Mock Version: 1.2.21
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/plumed.spec'], env={'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'SHELL': '/bin/bash', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'HOSTNAME': 'mock', 'HOME': '/builddir'}user='mockbuild'logger=<mockbuild.trace_decorator.getLog object at 0x7fcbfb8346d8>gid=135chrootPath='/var/lib/mock/epel-7-x86_64-mockbuilder-4092/root'timeout=0printOutput=Falseuid=1001shell=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/plumed.spec'] with env {'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'SHELL': '/bin/bash', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'HOSTNAME': 'mock', 'HOME': '/builddir'} and shell False
warning: Could not canonicalize hostname: copr-builder-720928416.novalocal
Building target platforms: x86_64
Building for target x86_64
Wrote: /builddir/build/SRPMS/plumed-2.2.1-2.el7.centos.src.rpm
Child return code was: 0
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/plumed.spec'], env={'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'SHELL': '/bin/bash', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'HOSTNAME': 'mock', 'HOME': '/builddir'}private_network=Trueuser='mockbuild'logger=<mockbuild.trace_decorator.getLog object at 0x7fcbfb8346d8>gid=135chrootPath='/var/lib/mock/epel-7-x86_64-mockbuilder-4092/root'timeout=0printOutput=Falseuid=1001shell=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/plumed.spec'] with env {'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'SHELL': '/bin/bash', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'HOSTNAME': 'mock', 'HOME': '/builddir'} and shell False
Building target platforms: x86_64
Building for target x86_64
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.uQEOOz
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf plumed-2.2.1
+ /usr/bin/mkdir -p plumed-2.2.1
+ cd plumed-2.2.1
+ /usr/bin/gzip -dc /builddir/build/SOURCES/plumed-2.2.1.tar.gz
+ /usr/bin/tar -xf -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ mv plumed2-2.2.1 serial
+ cp -a serial openmpi
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.QGBG2i
+ umask 022
+ cd /builddir/build/BUILD
+ cd plumed-2.2.1
+ export LIBS=-lopenblas
+ LIBS=-lopenblas
+ export LDFLAGS=-Wl,--as-needed
+ LDFLAGS=-Wl,--as-needed
+ pushd serial
~/build/BUILD/plumed-2.2.1/serial ~/build/BUILD/plumed-2.2.1
+ CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic'
+ export CFLAGS
+ CXXFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic'
+ export CXXFLAGS
+ FFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS=-Wl,--as-needed
+ export LDFLAGS
+ '[' 1 == 1 ']'
+ '[' x86_64 == ppc64le ']'
++ find . -name config.guess -o -name config.sub
+ ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --disable-mpi
configure: WARNING: unrecognized options: --disable-dependency-tracking
checking for x86_64-redhat-linux-gnu-g++... no
checking for x86_64-redhat-linux-gnu-cxx... no
checking for x86_64-redhat-linux-gnu-icpc... no
checking for x86_64-redhat-linux-gnu-gpp... no
checking for x86_64-redhat-linux-gnu-aCC... no
checking for x86_64-redhat-linux-gnu-CC... no
checking for x86_64-redhat-linux-gnu-cxx... no
checking for x86_64-redhat-linux-gnu-cc++... no
checking for x86_64-redhat-linux-gnu-cl.exe... no
checking for x86_64-redhat-linux-gnu-FCC... no
checking for x86_64-redhat-linux-gnu-KCC... no
checking for x86_64-redhat-linux-gnu-RCC... no
checking for x86_64-redhat-linux-gnu-xlC_r... no
checking for x86_64-redhat-linux-gnu-xlC... no
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for x86_64-redhat-linux-gnu-gcc... no
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for x86_64-redhat-linux-gnu-gfortran... no
checking for x86_64-redhat-linux-gnu-g95... no
checking for x86_64-redhat-linux-gnu-xlf95... no
checking for x86_64-redhat-linux-gnu-f95... no
checking for x86_64-redhat-linux-gnu-fort... no
checking for x86_64-redhat-linux-gnu-ifort... no
checking for x86_64-redhat-linux-gnu-ifc... no
checking for x86_64-redhat-linux-gnu-efc... no
checking for x86_64-redhat-linux-gnu-pgfortran... no
checking for x86_64-redhat-linux-gnu-pgf95... no
checking for x86_64-redhat-linux-gnu-lf95... no
checking for x86_64-redhat-linux-gnu-ftn... no
checking for x86_64-redhat-linux-gnu-nagfor... no
checking for x86_64-redhat-linux-gnu-xlf90... no
checking for x86_64-redhat-linux-gnu-f90... no
checking for x86_64-redhat-linux-gnu-pgf90... no
checking for x86_64-redhat-linux-gnu-pghpf... no
checking for x86_64-redhat-linux-gnu-epcf90... no
checking for x86_64-redhat-linux-gnu-g77... no
checking for x86_64-redhat-linux-gnu-xlf... no
checking for x86_64-redhat-linux-gnu-f77... no
checking for x86_64-redhat-linux-gnu-frt... no
checking for x86_64-redhat-linux-gnu-pgf77... no
checking for x86_64-redhat-linux-gnu-cf77... no
checking for x86_64-redhat-linux-gnu-fort77... no
checking for x86_64-redhat-linux-gnu-fl32... no
checking for x86_64-redhat-linux-gnu-af77... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
configure: Initial CXX:         g++
configure: Initial CXXFLAGS:    -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic
configure: Initial CPPFLAGS:    
configure: Initial CFLAGS:      -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic
configure: Initial LDFLAGS:     -Wl,--as-needed
configure: Initial LIBS:        -Wl,--as-needed
configure: Initial STATIC_LIBS: -Wl,--as-needed
configure: Initial LD:          g++
configure: Initial LDSO:        g++
configure: Initial SOEXT:       
checking whether g++ accepts -fPIC... yes
checking whether gcc accepts -fPIC... yes
checking whether g++ accepts -Wall... yes
checking whether g++ accepts -pedantic... yes
checking whether g++ accepts -ansi... yes
checking whether g++ supports explicit... yes
configure: Now we will check compulsory headers and libraries
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dirent.h usability... yes
checking dirent.h presence... yes
checking for dirent.h... yes
checking for readdir... yes
checking for dgemv... no
checking for dgemv_... yes
checking for dsyevr_... yes
configure: Now we will check for optional headers and libraries
checking for molfile_dcdplugin_init in -lmolfile_plugin... no
checking for dlopen in -ldl... configure: WARNING: using internal molfile_plugins, which only support dcd/xtc/trr/trj/crd files
yes
checking for g++ option to support OpenMP... -fopenmp
checking matheval.h usability... yes
checking matheval.h presence... yes
checking for matheval.h... yes
checking for evaluator_create... no
checking for evaluator_create in -lmatheval... yes
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking for clock_gettime... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for gettimeofday... yes
checking for dirent.h... (cached) yes
checking for readdir_r... yes
checking regex.h usability... yes
checking regex.h presence... yes
checking for regex.h... yes
checking for regcomp... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking for dlopen... yes
checking execinfo.h usability... yes
checking execinfo.h presence... yes
checking for execinfo.h... yes
checking for backtrace... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for gzopen... no
checking for gzopen in -lz... yes
checking xdrfile/xdrfile_xtc.h usability... no
checking xdrfile/xdrfile_xtc.h presence... no
checking for xdrfile/xdrfile_xtc.h... no
configure: Release mode, adding -DNDEBUG
configure: WARNING: cannot enable __PLUMED_HAS_XDRFILE
configure: *** Special settings for dynamic libraries on Linux ***
configure: Dynamic library extension is 'so'
configure: LDSO and LDFLAGS need special flags
checking whether LDFLAGS can contain -rdynamic... yes
configure: Using LDSO='g++ -shared'
configure: Using LDFLAGS='-Wl,--as-needed -rdynamic'
checking whether LDSO can create dynamic libraries... yes
checking for doxygen... found
configure: Doxygen version is fine
checking for dot... found
checking for xxd... found
checking whether a program can be run on this machine... yes
configure: PLUMED seems to be configured properly!
configure: **************************
checking whether C++ objects can be grouped with ld -r... yes
configure: I will now check if C++ objects can be linked by C/Fortran compilers
configure: This is relevant if you want to use plumed patch --static on a non-C++ code
checking whether C can link a C++ object... no
checking whether C can link a C++ object with library -lstdc++... no
checking whether C can link a C++ object with library -lc++... no
checking whether C can link a C++ object with library -lmpi_cxx... no
configure: WARNING: You might have problems linking C programs.
configure: WARNING: Please add c++ library to LIBS
checking whether FORTRAN can link a C++ object... no
checking whether FORTRAN can link a C++ object with library -lstdc++... no
checking whether FORTRAN can link a C++ object with library -lc++... no
checking whether FORTRAN can link a C++ object with library -lmpi_cxx... no
configure: WARNING: You might have problems linking FORTRAN programs.
configure: WARNING: Please add c++ library to LIBS
configure: **** PLUMED will be installed using the following paths:
configure: **** prefix: /usr
configure: **** exec_prefix: /usr
configure: **** bindir: /usr/bin
configure: **** libdir: /usr/lib64
configure: **** includedir: /usr/include
configure: **** datarootdir: ${prefix}/share
configure: **** datadir: /usr/share
configure: **** docdir: ${prefix}/share/doc/plumed
configure: **** htmldir: ${docdir}
configure: **** Executable will be named plumed
configure: **** You can change paths later using options to "make install"
configure: **** e.g. with "make install prefix=/path"
configure: **** PLUMED will be compiled without MPI
configure: creating ./config.status
config.status: creating Makefile.conf
config.status: creating sourceme.sh
config.status: creating stamp-h
configure: WARNING: unrecognized options: --disable-dependency-tracking
+ make -j2
make lib
make[1]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial'
make	-C src
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src'
make -C lib
make[3]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make dirslinks
make[4]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
*** Updating links to used modules in all directories ***
make ../analysis.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../lapack.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links
make[5]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make -C ../analysis links
make -C ../bias links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/analysis'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/analysis
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/bias'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/bias
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/bias'
make -C ../blas links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/blas'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/blas
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/blas'
make -C ../cltools links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/cltools'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/cltools
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/analysis'
make -C ../colvar links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/colvar'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/colvar
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/cltools'
make -C ../config links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
Nothing to do in /builddir/build/BUILD/plumed-2.2.1/serial/src/config
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make -C ../core links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/core'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/core
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/colvar'
make -C ../function links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/function'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/function
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/core'
make -C ../generic links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/generic'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/generic
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/function'
make -C ../lapack links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lapack'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/lapack
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lapack'
make -C ../main links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/main'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/main
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/generic'
make -C ../mapping links
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/main'
make -C ../molfile links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/mapping'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/mapping
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/molfile'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/molfile
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/molfile'
make -C ../multicolvar links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/multicolvar'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/multicolvar
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/multicolvar'
make -C ../reference links
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/mapping'
make -C ../secondarystructure links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/reference'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/reference
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/secondarystructure'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/secondarystructure
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/reference'
make -C ../setup links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/setup'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/setup
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/secondarystructure'
make -C ../tools links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/tools'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/tools
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/setup'
make -C ../vatom links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vatom'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/vatom
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/tools'
make -C ../vesselbase links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vesselbase'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/vesselbase
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vatom'
make -C ../wrapper links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/wrapper'
Nothing to do in /builddir/build/BUILD/plumed-2.2.1/serial/src/wrapper
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/wrapper'
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vesselbase'
make[5]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make[4]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make dirs
make[4]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
*** Compiling all directories ***
make ../analysis ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../lapack ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper
make[5]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make -C ../analysis obj
make -C ../bias obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/analysis'
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/bias'
compiling  Restraint.cpp
compiling  AnalysisWithLandmarks.cpp
compiling  ClassicalScaling.cpp
compiling  PBMetaD.cpp
compiling  Commit.cpp
PBMetaD.cpp: In destructor 'virtual PLMD::bias::PBMetaD::~PBMetaD()':
PBMetaD.cpp:256:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0; i<BiasGrids_.size();   ++i) delete BiasGrids_[i];
                                  ^
PBMetaD.cpp:257:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0; i<hillsOfiles_.size(); ++i){
                                    ^
PBMetaD.cpp: In constructor 'PLMD::bias::PBMetaD::PBMetaD(const PLMD::ActionOptions&)':
PBMetaD.cpp:202:11: warning: 'PLMD::bias::PBMetaD::kbt_' will be initialized after [-Wreorder]
   double  kbt_;
           ^
PBMetaD.cpp:199:11: warning:   'bool PLMD::bias::PBMetaD::grid_' [-Wreorder]
   bool    grid_;
           ^
PBMetaD.cpp:263:1: warning:   when initialized here [-Wreorder]
 PBMetaD::PBMetaD(const ActionOptions& ao):
 ^
PBMetaD.cpp:431:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<hillsfname.size();++i){
                                 ^
PBMetaD.cpp:447:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<hillsfname.size();++i){
                                ^
compiling  LandmarkSelectionBase.cpp
compiling  Histogram.cpp
compiling  ExtendedLagrangian.cpp
compiling  SelectAllFrames.cpp
compiling  Analysis.cpp
compiling  UWalls.cpp
compiling  MovingRestraint.cpp
compiling  ClassicalMultiDimensionalScaling.cpp
compiling  LandmarkRegister.cpp
compiling  External.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/analysis'
make -C ../blas obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/blas'
compiling  blas.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/blas'
make -C ../cltools obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/cltools'
compiling  Manual.cpp
compiling  MetaD.cpp
compiling  SumHills.cpp
compiling  SimpleMD.cpp
SimpleMD.cpp: In member function 'void PLMD::cltools::SimpleMD::read_natoms(const string&, int&)':
SimpleMD.cpp:197:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fp,"%1000d",&natoms);
                              ^
SimpleMD.cpp: In member function 'void PLMD::cltools::SimpleMD::read_positions(const string&, int, std::vector<PLMD::VectorGeneric<3u> >&, double*)':
SimpleMD.cpp:211:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(buffer,256,fp);
                       ^
SimpleMD.cpp:212:66: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fp,"%1000lf %1000lf %1000lf",&cell[0],&cell[1],&cell[2]);
                                                                  ^
SimpleMD.cpp:214:107: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%255s %1000lf %1000lf %1000lf",atomname,&positions[i][0],&positions[i][1],&positions[i][2]);
                                                                                                           ^
compiling  kT.cpp
compiling  Driver.cpp
compiling  GenTemplate.cpp
compiling  DriverFloat.cpp
compiling  BiasValue.cpp
compiling  LWalls.cpp
compiling  Bias.cpp
compiling  ABMD.cpp
compiling  Info.cpp
compiling  DriverDouble.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/bias'
make -C ../colvar obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/colvar'
compiling  Torsion.cpp
compiling  PathMSD.cpp
compiling  PathMSDBase.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/cltools'
make -C ../config obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make PLUMED_FORCE=yes ConfigInstall.cpp Config.cpp version.h
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
Updating ConfigInstall.cpp
cmp -s ConfigInstall.cpp~ ConfigInstall.cpp || cp ConfigInstall.cpp~ ConfigInstall.cpp
rm ConfigInstall.cpp~
Updating Config.cpp
cmp -s Config.cpp~ Config.cpp || cp Config.cpp~ Config.cpp
rm Config.cpp~
Updating version.h
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make Config.o ConfigInstall.o compile_options.sh
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
cat ../../Makefile.conf | xxd -i > Makefile.conf.xxd
Building compile_options.sh, a sourceable bash script with some compilation options
compiling  Config.cpp
compiling  ConfigInstall.cpp
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make -C ../core obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/core'
compiling  Value.cpp
compiling  ActionWithArguments.cpp
compiling  Volume.cpp
compiling  RDC.cpp
compiling  PlumedMainInitializer.cpp
compiling  CLToolRegister.cpp
compiling  PCARMSD.cpp
compiling  FlexibleBin.cpp
PCARMSD.cpp: In member function 'virtual void PLMD::colvar::PCARMSD::calculate()':
PCARMSD.cpp:217:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
          for(unsigned i=0;i<getNumberOfComponents();++i) setBoxDerivativesNoPbc( getPntrToComponent(i) );
                                                   ^
compiling  SetupMolInfo.cpp
compiling  Distance.cpp
compiling  ActionRegister.cpp
compiling  DRMSD.cpp
compiling  ActionPilot.cpp
compiling  TargetDist.cpp
compiling  CS2Backbone.cpp
compiling  Puckering.cpp
compiling  PlumedMain.cpp
PlumedMain.cpp: In member function 'void PLMD::PlumedMain::load(const string&)':
PlumedMain.cpp:732:50: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
        if(comm.Get_rank()==0) system(cmd.c_str());
                                                  ^
compiling  RMSD.cpp
compiling  CoordinationBase.cpp
CoordinationBase.cpp: In member function 'virtual void PLMD::colvar::CoordinationBase::calculate()':
CoordinationBase.cpp:198:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<getPositions().size();i++) deriv[i]+=omp_deriv[i];
                                     ^
compiling  CH3Shifts.cpp
compiling  Position.cpp
compiling  CLToolMain.cpp
CLToolMain.cpp: In static member function 'static int PLMD::CLToolMain::run(int, char**, FILE*, FILE*, PLMD::Communicator&)':
CLToolMain.cpp:246:24: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
     system(cmd.c_str());
                        ^
compiling  Cell.cpp
compiling  Action.cpp
compiling  Angle.cpp
compiling  Coordination.cpp
compiling  Atoms.cpp
Atoms.cpp: In member function 'void PLMD::Atoms::share(const std::set<PLMD::AtomNumber>&)':
Atoms.cpp:171:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned i=0;i<natoms;i++) forces[i].zero();
                        ^
Atoms.cpp: In member function 'void PLMD::Atoms::setAtomsGatindex(int*, bool)':
Atoms.cpp:355:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if( gatindex.size()==natoms ){
                        ^
Atoms.cpp:358:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           if( gatindex[i]!=i ){ shuffledAtoms=1; break; }
                            ^
Atoms.cpp: In member function 'void PLMD::Atoms::setAtomsContiguous(int)':
Atoms.cpp:374:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(gatindex.size()<natoms) shuffledAtoms=1;
                      ^
Atoms.cpp: In member function 'void PLMD::Atoms::getLocalForces(std::vector<PLMD::VectorGeneric<3u> >&)':
Atoms.cpp:510:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0; i<gatindex.size(); i++) localForces[i] = forces[gatindex[i]];
                                ^
compiling  DHEnergy.cpp
compiling  Colvar.cpp
compiling  ContactMap.cpp
compiling  ExchangePatterns.cpp
compiling  ActionAtomistic.cpp
ActionAtomistic.cpp: In member function 'void PLMD::ActionAtomistic::requestAtoms(const std::vector<PLMD::AtomNumber>&)':
ActionAtomistic.cpp:74:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(indexes[i].index()>=n) error("atom out of range");
                            ^
compiling  Dipole.cpp
compiling  ActionWithVirtualAtom.cpp
compiling  Constant.cpp
compiling  MultiRMSD.cpp
compiling  GREX.cpp
compiling  ActionSet.cpp
compiling  NOE.cpp
compiling  ActionWithValue.cpp
compiling  CLTool.cpp
compiling  PropertyMap.cpp
compiling  MDAtoms.cpp
compiling  ActionSetup.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/core'
compiling  Gyration.cpp
compiling  Template.cpp
make -C ../function obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/function'
compiling  FuncSumHills.cpp
compiling  Energy.cpp
compiling  Fake.cpp
In file included from core/../../core/tools/../../tools/Keywords.h:29:0,
                 from core/../../core/tools/Keywords.h:1,
                 from core/../../core/Action.h:27,
                 from core/../../core/ActionAtomistic.h:25,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from Fake.cpp:22:
Fake.cpp: In constructor 'PLMD::colvar::ColvarFake::ColvarFake(const PLMD::ActionOptions&)':
Fake.cpp:90:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    plumed_massert(getNumberOfComponents()*2==period.size(),"the periodicty should coincide with the number of components");
                                                          ^
core/../../core/tools/../../tools/Exception.h:132:39: note: in definition of macro 'plumed_massert'
 #define plumed_massert(test,msg) if(!(test)) throw PLMD::Exception("assertion failed " #test ", " msg,__FILE__,__LINE__,__PRETTY_FUNCTION__)
                                       ^
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/colvar'
make -C ../generic obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/generic'
compiling  WrapAround.cpp
compiling  DumpForces.cpp
compiling  Include.cpp
compiling  RandomExchanges.cpp
compiling  Ensemble.cpp
compiling  WholeMolecules.cpp
compiling  Combine.cpp
compiling  Sort.cpp
compiling  Flush.cpp
compiling  DumpProjections.cpp
compiling  Function.cpp
compiling  Read.cpp
compiling  Target.cpp
compiling  FuncPathMSD.cpp
FuncPathMSD.cpp: In constructor 'PLMD::function::FuncPathMSD::FuncPathMSD(const PLMD::ActionOptions&)':
FuncPathMSD.cpp:184:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
            if(neigh_size>getNumberOfArguments()){
                                               ^
compiling  Print.cpp
compiling  FitToTemplate.cpp
compiling  Matheval.cpp
compiling  EffectiveEnergyDrift.cpp
compiling  Piecewise.cpp
EffectiveEnergyDrift.cpp: In constructor 'PLMD::generic::EffectiveEnergyDrift::EffectiveEnergyDrift(const PLMD::ActionOptions&)':
EffectiveEnergyDrift.cpp:160:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<tmpActions.size();i++) if(tmpActions[i]->exists(tmpActions[i]->getLabel()+".bias")) biases.push_back(tmpActions[i]);
                                 ^
EffectiveEnergyDrift.cpp: In member function 'virtual void PLMD::generic::EffectiveEnergyDrift::update()':
EffectiveEnergyDrift.cpp:189:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<positions.size();++i){
                                  ^
EffectiveEnergyDrift.cpp:249:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<indexR.size();j++) backmap[indexR[j]]=j;
                               ^
EffectiveEnergyDrift.cpp:289:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<biases.size();i++) bias+=biases[i]->getOutputQuantity("bias");
                               ^
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/function'
compiling  DumpAtoms.cpp
compiling  DumpMassCharge.cpp
DumpMassCharge.cpp: In constructor 'PLMD::generic::DumpMassCharge::DumpMassCharge(const PLMD::ActionOptions&)':
DumpMassCharge.cpp:132:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned i=0;i<plumed.getAtoms().getNatoms();i++){
                                                    ^
DumpMassCharge.cpp: In member function 'virtual void PLMD::generic::DumpMassCharge::update()':
DumpMassCharge.cpp:153:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<getNumberOfAtoms();i++){
                                  ^
compiling  Group.cpp
make -C ../lapack obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lapack'
compiling  lapack.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lapack'
make -C ../main obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/main'
compiling  main.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/main'
make -C ../mapping obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/mapping'
compiling  ZpathVessel.cpp
compiling  DumpDerivatives.cpp
compiling  PathBase.cpp
compiling  Time.cpp
compiling  Path.cpp
compiling  Debug.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/generic'
make -C ../molfile obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/molfile'
compiling  dcdplugin.cpp
compiling  SpathVessel.cpp
dcdplugin.cpp:618:5: warning: "/*" within comment [-Wcomment]
     /*  Some platforms implement readv() as user level code in libc,     */
 ^
In file included from dcdplugin.cpp:83:0:
fastio.h: In function 'PLMD::molfile::fio_size_t PLMD::molfile::fio_readv(PLMD::molfile::fio_fd, const fio_iovec*, int)':
fastio.h:580:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (rc != iov[i].iov_len)
                        ^
dcdplugin.cpp: In function 'int PLMD::molfile::read_dcdheader(PLMD::molfile::fio_fd, int*, int*, int*, int*, double*, int*, int**, float**, int*, int*)':
dcdplugin.cpp:226:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {
                                                            ^
dcdplugin.cpp:239:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {
                                                         ^
dcdplugin.cpp:257:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (input_integer[0] != dcdcordmagic) {
                             ^
dcdplugin.cpp:296:31: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   (*NSET) = *((int *) (hdrbuf));
                               ^
dcdplugin.cpp:434:64: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {
                                                                ^
dcdplugin.cpp:451:64: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {
                                                                ^
dcdplugin.cpp: In function 'int PLMD::molfile::read_dcdstep(PLMD::molfile::fio_fd, int, float*, float*, float*, float*, int, int, int*, float*, int, int)':
dcdplugin.cpp:656:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT;
                                        ^
dcdplugin.cpp:660:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT;
                                                            ^
dcdplugin.cpp:581:16: warning: variable 'readlen' set but not used [-Wunused-but-set-variable]
     fio_size_t readlen; /* number of bytes actually read            */
                ^
In file included from dcdplugin.cpp:83:0:
fastio.h: At global scope:
fastio.h:520:19: warning: 'PLMD::molfile::fio_size_t PLMD::molfile::fio_readv(PLMD::molfile::fio_fd, const fio_iovec*, int)' defined but not used [-Wunused-function]
 static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) {
                   ^
fastio.h:662:12: warning: 'int PLMD::molfile::fio_read_int32(PLMD::molfile::fio_fd, int*)' defined but not used [-Wunused-function]
 static int fio_read_int32(fio_fd fd, int *i) {
            ^
fastio.h:666:12: warning: 'int PLMD::molfile::fio_write_str(PLMD::molfile::fio_fd, const char*)' defined but not used [-Wunused-function]
 static int fio_write_str(fio_fd fd, const char *str) {
            ^
In file included from dcdplugin.cpp:92:0:
endianswap.h:72:13: warning: 'void PLMD::molfile::swap2_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
endianswap.h:136:13: warning: 'void PLMD::molfile::swap2_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_aligned(void *v, long ndata) {
             ^
compiling  crdplugin.cpp
compiling  gromacsplugin.cpp
In file included from gromacsplugin.cpp:62:0:
Gromacs.h: In function 'int PLMD::molfile::mdio_readline(PLMD::molfile::md_file*, char*, int, int)':
Gromacs.h:467:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
  fgets(buf, n, mf->f);
                      ^
compiling  PCAVars.cpp
In file included from Gromacs.h:86:0,
                 from gromacsplugin.cpp:62:
endianswap.h: At global scope:
endianswap.h:72:13: warning: 'void PLMD::molfile::swap2_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
endianswap.h:86:13: warning: 'void PLMD::molfile::swap4_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap4_unaligned(void *v, long ndata) {
             ^
endianswap.h:105:13: warning: 'void PLMD::molfile::swap8_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_unaligned(void *v, long ndata) {
             ^
endianswap.h:136:13: warning: 'void PLMD::molfile::swap2_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_aligned(void *v, long ndata) {
             ^
compiling  pdbplugin.cpp
PCAVars.cpp: In constructor 'PLMD::mapping::PCAVars::PCAVars(const PLMD::ActionOptions&)':
PCAVars.cpp:296:14: warning: unused variable 'dist' [-Wunused-variable]
       double dist=myframes.getFrame(i)->calc( myref->getReferencePositions(), fake_pbc, getArguments(), myref->getReferenceArguments(), mypack, true );
              ^
PCAVars.cpp:326:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned i=0;i<getNumberOfComponents();++i) getPntrToComponent(i)->resizeDerivatives(nder);
                                            ^
PCAVars.cpp: In member function 'virtual void PLMD::mapping::PCAVars::calculate()':
PCAVars.cpp:366:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned i=0;i<getNumberOfComponents()-1;++i){  // One less component as we also have residual
                                              ^
PCAVars.cpp: In member function 'virtual void PLMD::mapping::PCAVars::calculateNumericalDerivatives(PLMD::ActionWithValue*)':
PCAVars.cpp:422:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(unsigned j=0;j<getNumberOfComponents();++j){
                                               ^
PCAVars.cpp:426:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(unsigned j=0;j<getNumberOfComponents();++j){
                                               ^
PCAVars.cpp: In member function 'virtual void PLMD::mapping::PCAVars::apply()':
PCAVars.cpp:435:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned i=0;i<getNumberOfComponents();++i){
                                            ^
In file included from pdbplugin.cpp:64:0:
periodic_table.h:173:12: warning: 'int PLMD::molfile::get_pte_idx(const char*)' defined but not used [-Wunused-function]
 static int get_pte_idx(const char *label)
            ^
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/molfile'
make -C ../multicolvar obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/multicolvar'
compiling  MultiColvarBase.cpp
In file included from ActionVolume.h:26:0,
                 from MultiColvarBase.cpp:24:
VolumeGradientBase.h: In member function 'PLMD::Vector PLMD::multicolvar::VolumeGradientBase::getPosition(int) const':
VolumeGradientBase.h:84:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                           ^
VolumeGradientBase.h:84:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                                                             ^
MultiColvarBase.cpp: In member function 'void PLMD::multicolvar::MultiColvarBase::setupLinkCells()':
MultiColvarBase.cpp:202:15: warning: unused variable 'justVolumes' [-Wunused-variable]
          bool justVolumes=true;
               ^
compiling  DihedralCorrelation.cpp
compiling  Mapping.cpp
Mapping.cpp: In member function 'virtual void PLMD::mapping::Mapping::prepare()':
Mapping.cpp:141:16: warning: unused variable 'nfram' [-Wunused-variable]
       unsigned nfram=getNumberOfReferencePoints();
                ^
Mapping.cpp: In member function 'virtual void PLMD::mapping::Mapping::calculateNumericalDerivatives(PLMD::ActionWithValue*)':
Mapping.cpp:203:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(unsigned j=0;j<getNumberOfComponents();++j){
                                               ^
Mapping.cpp:207:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(unsigned j=0;j<getNumberOfComponents();++j){ 
                                               ^
compiling  Bridge.cpp
compiling  BridgedMultiColvarFunction.cpp
compiling  PropertyMap.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/mapping'
make -C ../reference obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/reference'
compiling  DRMSD.cpp
compiling  Torsions.cpp
compiling  Direction.cpp
compiling  MultiColvarDensity.cpp
compiling  ReferenceConfiguration.cpp
compiling  ReferenceAtoms.cpp
compiling  ArgumentOnlyDistance.cpp
compiling  FilterBetween.cpp
compiling  EuclideanDistance.cpp
compiling  MultiDomainRMSD.cpp
compiling  CatomPack.cpp
compiling  AtomValuePack.cpp
compiling  Angles.cpp
compiling  SimpleRMSD.cpp
compiling  RMSDBase.cpp
compiling  VolumeCavity.cpp
compiling  ReferenceValuePack.cpp
In file included from ActionVolume.h:26:0,
                 from VolumeCavity.cpp:27:
VolumeGradientBase.h: In member function 'PLMD::Vector PLMD::multicolvar::VolumeGradientBase::getPosition(int) const':
VolumeGradientBase.h:84:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                           ^
VolumeGradientBase.h:84:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                                                             ^
compiling  SingleDomainRMSD.cpp
compiling  ReferenceArguments.cpp
compiling  AdjacencyMatrixAction.cpp
compiling  PointWiseMapping.cpp
compiling  OptimalRMSD.cpp
AdjacencyMatrixAction.cpp: In constructor 'PLMD::multicolvar::AdjacencyMatrixAction::AdjacencyMatrixAction(const PLMD::ActionOptions&)':
AdjacencyMatrixAction.cpp:56:20: warning: 'ibase' may be used uninitialized in this function [-Wmaybe-uninitialized]
           unsigned ibase;
                    ^
AdjacencyMatrixAction.cpp: In constructor 'PLMD::multicolvar::AdjacencyMatrixAction::AdjacencyMatrixAction(const PLMD::ActionOptions&)':
AdjacencyMatrixAction.cpp:56:20: warning: 'ibase' may be used uninitialized in this function [-Wmaybe-uninitialized]
compiling  MultiColvar.cpp
compiling  MultiReferenceBase.cpp
MultiColvar.cpp: In member function 'void PLMD::multicolvar::MultiColvar::readAtomsLikeKeyword(const string&, int&, std::vector<PLMD::AtomNumber>&)':
MultiColvar.cpp:95:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if( t.size()!=natoms ){
                    ^
MultiColvar.cpp:99:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(unsigned j=0;j<natoms;++j){ 
                         ^
MultiColvar.cpp:111:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for(unsigned j=0;j<natoms;++j){ cvcode += i*tmpc; tmpc *= nblock; }
                                ^
compiling  MetricRegister.cpp
compiling  DotProductDistance.cpp
compiling  InPlaneDistances.cpp
compiling  NormalizedEuclideanDistance.cpp
compiling  MahalanobisDistance.cpp
compiling  AdjacencyMatrixVessel.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/reference'
make -C ../secondarystructure obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/secondarystructure'
compiling  ParabetaRMSD.cpp
compiling  FilterLessThan.cpp
compiling  AntibetaRMSD.cpp
compiling  DumpMultiColvar.cpp
compiling  AlphaRMSD.cpp
compiling  SecondaryStructureRMSD.cpp
compiling  VolumeInCylinder.cpp
In file included from ActionVolume.h:26:0,
                 from VolumeInCylinder.cpp:25:
VolumeGradientBase.h: In member function 'PLMD::Vector PLMD::multicolvar::VolumeGradientBase::getPosition(int) const':
VolumeGradientBase.h:84:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                           ^
VolumeGradientBase.h:84:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                                                             ^
compiling  CoordinationNumbers.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/secondarystructure'
compiling  Density.cpp
make -C ../setup obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/setup'
compiling  Units.cpp
compiling  MultiColvarFunction.cpp
MultiColvarFunction.cpp: In member function 'virtual void PLMD::multicolvar::MultiColvarFunction::calculateNumericalDerivatives(PLMD::ActionWithValue*)':
MultiColvarFunction.cpp:236:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(unsigned k=0;k<getNumberOfComponents();++k){
                                                  ^
MultiColvarFunction.cpp:245:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(unsigned k=0;k<getNumberOfComponents();++k){
                                                  ^
MultiColvarFunction.cpp:257:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(unsigned k=0;k<getNumberOfComponents();++k){
                                                ^
MultiColvarFunction.cpp:265:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned j=0;j<getNumberOfComponents();++j){
                                            ^
compiling  Restart.cpp
compiling  MolInfo.cpp
compiling  Load.cpp
compiling  Sprint.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/setup'
compiling  FilterMoreThan.cpp
Sprint.cpp: In member function 'virtual void PLMD::multicolvar::Sprint::completeCalculation()':
Sprint.cpp:162:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned icomp=0;icomp<getNumberOfComponents();++icomp){
                                                     ^
Sprint.cpp:178:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(unsigned icomp=0;icomp<getNumberOfComponents();++icomp){
                                                        ^
Sprint.cpp:193:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned j=0;j<getNumberOfComponents();++j){
                                             ^
Sprint.cpp: In member function 'virtual void PLMD::multicolvar::Sprint::apply()':
Sprint.cpp:205:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned i=0;i<getNumberOfComponents();++i){
                                            ^
compiling  VolumeGradientBase.cpp
In file included from VolumeGradientBase.cpp:22:0:
VolumeGradientBase.h: In member function 'PLMD::Vector PLMD::multicolvar::VolumeGradientBase::getPosition(int) const':
VolumeGradientBase.h:84:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                           ^
VolumeGradientBase.h:84:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                                                             ^
compiling  Distances.cpp
compiling  XYDistances.cpp
compiling  AlphaBeta.cpp
compiling  NumberOfLinks.cpp
compiling  VolumeAround.cpp
In file included from ActionVolume.h:26:0,
                 from VolumeAround.cpp:24:
VolumeGradientBase.h: In member function 'PLMD::Vector PLMD::multicolvar::VolumeGradientBase::getPosition(int) const':
VolumeGradientBase.h:84:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                           ^
VolumeGradientBase.h:84:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                                                             ^
compiling  ActionVolume.cpp
In file included from ActionVolume.h:26:0,
                 from ActionVolume.cpp:22:
VolumeGradientBase.h: In member function 'PLMD::Vector PLMD::multicolvar::VolumeGradientBase::getPosition(int) const':
VolumeGradientBase.h:84:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                           ^
VolumeGradientBase.h:84:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                                                             ^
compiling  XDistances.cpp
compiling  VolumeTetrapore.cpp
In file included from ActionVolume.h:26:0,
                 from VolumeTetrapore.cpp:27:
VolumeGradientBase.h: In member function 'PLMD::Vector PLMD::multicolvar::VolumeGradientBase::getPosition(int) const':
VolumeGradientBase.h:84:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                           ^
VolumeGradientBase.h:84:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                                                             ^
compiling  LocalAverage.cpp
LocalAverage.cpp: In member function 'virtual double PLMD::multicolvar::LocalAverage::compute(const unsigned int&, PLMD::multicolvar::AtomValuePack&) const':
LocalAverage.cpp:155:10: warning: variable 'catom_pos' set but not used [-Wunused-but-set-variable]
   Vector catom_pos=myatoms.getPosition(0);
          ^
compiling  MultiColvarFilter.cpp
make -C ../tools obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/tools'
compiling  Torsion.cpp
compiling  CubicInterpolation.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/multicolvar'
make -C ../vatom obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vatom'
compiling  Ghost.cpp
CubicInterpolation.cpp: In member function 'unsigned int PLMD::CInterpolation::search1(const unsigned int&, const double&, const unsigned int&) const':
CubicInterpolation.cpp:83:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 else if( ju>=(np[kk]-1)*inc ){ju=(np[kk]-1)*inc; break; } 
                                         ^
compiling  HistogramBead.cpp
compiling  COM.cpp
compiling  OFile.cpp
compiling  Center.cpp
OFile.cpp: In constructor 'PLMD::OFile::OFile()':
OFile.cpp:73:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned i=0;i<buflen;++i) buffer[i]=0;
                      ^
OFile.cpp: In member function 'int PLMD::OFile::printf(const char*, ...)':
OFile.cpp:101:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(r>=buflen-actual_buffer_length){
                ^
OFile.cpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     while(newlen<=r+actual_buffer_length) newlen*=2;
                     ^
In file included from OFile.cpp:23:0:
OFile.cpp:115:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   plumed_massert(r>-1 && r<buflen-actual_buffer_length,"error using fmt string " + std::string(fmt));
                                   ^
Exception.h:132:39: note: in definition of macro 'plumed_massert'
 #define plumed_massert(test,msg) if(!(test)) throw PLMD::Exception("assertion failed " #test ", " msg,__FILE__,__LINE__,__PRETTY_FUNCTION__)
                                       ^
compiling  Kearsley.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vatom'
make -C ../vesselbase obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vesselbase'
compiling  LessThan.cpp
compiling  Lowest.cpp
compiling  ActionWithVessel.cpp
In file included from ActionWithVessel.cpp:23:0:
ActionWithVessel.h: In constructor 'PLMD::vesselbase::ActionWithVessel::ActionWithVessel(const PLMD::ActionOptions&)':
ActionWithVessel.h:98:8: warning: 'PLMD::vesselbase::ActionWithVessel::weightHasDerivatives' will be initialized after [-Wreorder]
   bool weightHasDerivatives;
        ^
ActionWithVessel.h:93:14: warning:   'PLMD::Stopwatch& PLMD::vesselbase::ActionWithVessel::stopwatch' [-Wreorder]
   Stopwatch& stopwatch;
              ^
ActionWithVessel.cpp:56:1: warning:   when initialized here [-Wreorder]
 ActionWithVessel::ActionWithVessel(const ActionOptions&ao):
 ^
compiling  Stopwatch.cpp
compiling  KernelFunctions.cpp
KernelFunctions.cpp: In constructor 'PLMD::KernelFunctions::KernelFunctions(const string&, const bool&)':
KernelFunctions.cpp:98:8: warning: unused variable 'founds' [-Wunused-variable]
   bool founds = Tools::parseVector(data,"SIGMA",sig);
        ^
compiling  Grid.cpp
compiling  AltMin.cpp
Grid.cpp: In member function 'std::vector<long unsigned int> PLMD::Grid::getNeighbors(const std::vector<unsigned int>&, const std::vector<unsigned int>&) const':
Grid.cpp:280:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(!pbc_[i] && i0>=nbin_[i]) continue;
                              ^
Grid.cpp:282:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if( pbc_[i] && i0>=nbin_[i]) i0%=nbin_[i];
                              ^
compiling  StoreDataVessel.cpp
In file included from StoreDataVessel.cpp:22:0:
StoreDataVessel.h: In constructor 'PLMD::vesselbase::StoreDataVessel::StoreDataVessel(const PLMD::vesselbase::VesselOptions&)':
StoreDataVessel.h:61:8: warning: 'PLMD::vesselbase::StoreDataVessel::hard_cut' will be initialized after [-Wreorder]
   bool hard_cut;
        ^
StoreDataVessel.h:52:12: warning:   'unsigned int PLMD::vesselbase::StoreDataVessel::nspace' [-Wreorder]
   unsigned nspace;
            ^
StoreDataVessel.cpp:31:1: warning:   when initialized here [-Wreorder]
 StoreDataVessel::StoreDataVessel( const VesselOptions& da ):
 ^
compiling  Max.cpp
compiling  BridgeVessel.cpp
BridgeVessel.cpp: In member function 'virtual void PLMD::vesselbase::BridgeVessel::setBufferStart(unsigned int&)':
BridgeVessel.cpp:64:12: warning: unused variable 'tmp' [-Wunused-variable]
   unsigned tmp=myOutputAction->getSizeOfBuffer( start );
            ^
compiling  Between.cpp
compiling  Units.cpp
compiling  Tensor.cpp
compiling  OrderingVessel.cpp
compiling  BiasRepresentation.cpp
compiling  ShortcutVessel.cpp
compiling  Moments.cpp
compiling  Angle.cpp
compiling  FileBase.cpp
compiling  Min.cpp
compiling  OpenMP.cpp
compiling  RMSD.cpp
RMSD.cpp: In member function 'std::vector<PLMD::VectorGeneric<3u> > PLMD::RMSDCoreData::getDDistanceDReferenceSOMA()':
RMSD.cpp:1057:10: warning: variable 't_ddist_drr01' set but not used [-Wunused-but-set-variable]
   Tensor t_ddist_drr01=ddist_drr01.transpose(); 
          ^
compiling  MoreThan.cpp
compiling  Histogram.cpp
compiling  ValueVessel.cpp
compiling  FunctionVessel.cpp
compiling  Mean.cpp
compiling  ActionWithInputVessel.cpp
compiling  Vessel.cpp
compiling  VesselRegister.cpp
compiling  NeighborList.cpp
compiling  Pbc.cpp
compiling  Highest.cpp
compiling  PDB.cpp
compiling  Sum.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vesselbase'
make -C ../wrapper obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/wrapper'
compiling  PlumedStatic.cpp
compiling  Plumed.c
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/wrapper'
compiling  IFile.cpp
compiling  LatticeReduction.cpp
compiling  Random.cpp
compiling  DLLoader.cpp
compiling  Log.cpp
compiling  Communicator.cpp
compiling  Citations.cpp
compiling  OptimalAlignment.cpp
compiling  MultiValue.cpp
compiling  MolDataClass.cpp
compiling  Tools.cpp
compiling  LinkCells.cpp
compiling  Keywords.cpp
compiling  Vector.cpp
compiling  SwitchingFunction.cpp
compiling  Exception.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/tools'
make[5]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make[4]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make lib
make[4]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
g++  ../main/main.o ../analysis/Analysis.o ../analysis/AnalysisWithLandmarks.o ../analysis/ClassicalMultiDimensionalScaling.o ../analysis/ClassicalScaling.o ../analysis/Commit.o ../analysis/Histogram.o ../analysis/LandmarkRegister.o ../analysis/LandmarkSelectionBase.o ../analysis/SelectAllFrames.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/UWalls.o ../blas/blas.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../colvar/Angle.o ../colvar/CH3Shifts.o ../colvar/CS2Backbone.o ../colvar/Cell.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/Energy.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/NOE.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RDC.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../function/Combine.o ../function/Ensemble.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/Matheval.o ../function/Piecewise.o ../function/Sort.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/Time.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../lapack/lapack.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AdjacencyMatrixAction.o ../multicolvar/AdjacencyMatrixVessel.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvar.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarFunction.o ../multicolvar/NumberOfLinks.o ../multicolvar/Sprint.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/MultiReferenceBase.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/PointWiseMapping.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/MolInfo.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/BiasRepresentation.o ../tools/Citations.o ../tools/Communicator.o ../tools/CubicInterpolation.o ../tools/DLLoader.o ../tools/Exception.o ../tools/FileBase.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/Kearsley.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/OptimalAlignment.o ../tools/PDB.o ../tools/Pbc.o ../tools/RMSD.o ../tools/Random.o ../tools/Stopwatch.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../vatom/COM.o ../vatom/Center.o ../vatom/Ghost.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/Config.o ../wrapper/PlumedStatic.o -o plumed -ldl  -lz -lmatheval -ldl -lopenblas -Wl,--as-needed -rdynamic -fopenmp
Building Plumed.inc
chmod a+x plumed-mklib
chmod a+x plumed-newcv
chmod a+x plumed-patch
g++ -shared -o libplumedKernel.so ../analysis/Analysis.o ../analysis/AnalysisWithLandmarks.o ../analysis/ClassicalMultiDimensionalScaling.o ../analysis/ClassicalScaling.o ../analysis/Commit.o ../analysis/Histogram.o ../analysis/LandmarkRegister.o ../analysis/LandmarkSelectionBase.o ../analysis/SelectAllFrames.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/UWalls.o ../blas/blas.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../colvar/Angle.o ../colvar/CH3Shifts.o ../colvar/CS2Backbone.o ../colvar/Cell.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/Energy.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/NOE.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RDC.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../function/Combine.o ../function/Ensemble.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/Matheval.o ../function/Piecewise.o ../function/Sort.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/Time.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../lapack/lapack.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AdjacencyMatrixAction.o ../multicolvar/AdjacencyMatrixVessel.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvar.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarFunction.o ../multicolvar/NumberOfLinks.o ../multicolvar/Sprint.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/MultiReferenceBase.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/PointWiseMapping.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/MolInfo.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/BiasRepresentation.o ../tools/Citations.o ../tools/Communicator.o ../tools/CubicInterpolation.o ../tools/DLLoader.o ../tools/Exception.o ../tools/FileBase.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/Kearsley.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/OptimalAlignment.o ../tools/PDB.o ../tools/Pbc.o ../tools/RMSD.o ../tools/Random.o ../tools/Stopwatch.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../vatom/COM.o ../vatom/Center.o ../vatom/Ghost.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/Config.o -lz -lmatheval -ldl -lopenblas -Wl,--as-needed -rdynamic -fopenmp
g++ -shared -o libplumed.so ../analysis/Analysis.o ../analysis/AnalysisWithLandmarks.o ../analysis/ClassicalMultiDimensionalScaling.o ../analysis/ClassicalScaling.o ../analysis/Commit.o ../analysis/Histogram.o ../analysis/LandmarkRegister.o ../analysis/LandmarkSelectionBase.o ../analysis/SelectAllFrames.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/UWalls.o ../blas/blas.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../colvar/Angle.o ../colvar/CH3Shifts.o ../colvar/CS2Backbone.o ../colvar/Cell.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/Energy.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/NOE.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RDC.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../function/Combine.o ../function/Ensemble.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/Matheval.o ../function/Piecewise.o ../function/Sort.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/Time.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../lapack/lapack.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AdjacencyMatrixAction.o ../multicolvar/AdjacencyMatrixVessel.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvar.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarFunction.o ../multicolvar/NumberOfLinks.o ../multicolvar/Sprint.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/MultiReferenceBase.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/PointWiseMapping.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/MolInfo.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/BiasRepresentation.o ../tools/Citations.o ../tools/Communicator.o ../tools/CubicInterpolation.o ../tools/DLLoader.o ../tools/Exception.o ../tools/FileBase.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/Kearsley.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/OptimalAlignment.o ../tools/PDB.o ../tools/Pbc.o ../tools/RMSD.o ../tools/Random.o ../tools/Stopwatch.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../vatom/COM.o ../vatom/Center.o ../vatom/Ghost.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/Config.o ../wrapper/PlumedStatic.o -lz -lmatheval -ldl -lopenblas -Wl,--as-needed -rdynamic -fopenmp
g++  ../main/main.o ../wrapper/Plumed.o -o plumed-runtime -ldl 
Building Plumed.inc, runtime-linking version
Building Plumed.inc, shared version
Building Plumed.inc, static version
Building Plumed.cmake
Building Plumed.cmake, static version
Building Plumed.cmake, runtime-linking version
Building Plumed.cmake, shared version
g++  ../main/main.o "/builddir/build/BUILD/plumed-2.2.1/serial/src/lib/libplumed.so" -o plumed-shared -ldl 
make[4]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make install-build
make[4]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
mkdir -p install/
make PLUMED_INSTALL=Install all
make[5]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make dirslinks
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
*** Updating links to used modules in all directories ***
make ../analysis.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../lapack.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make -C ../analysis links
make -C ../bias links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/bias'
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/analysis'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/analysis
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/bias
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/bias'
make -C ../blas links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/blas'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/blas
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/blas'
make -C ../cltools links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/cltools'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/cltools
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/analysis'
make -C ../colvar links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/colvar'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/colvar
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/cltools'
make -C ../config links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
Nothing to do in /builddir/build/BUILD/plumed-2.2.1/serial/src/config
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make -C ../core links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/core'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/core
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/colvar'
make -C ../function links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/function'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/function
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/core'
make -C ../generic links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/generic'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/generic
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/function'
make -C ../lapack links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lapack'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/lapack
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/generic'
make -C ../main links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/main'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/main
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lapack'
make -C ../mapping links
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/main'
make -C ../molfile links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/molfile'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/molfile
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/mapping'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/mapping
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/molfile'
make -C ../multicolvar links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/multicolvar'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/multicolvar
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/mapping'
make -C ../reference links
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/multicolvar'
make -C ../secondarystructure links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/secondarystructure'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/secondarystructure
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/reference'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/reference
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/reference'
make -C ../setup links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/setup'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/setup
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/secondarystructure'
make -C ../tools links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/tools'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/tools
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/setup'
make -C ../vatom links
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/tools'
make -C ../vesselbase links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vatom'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/vatom
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vesselbase'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/vesselbase
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vatom'
make -C ../wrapper links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/wrapper'
Nothing to do in /builddir/build/BUILD/plumed-2.2.1/serial/src/wrapper
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/wrapper'
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vesselbase'
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make dirs
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
*** Compiling all directories ***
make ../analysis ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../lapack ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make -C ../analysis obj
make -C ../bias obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/bias'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/bias'
make -C ../blas obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/blas'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/blas'
make -C ../cltools obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/analysis'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/analysis'
make -C ../colvar obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/cltools'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/cltools'
make -C ../config obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make PLUMED_FORCE=yes ConfigInstall.cpp Config.cpp version.h
make[9]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
Updating ConfigInstall.cpp
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/colvar'
make[8]: Nothing to be done for `obj'.
cmp -s ConfigInstall.cpp~ ConfigInstall.cpp || cp ConfigInstall.cpp~ ConfigInstall.cpp
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/colvar'
Updating Config.cpp
rm ConfigInstall.cpp~
Updating version.h
cmp -s Config.cpp~ Config.cpp || cp Config.cpp~ Config.cpp
rm Config.cpp~
make -C ../core obj
make[9]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make Config.o ConfigInstall.o compile_options.sh
make[9]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make[9]: `Config.o' is up to date.
make[9]: `ConfigInstall.o' is up to date.
make[9]: `compile_options.sh' is up to date.
make[9]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make -C ../function obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/function'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/function'
make -C ../generic obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/core'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/core'
make -C ../lapack obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lapack'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lapack'
make -C ../main obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/main'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/main'
make -C ../mapping obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/generic'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/generic'
make -C ../molfile obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/molfile'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/molfile'
make -C ../multicolvar obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/mapping'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/mapping'
make -C ../reference obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/reference'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/reference'
make -C ../secondarystructure obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/secondarystructure'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/secondarystructure'
make -C ../setup obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/multicolvar'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/multicolvar'
make -C ../tools obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/setup'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/setup'
make -C ../vatom obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vatom'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vatom'
make -C ../vesselbase obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/tools'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/tools'
make -C ../wrapper obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/wrapper'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/wrapper'
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vesselbase'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vesselbase'
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make lib
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
g++  ../main/main.o ../analysis/Analysis.o ../analysis/AnalysisWithLandmarks.o ../analysis/ClassicalMultiDimensionalScaling.o ../analysis/ClassicalScaling.o ../analysis/Commit.o ../analysis/Histogram.o ../analysis/LandmarkRegister.o ../analysis/LandmarkSelectionBase.o ../analysis/SelectAllFrames.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/UWalls.o ../blas/blas.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../colvar/Angle.o ../colvar/CH3Shifts.o ../colvar/CS2Backbone.o ../colvar/Cell.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/Energy.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/NOE.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RDC.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../function/Combine.o ../function/Ensemble.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/Matheval.o ../function/Piecewise.o ../function/Sort.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/Time.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../lapack/lapack.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AdjacencyMatrixAction.o ../multicolvar/AdjacencyMatrixVessel.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvar.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarFunction.o ../multicolvar/NumberOfLinks.o ../multicolvar/Sprint.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/MultiReferenceBase.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/PointWiseMapping.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/MolInfo.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/BiasRepresentation.o ../tools/Citations.o ../tools/Communicator.o ../tools/CubicInterpolation.o ../tools/DLLoader.o ../tools/Exception.o ../tools/FileBase.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/Kearsley.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/OptimalAlignment.o ../tools/PDB.o ../tools/Pbc.o ../tools/RMSD.o ../tools/Random.o ../tools/Stopwatch.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../vatom/COM.o ../vatom/Center.o ../vatom/Ghost.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/ConfigInstall.o ../wrapper/PlumedStatic.o -o install/plumed -ldl  -lz -lmatheval -ldl -lopenblas -Wl,--as-needed -rdynamic -fopenmp
Building Plumed.inc
chmod a+x install/plumed-mklib
chmod a+x install/plumed-newcv
chmod a+x install/plumed-patch
mkdir -p install
cd install && g++ -shared -o libplumedKernel.so ../../analysis/Analysis.o ../../analysis/AnalysisWithLandmarks.o ../../analysis/ClassicalMultiDimensionalScaling.o ../../analysis/ClassicalScaling.o ../../analysis/Commit.o ../../analysis/Histogram.o ../../analysis/LandmarkRegister.o ../../analysis/LandmarkSelectionBase.o ../../analysis/SelectAllFrames.o ../../bias/ABMD.o ../../bias/Bias.o ../../bias/BiasValue.o ../../bias/ExtendedLagrangian.o ../../bias/External.o ../../bias/LWalls.o ../../bias/MetaD.o ../../bias/MovingRestraint.o ../../bias/PBMetaD.o ../../bias/Restraint.o ../../bias/UWalls.o ../../blas/blas.o ../../cltools/Driver.o ../../cltools/DriverDouble.o ../../cltools/DriverFloat.o ../../cltools/GenTemplate.o ../../cltools/Info.o ../../cltools/Manual.o ../../cltools/SimpleMD.o ../../cltools/SumHills.o ../../cltools/kT.o ../../colvar/Angle.o ../../colvar/CH3Shifts.o ../../colvar/CS2Backbone.o ../../colvar/Cell.o ../../colvar/Constant.o ../../colvar/ContactMap.o ../../colvar/Coordination.o ../../colvar/CoordinationBase.o ../../colvar/DHEnergy.o ../../colvar/DRMSD.o ../../colvar/Dipole.o ../../colvar/Distance.o ../../colvar/Energy.o ../../colvar/Fake.o ../../colvar/Gyration.o ../../colvar/MultiRMSD.o ../../colvar/NOE.o ../../colvar/PCARMSD.o ../../colvar/PathMSD.o ../../colvar/PathMSDBase.o ../../colvar/Position.o ../../colvar/PropertyMap.o ../../colvar/Puckering.o ../../colvar/RDC.o ../../colvar/RMSD.o ../../colvar/Template.o ../../colvar/Torsion.o ../../colvar/Volume.o ../../core/Action.o ../../core/ActionAtomistic.o ../../core/ActionPilot.o ../../core/ActionRegister.o ../../core/ActionSet.o ../../core/ActionSetup.o ../../core/ActionWithArguments.o ../../core/ActionWithValue.o ../../core/ActionWithVirtualAtom.o ../../core/Atoms.o ../../core/CLTool.o ../../core/CLToolMain.o ../../core/CLToolRegister.o ../../core/Colvar.o ../../core/ExchangePatterns.o ../../core/FlexibleBin.o ../../core/GREX.o ../../core/MDAtoms.o ../../core/PlumedMain.o ../../core/PlumedMainInitializer.o ../../core/SetupMolInfo.o ../../core/TargetDist.o ../../core/Value.o ../../function/Combine.o ../../function/Ensemble.o ../../function/FuncPathMSD.o ../../function/FuncSumHills.o ../../function/Function.o ../../function/Matheval.o ../../function/Piecewise.o ../../function/Sort.o ../../function/Target.o ../../generic/Debug.o ../../generic/DumpAtoms.o ../../generic/DumpDerivatives.o ../../generic/DumpForces.o ../../generic/DumpMassCharge.o ../../generic/DumpProjections.o ../../generic/EffectiveEnergyDrift.o ../../generic/FitToTemplate.o ../../generic/Flush.o ../../generic/Group.o ../../generic/Include.o ../../generic/Print.o ../../generic/RandomExchanges.o ../../generic/Read.o ../../generic/Time.o ../../generic/WholeMolecules.o ../../generic/WrapAround.o ../../lapack/lapack.o ../../mapping/Mapping.o ../../mapping/PCAVars.o ../../mapping/Path.o ../../mapping/PathBase.o ../../mapping/PropertyMap.o ../../mapping/SpathVessel.o ../../mapping/ZpathVessel.o ../../molfile/crdplugin.o ../../molfile/dcdplugin.o ../../molfile/gromacsplugin.o ../../molfile/pdbplugin.o ../../multicolvar/ActionVolume.o ../../multicolvar/AdjacencyMatrixAction.o ../../multicolvar/AdjacencyMatrixVessel.o ../../multicolvar/AlphaBeta.o ../../multicolvar/Angles.o ../../multicolvar/AtomValuePack.o ../../multicolvar/Bridge.o ../../multicolvar/BridgedMultiColvarFunction.o ../../multicolvar/CatomPack.o ../../multicolvar/CoordinationNumbers.o ../../multicolvar/Density.o ../../multicolvar/DihedralCorrelation.o ../../multicolvar/Distances.o ../../multicolvar/DumpMultiColvar.o ../../multicolvar/FilterBetween.o ../../multicolvar/FilterLessThan.o ../../multicolvar/FilterMoreThan.o ../../multicolvar/InPlaneDistances.o ../../multicolvar/LocalAverage.o ../../multicolvar/MultiColvar.o ../../multicolvar/MultiColvarBase.o ../../multicolvar/MultiColvarDensity.o ../../multicolvar/MultiColvarFilter.o ../../multicolvar/MultiColvarFunction.o ../../multicolvar/NumberOfLinks.o ../../multicolvar/Sprint.o ../../multicolvar/Torsions.o ../../multicolvar/VolumeAround.o ../../multicolvar/VolumeCavity.o ../../multicolvar/VolumeGradientBase.o ../../multicolvar/VolumeInCylinder.o ../../multicolvar/VolumeTetrapore.o ../../multicolvar/XDistances.o ../../multicolvar/XYDistances.o ../../reference/ArgumentOnlyDistance.o ../../reference/DRMSD.o ../../reference/Direction.o ../../reference/DotProductDistance.o ../../reference/EuclideanDistance.o ../../reference/MahalanobisDistance.o ../../reference/MetricRegister.o ../../reference/MultiDomainRMSD.o ../../reference/MultiReferenceBase.o ../../reference/NormalizedEuclideanDistance.o ../../reference/OptimalRMSD.o ../../reference/PointWiseMapping.o ../../reference/RMSDBase.o ../../reference/ReferenceArguments.o ../../reference/ReferenceAtoms.o ../../reference/ReferenceConfiguration.o ../../reference/ReferenceValuePack.o ../../reference/SimpleRMSD.o ../../reference/SingleDomainRMSD.o ../../secondarystructure/AlphaRMSD.o ../../secondarystructure/AntibetaRMSD.o ../../secondarystructure/ParabetaRMSD.o ../../secondarystructure/SecondaryStructureRMSD.o ../../setup/Load.o ../../setup/MolInfo.o ../../setup/Restart.o ../../setup/Units.o ../../tools/Angle.o ../../tools/BiasRepresentation.o ../../tools/Citations.o ../../tools/Communicator.o ../../tools/CubicInterpolation.o ../../tools/DLLoader.o ../../tools/Exception.o ../../tools/FileBase.o ../../tools/Grid.o ../../tools/HistogramBead.o ../../tools/IFile.o ../../tools/Kearsley.o ../../tools/KernelFunctions.o ../../tools/Keywords.o ../../tools/LatticeReduction.o ../../tools/LinkCells.o ../../tools/Log.o ../../tools/MolDataClass.o ../../tools/MultiValue.o ../../tools/NeighborList.o ../../tools/OFile.o ../../tools/OpenMP.o ../../tools/OptimalAlignment.o ../../tools/PDB.o ../../tools/Pbc.o ../../tools/RMSD.o ../../tools/Random.o ../../tools/Stopwatch.o ../../tools/SwitchingFunction.o ../../tools/Tensor.o ../../tools/Tools.o ../../tools/Torsion.o ../../tools/Units.o ../../tools/Vector.o ../../vatom/COM.o ../../vatom/Center.o ../../vatom/Ghost.o ../../vesselbase/ActionWithInputVessel.o ../../vesselbase/ActionWithVessel.o ../../vesselbase/AltMin.o ../../vesselbase/Between.o ../../vesselbase/BridgeVessel.o ../../vesselbase/FunctionVessel.o ../../vesselbase/Highest.o ../../vesselbase/Histogram.o ../../vesselbase/LessThan.o ../../vesselbase/Lowest.o ../../vesselbase/Max.o ../../vesselbase/Mean.o ../../vesselbase/Min.o ../../vesselbase/Moments.o ../../vesselbase/MoreThan.o ../../vesselbase/OrderingVessel.o ../../vesselbase/ShortcutVessel.o ../../vesselbase/StoreDataVessel.o ../../vesselbase/Sum.o ../../vesselbase/ValueVessel.o ../../vesselbase/Vessel.o ../../vesselbase/VesselRegister.o ../../config/ConfigInstall.o -lz -lmatheval -ldl -lopenblas -Wl,--as-needed -rdynamic -fopenmp
mkdir -p install
cd install && g++ -shared -o libplumed.so ../../analysis/Analysis.o ../../analysis/AnalysisWithLandmarks.o ../../analysis/ClassicalMultiDimensionalScaling.o ../../analysis/ClassicalScaling.o ../../analysis/Commit.o ../../analysis/Histogram.o ../../analysis/LandmarkRegister.o ../../analysis/LandmarkSelectionBase.o ../../analysis/SelectAllFrames.o ../../bias/ABMD.o ../../bias/Bias.o ../../bias/BiasValue.o ../../bias/ExtendedLagrangian.o ../../bias/External.o ../../bias/LWalls.o ../../bias/MetaD.o ../../bias/MovingRestraint.o ../../bias/PBMetaD.o ../../bias/Restraint.o ../../bias/UWalls.o ../../blas/blas.o ../../cltools/Driver.o ../../cltools/DriverDouble.o ../../cltools/DriverFloat.o ../../cltools/GenTemplate.o ../../cltools/Info.o ../../cltools/Manual.o ../../cltools/SimpleMD.o ../../cltools/SumHills.o ../../cltools/kT.o ../../colvar/Angle.o ../../colvar/CH3Shifts.o ../../colvar/CS2Backbone.o ../../colvar/Cell.o ../../colvar/Constant.o ../../colvar/ContactMap.o ../../colvar/Coordination.o ../../colvar/CoordinationBase.o ../../colvar/DHEnergy.o ../../colvar/DRMSD.o ../../colvar/Dipole.o ../../colvar/Distance.o ../../colvar/Energy.o ../../colvar/Fake.o ../../colvar/Gyration.o ../../colvar/MultiRMSD.o ../../colvar/NOE.o ../../colvar/PCARMSD.o ../../colvar/PathMSD.o ../../colvar/PathMSDBase.o ../../colvar/Position.o ../../colvar/PropertyMap.o ../../colvar/Puckering.o ../../colvar/RDC.o ../../colvar/RMSD.o ../../colvar/Template.o ../../colvar/Torsion.o ../../colvar/Volume.o ../../core/Action.o ../../core/ActionAtomistic.o ../../core/ActionPilot.o ../../core/ActionRegister.o ../../core/ActionSet.o ../../core/ActionSetup.o ../../core/ActionWithArguments.o ../../core/ActionWithValue.o ../../core/ActionWithVirtualAtom.o ../../core/Atoms.o ../../core/CLTool.o ../../core/CLToolMain.o ../../core/CLToolRegister.o ../../core/Colvar.o ../../core/ExchangePatterns.o ../../core/FlexibleBin.o ../../core/GREX.o ../../core/MDAtoms.o ../../core/PlumedMain.o ../../core/PlumedMainInitializer.o ../../core/SetupMolInfo.o ../../core/TargetDist.o ../../core/Value.o ../../function/Combine.o ../../function/Ensemble.o ../../function/FuncPathMSD.o ../../function/FuncSumHills.o ../../function/Function.o ../../function/Matheval.o ../../function/Piecewise.o ../../function/Sort.o ../../function/Target.o ../../generic/Debug.o ../../generic/DumpAtoms.o ../../generic/DumpDerivatives.o ../../generic/DumpForces.o ../../generic/DumpMassCharge.o ../../generic/DumpProjections.o ../../generic/EffectiveEnergyDrift.o ../../generic/FitToTemplate.o ../../generic/Flush.o ../../generic/Group.o ../../generic/Include.o ../../generic/Print.o ../../generic/RandomExchanges.o ../../generic/Read.o ../../generic/Time.o ../../generic/WholeMolecules.o ../../generic/WrapAround.o ../../lapack/lapack.o ../../mapping/Mapping.o ../../mapping/PCAVars.o ../../mapping/Path.o ../../mapping/PathBase.o ../../mapping/PropertyMap.o ../../mapping/SpathVessel.o ../../mapping/ZpathVessel.o ../../molfile/crdplugin.o ../../molfile/dcdplugin.o ../../molfile/gromacsplugin.o ../../molfile/pdbplugin.o ../../multicolvar/ActionVolume.o ../../multicolvar/AdjacencyMatrixAction.o ../../multicolvar/AdjacencyMatrixVessel.o ../../multicolvar/AlphaBeta.o ../../multicolvar/Angles.o ../../multicolvar/AtomValuePack.o ../../multicolvar/Bridge.o ../../multicolvar/BridgedMultiColvarFunction.o ../../multicolvar/CatomPack.o ../../multicolvar/CoordinationNumbers.o ../../multicolvar/Density.o ../../multicolvar/DihedralCorrelation.o ../../multicolvar/Distances.o ../../multicolvar/DumpMultiColvar.o ../../multicolvar/FilterBetween.o ../../multicolvar/FilterLessThan.o ../../multicolvar/FilterMoreThan.o ../../multicolvar/InPlaneDistances.o ../../multicolvar/LocalAverage.o ../../multicolvar/MultiColvar.o ../../multicolvar/MultiColvarBase.o ../../multicolvar/MultiColvarDensity.o ../../multicolvar/MultiColvarFilter.o ../../multicolvar/MultiColvarFunction.o ../../multicolvar/NumberOfLinks.o ../../multicolvar/Sprint.o ../../multicolvar/Torsions.o ../../multicolvar/VolumeAround.o ../../multicolvar/VolumeCavity.o ../../multicolvar/VolumeGradientBase.o ../../multicolvar/VolumeInCylinder.o ../../multicolvar/VolumeTetrapore.o ../../multicolvar/XDistances.o ../../multicolvar/XYDistances.o ../../reference/ArgumentOnlyDistance.o ../../reference/DRMSD.o ../../reference/Direction.o ../../reference/DotProductDistance.o ../../reference/EuclideanDistance.o ../../reference/MahalanobisDistance.o ../../reference/MetricRegister.o ../../reference/MultiDomainRMSD.o ../../reference/MultiReferenceBase.o ../../reference/NormalizedEuclideanDistance.o ../../reference/OptimalRMSD.o ../../reference/PointWiseMapping.o ../../reference/RMSDBase.o ../../reference/ReferenceArguments.o ../../reference/ReferenceAtoms.o ../../reference/ReferenceConfiguration.o ../../reference/ReferenceValuePack.o ../../reference/SimpleRMSD.o ../../reference/SingleDomainRMSD.o ../../secondarystructure/AlphaRMSD.o ../../secondarystructure/AntibetaRMSD.o ../../secondarystructure/ParabetaRMSD.o ../../secondarystructure/SecondaryStructureRMSD.o ../../setup/Load.o ../../setup/MolInfo.o ../../setup/Restart.o ../../setup/Units.o ../../tools/Angle.o ../../tools/BiasRepresentation.o ../../tools/Citations.o ../../tools/Communicator.o ../../tools/CubicInterpolation.o ../../tools/DLLoader.o ../../tools/Exception.o ../../tools/FileBase.o ../../tools/Grid.o ../../tools/HistogramBead.o ../../tools/IFile.o ../../tools/Kearsley.o ../../tools/KernelFunctions.o ../../tools/Keywords.o ../../tools/LatticeReduction.o ../../tools/LinkCells.o ../../tools/Log.o ../../tools/MolDataClass.o ../../tools/MultiValue.o ../../tools/NeighborList.o ../../tools/OFile.o ../../tools/OpenMP.o ../../tools/OptimalAlignment.o ../../tools/PDB.o ../../tools/Pbc.o ../../tools/RMSD.o ../../tools/Random.o ../../tools/Stopwatch.o ../../tools/SwitchingFunction.o ../../tools/Tensor.o ../../tools/Tools.o ../../tools/Torsion.o ../../tools/Units.o ../../tools/Vector.o ../../vatom/COM.o ../../vatom/Center.o ../../vatom/Ghost.o ../../vesselbase/ActionWithInputVessel.o ../../vesselbase/ActionWithVessel.o ../../vesselbase/AltMin.o ../../vesselbase/Between.o ../../vesselbase/BridgeVessel.o ../../vesselbase/FunctionVessel.o ../../vesselbase/Highest.o ../../vesselbase/Histogram.o ../../vesselbase/LessThan.o ../../vesselbase/Lowest.o ../../vesselbase/Max.o ../../vesselbase/Mean.o ../../vesselbase/Min.o ../../vesselbase/Moments.o ../../vesselbase/MoreThan.o ../../vesselbase/OrderingVessel.o ../../vesselbase/ShortcutVessel.o ../../vesselbase/StoreDataVessel.o ../../vesselbase/Sum.o ../../vesselbase/ValueVessel.o ../../vesselbase/Vessel.o ../../vesselbase/VesselRegister.o ../../config/ConfigInstall.o ../../wrapper/PlumedStatic.o -lz -lmatheval -ldl -lopenblas -Wl,--as-needed -rdynamic -fopenmp
g++  ../main/main.o ../wrapper/Plumed.o -o install/plumed-runtime -ldl 
Building Plumed.inc, runtime-linking version
Building Plumed.inc, shared version
Building Plumed.inc, static version
Building Plumed.cmake
Building Plumed.cmake, static version
Building Plumed.cmake, runtime-linking version
Building Plumed.cmake, shared version
g++  ../main/main.o "/builddir/build/BUILD/plumed-2.2.1/serial/src/lib/install/libplumed.so" -o install/plumed-shared -ldl 
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make[5]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make install/kernel.o
make[5]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
ld -r -o install/kernel.o ../analysis/Analysis.o ../analysis/AnalysisWithLandmarks.o ../analysis/ClassicalMultiDimensionalScaling.o ../analysis/ClassicalScaling.o ../analysis/Commit.o ../analysis/Histogram.o ../analysis/LandmarkRegister.o ../analysis/LandmarkSelectionBase.o ../analysis/SelectAllFrames.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/UWalls.o ../blas/blas.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../colvar/Angle.o ../colvar/CH3Shifts.o ../colvar/CS2Backbone.o ../colvar/Cell.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/Energy.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/NOE.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RDC.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../function/Combine.o ../function/Ensemble.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/Matheval.o ../function/Piecewise.o ../function/Sort.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/Time.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../lapack/lapack.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AdjacencyMatrixAction.o ../multicolvar/AdjacencyMatrixVessel.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvar.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarFunction.o ../multicolvar/NumberOfLinks.o ../multicolvar/Sprint.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/MultiReferenceBase.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/PointWiseMapping.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/MolInfo.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/BiasRepresentation.o ../tools/Citations.o ../tools/Communicator.o ../tools/CubicInterpolation.o ../tools/DLLoader.o ../tools/Exception.o ../tools/FileBase.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/Kearsley.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/OptimalAlignment.o ../tools/PDB.o ../tools/Pbc.o ../tools/RMSD.o ../tools/Random.o ../tools/Stopwatch.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../vatom/COM.o ../vatom/Center.o ../vatom/Ghost.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/Config.o
make[5]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make[4]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make[3]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src'
make[1]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial'
~/build/BUILD/plumed-2.2.1
~/build/BUILD/plumed-2.2.1/openmpi ~/build/BUILD/plumed-2.2.1
+ popd
+ pushd openmpi
+ . /etc/profile.d/modules.sh
++++ /bin/ps -p 5899 -ocomm=
+++ /bin/basename sh
++ shell=sh
++ '[' -f /usr/share/Modules/init/sh ']'
++ . /usr/share/Modules/init/sh
+++ MODULESHOME=/usr/share/Modules
+++ export MODULESHOME
+++ '[' '' = '' ']'
+++ LOADEDMODULES=
+++ export LOADEDMODULES
+++ '[' /usr/share/Modules/modulefiles:/etc/modulefiles = '' ']'
+ module load mpi/openmpi-x86_64
++ /usr/bin/modulecmd sh load mpi/openmpi-x86_64
+ eval LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ';export' 'LD_LIBRARY_PATH;LOADEDMODULES=mpi/openmpi-x86_64' ';export' 'LOADEDMODULES;MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man:/usr/local/share/man' ';export' 'MANPATH;MPI_BIN=/usr/lib64/openmpi/bin' ';export' 'MPI_BIN;MPI_COMPILER=openmpi-x86_64' ';export' 'MPI_COMPILER;MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-x86_64' ';export' 'MPI_FORTRAN_MOD_DIR;MPI_HOME=/usr/lib64/openmpi' ';export' 'MPI_HOME;MPI_INCLUDE=/usr/include/openmpi-x86_64' ';export' 'MPI_INCLUDE;MPI_LIB=/usr/lib64/openmpi/lib' ';export' 'MPI_LIB;MPI_MAN=/usr/share/man/openmpi-x86_64' ';export' 'MPI_MAN;MPI_PYTHON_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi' ';export' 'MPI_PYTHON_SITEARCH;MPI_SUFFIX=_openmpi' ';export' 'MPI_SUFFIX;MPI_SYSCONFIG=/etc/openmpi-x86_64' ';export' 'MPI_SYSCONFIG;PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin' ';export' 'PATH;PYTHONPATH=/usr/lib64/python2.7/site-packages/openmpi' ';export' 'PYTHONPATH;_LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64' ';export' '_LMFILES_;'
++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib
++ export LD_LIBRARY_PATH
++ LOADEDMODULES=mpi/openmpi-x86_64
++ export LOADEDMODULES
++ MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man:/usr/local/share/man
++ export MANPATH
++ MPI_BIN=/usr/lib64/openmpi/bin
++ export MPI_BIN
++ MPI_COMPILER=openmpi-x86_64
++ export MPI_COMPILER
++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-x86_64
++ export MPI_FORTRAN_MOD_DIR
++ MPI_HOME=/usr/lib64/openmpi
++ export MPI_HOME
++ MPI_INCLUDE=/usr/include/openmpi-x86_64
++ export MPI_INCLUDE
++ MPI_LIB=/usr/lib64/openmpi/lib
++ export MPI_LIB
++ MPI_MAN=/usr/share/man/openmpi-x86_64
++ export MPI_MAN
++ MPI_PYTHON_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi
++ export MPI_PYTHON_SITEARCH
++ MPI_SUFFIX=_openmpi
++ export MPI_SUFFIX
++ MPI_SYSCONFIG=/etc/openmpi-x86_64
++ export MPI_SYSCONFIG
++ PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin
++ export PATH
++ PYTHONPATH=/usr/lib64/python2.7/site-packages/openmpi
++ export PYTHONPATH
++ _LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64
++ export _LMFILES_
+ export 'CFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic'
+ CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic'
+ CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic'
+ export CFLAGS
+ CXXFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic'
+ export CXXFLAGS
+ FFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS=-Wl,--as-needed
+ export LDFLAGS
+ '[' 1 == 1 ']'
+ '[' x86_64 == ppc64le ']'
++ find . -name config.guess -o -name config.sub
+ ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --libdir=/usr/lib64/openmpi/lib --includedir=/usr/include/openmpi-x86_64 --bindir=/usr/lib64/openmpi/bin
configure: WARNING: unrecognized options: --disable-dependency-tracking
checking for x86_64-redhat-linux-gnu-mpic++... no
checking for x86_64-redhat-linux-gnu-mpicxx... no
checking for x86_64-redhat-linux-gnu-mpiicpc... no
checking for x86_64-redhat-linux-gnu-openmpic++... no
checking for x86_64-redhat-linux-gnu-openmpicxx... no
checking for x86_64-redhat-linux-gnu-g++... no
checking for x86_64-redhat-linux-gnu-cxx... no
checking for x86_64-redhat-linux-gnu-icpc... no
checking for x86_64-redhat-linux-gnu-gpp... no
checking for x86_64-redhat-linux-gnu-aCC... no
checking for x86_64-redhat-linux-gnu-CC... no
checking for x86_64-redhat-linux-gnu-cxx... no
checking for x86_64-redhat-linux-gnu-cc++... no
checking for x86_64-redhat-linux-gnu-cl.exe... no
checking for x86_64-redhat-linux-gnu-FCC... no
checking for x86_64-redhat-linux-gnu-KCC... no
checking for x86_64-redhat-linux-gnu-RCC... no
checking for x86_64-redhat-linux-gnu-xlC_r... no
checking for x86_64-redhat-linux-gnu-xlC... no
checking for mpic++... mpic++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether mpic++ accepts -g... yes
checking for x86_64-redhat-linux-gnu-gcc... no
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for x86_64-redhat-linux-gnu-gfortran... no
checking for x86_64-redhat-linux-gnu-g95... no
checking for x86_64-redhat-linux-gnu-xlf95... no
checking for x86_64-redhat-linux-gnu-f95... no
checking for x86_64-redhat-linux-gnu-fort... no
checking for x86_64-redhat-linux-gnu-ifort... no
checking for x86_64-redhat-linux-gnu-ifc... no
checking for x86_64-redhat-linux-gnu-efc... no
checking for x86_64-redhat-linux-gnu-pgfortran... no
checking for x86_64-redhat-linux-gnu-pgf95... no
checking for x86_64-redhat-linux-gnu-lf95... no
checking for x86_64-redhat-linux-gnu-ftn... no
checking for x86_64-redhat-linux-gnu-nagfor... no
checking for x86_64-redhat-linux-gnu-xlf90... no
checking for x86_64-redhat-linux-gnu-f90... no
checking for x86_64-redhat-linux-gnu-pgf90... no
checking for x86_64-redhat-linux-gnu-pghpf... no
checking for x86_64-redhat-linux-gnu-epcf90... no
checking for x86_64-redhat-linux-gnu-g77... no
checking for x86_64-redhat-linux-gnu-xlf... no
checking for x86_64-redhat-linux-gnu-f77... no
checking for x86_64-redhat-linux-gnu-frt... no
checking for x86_64-redhat-linux-gnu-pgf77... no
checking for x86_64-redhat-linux-gnu-cf77... no
checking for x86_64-redhat-linux-gnu-fort77... no
checking for x86_64-redhat-linux-gnu-fl32... no
checking for x86_64-redhat-linux-gnu-af77... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
configure: Initial CXX:         mpic++
configure: Initial CXXFLAGS:    -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic
configure: Initial CPPFLAGS:    
configure: Initial CFLAGS:      -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic
configure: Initial LDFLAGS:     -Wl,--as-needed
configure: Initial LIBS:        -Wl,--as-needed
configure: Initial STATIC_LIBS: -Wl,--as-needed
configure: Initial LD:          mpic++
configure: Initial LDSO:        mpic++
configure: Initial SOEXT:       
checking whether mpic++ accepts -fPIC... yes
checking whether gcc accepts -fPIC... yes
checking whether mpic++ accepts -Wall... yes
checking whether mpic++ accepts -pedantic... yes
checking whether mpic++ accepts -ansi... yes
checking whether mpic++ supports explicit... yes
configure: Now we will check compulsory headers and libraries
checking how to run the C++ preprocessor... mpic++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dirent.h usability... yes
checking dirent.h presence... yes
checking for dirent.h... yes
checking for readdir... yes
checking for dgemv... no
checking for dgemv_... yes
checking for dsyevr_... yes
configure: Now we will check for optional headers and libraries
checking for molfile_dcdplugin_init in -lmolfile_plugin... no
checking for dlopen in -ldl... configure: WARNING: using internal molfile_plugins, which only support dcd/xtc/trr/trj/crd files
yes
checking mpi.h usability... yes
checking mpi.h presence... yes
checking for mpi.h... yes
checking for MPI_Init... yes
checking for mpic++ option to support OpenMP... -fopenmp
checking matheval.h usability... yes
checking matheval.h presence... yes
checking for matheval.h... yes
checking for evaluator_create... no
checking for evaluator_create in -lmatheval... yes
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking for clock_gettime... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for gettimeofday... yes
checking for dirent.h... (cached) yes
checking for readdir_r... yes
checking regex.h usability... yes
checking regex.h presence... yes
checking for regex.h... yes
checking for regcomp... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking for dlopen... yes
checking execinfo.h usability... yes
checking execinfo.h presence... yes
checking for execinfo.h... yes
checking for backtrace... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for gzopen... no
checking for gzopen in -lz... yes
checking xdrfile/xdrfile_xtc.h usability... no
checking xdrfile/xdrfile_xtc.h presence... no
checking for xdrfile/xdrfile_xtc.h... no
configure: Release mode, adding -DNDEBUG
configure: WARNING: cannot enable __PLUMED_HAS_XDRFILE
configure: *** Special settings for dynamic libraries on Linux ***
configure: Dynamic library extension is 'so'
configure: LDSO and LDFLAGS need special flags
checking whether LDFLAGS can contain -rdynamic... yes
configure: Using LDSO='mpic++ -shared'
configure: Using LDFLAGS='-Wl,--as-needed -rdynamic'
checking whether LDSO can create dynamic libraries... yes
checking for doxygen... found
configure: Doxygen version is fine
checking for dot... found
checking for xxd... found
checking whether a program can be run on this machine... yes
checking whether a program compiled with mpi can be run on this machine... yes
configure: PLUMED seems to be configured properly!
configure: **************************
checking whether C++ objects can be grouped with ld -r... yes
configure: I will now check if C++ objects can be linked by C/Fortran compilers
configure: This is relevant if you want to use plumed patch --static on a non-C++ code
checking whether C can link a C++ object... no
checking whether C can link a C++ object with library -lstdc++... no
checking whether C can link a C++ object with library -lc++... no
checking whether C can link a C++ object with library -lmpi_cxx... no
configure: WARNING: You might have problems linking C programs.
configure: WARNING: Please add c++ library to LIBS
checking whether FORTRAN can link a C++ object... no
checking whether FORTRAN can link a C++ object with library -lstdc++... no
checking whether FORTRAN can link a C++ object with library -lc++... no
checking whether FORTRAN can link a C++ object with library -lmpi_cxx... no
configure: WARNING: You might have problems linking FORTRAN programs.
configure: WARNING: Please add c++ library to LIBS
configure: **** PLUMED will be installed using the following paths:
configure: **** prefix: /usr
configure: **** exec_prefix: /usr
configure: **** bindir: /usr/lib64/openmpi/bin
configure: **** libdir: /usr/lib64/openmpi/lib
configure: **** includedir: /usr/include/openmpi-x86_64
configure: **** datarootdir: ${prefix}/share
configure: **** datadir: /usr/share
configure: **** docdir: ${prefix}/share/doc/plumed
configure: **** htmldir: ${docdir}
configure: **** Executable will be named plumed
configure: **** You can change paths later using options to "make install"
configure: **** e.g. with "make install prefix=/path"
configure: **** PLUMED will be compiled using MPI
configure: creating ./config.status
config.status: creating Makefile.conf
config.status: creating sourceme.sh
config.status: creating stamp-h
configure: WARNING: unrecognized options: --disable-dependency-tracking
+ make -j2
make lib
make[1]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi'
make	-C src
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src'
make -C lib
make[3]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make dirslinks
make[4]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
*** Updating links to used modules in all directories ***
make ../analysis.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../lapack.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links
make[5]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make -C ../analysis links
make -C ../bias links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/analysis'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/analysis
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/bias'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/bias
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/bias'
make -C ../blas links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/blas'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/blas
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/blas'
make -C ../cltools links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/cltools'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/cltools
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/analysis'
make -C ../colvar links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/colvar'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/colvar
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/cltools'
make -C ../config links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
Nothing to do in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/config
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make -C ../core links
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/colvar'
make -C ../function links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/function'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/function
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/core'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/core
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/core'
make -C ../generic links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/generic'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/generic
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/function'
make -C ../lapack links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lapack'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/lapack
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lapack'
make -C ../main links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/main'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/main
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/main'
make -C ../mapping links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/mapping'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/mapping
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/generic'
make -C ../molfile links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/molfile'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/molfile
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/molfile'
make -C ../multicolvar links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/multicolvar'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/multicolvar
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/mapping'
make -C ../reference links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/reference'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/reference
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/multicolvar'
make -C ../secondarystructure links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/secondarystructure'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/secondarystructure
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/reference'
make -C ../setup links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/setup'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/setup
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/secondarystructure'
make -C ../tools links
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/setup'
make -C ../vatom links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vatom'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/vatom
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/tools'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/tools
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/tools'
make -C ../vesselbase links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vesselbase'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/vesselbase
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vatom'
make -C ../wrapper links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/wrapper'
Nothing to do in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/wrapper
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/wrapper'
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vesselbase'
make[5]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make[4]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make dirs
make[4]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
*** Compiling all directories ***
make ../analysis ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../lapack ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper
make[5]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make -C ../analysis obj
make -C ../bias obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/analysis'
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/bias'
compiling  AnalysisWithLandmarks.cpp
compiling  Restraint.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from Analysis.h:26,
                 from AnalysisWithLandmarks.h:25,
                 from AnalysisWithLandmarks.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  PBMetaD.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/Atoms.h:1,
                 from PBMetaD.cpp:27:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  ClassicalScaling.cpp
PBMetaD.cpp: In destructor 'virtual PLMD::bias::PBMetaD::~PBMetaD()':
PBMetaD.cpp:256:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0; i<BiasGrids_.size();   ++i) delete BiasGrids_[i];
                                  ^
PBMetaD.cpp:257:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0; i<hillsOfiles_.size(); ++i){
                                    ^
PBMetaD.cpp: In constructor 'PLMD::bias::PBMetaD::PBMetaD(const PLMD::ActionOptions&)':
PBMetaD.cpp:202:11: warning: 'PLMD::bias::PBMetaD::kbt_' will be initialized after [-Wreorder]
   double  kbt_;
           ^
PBMetaD.cpp:199:11: warning:   'bool PLMD::bias::PBMetaD::grid_' [-Wreorder]
   bool    grid_;
           ^
PBMetaD.cpp:263:1: warning:   when initialized here [-Wreorder]
 PBMetaD::PBMetaD(const ActionOptions& ao):
 ^
PBMetaD.cpp:431:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<hillsfname.size();++i){
                                 ^
PBMetaD.cpp:447:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<hillsfname.size();++i){
                                ^
In file included from reference/../../reference/tools/../../tools/Communicator.h:25:0,
                 from reference/../../reference/tools/../../tools/DynamicList.h:26,
                 from reference/../../reference/tools/../../tools/MultiValue.h:27,
                 from reference/../../reference/tools/MultiValue.h:1,
                 from reference/../../reference/ReferenceValuePack.h:25,
                 from reference/../../reference/ReferenceConfiguration.h:31,
                 from reference/../../reference/MultiReferenceBase.h:25,
                 from reference/../../reference/PointWiseMapping.h:25,
                 from reference/PointWiseMapping.h:1,
                 from ClassicalScaling.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Commit.cpp
compiling  LandmarkSelectionBase.cpp
In file included from reference/../../reference/tools/../../tools/Communicator.h:25:0,
                 from reference/../../reference/tools/../../tools/DynamicList.h:26,
                 from reference/../../reference/tools/../../tools/MultiValue.h:27,
                 from reference/../../reference/tools/MultiValue.h:1,
                 from reference/../../reference/ReferenceValuePack.h:25,
                 from reference/../../reference/ReferenceConfiguration.h:31,
                 from reference/ReferenceConfiguration.h:1,
                 from LandmarkSelectionBase.h:25,
                 from LandmarkSelectionBase.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Histogram.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from Analysis.h:26,
                 from Histogram.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  ExtendedLagrangian.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/Atoms.h:1,
                 from ExtendedLagrangian.cpp:26:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Analysis.cpp
compiling  LWalls.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from Analysis.h:26,
                 from Analysis.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  MovingRestraint.cpp
compiling  SelectAllFrames.cpp
In file included from reference/../../reference/tools/../../tools/Communicator.h:25:0,
                 from reference/../../reference/tools/../../tools/DynamicList.h:26,
                 from reference/../../reference/tools/../../tools/MultiValue.h:27,
                 from reference/../../reference/tools/MultiValue.h:1,
                 from reference/../../reference/ReferenceValuePack.h:25,
                 from reference/../../reference/ReferenceConfiguration.h:31,
                 from reference/ReferenceConfiguration.h:1,
                 from LandmarkSelectionBase.h:25,
                 from SelectAllFrames.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  External.cpp
compiling  ClassicalMultiDimensionalScaling.cpp
compiling  MetaD.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from Analysis.h:26,
                 from AnalysisWithLandmarks.h:25,
                 from ClassicalMultiDimensionalScaling.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/Atoms.h:1,
                 from MetaD.cpp:27:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  LandmarkRegister.cpp
In file included from reference/../../reference/tools/../../tools/Communicator.h:25:0,
                 from reference/../../reference/tools/../../tools/DynamicList.h:26,
                 from reference/../../reference/tools/../../tools/MultiValue.h:27,
                 from reference/../../reference/tools/MultiValue.h:1,
                 from reference/../../reference/ReferenceValuePack.h:25,
                 from reference/../../reference/ReferenceConfiguration.h:31,
                 from reference/ReferenceConfiguration.h:1,
                 from LandmarkSelectionBase.h:25,
                 from LandmarkRegister.h:29,
                 from LandmarkRegister.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/analysis'
make -C ../blas obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/blas'
compiling  blas.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/blas'
make -C ../cltools obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/cltools'
compiling  Manual.cpp
compiling  SumHills.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/Communicator.h:1,
                 from SumHills.cpp:28:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  SimpleMD.cpp
SimpleMD.cpp: In member function 'void PLMD::cltools::SimpleMD::read_natoms(const string&, int&)':
SimpleMD.cpp:197:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fp,"%1000d",&natoms);
                              ^
SimpleMD.cpp: In member function 'void PLMD::cltools::SimpleMD::read_positions(const string&, int, std::vector<PLMD::VectorGeneric<3u> >&, double*)':
SimpleMD.cpp:211:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(buffer,256,fp);
                       ^
SimpleMD.cpp:212:66: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fp,"%1000lf %1000lf %1000lf",&cell[0],&cell[1],&cell[2]);
                                                                  ^
SimpleMD.cpp:214:107: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%255s %1000lf %1000lf %1000lf",atomname,&positions[i][0],&positions[i][1],&positions[i][2]);
                                                                                                           ^
compiling  BiasValue.cpp
compiling  UWalls.cpp
compiling  kT.cpp
compiling  Driver.cpp
compiling  Bias.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/Communicator.h:1,
                 from Driver.cpp:26:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  ABMD.cpp
compiling  GenTemplate.cpp
compiling  DriverFloat.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/Communicator.h:1,
                 from Driver.cpp:26,
                 from DriverFloat.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/bias'
make -C ../colvar obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/colvar'
compiling  Torsion.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from Torsion.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Coordination.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from CoordinationBase.h:24,
                 from Coordination.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  PathMSDBase.cpp
compiling  Info.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from PathMSDBase.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  DriverDouble.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/Communicator.h:1,
                 from Driver.cpp:26,
                 from DriverDouble.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Volume.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from Volume.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/cltools'
compiling  RDC.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from RDC.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
make -C ../config obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make PLUMED_FORCE=yes ConfigInstall.cpp Config.cpp version.h
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
Updating ConfigInstall.cpp
cmp -s ConfigInstall.cpp~ ConfigInstall.cpp || cp ConfigInstall.cpp~ ConfigInstall.cpp
rm ConfigInstall.cpp~
Updating Config.cpp
cmp -s Config.cpp~ Config.cpp || cp Config.cpp~ Config.cpp
rm Config.cpp~
Updating version.h
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make Config.o ConfigInstall.o compile_options.sh
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
cat ../../Makefile.conf | xxd -i > Makefile.conf.xxd
Building compile_options.sh, a sourceable bash script with some compilation options
compiling  Config.cpp
compiling  ConfigInstall.cpp
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make -C ../core obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/core'
compiling  Value.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/Communicator.h:1,
                 from Atoms.h:25,
                 from ActionAtomistic.h:27,
                 from Value.cpp:24:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  PathMSD.cpp
compiling  SetupMolInfo.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from PathMSDBase.h:25,
                 from PathMSD.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/Communicator.h:1,
                 from Atoms.h:25,
                 from ActionAtomistic.h:27,
                 from SetupMolInfo.h:26,
                 from SetupMolInfo.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  NOE.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from NOE.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  PlumedMainInitializer.cpp
compiling  CLTool.cpp
compiling  FlexibleBin.cpp
compiling  Distance.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from Distance.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  ActionRegister.cpp
compiling  Energy.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from Energy.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Action.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/Communicator.h:1,
                 from Atoms.h:25,
                 from Action.cpp:27:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  DRMSD.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from DRMSD.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  ActionWithArguments.cpp
compiling  CS2Backbone.cpp
compiling  RMSD.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from RMSD.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  ActionPilot.cpp
compiling  ActionWithValue.cpp
compiling  PCARMSD.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from PCARMSD.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
PCARMSD.cpp: In member function 'virtual void PLMD::colvar::PCARMSD::calculate()':
PCARMSD.cpp:217:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
          for(unsigned i=0;i<getNumberOfComponents();++i) setBoxDerivativesNoPbc( getPntrToComponent(i) );
                                                   ^
compiling  PlumedMain.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/Communicator.h:1,
                 from Atoms.h:25,
                 from ActionAtomistic.h:27,
                 from PlumedMain.cpp:28:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
PlumedMain.cpp: In member function 'void PLMD::PlumedMain::load(const string&)':
PlumedMain.cpp:732:50: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
        if(comm.Get_rank()==0) system(cmd.c_str());
                                                  ^
compiling  MultiRMSD.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from MultiRMSD.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Atoms.cpp
compiling  CH3Shifts.cpp
compiling  Position.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/Communicator.h:1,
                 from Atoms.h:25,
                 from Atoms.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from Position.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
Atoms.cpp: In member function 'void PLMD::Atoms::share(const std::set<PLMD::AtomNumber>&)':
Atoms.cpp:171:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned i=0;i<natoms;i++) forces[i].zero();
                        ^
Atoms.cpp: In member function 'void PLMD::Atoms::setAtomsGatindex(int*, bool)':
Atoms.cpp:355:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if( gatindex.size()==natoms ){
                        ^
Atoms.cpp:358:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           if( gatindex[i]!=i ){ shuffledAtoms=1; break; }
                            ^
Atoms.cpp: In member function 'void PLMD::Atoms::setAtomsContiguous(int)':
Atoms.cpp:374:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(gatindex.size()<natoms) shuffledAtoms=1;
                      ^
Atoms.cpp: In member function 'void PLMD::Atoms::getLocalForces(std::vector<PLMD::VectorGeneric<3u> >&)':
Atoms.cpp:510:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0; i<gatindex.size(); i++) localForces[i] = forces[gatindex[i]];
                                ^
compiling  Angle.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from Angle.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  CLToolRegister.cpp
compiling  CoordinationBase.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from CoordinationBase.h:24,
                 from CoordinationBase.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
CoordinationBase.cpp: In member function 'virtual void PLMD::colvar::CoordinationBase::calculate()':
CoordinationBase.cpp:198:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<getPositions().size();i++) deriv[i]+=omp_deriv[i];
                                     ^
compiling  Colvar.cpp
compiling  ContactMap.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/Communicator.h:1,
                 from Atoms.h:25,
                 from ActionAtomistic.h:27,
                 from Colvar.h:25,
                 from Colvar.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from ContactMap.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  ExchangePatterns.cpp
compiling  ActionAtomistic.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/Communicator.h:1,
                 from Atoms.h:25,
                 from ActionAtomistic.h:27,
                 from ActionAtomistic.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
ActionAtomistic.cpp: In member function 'void PLMD::ActionAtomistic::requestAtoms(const std::vector<PLMD::AtomNumber>&)':
ActionAtomistic.cpp:74:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(indexes[i].index()>=n) error("atom out of range");
                            ^
compiling  Dipole.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from Dipole.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  TargetDist.cpp
compiling  Constant.cpp
compiling  ActionWithVirtualAtom.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from Constant.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/Communicator.h:1,
                 from Atoms.h:25,
                 from ActionAtomistic.h:27,
                 from ActionWithVirtualAtom.h:25,
                 from ActionWithVirtualAtom.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Puckering.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from Puckering.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  GREX.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/Communicator.h:1,
                 from Atoms.h:25,
                 from GREX.cpp:24:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Cell.cpp
compiling  CLToolMain.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from Cell.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/Communicator.h:1,
                 from CLToolMain.cpp:24:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
CLToolMain.cpp: In static member function 'static int PLMD::CLToolMain::run(int, char**, FILE*, FILE*, PLMD::Communicator&)':
CLToolMain.cpp:246:24: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
     system(cmd.c_str());
                        ^
compiling  PropertyMap.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from PathMSDBase.h:25,
                 from PropertyMap.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  ActionSet.cpp
compiling  MDAtoms.cpp
compiling  ActionSetup.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/core'
make -C ../function obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/function'
compiling  FuncSumHills.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/Communicator.h:1,
                 from FuncSumHills.cpp:25:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Gyration.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from Gyration.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Template.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from Template.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  DHEnergy.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from CoordinationBase.h:24,
                 from DHEnergy.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Ensemble.cpp
compiling  Fake.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/Communicator.h:1,
                 from Ensemble.cpp:24:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from Fake.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from core/../../core/tools/../../tools/Keywords.h:29:0,
                 from core/../../core/tools/Keywords.h:1,
                 from core/../../core/Action.h:27,
                 from core/../../core/ActionAtomistic.h:25,
                 from core/../../core/Colvar.h:25,
                 from core/Colvar.h:1,
                 from Colvar.h:24,
                 from Fake.cpp:22:
Fake.cpp: In constructor 'PLMD::colvar::ColvarFake::ColvarFake(const PLMD::ActionOptions&)':
Fake.cpp:90:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    plumed_massert(getNumberOfComponents()*2==period.size(),"the periodicty should coincide with the number of components");
                                                          ^
core/../../core/tools/../../tools/Exception.h:132:39: note: in definition of macro 'plumed_massert'
 #define plumed_massert(test,msg) if(!(test)) throw PLMD::Exception("assertion failed " #test ", " msg,__FILE__,__LINE__,__PRETTY_FUNCTION__)
                                       ^
compiling  Combine.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/colvar'
make -C ../generic obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/generic'
compiling  DumpAtoms.cpp
compiling  Target.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from DumpAtoms.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from reference/../../reference/tools/../../tools/Communicator.h:25:0,
                 from reference/../../reference/tools/../../tools/DynamicList.h:26,
                 from reference/../../reference/tools/../../tools/MultiValue.h:27,
                 from reference/../../reference/tools/MultiValue.h:1,
                 from reference/../../reference/ReferenceValuePack.h:25,
                 from reference/../../reference/ReferenceConfiguration.h:31,
                 from reference/../../reference/MetricRegister.h:32,
                 from reference/MetricRegister.h:1,
                 from Target.cpp:25:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Function.cpp
compiling  DumpForces.cpp
compiling  Sort.cpp
compiling  Include.cpp
compiling  FuncPathMSD.cpp
FuncPathMSD.cpp: In constructor 'PLMD::function::FuncPathMSD::FuncPathMSD(const PLMD::ActionOptions&)':
FuncPathMSD.cpp:184:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
            if(neigh_size>getNumberOfArguments()){
                                               ^
compiling  RandomExchanges.cpp
compiling  WholeMolecules.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from WholeMolecules.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Matheval.cpp
compiling  Piecewise.cpp
compiling  Flush.cpp
compiling  DumpProjections.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/function'
make -C ../lapack obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lapack'
compiling  lapack.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lapack'
make -C ../main obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/main'
compiling  main.cpp
In file included from main.cpp:26:0:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Read.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/Atoms.h:1,
                 from Read.cpp:27:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/main'
make -C ../mapping obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/mapping'
compiling  ZpathVessel.cpp
In file included from vesselbase/../../vesselbase/core/../../core/tools/../../tools/Communicator.h:25:0,
                 from vesselbase/../../vesselbase/core/../../core/tools/Communicator.h:1,
                 from vesselbase/../../vesselbase/core/../../core/Atoms.h:25,
                 from vesselbase/../../vesselbase/core/../../core/ActionAtomistic.h:27,
                 from vesselbase/../../vesselbase/core/ActionAtomistic.h:1,
                 from vesselbase/../../vesselbase/ActionWithVessel.h:26,
                 from vesselbase/../../vesselbase/Vessel.h:31,
                 from vesselbase/../../vesselbase/ValueVessel.h:29,
                 from vesselbase/../../vesselbase/FunctionVessel.h:28,
                 from vesselbase/FunctionVessel.h:1,
                 from ZpathVessel.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  PathBase.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from Mapping.h:25,
                 from PathBase.h:25,
                 from PathBase.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Print.cpp
compiling  Path.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from Mapping.h:25,
                 from PathBase.h:25,
                 from Path.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  FitToTemplate.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from FitToTemplate.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  SpathVessel.cpp
In file included from vesselbase/../../vesselbase/core/../../core/tools/../../tools/Communicator.h:25:0,
                 from vesselbase/../../vesselbase/core/../../core/tools/Communicator.h:1,
                 from vesselbase/../../vesselbase/core/../../core/Atoms.h:25,
                 from vesselbase/../../vesselbase/core/../../core/ActionAtomistic.h:27,
                 from vesselbase/../../vesselbase/core/ActionAtomistic.h:1,
                 from vesselbase/../../vesselbase/ActionWithVessel.h:26,
                 from vesselbase/../../vesselbase/Vessel.h:31,
                 from vesselbase/../../vesselbase/ValueVessel.h:29,
                 from vesselbase/../../vesselbase/FunctionVessel.h:28,
                 from vesselbase/FunctionVessel.h:1,
                 from SpathVessel.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  EffectiveEnergyDrift.cpp
compiling  PCAVars.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/Atoms.h:1,
                 from EffectiveEnergyDrift.cpp:34:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
EffectiveEnergyDrift.cpp: In constructor 'PLMD::generic::EffectiveEnergyDrift::EffectiveEnergyDrift(const PLMD::ActionOptions&)':
EffectiveEnergyDrift.cpp:160:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<tmpActions.size();i++) if(tmpActions[i]->exists(tmpActions[i]->getLabel()+".bias")) biases.push_back(tmpActions[i]);
                                 ^
EffectiveEnergyDrift.cpp: In member function 'virtual void PLMD::generic::EffectiveEnergyDrift::update()':
EffectiveEnergyDrift.cpp:189:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<positions.size();++i){
                                  ^
EffectiveEnergyDrift.cpp:249:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<indexR.size();j++) backmap[indexR[j]]=j;
                               ^
EffectiveEnergyDrift.cpp:289:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<biases.size();i++) bias+=biases[i]->getOutputQuantity("bias");
                               ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from PCAVars.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
PCAVars.cpp: In constructor 'PLMD::mapping::PCAVars::PCAVars(const PLMD::ActionOptions&)':
PCAVars.cpp:296:14: warning: unused variable 'dist' [-Wunused-variable]
       double dist=myframes.getFrame(i)->calc( myref->getReferencePositions(), fake_pbc, getArguments(), myref->getReferenceArguments(), mypack, true );
              ^
PCAVars.cpp:326:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned i=0;i<getNumberOfComponents();++i) getPntrToComponent(i)->resizeDerivatives(nder);
                                            ^
PCAVars.cpp: In member function 'virtual void PLMD::mapping::PCAVars::calculate()':
PCAVars.cpp:366:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned i=0;i<getNumberOfComponents()-1;++i){  // One less component as we also have residual
                                              ^
PCAVars.cpp: In member function 'virtual void PLMD::mapping::PCAVars::calculateNumericalDerivatives(PLMD::ActionWithValue*)':
PCAVars.cpp:422:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(unsigned j=0;j<getNumberOfComponents();++j){
                                               ^
PCAVars.cpp:426:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(unsigned j=0;j<getNumberOfComponents();++j){
                                               ^
PCAVars.cpp: In member function 'virtual void PLMD::mapping::PCAVars::apply()':
PCAVars.cpp:435:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned i=0;i<getNumberOfComponents();++i){
                                            ^
compiling  WrapAround.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from WrapAround.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Mapping.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from Mapping.h:25,
                 from Mapping.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  DumpMassCharge.cpp
Mapping.cpp: In member function 'virtual void PLMD::mapping::Mapping::prepare()':
Mapping.cpp:141:16: warning: unused variable 'nfram' [-Wunused-variable]
       unsigned nfram=getNumberOfReferencePoints();
                ^
Mapping.cpp: In member function 'virtual void PLMD::mapping::Mapping::calculateNumericalDerivatives(PLMD::ActionWithValue*)':
Mapping.cpp:203:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(unsigned j=0;j<getNumberOfComponents();++j){
                                               ^
Mapping.cpp:207:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(unsigned j=0;j<getNumberOfComponents();++j){ 
                                               ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from DumpMassCharge.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
DumpMassCharge.cpp: In constructor 'PLMD::generic::DumpMassCharge::DumpMassCharge(const PLMD::ActionOptions&)':
DumpMassCharge.cpp:132:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned i=0;i<plumed.getAtoms().getNatoms();i++){
                                                    ^
DumpMassCharge.cpp: In member function 'virtual void PLMD::generic::DumpMassCharge::update()':
DumpMassCharge.cpp:153:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<getNumberOfAtoms();i++){
                                  ^
compiling  Group.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from Group.cpp:24:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  PropertyMap.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from Mapping.h:25,
                 from PathBase.h:25,
                 from PropertyMap.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  DumpDerivatives.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/mapping'
make -C ../molfile obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/molfile'
compiling  dcdplugin.cpp
dcdplugin.cpp:618:5: warning: "/*" within comment [-Wcomment]
     /*  Some platforms implement readv() as user level code in libc,     */
 ^
In file included from dcdplugin.cpp:83:0:
fastio.h: In function 'PLMD::molfile::fio_size_t PLMD::molfile::fio_readv(PLMD::molfile::fio_fd, const fio_iovec*, int)':
fastio.h:580:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (rc != iov[i].iov_len)
                        ^
dcdplugin.cpp: In function 'int PLMD::molfile::read_dcdheader(PLMD::molfile::fio_fd, int*, int*, int*, int*, double*, int*, int**, float**, int*, int*)':
dcdplugin.cpp:226:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {
                                                            ^
dcdplugin.cpp:239:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {
                                                         ^
dcdplugin.cpp:257:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (input_integer[0] != dcdcordmagic) {
                             ^
dcdplugin.cpp:296:31: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   (*NSET) = *((int *) (hdrbuf));
                               ^
dcdplugin.cpp:434:64: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {
                                                                ^
dcdplugin.cpp:451:64: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {
                                                                ^
dcdplugin.cpp: In function 'int PLMD::molfile::read_dcdstep(PLMD::molfile::fio_fd, int, float*, float*, float*, float*, int, int, int*, float*, int, int)':
dcdplugin.cpp:656:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT;
                                        ^
dcdplugin.cpp:660:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT;
                                                            ^
dcdplugin.cpp:581:16: warning: variable 'readlen' set but not used [-Wunused-but-set-variable]
     fio_size_t readlen; /* number of bytes actually read            */
                ^
In file included from dcdplugin.cpp:83:0:
fastio.h: At global scope:
fastio.h:520:19: warning: 'PLMD::molfile::fio_size_t PLMD::molfile::fio_readv(PLMD::molfile::fio_fd, const fio_iovec*, int)' defined but not used [-Wunused-function]
 static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) {
                   ^
fastio.h:662:12: warning: 'int PLMD::molfile::fio_read_int32(PLMD::molfile::fio_fd, int*)' defined but not used [-Wunused-function]
 static int fio_read_int32(fio_fd fd, int *i) {
            ^
fastio.h:666:12: warning: 'int PLMD::molfile::fio_write_str(PLMD::molfile::fio_fd, const char*)' defined but not used [-Wunused-function]
 static int fio_write_str(fio_fd fd, const char *str) {
            ^
In file included from dcdplugin.cpp:92:0:
endianswap.h:72:13: warning: 'void PLMD::molfile::swap2_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
endianswap.h:136:13: warning: 'void PLMD::molfile::swap2_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_aligned(void *v, long ndata) {
             ^
compiling  crdplugin.cpp
compiling  gromacsplugin.cpp
In file included from gromacsplugin.cpp:62:0:
Gromacs.h: In function 'int PLMD::molfile::mdio_readline(PLMD::molfile::md_file*, char*, int, int)':
Gromacs.h:467:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
  fgets(buf, n, mf->f);
                      ^
compiling  Time.cpp
In file included from Gromacs.h:86:0,
                 from gromacsplugin.cpp:62:
endianswap.h: At global scope:
endianswap.h:72:13: warning: 'void PLMD::molfile::swap2_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
endianswap.h:86:13: warning: 'void PLMD::molfile::swap4_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap4_unaligned(void *v, long ndata) {
             ^
endianswap.h:105:13: warning: 'void PLMD::molfile::swap8_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_unaligned(void *v, long ndata) {
             ^
endianswap.h:136:13: warning: 'void PLMD::molfile::swap2_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_aligned(void *v, long ndata) {
             ^
compiling  pdbplugin.cpp
compiling  Debug.cpp
In file included from pdbplugin.cpp:64:0:
periodic_table.h:173:12: warning: 'int PLMD::molfile::get_pte_idx(const char*)' defined but not used [-Wunused-function]
 static int get_pte_idx(const char *label)
            ^
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/molfile'
make -C ../multicolvar obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/multicolvar'
compiling  MultiColvarBase.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/generic'
make -C ../reference obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/reference'
compiling  Direction.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvarBase.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from ActionVolume.h:26:0,
                 from MultiColvarBase.cpp:24:
VolumeGradientBase.h: In member function 'PLMD::Vector PLMD::multicolvar::VolumeGradientBase::getPosition(int) const':
VolumeGradientBase.h:84:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                           ^
VolumeGradientBase.h:84:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                                                             ^
MultiColvarBase.cpp: In member function 'void PLMD::multicolvar::MultiColvarBase::setupLinkCells()':
MultiColvarBase.cpp:202:15: warning: unused variable 'justVolumes' [-Wunused-variable]
          bool justVolumes=true;
               ^
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from MetricRegister.h:32,
                 from Direction.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  ReferenceConfiguration.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from ReferenceConfiguration.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  BridgedMultiColvarFunction.cpp
In file included from vesselbase/../../vesselbase/core/../../core/tools/../../tools/Communicator.h:25:0,
                 from vesselbase/../../vesselbase/core/../../core/tools/Communicator.h:1,
                 from vesselbase/../../vesselbase/core/../../core/Atoms.h:25,
                 from vesselbase/../../vesselbase/core/../../core/ActionAtomistic.h:27,
                 from vesselbase/../../vesselbase/core/ActionAtomistic.h:1,
                 from vesselbase/../../vesselbase/ActionWithVessel.h:26,
                 from vesselbase/../../vesselbase/Vessel.h:31,
                 from vesselbase/../../vesselbase/BridgeVessel.h:28,
                 from vesselbase/BridgeVessel.h:1,
                 from BridgedMultiColvarFunction.h:25,
                 from BridgedMultiColvarFunction.cpp:25:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  EuclideanDistance.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from MetricRegister.h:32,
                 from EuclideanDistance.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Torsions.cpp
compiling  DRMSD.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvar.h:25,
                 from Torsions.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from ReferenceAtoms.h:25,
                 from SingleDomainRMSD.h:25,
                 from DRMSD.h:28,
                 from DRMSD.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  MahalanobisDistance.cpp
compiling  AlphaBeta.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from MetricRegister.h:32,
                 from MahalanobisDistance.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvar.h:25,
                 from AlphaBeta.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  ArgumentOnlyDistance.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from ReferenceArguments.h:25,
                 from ArgumentOnlyDistance.h:27,
                 from ArgumentOnlyDistance.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  MultiColvarFunction.cpp
compiling  MultiDomainRMSD.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvarFunction.h:26,
                 from MultiColvarFunction.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
MultiColvarFunction.cpp: In member function 'virtual void PLMD::multicolvar::MultiColvarFunction::calculateNumericalDerivatives(PLMD::ActionWithValue*)':
MultiColvarFunction.cpp:236:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(unsigned k=0;k<getNumberOfComponents();++k){
                                                  ^
MultiColvarFunction.cpp:245:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(unsigned k=0;k<getNumberOfComponents();++k){
                                                  ^
MultiColvarFunction.cpp:257:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(unsigned k=0;k<getNumberOfComponents();++k){
                                                ^
MultiColvarFunction.cpp:265:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned j=0;j<getNumberOfComponents();++j){
                                            ^
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from ReferenceAtoms.h:25,
                 from SingleDomainRMSD.h:25,
                 from MultiDomainRMSD.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  SimpleRMSD.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from ReferenceAtoms.h:25,
                 from SingleDomainRMSD.h:25,
                 from RMSDBase.h:27,
                 from SimpleRMSD.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  NumberOfLinks.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvarFunction.h:26,
                 from NumberOfLinks.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  RMSDBase.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from ReferenceAtoms.h:25,
                 from SingleDomainRMSD.h:25,
                 from RMSDBase.h:27,
                 from RMSDBase.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  SingleDomainRMSD.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from ReferenceAtoms.h:25,
                 from SingleDomainRMSD.h:25,
                 from SingleDomainRMSD.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  FilterBetween.cpp
In file included from vesselbase/../../vesselbase/core/../../core/tools/../../tools/Communicator.h:25:0,
                 from vesselbase/../../vesselbase/core/../../core/tools/Communicator.h:1,
                 from vesselbase/../../vesselbase/core/../../core/Atoms.h:25,
                 from vesselbase/../../vesselbase/core/../../core/ActionAtomistic.h:27,
                 from vesselbase/../../vesselbase/core/ActionAtomistic.h:1,
                 from vesselbase/../../vesselbase/ActionWithVessel.h:26,
                 from vesselbase/../../vesselbase/Vessel.h:31,
                 from vesselbase/../../vesselbase/BridgeVessel.h:28,
                 from vesselbase/BridgeVessel.h:1,
                 from BridgedMultiColvarFunction.h:25,
                 from MultiColvarFilter.h:26,
                 from FilterBetween.cpp:24:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  ReferenceArguments.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from ReferenceArguments.h:25,
                 from ReferenceArguments.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  CatomPack.cpp
compiling  AtomValuePack.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from AtomValuePack.h:25,
                 from AtomValuePack.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  PointWiseMapping.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from MultiReferenceBase.h:25,
                 from PointWiseMapping.h:25,
                 from PointWiseMapping.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Angles.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvar.h:25,
                 from Angles.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  OptimalRMSD.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from MetricRegister.h:32,
                 from OptimalRMSD.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  VolumeCavity.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/Atoms.h:1,
                 from VolumeCavity.cpp:24:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from ActionVolume.h:26:0,
                 from VolumeCavity.cpp:27:
VolumeGradientBase.h: In member function 'PLMD::Vector PLMD::multicolvar::VolumeGradientBase::getPosition(int) const':
VolumeGradientBase.h:84:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                           ^
VolumeGradientBase.h:84:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                                                             ^
compiling  MultiReferenceBase.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from MultiReferenceBase.h:25,
                 from MultiReferenceBase.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  MetricRegister.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from MetricRegister.h:32,
                 from MetricRegister.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  MultiColvarDensity.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarDensity.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  ReferenceAtoms.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from ReferenceAtoms.h:25,
                 from ReferenceAtoms.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  DotProductDistance.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from MetricRegister.h:32,
                 from DotProductDistance.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  MultiColvar.cpp
compiling  NormalizedEuclideanDistance.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvar.h:25,
                 from MultiColvar.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
MultiColvar.cpp: In member function 'void PLMD::multicolvar::MultiColvar::readAtomsLikeKeyword(const string&, int&, std::vector<PLMD::AtomNumber>&)':
MultiColvar.cpp:95:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      if( t.size()!=natoms ){
                    ^
MultiColvar.cpp:99:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(unsigned j=0;j<natoms;++j){ 
                         ^
MultiColvar.cpp:111:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for(unsigned j=0;j<natoms;++j){ cvcode += i*tmpc; tmpc *= nblock; }
                                ^
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceConfiguration.h:31,
                 from MetricRegister.h:32,
                 from NormalizedEuclideanDistance.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  ReferenceValuePack.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/../../tools/DynamicList.h:26,
                 from tools/../../tools/MultiValue.h:27,
                 from tools/MultiValue.h:1,
                 from ReferenceValuePack.h:25,
                 from ReferenceValuePack.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/reference'
make -C ../secondarystructure obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/secondarystructure'
compiling  ParabetaRMSD.cpp
compiling  InPlaneDistances.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from SecondaryStructureRMSD.h:25,
                 from ParabetaRMSD.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvar.h:25,
                 from InPlaneDistances.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  AntibetaRMSD.cpp
compiling  AdjacencyMatrixVessel.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from SecondaryStructureRMSD.h:25,
                 from AntibetaRMSD.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from vesselbase/../../vesselbase/core/../../core/tools/../../tools/Communicator.h:25:0,
                 from vesselbase/../../vesselbase/core/../../core/tools/Communicator.h:1,
                 from vesselbase/../../vesselbase/core/../../core/Atoms.h:25,
                 from vesselbase/../../vesselbase/core/../../core/ActionAtomistic.h:27,
                 from vesselbase/../../vesselbase/core/ActionAtomistic.h:1,
                 from vesselbase/../../vesselbase/ActionWithVessel.h:26,
                 from vesselbase/ActionWithVessel.h:1,
                 from AdjacencyMatrixVessel.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  FilterLessThan.cpp
compiling  AlphaRMSD.cpp
In file included from vesselbase/../../vesselbase/core/../../core/tools/../../tools/Communicator.h:25:0,
                 from vesselbase/../../vesselbase/core/../../core/tools/Communicator.h:1,
                 from vesselbase/../../vesselbase/core/../../core/Atoms.h:25,
                 from vesselbase/../../vesselbase/core/../../core/ActionAtomistic.h:27,
                 from vesselbase/../../vesselbase/core/ActionAtomistic.h:1,
                 from vesselbase/../../vesselbase/ActionWithVessel.h:26,
                 from vesselbase/../../vesselbase/Vessel.h:31,
                 from vesselbase/../../vesselbase/BridgeVessel.h:28,
                 from vesselbase/BridgeVessel.h:1,
                 from BridgedMultiColvarFunction.h:25,
                 from MultiColvarFilter.h:26,
                 from FilterLessThan.cpp:24:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from SecondaryStructureRMSD.h:25,
                 from AlphaRMSD.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  SecondaryStructureRMSD.cpp
compiling  VolumeAround.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from SecondaryStructureRMSD.h:25,
                 from SecondaryStructureRMSD.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from vesselbase/../../vesselbase/core/../../core/tools/../../tools/Communicator.h:25:0,
                 from vesselbase/../../vesselbase/core/../../core/tools/Communicator.h:1,
                 from vesselbase/../../vesselbase/core/../../core/Atoms.h:25,
                 from vesselbase/../../vesselbase/core/../../core/ActionAtomistic.h:27,
                 from vesselbase/../../vesselbase/core/ActionAtomistic.h:1,
                 from vesselbase/../../vesselbase/ActionWithVessel.h:26,
                 from vesselbase/../../vesselbase/Vessel.h:31,
                 from vesselbase/../../vesselbase/BridgeVessel.h:28,
                 from vesselbase/BridgeVessel.h:1,
                 from BridgedMultiColvarFunction.h:25,
                 from VolumeGradientBase.h:25,
                 from ActionVolume.h:26,
                 from VolumeAround.cpp:24:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from ActionVolume.h:26:0,
                 from VolumeAround.cpp:24:
VolumeGradientBase.h: In member function 'PLMD::Vector PLMD::multicolvar::VolumeGradientBase::getPosition(int) const':
VolumeGradientBase.h:84:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                           ^
VolumeGradientBase.h:84:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                                                             ^
compiling  DumpMultiColvar.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from DumpMultiColvar.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/secondarystructure'
make -C ../setup obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/setup'
compiling  Units.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/Atoms.h:1,
                 from Units.cpp:25:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  VolumeInCylinder.cpp
compiling  Restart.cpp
In file included from vesselbase/../../vesselbase/core/../../core/tools/../../tools/Communicator.h:25:0,
                 from vesselbase/../../vesselbase/core/../../core/tools/Communicator.h:1,
                 from vesselbase/../../vesselbase/core/../../core/Atoms.h:25,
                 from vesselbase/../../vesselbase/core/../../core/ActionAtomistic.h:27,
                 from vesselbase/../../vesselbase/core/ActionAtomistic.h:1,
                 from vesselbase/../../vesselbase/ActionWithVessel.h:26,
                 from vesselbase/../../vesselbase/Vessel.h:31,
                 from vesselbase/../../vesselbase/BridgeVessel.h:28,
                 from vesselbase/BridgeVessel.h:1,
                 from BridgedMultiColvarFunction.h:25,
                 from VolumeGradientBase.h:25,
                 from ActionVolume.h:26,
                 from VolumeInCylinder.cpp:25:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from ActionVolume.h:26:0,
                 from VolumeInCylinder.cpp:25:
VolumeGradientBase.h: In member function 'PLMD::Vector PLMD::multicolvar::VolumeGradientBase::getPosition(int) const':
VolumeGradientBase.h:84:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                           ^
VolumeGradientBase.h:84:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                                                             ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/Atoms.h:1,
                 from Restart.cpp:25:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  MolInfo.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/SetupMolInfo.h:26,
                 from core/SetupMolInfo.h:1,
                 from MolInfo.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  CoordinationNumbers.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvar.h:25,
                 from CoordinationNumbers.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Load.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/setup'
make -C ../tools obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/tools'
compiling  Torsion.cpp
compiling  Tensor.cpp
compiling  CubicInterpolation.cpp
compiling  Density.cpp
CubicInterpolation.cpp: In member function 'unsigned int PLMD::CInterpolation::search1(const unsigned int&, const double&, const unsigned int&) const':
CubicInterpolation.cpp:83:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 else if( ju>=(np[kk]-1)*inc ){ju=(np[kk]-1)*inc; break; } 
                                         ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvar.h:25,
                 from Density.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  HistogramBead.cpp
compiling  XDistances.cpp
compiling  RMSD.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvar.h:25,
                 from XDistances.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
RMSD.cpp: In member function 'std::vector<PLMD::VectorGeneric<3u> > PLMD::RMSDCoreData::getDDistanceDReferenceSOMA()':
RMSD.cpp:1057:10: warning: variable 't_ddist_drr01' set but not used [-Wunused-but-set-variable]
   Tensor t_ddist_drr01=ddist_drr01.transpose(); 
          ^
compiling  Bridge.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvar.h:25,
                 from Bridge.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Sprint.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvarFunction.h:26,
                 from AdjacencyMatrixAction.h:25,
                 from Sprint.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
Sprint.cpp: In member function 'virtual void PLMD::multicolvar::Sprint::completeCalculation()':
Sprint.cpp:162:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned icomp=0;icomp<getNumberOfComponents();++icomp){
                                                     ^
Sprint.cpp:178:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(unsigned icomp=0;icomp<getNumberOfComponents();++icomp){
                                                        ^
Sprint.cpp:193:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned j=0;j<getNumberOfComponents();++j){
                                             ^
Sprint.cpp: In member function 'virtual void PLMD::multicolvar::Sprint::apply()':
Sprint.cpp:205:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned i=0;i<getNumberOfComponents();++i){
                                            ^
compiling  IFile.cpp
compiling  FilterMoreThan.cpp
In file included from Communicator.h:25:0,
                 from IFile.cpp:27:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from vesselbase/../../vesselbase/core/../../core/tools/../../tools/Communicator.h:25:0,
                 from vesselbase/../../vesselbase/core/../../core/tools/Communicator.h:1,
                 from vesselbase/../../vesselbase/core/../../core/Atoms.h:25,
                 from vesselbase/../../vesselbase/core/../../core/ActionAtomistic.h:27,
                 from vesselbase/../../vesselbase/core/ActionAtomistic.h:1,
                 from vesselbase/../../vesselbase/ActionWithVessel.h:26,
                 from vesselbase/../../vesselbase/Vessel.h:31,
                 from vesselbase/../../vesselbase/BridgeVessel.h:28,
                 from vesselbase/BridgeVessel.h:1,
                 from BridgedMultiColvarFunction.h:25,
                 from MultiColvarFilter.h:26,
                 from FilterMoreThan.cpp:24:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Stopwatch.cpp
compiling  Distances.cpp
compiling  Random.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvar.h:25,
                 from Distances.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Units.cpp
compiling  Grid.cpp
Grid.cpp: In member function 'std::vector<long unsigned int> PLMD::Grid::getNeighbors(const std::vector<unsigned int>&, const std::vector<unsigned int>&) const':
Grid.cpp:280:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(!pbc_[i] && i0>=nbin_[i]) continue;
                              ^
Grid.cpp:282:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if( pbc_[i] && i0>=nbin_[i]) i0%=nbin_[i];
                              ^
compiling  XYDistances.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvar.h:25,
                 from XYDistances.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  VolumeGradientBase.cpp
In file included from vesselbase/../../vesselbase/core/../../core/tools/../../tools/Communicator.h:25:0,
                 from vesselbase/../../vesselbase/core/../../core/tools/Communicator.h:1,
                 from vesselbase/../../vesselbase/core/../../core/Atoms.h:25,
                 from vesselbase/../../vesselbase/core/../../core/ActionAtomistic.h:27,
                 from vesselbase/../../vesselbase/core/ActionAtomistic.h:1,
                 from vesselbase/../../vesselbase/ActionWithVessel.h:26,
                 from vesselbase/../../vesselbase/Vessel.h:31,
                 from vesselbase/../../vesselbase/BridgeVessel.h:28,
                 from vesselbase/BridgeVessel.h:1,
                 from BridgedMultiColvarFunction.h:25,
                 from VolumeGradientBase.h:25,
                 from VolumeGradientBase.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from VolumeGradientBase.cpp:22:0:
VolumeGradientBase.h: In member function 'PLMD::Vector PLMD::multicolvar::VolumeGradientBase::getPosition(int) const':
VolumeGradientBase.h:84:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                           ^
VolumeGradientBase.h:84:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                                                             ^
compiling  BiasRepresentation.cpp
In file included from Communicator.h:25:0,
                 from BiasRepresentation.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  LocalAverage.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvarFunction.h:26,
                 from LocalAverage.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
LocalAverage.cpp: In member function 'virtual double PLMD::multicolvar::LocalAverage::compute(const unsigned int&, PLMD::multicolvar::AtomValuePack&) const':
LocalAverage.cpp:155:10: warning: variable 'catom_pos' set but not used [-Wunused-but-set-variable]
   Vector catom_pos=myatoms.getPosition(0);
          ^
compiling  Tools.cpp
compiling  AdjacencyMatrixAction.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvarFunction.h:26,
                 from AdjacencyMatrixAction.h:25,
                 from AdjacencyMatrixAction.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  SwitchingFunction.cpp
compiling  OpenMP.cpp
compiling  LinkCells.cpp
In file included from Communicator.h:25:0,
                 from LinkCells.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
AdjacencyMatrixAction.cpp: In constructor 'PLMD::multicolvar::AdjacencyMatrixAction::AdjacencyMatrixAction(const PLMD::ActionOptions&)':
AdjacencyMatrixAction.cpp:56:20: warning: 'ibase' may be used uninitialized in this function [-Wmaybe-uninitialized]
           unsigned ibase;
                    ^
AdjacencyMatrixAction.cpp: In constructor 'PLMD::multicolvar::AdjacencyMatrixAction::AdjacencyMatrixAction(const PLMD::ActionOptions&)':
AdjacencyMatrixAction.cpp:56:20: warning: 'ibase' may be used uninitialized in this function [-Wmaybe-uninitialized]
compiling  ActionVolume.cpp
compiling  NeighborList.cpp
In file included from vesselbase/../../vesselbase/core/../../core/tools/../../tools/Communicator.h:25:0,
                 from vesselbase/../../vesselbase/core/../../core/tools/Communicator.h:1,
                 from vesselbase/../../vesselbase/core/../../core/Atoms.h:25,
                 from vesselbase/../../vesselbase/core/../../core/ActionAtomistic.h:27,
                 from vesselbase/../../vesselbase/core/ActionAtomistic.h:1,
                 from vesselbase/../../vesselbase/ActionWithVessel.h:26,
                 from vesselbase/../../vesselbase/Vessel.h:31,
                 from vesselbase/../../vesselbase/BridgeVessel.h:28,
                 from vesselbase/BridgeVessel.h:1,
                 from BridgedMultiColvarFunction.h:25,
                 from VolumeGradientBase.h:25,
                 from ActionVolume.h:26,
                 from ActionVolume.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from ActionVolume.h:26:0,
                 from ActionVolume.cpp:22:
VolumeGradientBase.h: In member function 'PLMD::Vector PLMD::multicolvar::VolumeGradientBase::getPosition(int) const':
VolumeGradientBase.h:84:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                           ^
VolumeGradientBase.h:84:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                                                             ^
compiling  MolDataClass.cpp
compiling  VolumeTetrapore.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/Atoms.h:1,
                 from VolumeTetrapore.cpp:24:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from ActionVolume.h:26:0,
                 from VolumeTetrapore.cpp:27:
VolumeGradientBase.h: In member function 'PLMD::Vector PLMD::multicolvar::VolumeGradientBase::getPosition(int) const':
VolumeGradientBase.h:84:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                           ^
VolumeGradientBase.h:84:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
                                                             ^
compiling  PDB.cpp
compiling  FileBase.cpp
In file included from Communicator.h:25:0,
                 from FileBase.cpp:27:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  DihedralCorrelation.cpp
compiling  LatticeReduction.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from MultiColvarBase.h:25,
                 from MultiColvar.h:25,
                 from DihedralCorrelation.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Exception.cpp
compiling  KernelFunctions.cpp
KernelFunctions.cpp: In constructor 'PLMD::KernelFunctions::KernelFunctions(const string&, const bool&)':
KernelFunctions.cpp:98:8: warning: unused variable 'founds' [-Wunused-variable]
   bool founds = Tools::parseVector(data,"SIGMA",sig);
        ^
compiling  MultiColvarFilter.cpp
In file included from vesselbase/../../vesselbase/core/../../core/tools/../../tools/Communicator.h:25:0,
                 from vesselbase/../../vesselbase/core/../../core/tools/Communicator.h:1,
                 from vesselbase/../../vesselbase/core/../../core/Atoms.h:25,
                 from vesselbase/../../vesselbase/core/../../core/ActionAtomistic.h:27,
                 from vesselbase/../../vesselbase/core/ActionAtomistic.h:1,
                 from vesselbase/../../vesselbase/ActionWithVessel.h:26,
                 from vesselbase/../../vesselbase/Vessel.h:31,
                 from vesselbase/../../vesselbase/BridgeVessel.h:28,
                 from vesselbase/BridgeVessel.h:1,
                 from BridgedMultiColvarFunction.h:25,
                 from MultiColvarFilter.h:26,
                 from MultiColvarFilter.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  DLLoader.cpp
compiling  OptimalAlignment.cpp
compiling  Angle.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/multicolvar'
make -C ../vatom obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vatom'
compiling  Ghost.cpp
compiling  Communicator.cpp
In file included from Communicator.h:25:0,
                 from Communicator.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/ActionWithVirtualAtom.h:25,
                 from core/ActionWithVirtualAtom.h:1,
                 from ActionWithVirtualAtom.h:24,
                 from Ghost.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Citations.cpp
compiling  Kearsley.cpp
compiling  COM.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/ActionWithVirtualAtom.h:25,
                 from core/ActionWithVirtualAtom.h:1,
                 from ActionWithVirtualAtom.h:24,
                 from COM.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Center.cpp
compiling  Log.cpp
compiling  OFile.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/../../core/ActionWithVirtualAtom.h:25,
                 from core/ActionWithVirtualAtom.h:1,
                 from ActionWithVirtualAtom.h:24,
                 from Center.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from Communicator.h:25:0,
                 from OFile.cpp:27:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
OFile.cpp: In constructor 'PLMD::OFile::OFile()':
OFile.cpp:73:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned i=0;i<buflen;++i) buffer[i]=0;
                      ^
OFile.cpp: In member function 'int PLMD::OFile::printf(const char*, ...)':
OFile.cpp:101:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(r>=buflen-actual_buffer_length){
                ^
OFile.cpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     while(newlen<=r+actual_buffer_length) newlen*=2;
                     ^
In file included from OFile.cpp:23:0:
OFile.cpp:115:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   plumed_massert(r>-1 && r<buflen-actual_buffer_length,"error using fmt string " + std::string(fmt));
                                   ^
Exception.h:132:39: note: in definition of macro 'plumed_massert'
 #define plumed_massert(test,msg) if(!(test)) throw PLMD::Exception("assertion failed " #test ", " msg,__FILE__,__LINE__,__PRETTY_FUNCTION__)
                                       ^
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vatom'
make -C ../vesselbase obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vesselbase'
compiling  LessThan.cpp
compiling  Keywords.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from ValueVessel.h:29,
                 from FunctionVessel.h:28,
                 from LessThan.h:25,
                 from LessThan.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Sum.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from ValueVessel.h:29,
                 from FunctionVessel.h:28,
                 from Sum.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Vessel.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  MultiValue.cpp
In file included from Communicator.h:25:0,
                 from DynamicList.h:26,
                 from MultiValue.h:27,
                 from MultiValue.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  AltMin.cpp
compiling  Vector.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from ValueVessel.h:29,
                 from FunctionVessel.h:28,
                 from AltMin.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Pbc.cpp
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/tools'
compiling  StoreDataVessel.cpp
compiling  Lowest.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from StoreDataVessel.h:28,
                 from StoreDataVessel.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from ValueVessel.h:29,
                 from OrderingVessel.h:28,
                 from Lowest.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from StoreDataVessel.cpp:22:0:
StoreDataVessel.h: In constructor 'PLMD::vesselbase::StoreDataVessel::StoreDataVessel(const PLMD::vesselbase::VesselOptions&)':
StoreDataVessel.h:61:8: warning: 'PLMD::vesselbase::StoreDataVessel::hard_cut' will be initialized after [-Wreorder]
   bool hard_cut;
        ^
StoreDataVessel.h:52:12: warning:   'unsigned int PLMD::vesselbase::StoreDataVessel::nspace' [-Wreorder]
   unsigned nspace;
            ^
StoreDataVessel.cpp:31:1: warning:   when initialized here [-Wreorder]
 StoreDataVessel::StoreDataVessel( const VesselOptions& da ):
 ^
compiling  ActionWithVessel.cpp
In file included from tools/../../tools/Communicator.h:25:0,
                 from tools/Communicator.h:1,
                 from ActionWithVessel.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
make -C ../wrapper obj
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/wrapper'
compiling  PlumedStatic.cpp
compiling  Plumed.c
In file included from ActionWithVessel.cpp:23:0:
ActionWithVessel.h: In constructor 'PLMD::vesselbase::ActionWithVessel::ActionWithVessel(const PLMD::ActionOptions&)':
ActionWithVessel.h:98:8: warning: 'PLMD::vesselbase::ActionWithVessel::weightHasDerivatives' will be initialized after [-Wreorder]
   bool weightHasDerivatives;
        ^
ActionWithVessel.h:93:14: warning:   'PLMD::Stopwatch& PLMD::vesselbase::ActionWithVessel::stopwatch' [-Wreorder]
   Stopwatch& stopwatch;
              ^
ActionWithVessel.cpp:56:1: warning:   when initialized here [-Wreorder]
 ActionWithVessel::ActionWithVessel(const ActionOptions&ao):
 ^
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/wrapper'
compiling  MoreThan.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from ValueVessel.h:29,
                 from FunctionVessel.h:28,
                 from MoreThan.cpp:24:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Max.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from ValueVessel.h:29,
                 from FunctionVessel.h:28,
                 from Max.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  BridgeVessel.cpp
compiling  Between.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from BridgeVessel.h:28,
                 from BridgeVessel.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from ValueVessel.h:29,
                 from FunctionVessel.h:28,
                 from Between.h:25,
                 from Between.cpp:24:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
BridgeVessel.cpp: In member function 'virtual void PLMD::vesselbase::BridgeVessel::setBufferStart(unsigned int&)':
BridgeVessel.cpp:64:12: warning: unused variable 'tmp' [-Wunused-variable]
   unsigned tmp=myOutputAction->getSizeOfBuffer( start );
            ^
compiling  ShortcutVessel.cpp
compiling  Min.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from ShortcutVessel.h:28,
                 from ShortcutVessel.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from ValueVessel.h:29,
                 from FunctionVessel.h:28,
                 from Min.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  OrderingVessel.cpp
compiling  Histogram.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from ValueVessel.h:29,
                 from OrderingVessel.h:28,
                 from OrderingVessel.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from ShortcutVessel.h:28,
                 from Histogram.cpp:24:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  FunctionVessel.cpp
compiling  Mean.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from ValueVessel.h:29,
                 from FunctionVessel.h:28,
                 from FunctionVessel.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from ValueVessel.h:29,
                 from FunctionVessel.h:28,
                 from Mean.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  ValueVessel.cpp
compiling  ActionWithInputVessel.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from ValueVessel.h:29,
                 from ValueVessel.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from ActionWithInputVessel.h:26,
                 from ActionWithInputVessel.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  VesselRegister.cpp
compiling  Highest.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from VesselRegister.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from ValueVessel.h:29,
                 from OrderingVessel.h:28,
                 from Highest.cpp:22:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
compiling  Moments.cpp
In file included from core/../../core/tools/../../tools/Communicator.h:25:0,
                 from core/../../core/tools/Communicator.h:1,
                 from core/../../core/Atoms.h:25,
                 from core/../../core/ActionAtomistic.h:27,
                 from core/ActionAtomistic.h:1,
                 from ActionWithVessel.h:26,
                 from Vessel.h:31,
                 from StoreDataVessel.h:28,
                 from Moments.cpp:23:
/usr/include/openmpi-x86_64/mpi.h:142:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_OFFSET_TYPE long long
                                   ^
/usr/include/openmpi-x86_64/mpi.h:322:9: note: in expansion of macro 'OMPI_MPI_OFFSET_TYPE'
 typedef OMPI_MPI_OFFSET_TYPE MPI_Offset;
         ^
/usr/include/openmpi-x86_64/mpi.h:151:34: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
 #define OMPI_MPI_COUNT_TYPE long long
                                  ^
/usr/include/openmpi-x86_64/mpi.h:323:9: note: in expansion of macro 'OMPI_MPI_COUNT_TYPE'
 typedef OMPI_MPI_COUNT_TYPE MPI_Count;
         ^
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vesselbase'
make[5]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make[4]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make lib
make[4]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
mpic++  ../main/main.o ../analysis/Analysis.o ../analysis/AnalysisWithLandmarks.o ../analysis/ClassicalMultiDimensionalScaling.o ../analysis/ClassicalScaling.o ../analysis/Commit.o ../analysis/Histogram.o ../analysis/LandmarkRegister.o ../analysis/LandmarkSelectionBase.o ../analysis/SelectAllFrames.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/UWalls.o ../blas/blas.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../colvar/Angle.o ../colvar/CH3Shifts.o ../colvar/CS2Backbone.o ../colvar/Cell.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/Energy.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/NOE.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RDC.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../function/Combine.o ../function/Ensemble.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/Matheval.o ../function/Piecewise.o ../function/Sort.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/Time.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../lapack/lapack.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AdjacencyMatrixAction.o ../multicolvar/AdjacencyMatrixVessel.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvar.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarFunction.o ../multicolvar/NumberOfLinks.o ../multicolvar/Sprint.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/MultiReferenceBase.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/PointWiseMapping.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/MolInfo.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/BiasRepresentation.o ../tools/Citations.o ../tools/Communicator.o ../tools/CubicInterpolation.o ../tools/DLLoader.o ../tools/Exception.o ../tools/FileBase.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/Kearsley.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/OptimalAlignment.o ../tools/PDB.o ../tools/Pbc.o ../tools/RMSD.o ../tools/Random.o ../tools/Stopwatch.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../vatom/COM.o ../vatom/Center.o ../vatom/Ghost.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/Config.o ../wrapper/PlumedStatic.o -o plumed -ldl  -lz -lmatheval -ldl -lopenblas -Wl,--as-needed -rdynamic -fopenmp
Building Plumed.inc
chmod a+x plumed-mklib
chmod a+x plumed-newcv
chmod a+x plumed-patch
mpic++ -shared -o libplumedKernel.so ../analysis/Analysis.o ../analysis/AnalysisWithLandmarks.o ../analysis/ClassicalMultiDimensionalScaling.o ../analysis/ClassicalScaling.o ../analysis/Commit.o ../analysis/Histogram.o ../analysis/LandmarkRegister.o ../analysis/LandmarkSelectionBase.o ../analysis/SelectAllFrames.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/UWalls.o ../blas/blas.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../colvar/Angle.o ../colvar/CH3Shifts.o ../colvar/CS2Backbone.o ../colvar/Cell.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/Energy.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/NOE.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RDC.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../function/Combine.o ../function/Ensemble.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/Matheval.o ../function/Piecewise.o ../function/Sort.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/Time.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../lapack/lapack.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AdjacencyMatrixAction.o ../multicolvar/AdjacencyMatrixVessel.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvar.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarFunction.o ../multicolvar/NumberOfLinks.o ../multicolvar/Sprint.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/MultiReferenceBase.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/PointWiseMapping.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/MolInfo.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/BiasRepresentation.o ../tools/Citations.o ../tools/Communicator.o ../tools/CubicInterpolation.o ../tools/DLLoader.o ../tools/Exception.o ../tools/FileBase.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/Kearsley.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/OptimalAlignment.o ../tools/PDB.o ../tools/Pbc.o ../tools/RMSD.o ../tools/Random.o ../tools/Stopwatch.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../vatom/COM.o ../vatom/Center.o ../vatom/Ghost.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/Config.o -lz -lmatheval -ldl -lopenblas -Wl,--as-needed -rdynamic -fopenmp
mpic++ -shared -o libplumed.so ../analysis/Analysis.o ../analysis/AnalysisWithLandmarks.o ../analysis/ClassicalMultiDimensionalScaling.o ../analysis/ClassicalScaling.o ../analysis/Commit.o ../analysis/Histogram.o ../analysis/LandmarkRegister.o ../analysis/LandmarkSelectionBase.o ../analysis/SelectAllFrames.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/UWalls.o ../blas/blas.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../colvar/Angle.o ../colvar/CH3Shifts.o ../colvar/CS2Backbone.o ../colvar/Cell.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/Energy.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/NOE.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RDC.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../function/Combine.o ../function/Ensemble.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/Matheval.o ../function/Piecewise.o ../function/Sort.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/Time.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../lapack/lapack.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AdjacencyMatrixAction.o ../multicolvar/AdjacencyMatrixVessel.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvar.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarFunction.o ../multicolvar/NumberOfLinks.o ../multicolvar/Sprint.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/MultiReferenceBase.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/PointWiseMapping.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/MolInfo.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/BiasRepresentation.o ../tools/Citations.o ../tools/Communicator.o ../tools/CubicInterpolation.o ../tools/DLLoader.o ../tools/Exception.o ../tools/FileBase.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/Kearsley.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/OptimalAlignment.o ../tools/PDB.o ../tools/Pbc.o ../tools/RMSD.o ../tools/Random.o ../tools/Stopwatch.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../vatom/COM.o ../vatom/Center.o ../vatom/Ghost.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/Config.o ../wrapper/PlumedStatic.o -lz -lmatheval -ldl -lopenblas -Wl,--as-needed -rdynamic -fopenmp
mpic++  ../main/main.o ../wrapper/Plumed.o -o plumed-runtime -ldl 
Building Plumed.inc, runtime-linking version
Building Plumed.inc, shared version
Building Plumed.inc, static version
Building Plumed.cmake
Building Plumed.cmake, static version
Building Plumed.cmake, runtime-linking version
Building Plumed.cmake, shared version
mpic++  ../main/main.o "/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib/libplumed.so" -o plumed-shared -ldl 
make[4]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make install-build
make[4]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
mkdir -p install/
make PLUMED_INSTALL=Install all
make[5]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make dirslinks
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
*** Updating links to used modules in all directories ***
make ../analysis.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../lapack.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make -C ../analysis links
make -C ../bias links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/bias'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/bias
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/analysis'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/analysis
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/bias'
make -C ../blas links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/blas'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/blas
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/blas'
make -C ../cltools links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/cltools'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/cltools
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/analysis'
make -C ../colvar links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/colvar'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/colvar
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/cltools'
make -C ../config links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
Nothing to do in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/config
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make -C ../core links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/core'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/core
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/colvar'
make -C ../function links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/function'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/function
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/core'
make -C ../generic links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/generic'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/generic
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/function'
make -C ../lapack links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lapack'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/lapack
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lapack'
make -C ../main links
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/generic'
make -C ../mapping links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/main'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/main
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/mapping'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/mapping
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/main'
make -C ../molfile links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/molfile'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/molfile
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/molfile'
make -C ../multicolvar links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/multicolvar'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/multicolvar
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/mapping'
make -C ../reference links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/reference'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/reference
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/multicolvar'
make -C ../secondarystructure links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/secondarystructure'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/secondarystructure
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/reference'
make -C ../setup links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/setup'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/setup
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/secondarystructure'
make -C ../tools links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/tools'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/tools
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/setup'
make -C ../vatom links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vatom'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/vatom
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/tools'
make -C ../vesselbase links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vesselbase'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/vesselbase
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vatom'
make -C ../wrapper links
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/wrapper'
Nothing to do in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/wrapper
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/wrapper'
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vesselbase'
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make dirs
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
*** Compiling all directories ***
make ../analysis ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../lapack ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make -C ../analysis obj
make -C ../bias obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/bias'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/bias'
make -C ../blas obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/analysis'
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/blas'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/blas'
make -C ../cltools obj
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/analysis'
make -C ../colvar obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/cltools'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/cltools'
make -C ../config obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make PLUMED_FORCE=yes ConfigInstall.cpp Config.cpp version.h
make[9]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
Updating ConfigInstall.cpp
cmp -s ConfigInstall.cpp~ ConfigInstall.cpp || cp ConfigInstall.cpp~ ConfigInstall.cpp
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/colvar'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/colvar'
make -C ../core obj
rm ConfigInstall.cpp~
Updating Config.cpp
cmp -s Config.cpp~ Config.cpp || cp Config.cpp~ Config.cpp
rm Config.cpp~
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/core'
Updating version.h
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/core'
make -C ../function obj
make[9]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make Config.o ConfigInstall.o compile_options.sh
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/function'
make[8]: Nothing to be done for `obj'.
make[9]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make[9]: `Config.o' is up to date.
make[9]: `ConfigInstall.o' is up to date.
make[9]: `compile_options.sh' is up to date.
make[9]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make -C ../generic obj
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/function'
make -C ../lapack obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lapack'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lapack'
make -C ../main obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/main'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/main'
make -C ../mapping obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/generic'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/generic'
make -C ../molfile obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/molfile'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/molfile'
make -C ../multicolvar obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/mapping'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/mapping'
make -C ../reference obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/reference'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/reference'
make -C ../secondarystructure obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/secondarystructure'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/secondarystructure'
make -C ../setup obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/setup'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/setup'
make -C ../tools obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/multicolvar'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/multicolvar'
make -C ../vatom obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vatom'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vatom'
make -C ../vesselbase obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/tools'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/tools'
make -C ../wrapper obj
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/wrapper'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/wrapper'
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vesselbase'
make[8]: Nothing to be done for `obj'.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vesselbase'
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make lib
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
mpic++  ../main/main.o ../analysis/Analysis.o ../analysis/AnalysisWithLandmarks.o ../analysis/ClassicalMultiDimensionalScaling.o ../analysis/ClassicalScaling.o ../analysis/Commit.o ../analysis/Histogram.o ../analysis/LandmarkRegister.o ../analysis/LandmarkSelectionBase.o ../analysis/SelectAllFrames.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/UWalls.o ../blas/blas.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../colvar/Angle.o ../colvar/CH3Shifts.o ../colvar/CS2Backbone.o ../colvar/Cell.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/Energy.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/NOE.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RDC.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../function/Combine.o ../function/Ensemble.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/Matheval.o ../function/Piecewise.o ../function/Sort.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/Time.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../lapack/lapack.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AdjacencyMatrixAction.o ../multicolvar/AdjacencyMatrixVessel.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvar.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarFunction.o ../multicolvar/NumberOfLinks.o ../multicolvar/Sprint.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/MultiReferenceBase.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/PointWiseMapping.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/MolInfo.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/BiasRepresentation.o ../tools/Citations.o ../tools/Communicator.o ../tools/CubicInterpolation.o ../tools/DLLoader.o ../tools/Exception.o ../tools/FileBase.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/Kearsley.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/OptimalAlignment.o ../tools/PDB.o ../tools/Pbc.o ../tools/RMSD.o ../tools/Random.o ../tools/Stopwatch.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../vatom/COM.o ../vatom/Center.o ../vatom/Ghost.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/ConfigInstall.o ../wrapper/PlumedStatic.o -o install/plumed -ldl  -lz -lmatheval -ldl -lopenblas -Wl,--as-needed -rdynamic -fopenmp
Building Plumed.inc
chmod a+x install/plumed-mklib
chmod a+x install/plumed-newcv
chmod a+x install/plumed-patch
mkdir -p install
cd install && mpic++ -shared -o libplumedKernel.so ../../analysis/Analysis.o ../../analysis/AnalysisWithLandmarks.o ../../analysis/ClassicalMultiDimensionalScaling.o ../../analysis/ClassicalScaling.o ../../analysis/Commit.o ../../analysis/Histogram.o ../../analysis/LandmarkRegister.o ../../analysis/LandmarkSelectionBase.o ../../analysis/SelectAllFrames.o ../../bias/ABMD.o ../../bias/Bias.o ../../bias/BiasValue.o ../../bias/ExtendedLagrangian.o ../../bias/External.o ../../bias/LWalls.o ../../bias/MetaD.o ../../bias/MovingRestraint.o ../../bias/PBMetaD.o ../../bias/Restraint.o ../../bias/UWalls.o ../../blas/blas.o ../../cltools/Driver.o ../../cltools/DriverDouble.o ../../cltools/DriverFloat.o ../../cltools/GenTemplate.o ../../cltools/Info.o ../../cltools/Manual.o ../../cltools/SimpleMD.o ../../cltools/SumHills.o ../../cltools/kT.o ../../colvar/Angle.o ../../colvar/CH3Shifts.o ../../colvar/CS2Backbone.o ../../colvar/Cell.o ../../colvar/Constant.o ../../colvar/ContactMap.o ../../colvar/Coordination.o ../../colvar/CoordinationBase.o ../../colvar/DHEnergy.o ../../colvar/DRMSD.o ../../colvar/Dipole.o ../../colvar/Distance.o ../../colvar/Energy.o ../../colvar/Fake.o ../../colvar/Gyration.o ../../colvar/MultiRMSD.o ../../colvar/NOE.o ../../colvar/PCARMSD.o ../../colvar/PathMSD.o ../../colvar/PathMSDBase.o ../../colvar/Position.o ../../colvar/PropertyMap.o ../../colvar/Puckering.o ../../colvar/RDC.o ../../colvar/RMSD.o ../../colvar/Template.o ../../colvar/Torsion.o ../../colvar/Volume.o ../../core/Action.o ../../core/ActionAtomistic.o ../../core/ActionPilot.o ../../core/ActionRegister.o ../../core/ActionSet.o ../../core/ActionSetup.o ../../core/ActionWithArguments.o ../../core/ActionWithValue.o ../../core/ActionWithVirtualAtom.o ../../core/Atoms.o ../../core/CLTool.o ../../core/CLToolMain.o ../../core/CLToolRegister.o ../../core/Colvar.o ../../core/ExchangePatterns.o ../../core/FlexibleBin.o ../../core/GREX.o ../../core/MDAtoms.o ../../core/PlumedMain.o ../../core/PlumedMainInitializer.o ../../core/SetupMolInfo.o ../../core/TargetDist.o ../../core/Value.o ../../function/Combine.o ../../function/Ensemble.o ../../function/FuncPathMSD.o ../../function/FuncSumHills.o ../../function/Function.o ../../function/Matheval.o ../../function/Piecewise.o ../../function/Sort.o ../../function/Target.o ../../generic/Debug.o ../../generic/DumpAtoms.o ../../generic/DumpDerivatives.o ../../generic/DumpForces.o ../../generic/DumpMassCharge.o ../../generic/DumpProjections.o ../../generic/EffectiveEnergyDrift.o ../../generic/FitToTemplate.o ../../generic/Flush.o ../../generic/Group.o ../../generic/Include.o ../../generic/Print.o ../../generic/RandomExchanges.o ../../generic/Read.o ../../generic/Time.o ../../generic/WholeMolecules.o ../../generic/WrapAround.o ../../lapack/lapack.o ../../mapping/Mapping.o ../../mapping/PCAVars.o ../../mapping/Path.o ../../mapping/PathBase.o ../../mapping/PropertyMap.o ../../mapping/SpathVessel.o ../../mapping/ZpathVessel.o ../../molfile/crdplugin.o ../../molfile/dcdplugin.o ../../molfile/gromacsplugin.o ../../molfile/pdbplugin.o ../../multicolvar/ActionVolume.o ../../multicolvar/AdjacencyMatrixAction.o ../../multicolvar/AdjacencyMatrixVessel.o ../../multicolvar/AlphaBeta.o ../../multicolvar/Angles.o ../../multicolvar/AtomValuePack.o ../../multicolvar/Bridge.o ../../multicolvar/BridgedMultiColvarFunction.o ../../multicolvar/CatomPack.o ../../multicolvar/CoordinationNumbers.o ../../multicolvar/Density.o ../../multicolvar/DihedralCorrelation.o ../../multicolvar/Distances.o ../../multicolvar/DumpMultiColvar.o ../../multicolvar/FilterBetween.o ../../multicolvar/FilterLessThan.o ../../multicolvar/FilterMoreThan.o ../../multicolvar/InPlaneDistances.o ../../multicolvar/LocalAverage.o ../../multicolvar/MultiColvar.o ../../multicolvar/MultiColvarBase.o ../../multicolvar/MultiColvarDensity.o ../../multicolvar/MultiColvarFilter.o ../../multicolvar/MultiColvarFunction.o ../../multicolvar/NumberOfLinks.o ../../multicolvar/Sprint.o ../../multicolvar/Torsions.o ../../multicolvar/VolumeAround.o ../../multicolvar/VolumeCavity.o ../../multicolvar/VolumeGradientBase.o ../../multicolvar/VolumeInCylinder.o ../../multicolvar/VolumeTetrapore.o ../../multicolvar/XDistances.o ../../multicolvar/XYDistances.o ../../reference/ArgumentOnlyDistance.o ../../reference/DRMSD.o ../../reference/Direction.o ../../reference/DotProductDistance.o ../../reference/EuclideanDistance.o ../../reference/MahalanobisDistance.o ../../reference/MetricRegister.o ../../reference/MultiDomainRMSD.o ../../reference/MultiReferenceBase.o ../../reference/NormalizedEuclideanDistance.o ../../reference/OptimalRMSD.o ../../reference/PointWiseMapping.o ../../reference/RMSDBase.o ../../reference/ReferenceArguments.o ../../reference/ReferenceAtoms.o ../../reference/ReferenceConfiguration.o ../../reference/ReferenceValuePack.o ../../reference/SimpleRMSD.o ../../reference/SingleDomainRMSD.o ../../secondarystructure/AlphaRMSD.o ../../secondarystructure/AntibetaRMSD.o ../../secondarystructure/ParabetaRMSD.o ../../secondarystructure/SecondaryStructureRMSD.o ../../setup/Load.o ../../setup/MolInfo.o ../../setup/Restart.o ../../setup/Units.o ../../tools/Angle.o ../../tools/BiasRepresentation.o ../../tools/Citations.o ../../tools/Communicator.o ../../tools/CubicInterpolation.o ../../tools/DLLoader.o ../../tools/Exception.o ../../tools/FileBase.o ../../tools/Grid.o ../../tools/HistogramBead.o ../../tools/IFile.o ../../tools/Kearsley.o ../../tools/KernelFunctions.o ../../tools/Keywords.o ../../tools/LatticeReduction.o ../../tools/LinkCells.o ../../tools/Log.o ../../tools/MolDataClass.o ../../tools/MultiValue.o ../../tools/NeighborList.o ../../tools/OFile.o ../../tools/OpenMP.o ../../tools/OptimalAlignment.o ../../tools/PDB.o ../../tools/Pbc.o ../../tools/RMSD.o ../../tools/Random.o ../../tools/Stopwatch.o ../../tools/SwitchingFunction.o ../../tools/Tensor.o ../../tools/Tools.o ../../tools/Torsion.o ../../tools/Units.o ../../tools/Vector.o ../../vatom/COM.o ../../vatom/Center.o ../../vatom/Ghost.o ../../vesselbase/ActionWithInputVessel.o ../../vesselbase/ActionWithVessel.o ../../vesselbase/AltMin.o ../../vesselbase/Between.o ../../vesselbase/BridgeVessel.o ../../vesselbase/FunctionVessel.o ../../vesselbase/Highest.o ../../vesselbase/Histogram.o ../../vesselbase/LessThan.o ../../vesselbase/Lowest.o ../../vesselbase/Max.o ../../vesselbase/Mean.o ../../vesselbase/Min.o ../../vesselbase/Moments.o ../../vesselbase/MoreThan.o ../../vesselbase/OrderingVessel.o ../../vesselbase/ShortcutVessel.o ../../vesselbase/StoreDataVessel.o ../../vesselbase/Sum.o ../../vesselbase/ValueVessel.o ../../vesselbase/Vessel.o ../../vesselbase/VesselRegister.o ../../config/ConfigInstall.o -lz -lmatheval -ldl -lopenblas -Wl,--as-needed -rdynamic -fopenmp
mkdir -p install
cd install && mpic++ -shared -o libplumed.so ../../analysis/Analysis.o ../../analysis/AnalysisWithLandmarks.o ../../analysis/ClassicalMultiDimensionalScaling.o ../../analysis/ClassicalScaling.o ../../analysis/Commit.o ../../analysis/Histogram.o ../../analysis/LandmarkRegister.o ../../analysis/LandmarkSelectionBase.o ../../analysis/SelectAllFrames.o ../../bias/ABMD.o ../../bias/Bias.o ../../bias/BiasValue.o ../../bias/ExtendedLagrangian.o ../../bias/External.o ../../bias/LWalls.o ../../bias/MetaD.o ../../bias/MovingRestraint.o ../../bias/PBMetaD.o ../../bias/Restraint.o ../../bias/UWalls.o ../../blas/blas.o ../../cltools/Driver.o ../../cltools/DriverDouble.o ../../cltools/DriverFloat.o ../../cltools/GenTemplate.o ../../cltools/Info.o ../../cltools/Manual.o ../../cltools/SimpleMD.o ../../cltools/SumHills.o ../../cltools/kT.o ../../colvar/Angle.o ../../colvar/CH3Shifts.o ../../colvar/CS2Backbone.o ../../colvar/Cell.o ../../colvar/Constant.o ../../colvar/ContactMap.o ../../colvar/Coordination.o ../../colvar/CoordinationBase.o ../../colvar/DHEnergy.o ../../colvar/DRMSD.o ../../colvar/Dipole.o ../../colvar/Distance.o ../../colvar/Energy.o ../../colvar/Fake.o ../../colvar/Gyration.o ../../colvar/MultiRMSD.o ../../colvar/NOE.o ../../colvar/PCARMSD.o ../../colvar/PathMSD.o ../../colvar/PathMSDBase.o ../../colvar/Position.o ../../colvar/PropertyMap.o ../../colvar/Puckering.o ../../colvar/RDC.o ../../colvar/RMSD.o ../../colvar/Template.o ../../colvar/Torsion.o ../../colvar/Volume.o ../../core/Action.o ../../core/ActionAtomistic.o ../../core/ActionPilot.o ../../core/ActionRegister.o ../../core/ActionSet.o ../../core/ActionSetup.o ../../core/ActionWithArguments.o ../../core/ActionWithValue.o ../../core/ActionWithVirtualAtom.o ../../core/Atoms.o ../../core/CLTool.o ../../core/CLToolMain.o ../../core/CLToolRegister.o ../../core/Colvar.o ../../core/ExchangePatterns.o ../../core/FlexibleBin.o ../../core/GREX.o ../../core/MDAtoms.o ../../core/PlumedMain.o ../../core/PlumedMainInitializer.o ../../core/SetupMolInfo.o ../../core/TargetDist.o ../../core/Value.o ../../function/Combine.o ../../function/Ensemble.o ../../function/FuncPathMSD.o ../../function/FuncSumHills.o ../../function/Function.o ../../function/Matheval.o ../../function/Piecewise.o ../../function/Sort.o ../../function/Target.o ../../generic/Debug.o ../../generic/DumpAtoms.o ../../generic/DumpDerivatives.o ../../generic/DumpForces.o ../../generic/DumpMassCharge.o ../../generic/DumpProjections.o ../../generic/EffectiveEnergyDrift.o ../../generic/FitToTemplate.o ../../generic/Flush.o ../../generic/Group.o ../../generic/Include.o ../../generic/Print.o ../../generic/RandomExchanges.o ../../generic/Read.o ../../generic/Time.o ../../generic/WholeMolecules.o ../../generic/WrapAround.o ../../lapack/lapack.o ../../mapping/Mapping.o ../../mapping/PCAVars.o ../../mapping/Path.o ../../mapping/PathBase.o ../../mapping/PropertyMap.o ../../mapping/SpathVessel.o ../../mapping/ZpathVessel.o ../../molfile/crdplugin.o ../../molfile/dcdplugin.o ../../molfile/gromacsplugin.o ../../molfile/pdbplugin.o ../../multicolvar/ActionVolume.o ../../multicolvar/AdjacencyMatrixAction.o ../../multicolvar/AdjacencyMatrixVessel.o ../../multicolvar/AlphaBeta.o ../../multicolvar/Angles.o ../../multicolvar/AtomValuePack.o ../../multicolvar/Bridge.o ../../multicolvar/BridgedMultiColvarFunction.o ../../multicolvar/CatomPack.o ../../multicolvar/CoordinationNumbers.o ../../multicolvar/Density.o ../../multicolvar/DihedralCorrelation.o ../../multicolvar/Distances.o ../../multicolvar/DumpMultiColvar.o ../../multicolvar/FilterBetween.o ../../multicolvar/FilterLessThan.o ../../multicolvar/FilterMoreThan.o ../../multicolvar/InPlaneDistances.o ../../multicolvar/LocalAverage.o ../../multicolvar/MultiColvar.o ../../multicolvar/MultiColvarBase.o ../../multicolvar/MultiColvarDensity.o ../../multicolvar/MultiColvarFilter.o ../../multicolvar/MultiColvarFunction.o ../../multicolvar/NumberOfLinks.o ../../multicolvar/Sprint.o ../../multicolvar/Torsions.o ../../multicolvar/VolumeAround.o ../../multicolvar/VolumeCavity.o ../../multicolvar/VolumeGradientBase.o ../../multicolvar/VolumeInCylinder.o ../../multicolvar/VolumeTetrapore.o ../../multicolvar/XDistances.o ../../multicolvar/XYDistances.o ../../reference/ArgumentOnlyDistance.o ../../reference/DRMSD.o ../../reference/Direction.o ../../reference/DotProductDistance.o ../../reference/EuclideanDistance.o ../../reference/MahalanobisDistance.o ../../reference/MetricRegister.o ../../reference/MultiDomainRMSD.o ../../reference/MultiReferenceBase.o ../../reference/NormalizedEuclideanDistance.o ../../reference/OptimalRMSD.o ../../reference/PointWiseMapping.o ../../reference/RMSDBase.o ../../reference/ReferenceArguments.o ../../reference/ReferenceAtoms.o ../../reference/ReferenceConfiguration.o ../../reference/ReferenceValuePack.o ../../reference/SimpleRMSD.o ../../reference/SingleDomainRMSD.o ../../secondarystructure/AlphaRMSD.o ../../secondarystructure/AntibetaRMSD.o ../../secondarystructure/ParabetaRMSD.o ../../secondarystructure/SecondaryStructureRMSD.o ../../setup/Load.o ../../setup/MolInfo.o ../../setup/Restart.o ../../setup/Units.o ../../tools/Angle.o ../../tools/BiasRepresentation.o ../../tools/Citations.o ../../tools/Communicator.o ../../tools/CubicInterpolation.o ../../tools/DLLoader.o ../../tools/Exception.o ../../tools/FileBase.o ../../tools/Grid.o ../../tools/HistogramBead.o ../../tools/IFile.o ../../tools/Kearsley.o ../../tools/KernelFunctions.o ../../tools/Keywords.o ../../tools/LatticeReduction.o ../../tools/LinkCells.o ../../tools/Log.o ../../tools/MolDataClass.o ../../tools/MultiValue.o ../../tools/NeighborList.o ../../tools/OFile.o ../../tools/OpenMP.o ../../tools/OptimalAlignment.o ../../tools/PDB.o ../../tools/Pbc.o ../../tools/RMSD.o ../../tools/Random.o ../../tools/Stopwatch.o ../../tools/SwitchingFunction.o ../../tools/Tensor.o ../../tools/Tools.o ../../tools/Torsion.o ../../tools/Units.o ../../tools/Vector.o ../../vatom/COM.o ../../vatom/Center.o ../../vatom/Ghost.o ../../vesselbase/ActionWithInputVessel.o ../../vesselbase/ActionWithVessel.o ../../vesselbase/AltMin.o ../../vesselbase/Between.o ../../vesselbase/BridgeVessel.o ../../vesselbase/FunctionVessel.o ../../vesselbase/Highest.o ../../vesselbase/Histogram.o ../../vesselbase/LessThan.o ../../vesselbase/Lowest.o ../../vesselbase/Max.o ../../vesselbase/Mean.o ../../vesselbase/Min.o ../../vesselbase/Moments.o ../../vesselbase/MoreThan.o ../../vesselbase/OrderingVessel.o ../../vesselbase/ShortcutVessel.o ../../vesselbase/StoreDataVessel.o ../../vesselbase/Sum.o ../../vesselbase/ValueVessel.o ../../vesselbase/Vessel.o ../../vesselbase/VesselRegister.o ../../config/ConfigInstall.o ../../wrapper/PlumedStatic.o -lz -lmatheval -ldl -lopenblas -Wl,--as-needed -rdynamic -fopenmp
mpic++  ../main/main.o ../wrapper/Plumed.o -o install/plumed-runtime -ldl 
Building Plumed.inc, runtime-linking version
Building Plumed.inc, shared version
Building Plumed.inc, static version
Building Plumed.cmake
Building Plumed.cmake, static version
Building Plumed.cmake, runtime-linking version
Building Plumed.cmake, shared version
mpic++  ../main/main.o "/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib/install/libplumed.so" -o install/plumed-shared -ldl 
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make[5]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make install/kernel.o
make[5]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
ld -r -o install/kernel.o ../analysis/Analysis.o ../analysis/AnalysisWithLandmarks.o ../analysis/ClassicalMultiDimensionalScaling.o ../analysis/ClassicalScaling.o ../analysis/Commit.o ../analysis/Histogram.o ../analysis/LandmarkRegister.o ../analysis/LandmarkSelectionBase.o ../analysis/SelectAllFrames.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/UWalls.o ../blas/blas.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/Manual.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../cltools/kT.o ../colvar/Angle.o ../colvar/CH3Shifts.o ../colvar/CS2Backbone.o ../colvar/Cell.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/Coordination.o ../colvar/CoordinationBase.o ../colvar/DHEnergy.o ../colvar/DRMSD.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/Energy.o ../colvar/Fake.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/NOE.o ../colvar/PCARMSD.o ../colvar/PathMSD.o ../colvar/PathMSDBase.o ../colvar/Position.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RDC.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/Action.o ../core/ActionAtomistic.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/SetupMolInfo.o ../core/TargetDist.o ../core/Value.o ../function/Combine.o ../function/Ensemble.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/Matheval.o ../function/Piecewise.o ../function/Sort.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/Time.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../lapack/lapack.o ../mapping/Mapping.o ../mapping/PCAVars.o ../mapping/Path.o ../mapping/PathBase.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AdjacencyMatrixAction.o ../multicolvar/AdjacencyMatrixVessel.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvar.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarFunction.o ../multicolvar/NumberOfLinks.o ../multicolvar/Sprint.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../reference/ArgumentOnlyDistance.o ../reference/DRMSD.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/EuclideanDistance.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/MultiReferenceBase.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/PointWiseMapping.o ../reference/RMSDBase.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/MolInfo.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/BiasRepresentation.o ../tools/Citations.o ../tools/Communicator.o ../tools/CubicInterpolation.o ../tools/DLLoader.o ../tools/Exception.o ../tools/FileBase.o ../tools/Grid.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/Kearsley.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/OptimalAlignment.o ../tools/PDB.o ../tools/Pbc.o ../tools/RMSD.o ../tools/Random.o ../tools/Stopwatch.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Units.o ../tools/Vector.o ../vatom/COM.o ../vatom/Center.o ../vatom/Ghost.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/Config.o
make[5]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make[4]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make[3]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src'
make[1]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi'
+ . /etc/profile.d/modules.sh
++++ /bin/ps -p 5899 -ocomm=
+++ /bin/basename sh
++ shell=sh
++ '[' -f /usr/share/Modules/init/sh ']'
++ . /usr/share/Modules/init/sh
+++ MODULESHOME=/usr/share/Modules
+++ export MODULESHOME
+++ '[' mpi/openmpi-x86_64 = '' ']'
+++ '[' /usr/share/Modules/modulefiles:/etc/modulefiles = '' ']'
+ module unload mpi/openmpi-x86_64
++ /usr/bin/modulecmd sh unload mpi/openmpi-x86_64
+ eval MANPATH=/usr/share/man:/usr/local/share/man ';export' 'MANPATH;PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin' ';export' 'PATH;unset' 'LD_LIBRARY_PATH;unset' 'LOADEDMODULES;unset' 'MPI_BIN;unset' 'MPI_COMPILER;unset' 'MPI_FORTRAN_MOD_DIR;unset' 'MPI_HOME;unset' 'MPI_INCLUDE;unset' 'MPI_LIB;unset' 'MPI_MAN;unset' 'MPI_PYTHON_SITEARCH;unset' 'MPI_SUFFIX;unset' 'MPI_SYSCONFIG;unset' 'PYTHONPATH;unset' '_LMFILES_;'
++ MANPATH=/usr/share/man:/usr/local/share/man
++ export MANPATH
++ PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin
++ export PATH
++ unset LD_LIBRARY_PATH
++ unset LOADEDMODULES
++ unset MPI_BIN
++ unset MPI_COMPILER
++ unset MPI_FORTRAN_MOD_DIR
++ unset MPI_HOME
++ unset MPI_INCLUDE
++ unset MPI_LIB
++ unset MPI_MAN
++ unset MPI_PYTHON_SITEARCH
++ unset MPI_SUFFIX
++ unset MPI_SYSCONFIG
++ unset PYTHONPATH
++ unset _LMFILES_
+ popd
~/build/BUILD/plumed-2.2.1
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.6XO4tG
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64
++ dirname /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64
+ cd plumed-2.2.1
+ make -C serial install DESTDIR=/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64
make: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial'
make -C src install
make[1]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src'
make -C lib install
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
cd ../config ; make
make[3]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make PLUMED_FORCE=yes ConfigInstall.cpp Config.cpp version.h
make[4]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
Updating ConfigInstall.cpp
cmp -s ConfigInstall.cpp~ ConfigInstall.cpp || cp ConfigInstall.cpp~ ConfigInstall.cpp
rm ConfigInstall.cpp~
Updating Config.cpp
cmp -s Config.cpp~ Config.cpp || cp Config.cpp~ Config.cpp
rm Config.cpp~
Updating version.h
make[4]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make Config.o ConfigInstall.o compile_options.sh
make[4]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make[4]: `Config.o' is up to date.
make[4]: `ConfigInstall.o' is up to date.
make[4]: `compile_options.sh' is up to date.
make[4]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make[3]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
# make uninstall
mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/bin"
mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64"
mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/include/plumed"
mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/plumed/obj"
mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/plumed/src/lib"
mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/plumed/src/config"
mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/plumed/src/colvar"
make install-build
make[3]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
mkdir -p install/
make PLUMED_INSTALL=Install all
make[4]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make dirslinks
make[5]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
*** Updating links to used modules in all directories ***
make ../analysis.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../lapack.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make -C ../analysis links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/analysis'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/analysis
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/analysis'
make -C ../bias links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/bias'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/bias
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/bias'
make -C ../blas links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/blas'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/blas
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/blas'
make -C ../cltools links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/cltools'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/cltools
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/cltools'
make -C ../colvar links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/colvar'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/colvar
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/colvar'
make -C ../config links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
Nothing to do in /builddir/build/BUILD/plumed-2.2.1/serial/src/config
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make -C ../core links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/core'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/core
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/core'
make -C ../function links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/function'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/function
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/function'
make -C ../generic links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/generic'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/generic
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/generic'
make -C ../lapack links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lapack'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/lapack
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lapack'
make -C ../main links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/main'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/main
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/main'
make -C ../mapping links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/mapping'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/mapping
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/mapping'
make -C ../molfile links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/molfile'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/molfile
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/molfile'
make -C ../multicolvar links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/multicolvar'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/multicolvar
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/multicolvar'
make -C ../reference links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/reference'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/reference
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/reference'
make -C ../secondarystructure links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/secondarystructure'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/secondarystructure
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/secondarystructure'
make -C ../setup links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/setup'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/setup
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/setup'
make -C ../tools links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/tools'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/tools
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/tools'
make -C ../vatom links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vatom'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/vatom
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vatom'
make -C ../vesselbase links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vesselbase'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/serial/src/vesselbase
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vesselbase'
make -C ../wrapper links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/wrapper'
Nothing to do in /builddir/build/BUILD/plumed-2.2.1/serial/src/wrapper
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/wrapper'
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make[5]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make dirs
make[5]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
*** Compiling all directories ***
make ../analysis ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../lapack ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make -C ../analysis obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/analysis'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/analysis'
make -C ../bias obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/bias'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/bias'
make -C ../blas obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/blas'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/blas'
make -C ../cltools obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/cltools'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/cltools'
make -C ../colvar obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/colvar'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/colvar'
make -C ../config obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make PLUMED_FORCE=yes ConfigInstall.cpp Config.cpp version.h
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
Updating ConfigInstall.cpp
cmp -s ConfigInstall.cpp~ ConfigInstall.cpp || cp ConfigInstall.cpp~ ConfigInstall.cpp
rm ConfigInstall.cpp~
Updating Config.cpp
cmp -s Config.cpp~ Config.cpp || cp Config.cpp~ Config.cpp
rm Config.cpp~
Updating version.h
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make Config.o ConfigInstall.o compile_options.sh
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make[8]: `Config.o' is up to date.
make[8]: `ConfigInstall.o' is up to date.
make[8]: `compile_options.sh' is up to date.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/config'
make -C ../core obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/core'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/core'
make -C ../function obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/function'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/function'
make -C ../generic obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/generic'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/generic'
make -C ../lapack obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lapack'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lapack'
make -C ../main obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/main'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/main'
make -C ../mapping obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/mapping'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/mapping'
make -C ../molfile obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/molfile'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/molfile'
make -C ../multicolvar obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/multicolvar'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/multicolvar'
make -C ../reference obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/reference'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/reference'
make -C ../secondarystructure obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/secondarystructure'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/secondarystructure'
make -C ../setup obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/setup'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/setup'
make -C ../tools obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/tools'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/tools'
make -C ../vatom obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vatom'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vatom'
make -C ../vesselbase obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vesselbase'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/vesselbase'
make -C ../wrapper obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/wrapper'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/wrapper'
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make[5]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make lib
make[5]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
Building Plumed.inc
Building Plumed.inc, static version
Building Plumed.cmake
Building Plumed.cmake, static version
chmod a+x install/plumed-mklib
chmod a+x install/plumed-newcv
chmod a+x install/plumed-patch
Building Plumed.inc, runtime-linking version
Building Plumed.inc, shared version
Building Plumed.cmake, runtime-linking version
Building Plumed.cmake, shared version
make[5]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make[4]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make install/kernel.o
make[4]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make[4]: `install/kernel.o' is up to date.
make[4]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make[3]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make install-html
make[3]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
if test -d ../../user-doc/html ; then mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed" && cd ../../ && tar cf - user-doc/html | tar xf - -C "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed/" ; fi
if test -d ../../developer-doc/html ; then mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed" && cd ../../ && tar cf - developer-doc/html | tar xf - -C "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed/" ; fi
if test -f ../../user-doc/manual.pdf ; then mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed/user-doc" && cp ../../user-doc/manual.pdf "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed/user-doc/" ; fi
make[3]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
cd ../../ ; tar cf - patches scripts | tar xf - -C "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/plumed/"
cp ../colvar/Template.cpp "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/plumed/src/colvar/"
cp ../config/compile_options.sh "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/plumed/src/config/compile_options.sh"
cp install/kernel.o "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/plumed/obj/kernel.o"
cp ../wrapper/PlumedStatic.o "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/plumed/obj/PlumedStatic.o"
cp ../wrapper/Plumed.o "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/plumed/obj/Plumed.o"
cd ../../src ; tar cf - */*.h */*/*.h | tar xf - -C "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/include/plumed/"
cp install/plumed "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/bin/plumed"
cp install/plumed-patch "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/bin/plumed-patch"
cp install/Plumed.cmake* "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/plumed/src/lib/"
cp install/Plumed.inc* "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/plumed/src/lib/"
for file in mklib newcv patch ; do cp install/plumed-$file "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/plumed/plumed-$file" ; done
cp install/libplumed.so "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/libplumed.so"
cp install/libplumedKernel.so "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/libplumedKernel.so"
cp install/modulefile "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/plumed/modulefile"
chmod -R go+rX,go-w "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/plumed"
chmod -R go+rX,go-w "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/include/plumed"
chmod -R go+rX,go-w "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/bin/plumed"
chmod -R go+rX,go-w "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/bin/plumed-patch"
*** PLUMED has been installed ***
WARNING: Staged install with DESTDIR = /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64
Install prefix : /usr
Full name      : plumed
Setup your environment
- Ensure this is in your execution path : /usr/bin
- Ensure this is in your include path   : /usr/include
- Ensure this is in your library path   : /usr/lib64
For runtime binding:
- Set this environment variable         : PLUMED_KERNEL=/usr/lib64/libplumedKernel.so
To create a tcl module that sets all the variables above, use this one as a starting point:
/usr/lib64/plumed/modulefile
To uninstall, remove the following files and directories:
/usr/lib64/plumed
/usr/share/doc/plumed
/usr/include/plumed
/usr/bin/plumed
/usr/bin/plumed-patch
/usr/lib64/libplumed.so
/usr/lib64/libplumedKernel.so
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src/lib'
make[1]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/src'
make: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial'
+ . /etc/profile.d/modules.sh
++++ /bin/ps -p 29105 -ocomm=
+++ /bin/basename sh
++ shell=sh
++ '[' -f /usr/share/Modules/init/sh ']'
++ . /usr/share/Modules/init/sh
+++ MODULESHOME=/usr/share/Modules
+++ export MODULESHOME
+++ '[' '' = '' ']'
+++ LOADEDMODULES=
+++ export LOADEDMODULES
+++ '[' /usr/share/Modules/modulefiles:/etc/modulefiles = '' ']'
+ module load mpi/openmpi-x86_64
++ /usr/bin/modulecmd sh load mpi/openmpi-x86_64
+ eval LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ';export' 'LD_LIBRARY_PATH;LOADEDMODULES=mpi/openmpi-x86_64' ';export' 'LOADEDMODULES;MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man:/usr/local/share/man' ';export' 'MANPATH;MPI_BIN=/usr/lib64/openmpi/bin' ';export' 'MPI_BIN;MPI_COMPILER=openmpi-x86_64' ';export' 'MPI_COMPILER;MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-x86_64' ';export' 'MPI_FORTRAN_MOD_DIR;MPI_HOME=/usr/lib64/openmpi' ';export' 'MPI_HOME;MPI_INCLUDE=/usr/include/openmpi-x86_64' ';export' 'MPI_INCLUDE;MPI_LIB=/usr/lib64/openmpi/lib' ';export' 'MPI_LIB;MPI_MAN=/usr/share/man/openmpi-x86_64' ';export' 'MPI_MAN;MPI_PYTHON_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi' ';export' 'MPI_PYTHON_SITEARCH;MPI_SUFFIX=_openmpi' ';export' 'MPI_SUFFIX;MPI_SYSCONFIG=/etc/openmpi-x86_64' ';export' 'MPI_SYSCONFIG;PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin' ';export' 'PATH;PYTHONPATH=/usr/lib64/python2.7/site-packages/openmpi' ';export' 'PYTHONPATH;_LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64' ';export' '_LMFILES_;'
++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib
++ export LD_LIBRARY_PATH
++ LOADEDMODULES=mpi/openmpi-x86_64
++ export LOADEDMODULES
++ MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man:/usr/local/share/man
++ export MANPATH
++ MPI_BIN=/usr/lib64/openmpi/bin
++ export MPI_BIN
++ MPI_COMPILER=openmpi-x86_64
++ export MPI_COMPILER
++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-x86_64
++ export MPI_FORTRAN_MOD_DIR
++ MPI_HOME=/usr/lib64/openmpi
++ export MPI_HOME
++ MPI_INCLUDE=/usr/include/openmpi-x86_64
++ export MPI_INCLUDE
++ MPI_LIB=/usr/lib64/openmpi/lib
++ export MPI_LIB
++ MPI_MAN=/usr/share/man/openmpi-x86_64
++ export MPI_MAN
++ MPI_PYTHON_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi
++ export MPI_PYTHON_SITEARCH
++ MPI_SUFFIX=_openmpi
++ export MPI_SUFFIX
++ MPI_SYSCONFIG=/etc/openmpi-x86_64
++ export MPI_SYSCONFIG
++ PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin
++ export PATH
++ PYTHONPATH=/usr/lib64/python2.7/site-packages/openmpi
++ export PYTHONPATH
++ _LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64
++ export _LMFILES_
+ export 'CFLAGS= -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic'
+ CFLAGS=' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic'
+ make -C openmpi install DESTDIR=/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64
make: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi'
make -C src install
make[1]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src'
make -C lib install
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
cd ../config ; make
make[3]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make PLUMED_FORCE=yes ConfigInstall.cpp Config.cpp version.h
make[4]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
Updating ConfigInstall.cpp
cmp -s ConfigInstall.cpp~ ConfigInstall.cpp || cp ConfigInstall.cpp~ ConfigInstall.cpp
rm ConfigInstall.cpp~
Updating Config.cpp
cmp -s Config.cpp~ Config.cpp || cp Config.cpp~ Config.cpp
rm Config.cpp~
Updating version.h
make[4]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make Config.o ConfigInstall.o compile_options.sh
make[4]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make[4]: `Config.o' is up to date.
make[4]: `ConfigInstall.o' is up to date.
make[4]: `compile_options.sh' is up to date.
make[4]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make[3]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
# make uninstall
mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/bin"
mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib"
mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/include/openmpi-x86_64/plumed"
mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/plumed/obj"
mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/plumed/src/lib"
mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/plumed/src/config"
mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/plumed/src/colvar"
make install-build
make[3]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
mkdir -p install/
make PLUMED_INSTALL=Install all
make[4]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make dirslinks
make[5]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
*** Updating links to used modules in all directories ***
make ../analysis.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../lapack.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make -C ../analysis links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/analysis'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/analysis
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/analysis'
make -C ../bias links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/bias'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/bias
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/bias'
make -C ../blas links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/blas'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/blas
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/blas'
make -C ../cltools links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/cltools'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/cltools
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/cltools'
make -C ../colvar links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/colvar'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/colvar
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/colvar'
make -C ../config links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
Nothing to do in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/config
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make -C ../core links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/core'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/core
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/core'
make -C ../function links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/function'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/function
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/function'
make -C ../generic links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/generic'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/generic
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/generic'
make -C ../lapack links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lapack'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/lapack
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lapack'
make -C ../main links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/main'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/main
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/main'
make -C ../mapping links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/mapping'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/mapping
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/mapping'
make -C ../molfile links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/molfile'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/molfile
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/molfile'
make -C ../multicolvar links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/multicolvar'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/multicolvar
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/multicolvar'
make -C ../reference links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/reference'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/reference
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/reference'
make -C ../secondarystructure links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/secondarystructure'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/secondarystructure
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/secondarystructure'
make -C ../setup links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/setup'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/setup
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/setup'
make -C ../tools links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/tools'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/tools
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/tools'
make -C ../vatom links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vatom'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/vatom
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vatom'
make -C ../vesselbase links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vesselbase'
Verify modules and create links in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/vesselbase
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vesselbase'
make -C ../wrapper links
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/wrapper'
Nothing to do in /builddir/build/BUILD/plumed-2.2.1/openmpi/src/wrapper
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/wrapper'
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make[5]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make dirs
make[5]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
*** Compiling all directories ***
make ../analysis ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../lapack ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper
make[6]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make -C ../analysis obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/analysis'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/analysis'
make -C ../bias obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/bias'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/bias'
make -C ../blas obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/blas'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/blas'
make -C ../cltools obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/cltools'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/cltools'
make -C ../colvar obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/colvar'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/colvar'
make -C ../config obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make PLUMED_FORCE=yes ConfigInstall.cpp Config.cpp version.h
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
Updating ConfigInstall.cpp
cmp -s ConfigInstall.cpp~ ConfigInstall.cpp || cp ConfigInstall.cpp~ ConfigInstall.cpp
rm ConfigInstall.cpp~
Updating Config.cpp
cmp -s Config.cpp~ Config.cpp || cp Config.cpp~ Config.cpp
rm Config.cpp~
Updating version.h
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make Config.o ConfigInstall.o compile_options.sh
make[8]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make[8]: `Config.o' is up to date.
make[8]: `ConfigInstall.o' is up to date.
make[8]: `compile_options.sh' is up to date.
make[8]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/config'
make -C ../core obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/core'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/core'
make -C ../function obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/function'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/function'
make -C ../generic obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/generic'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/generic'
make -C ../lapack obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lapack'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lapack'
make -C ../main obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/main'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/main'
make -C ../mapping obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/mapping'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/mapping'
make -C ../molfile obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/molfile'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/molfile'
make -C ../multicolvar obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/multicolvar'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/multicolvar'
make -C ../reference obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/reference'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/reference'
make -C ../secondarystructure obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/secondarystructure'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/secondarystructure'
make -C ../setup obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/setup'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/setup'
make -C ../tools obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/tools'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/tools'
make -C ../vatom obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vatom'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vatom'
make -C ../vesselbase obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vesselbase'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/vesselbase'
make -C ../wrapper obj
make[7]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/wrapper'
make[7]: Nothing to be done for `obj'.
make[7]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/wrapper'
make[6]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make[5]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make lib
make[5]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
Building Plumed.inc
Building Plumed.inc, static version
Building Plumed.cmake
Building Plumed.cmake, static version
chmod a+x install/plumed-mklib
chmod a+x install/plumed-newcv
chmod a+x install/plumed-patch
Building Plumed.inc, runtime-linking version
Building Plumed.inc, shared version
Building Plumed.cmake, runtime-linking version
Building Plumed.cmake, shared version
make[5]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make[4]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make install/kernel.o
make[4]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make[4]: `install/kernel.o' is up to date.
make[4]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make[3]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make install-html
make[3]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
if test -d ../../user-doc/html ; then mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed" && cd ../../ && tar cf - user-doc/html | tar xf - -C "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed/" ; fi
if test -d ../../developer-doc/html ; then mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed" && cd ../../ && tar cf - developer-doc/html | tar xf - -C "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed/" ; fi
if test -f ../../user-doc/manual.pdf ; then mkdir -p "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed/user-doc" && cp ../../user-doc/manual.pdf "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed/user-doc/" ; fi
make[3]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
cd ../../ ; tar cf - patches scripts | tar xf - -C "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/plumed/"
cp ../colvar/Template.cpp "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/plumed/src/colvar/"
cp ../config/compile_options.sh "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/plumed/src/config/compile_options.sh"
cp install/kernel.o "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/plumed/obj/kernel.o"
cp ../wrapper/PlumedStatic.o "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/plumed/obj/PlumedStatic.o"
cp ../wrapper/Plumed.o "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/plumed/obj/Plumed.o"
cd ../../src ; tar cf - */*.h */*/*.h | tar xf - -C "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/include/openmpi-x86_64/plumed/"
cp install/plumed "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/bin/plumed"
cp install/plumed-patch "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/bin/plumed-patch"
cp install/Plumed.cmake* "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/plumed/src/lib/"
cp install/Plumed.inc* "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/plumed/src/lib/"
for file in mklib newcv patch ; do cp install/plumed-$file "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/plumed/plumed-$file" ; done
cp install/libplumed.so "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/libplumed.so"
cp install/libplumedKernel.so "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/libplumedKernel.so"
cp install/modulefile "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/plumed/modulefile"
chmod -R go+rX,go-w "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/plumed"
chmod -R go+rX,go-w "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/include/openmpi-x86_64/plumed"
chmod -R go+rX,go-w "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/bin/plumed"
chmod -R go+rX,go-w "/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/bin/plumed-patch"
*** PLUMED has been installed ***
WARNING: Staged install with DESTDIR = /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64
Install prefix : /usr
Full name      : plumed
Setup your environment
- Ensure this is in your execution path : /usr/lib64/openmpi/bin
- Ensure this is in your include path   : /usr/include/openmpi-x86_64
- Ensure this is in your library path   : /usr/lib64/openmpi/lib
For runtime binding:
- Set this environment variable         : PLUMED_KERNEL=/usr/lib64/openmpi/lib/libplumedKernel.so
To create a tcl module that sets all the variables above, use this one as a starting point:
/usr/lib64/openmpi/lib/plumed/modulefile
To uninstall, remove the following files and directories:
/usr/lib64/openmpi/lib/plumed
/usr/share/doc/plumed
/usr/include/openmpi-x86_64/plumed
/usr/lib64/openmpi/bin/plumed
/usr/lib64/openmpi/bin/plumed-patch
/usr/lib64/openmpi/lib/libplumed.so
/usr/lib64/openmpi/lib/libplumedKernel.so
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src/lib'
make[1]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi/src'
make: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/openmpi'
+ . /etc/profile.d/modules.sh
++++ /bin/ps -p 29105 -ocomm=
+++ /bin/basename sh
++ shell=sh
++ '[' -f /usr/share/Modules/init/sh ']'
++ . /usr/share/Modules/init/sh
+++ MODULESHOME=/usr/share/Modules
+++ export MODULESHOME
+++ '[' mpi/openmpi-x86_64 = '' ']'
+++ '[' /usr/share/Modules/modulefiles:/etc/modulefiles = '' ']'
+ module unload mpi/openmpi-x86_64
++ /usr/bin/modulecmd sh unload mpi/openmpi-x86_64
+ eval MANPATH=/usr/share/man:/usr/local/share/man ';export' 'MANPATH;PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin' ';export' 'PATH;unset' 'LD_LIBRARY_PATH;unset' 'LOADEDMODULES;unset' 'MPI_BIN;unset' 'MPI_COMPILER;unset' 'MPI_FORTRAN_MOD_DIR;unset' 'MPI_HOME;unset' 'MPI_INCLUDE;unset' 'MPI_LIB;unset' 'MPI_MAN;unset' 'MPI_PYTHON_SITEARCH;unset' 'MPI_SUFFIX;unset' 'MPI_SYSCONFIG;unset' 'PYTHONPATH;unset' '_LMFILES_;'
++ MANPATH=/usr/share/man:/usr/local/share/man
++ export MANPATH
++ PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin
++ export PATH
++ unset LD_LIBRARY_PATH
++ unset LOADEDMODULES
++ unset MPI_BIN
++ unset MPI_COMPILER
++ unset MPI_FORTRAN_MOD_DIR
++ unset MPI_HOME
++ unset MPI_INCLUDE
++ unset MPI_LIB
++ unset MPI_MAN
++ unset MPI_PYTHON_SITEARCH
++ unset MPI_SUFFIX
++ unset MPI_SYSCONFIG
++ unset PYTHONPATH
++ unset _LMFILES_
+ /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 /builddir/build/BUILD/plumed-2.2.1
extracting debug info from /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/libplumedKernel.so
extracting debug info from /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/lib/libplumed.so
extracting debug info from /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/openmpi/bin/plumed
extracting debug info from /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/libplumedKernel.so
extracting debug info from /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/lib64/libplumed.so
extracting debug info from /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/bin/plumed
/usr/lib/rpm/sepdebugcrcfix: Updated 6 CRC32s, 0 CRC32s did match.
9769 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-java-repack-jars
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.6kWhvw
+ umask 022
+ cd /builddir/build/BUILD
+ cd plumed-2.2.1
+ pushd serial
~/build/BUILD/plumed-2.2.1/serial ~/build/BUILD/plumed-2.2.1
+ make -C regtest
make: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest'
make -C basic
make[1]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic'
make -C rt42
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt42'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt42
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --ixyz trajectory.xyz
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt42'
make -C rt46
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt46'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt46
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed=plumed.dat --timestep=0.05 --ixyz amyloid.xyz --dump-forces ff
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt46'
make -C rt54-xdrfile
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt54-xdrfile'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt54-xdrfile
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixtc traj.xtc
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt54-xdrfile'
make -C rt-mpi0
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi0'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi0
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff
++ Processors: 4
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi0'
make -C rt19
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt19'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt19
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt19'
make -C rt22
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt22'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt22
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt22'
make -C rt17
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt17'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt17
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt17'
make -C rt32
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt32'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt32
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt32'
make -C rt-dhenergy
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-dhenergy'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-dhenergy
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f --pdb test.pdb
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-dhenergy'
make -C rt10-mpi
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt10-mpi'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt10-mpi
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
  --box 5.0388,5.0388,5.0388
++ Processors: 2
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt10-mpi'
make -C rt51
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt51'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt51
cp: omitting directory '../tmp'
++ Test type: sum_hills
++ Arguments:  --kt 0.6 --sigma 0.2,0.2 --bin 30,30 --histo HILLS_t1 --fmt %8.3f --outhisto correction.dat
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt51'
make -C rt15
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt15'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt15
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt15'
make -C rt1
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt1'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt1
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
../../scripts/run: line 48: plumed: command not found
++ Processors: 0
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt1'
make -C rt39
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt39'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt39
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 50 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt39'
make -C rt65-mpi
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt65-mpi'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt65-mpi
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --multi 2 --dump-forces ff
++ Processors: 4
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt65-mpi'
make -C rt42b
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt42b'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt42b
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --igro trajectory.gro
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt42b'
make -C rt64
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt64'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt64
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz
../../scripts/run: line 48: plumed: command not found
++ Processors: 0
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt64'
make -C rt39-mpi
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt39-mpi'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt39-mpi
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 50 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 2
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt39-mpi'
make -C rt48
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt48'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt48
cp: omitting directory '../tmp'
++ Test type: sum_hills
++ Arguments:  --min -pi,pi --max -pi,pi --bin 49,49 --hills HILLS_t1a,HILLS_t1b  --fmt %8.3f 
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt48'
make -C rt18
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt18'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt18
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt18'
make -C rt-make-0
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-make-0'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-make-0
cp: omitting directory '../tmp'
++ Test type: make
++ Arguments: 
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-make-0'
make -C rt64-mpi
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt64-mpi'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt64-mpi
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --multi 2
++ Processors: 2
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt64-mpi'
make -C rt-molfile-3
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-3'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-3
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --mf_xtc test.xtc
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-3'
make -C rt-molfile-1
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-1'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-1
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 1 --timestep 0.005 --pdb diala.pdb --mf_xtc traj.xtc --dump-forces forces --dump-forces-fmt=%10.6f
../../scripts/run: line 48: plumed: command not found
++ Processors: 0
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-1'
make -C rt35
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt35'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt35
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f
../../scripts/run: line 48: plumed: command not found
++ Processors: 0
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt35'
make -C rt44
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt44'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt44
cp: omitting directory '../tmp'
++ Test type: sum_hills
++ Arguments:  --min -pi,pi --max -pi,pi --bin 99,99 --hills HILLS_t1 --fmt %12.7f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt44'
make -C rt28
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt28'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt28
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --ixyz trajectory.xyz
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt28'
make -C rt27
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt27'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt27
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt27'
make -C rt52
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt52'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt52
cp: omitting directory '../tmp'
++ Test type: sum_hills
++ Arguments:  --negbias --bin 30,30 --hills HILLS_t2 --fmt %8.3f 
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt52'
make -C rt20
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt20'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt20
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --ixyz trajectory.xyz
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt20'
make -C rt54
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt54'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt54
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --igro helix.input.gro
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt54'
make -C rt42c
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt42c'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt42c
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --ixyz trajectory.xyz
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt42c'
make -C rt2
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt2'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt2
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt2'
make -C rt11-mpi
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt11-mpi'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt11-mpi
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
../../scripts/run: line 48: plumed: command not found
++ Processors: 2
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt11-mpi'
make -C rt-xdrfile-1
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-xdrfile-1'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-xdrfile-1
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 1 --timestep 0.005 --itrr traj.trr
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-xdrfile-1'
make -C rt-newline
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-newline'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-newline
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-newline'
make -C rt10-restart
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt10-restart'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt10-restart
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
  --box 5.0388,5.0388,5.0388
../../scripts/run: line 48: plumed: command not found
++ Processors: 0
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt10-restart'
make -C rt-mpi7
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi7'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi7
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --multi 3
++ Processors: 3
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi7'
make -C rt59
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt59'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt59
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 1 --timestep 0.005 --igro traj_10dec.gro 
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt59'
make -C rt11
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt11'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt11
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
../../scripts/run: line 48: plumed: command not found
++ Processors: 0
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt11'
make -C rt-make-3
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-make-3'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-make-3
cp: omitting directory '../tmp'
++ Test type: make
++ Arguments: 
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-make-3'
make -C rt49
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt49'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt49
cp: omitting directory '../tmp'
++ Test type: sum_hills
++ Arguments:  --hills HILLS_t1  --fmt %8.3f 
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt49'
make -C rt61-cregex
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt61-cregex'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt61-cregex
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 1 --ixyz diala_traj_nm.xyz  
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt61-cregex'
make -C rt47
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt47'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt47
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt47'
make -C rt56
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt56'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt56
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 1 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt56'
make -C rt-mpi6b
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi6b'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi6b
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb --multi 3
++ Processors: 3
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi6b'
make -C rt4
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt4'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt4
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt4'
make -C rt0
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt0'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt0
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt0'
make -C rt-multirmsd
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-multirmsd'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-multirmsd
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-multirmsd'
make -C rt-mpi3
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi3'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi3
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb --multi 3
     --debug-dd --debug-grex 2 --debug-grex-log log.grex
++ Processors: 6
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi3'
make -C rt-mpi1
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi1'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi1
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff  --debug-pd
++ Processors: 4
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi1'
make -C rt21
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt21'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt21
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --ixyz traj.xyz
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt21'
make -C rt22-mpi
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt22-mpi'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt22-mpi
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --multi 2
++ Processors: 2
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt22-mpi'
make -C rt-mpi6
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi6'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi6
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb --multi 3
++ Processors: 6
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi6'
make -C rt-molfile-2
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-2'
../../scripts/run
Fri Oct  7 14:09:04 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-2
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 1 --timestep 0.005 --pdb diala.pdb --mf_dcd traj.dcd --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-2'
make -C rt50
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt50'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt50
cp: omitting directory '../tmp'
++ Test type: sum_hills
++ Arguments:  --idw t1 --kt 0.6 --stride 300 --hills HILLS_t1 --fmt %8.3f 
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt50'
make -C rt40
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt40'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt40
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 50 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt40'
make -C rt-simplemd1
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-simplemd1'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-simplemd1
cp: omitting directory '../tmp'
++ Test type: simplemd
++ Arguments: 
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-simplemd1'
make -C rt-simplemd2
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-simplemd2'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-simplemd2
cp: omitting directory '../tmp'
++ Test type: simplemd
++ Arguments: 
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-simplemd2'
make -C rt13
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt13'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt13
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt13'
make -C rt67
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt67'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt67
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 500 --timestep 0.002 --igro traj.gro
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt67'
make -C rt62-cregex
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt62-cregex'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt62-cregex
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 1 --ixyz diala_traj_nm.xyz  
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt62-cregex'
make -C rt63
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt63'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt63
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --igro helix.input.gro --dump-forces ff --dump-full-virial
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt63'
make -C rt16b
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt16b'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt16b
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f --mc mc
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt16b'
make -C rt-molfile-6
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-6'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-6
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --mf_pdb input.pdb
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-6'
make -C rt63b
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt63b'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt63b
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --igro helix.input.gro --dump-forces ff --dump-full-virial
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt63b'
make -C rt16
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt16'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt16
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f --pdb test.pdb
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt16'
make -C rt12
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt12'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt12
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt12'
make -C rt-mpi4
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi4'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi4
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb --multi 3
      --debug-dd --debug-grex 2 --debug-grex-log log.grex
++ Processors: 6
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi4'
make -C rt-molfile-5
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-5'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-5
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --mf_crdbox test.crd --natoms 9560
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-5'
make -C rt41
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt41'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt41
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 50 --timestep 0.005 --noatoms
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt41'
make -C rt38
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt38'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt38
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt38'
make -C rt37
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt37'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt37
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt37'
make -C rt67-mpi
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt67-mpi'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt67-mpi
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 500 --timestep 0.002 --igro traj.gro
++ Processors: 4
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt67-mpi'
make -C rt55
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt55'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt55
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --ixyz trajectory.xyz
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt55'
make -C rt-mpi8
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi8'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi8
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --multi 3
      --debug-dd --debug-grex 2 --debug-grex-log log.grex
++ Processors: 6
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi8'
make -C rt3
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt3'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt3
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt3'
make -C rt-combine-periodic
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-combine-periodic'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-combine-periodic
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz tmp.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-combine-periodic'
make -C rt-ghost-1
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-ghost-1'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-ghost-1
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --ixyz trajectory.xyz --dump-forces ff --dump-forces-fmt=%10.6f --dump-full-virial
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-ghost-1'
make -C rt-tg1
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-tg1'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-tg1
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --length-units A --ixyz tip3.A.xyz --pdb tip3.plumed.pdb
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-tg1'
make -C rt65-rmsd2
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt65-rmsd2'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt65-rmsd2
cp: omitting directory '../tmp'
++ Test type: make
++ Arguments: 
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt65-rmsd2'
make -C rt36
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt36'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt36
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt36'
make -C rt-make-1
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-make-1'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-make-1
cp: omitting directory '../tmp'
++ Test type: make
++ Arguments: 
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-make-1'
make -C rt-ghost-2
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-ghost-2'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-ghost-2
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --ixyz trajectory.xyz --dump-forces ff --dump-forces-fmt=%10.6f --dump-full-virial
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-ghost-2'
make -C rt40-mpi
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt40-mpi'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt40-mpi
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 50 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 2
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt40-mpi'
make -C rt10
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt10'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt10
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
  --box 5.0388,5.0388,5.0388
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt10'
make -C rt-molfile-4
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-4'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-4
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --mf_crd test.crd --natoms 2257
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-molfile-4'
make -C rt23
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt23'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt23
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --ixyz trajectory.xyz --dump-forces forces.xyz --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt23'
make -C rt58
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt58'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt58
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 1 --timestep 0.005 --igro traj_5dec.gro 
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt58'
make -C rt-make-2
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-make-2'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-make-2
cp: omitting directory '../tmp'
++ Test type: make
++ Arguments: 
++ Processors: 3
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-make-2'
make -C rt-mpi2
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi2'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi2
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --dump-forces ff --pdb test.pdb --debug-dd
++ Processors: 4
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi2'
make -C rt60-cregex
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt60-cregex'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt60-cregex
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 1 --ixyz diala_traj_nm.xyz  
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt60-cregex'
make -C rt31
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt31'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt31
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt31'
make -C rt-mpi9
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi9'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi9
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --multi 3
++ Processors: 3
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi9'
make -C rt19-mpi
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt19-mpi'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt19-mpi
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f --multi 2
++ Processors: 2
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt19-mpi'
make -C rt57
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt57'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt57
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 1 --timestep 0.005 --igro traj_3dec.gro 
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt57'
make -C rt6
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt6'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt6
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt6'
make -C rt66b
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt66b'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt66b
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --ixyz traj.xyz
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt66b'
make -C rt9
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt9'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt9
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt9'
make -C rt8
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt8'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt8
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt8'
make -C rt7
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt7'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt7
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt7'
make -C rt66
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt66'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt66
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --ixyz traj.xyz
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt66'
make -C rt5
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt5'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt5
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt5'
make -C rt64-pca
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt64-pca'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt64-pca
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 1 --ixyz diala_traj_nm.xyz  
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt64-pca'
make -C rt-xdrfile-2
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-xdrfile-2'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-xdrfile-2
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 1 --timestep 0.005 --itrr traj.trr --multi 2
++ Processors: 2
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-xdrfile-2'
make -C rt44b
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt44b'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt44b
cp: omitting directory '../tmp'
++ Test type: sum_hills
++ Arguments:  --min -pi,-pi --max pi,pi --bin 20,20 --hills HILLS --fmt %12.7f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt44b'
make -C rt-simplemd0
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-simplemd0'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-simplemd0
cp: omitting directory '../tmp'
++ Test type: simplemd
++ Arguments: 
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-simplemd0'
make -C rt24
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt24'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt24
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 1 --timestep 0.005 --ixyz ala12_trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt24'
make -C rt26
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt26'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt26
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt26'
make -C rt14
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt14'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt14
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt14'
make -C rt-mpi7b
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi7b'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi7b
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz --multi 3
++ Processors: 3
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-mpi7b'
make -C rt25
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt25'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt25
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 1 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt25'
make -C rt34
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt34'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt34
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt34'
make -C rt-make-4
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-make-4'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-make-4
cp: omitting directory '../tmp'
++ Test type: make
++ Arguments: 
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt-make-4'
make -C rt30
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt30'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt30
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic/rt30'
make[1]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/basic'
make -C analysis
make[1]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/analysis'
make -C rt0
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/analysis/rt0'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/analysis/rt0
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --ixyz trajectory.xyz
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/analysis/rt0'
make -C rt-mds
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/analysis/rt-mds'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/analysis/rt-mds
cp: omitting directory '../tmp'
++ Test type: simplemd
++ Arguments: 
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/analysis/rt-mds'
make[1]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/analysis'
make -C mapping
make[1]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping'
make -C rt39
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt39'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt39
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 50 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt39'
make -C rt-pca
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt-pca'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt-pca
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --length-units A --ixyz pca-test.xyz --box 100.,100.,100.
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt-pca'
make -C rt40-mpi
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt40-mpi'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt40-mpi
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 50 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 2
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt40-mpi'
make -C rt-pca-multi
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt-pca-multi'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt-pca-multi
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --length-units A --ixyz pca-test.xyz --box 100.,100.,100.
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt-pca-multi'
make -C rt40
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt40'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt40
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 50 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt40'
make -C rt39-mpi
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt39-mpi'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt39-mpi
cp: omitting directory '../tmp'
cp: cannot stat '../../trajectories/path_msd/all.pdb': No such file or directory
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 50 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 2
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping/rt39-mpi'
make[1]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/mapping'
make -C multicolvar
make[1]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar'
make -C rt20-mpi
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt20-mpi'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt20-mpi
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 4
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt20-mpi'
make -C rt-dihcor
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-dihcor'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-dihcor
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-dihcor'
make -C rt22
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt22'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt22
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt22'
make -C rt25
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt25'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt25
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt25'
make -C rt19-mpi
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt19-mpi'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt19-mpi
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 4
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt19-mpi'
make -C rt-waterbridge
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-waterbridge'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-waterbridge
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-waterbridge'
make -C rt20
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt20'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt20
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt20'
make -C rt24
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt24'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt24
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt24'
make -C rt19
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt19'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt19
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt19'
make -C rt15
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt15'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt15
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt15'
make -C rt-filters
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-filters'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-filters
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-filters'
make -C rt23
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt23'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt23
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt23'
make -C rt24-lowmem
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt24-lowmem'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt24-lowmem
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt24-lowmem'
make -C rt-cavity
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-cavity'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-cavity
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz rotating_box.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-cavity'
make -C rt45
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt45'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt45
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt45'
make -C rt-sprint
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-sprint'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-sprint
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --ixyz isomers.xyz
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-sprint'
make -C rt-link
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-link'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-link
cp: omitting directory '../tmp'
++ Test type: make
++ Arguments: 
++ Processors: 2
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt-link'
make -C rt21
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt21'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt21
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar/rt21'
make[1]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/multicolvar'
make -C secondarystructure
make[1]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/secondarystructure'
make -C rt32
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/secondarystructure/rt32'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/secondarystructure/rt32
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/secondarystructure/rt32'
make -C rt33
make[2]: Entering directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/secondarystructure/rt33'
../../scripts/run
Fri Oct  7 14:09:05 UTC 2016
Running regtest in /builddir/build/BUILD/plumed-2.2.1/serial/regtest/secondarystructure/rt33
cp: omitting directory '../tmp'
++ Test type: driver
++ Arguments: --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz amyloid.xyz --dump-forces forces --dump-forces-fmt=%10.6f
++ Processors: 0
../../scripts/run: line 48: plumed: command not found
FAILURE: plumed executable not available
make[2]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/secondarystructure/rt33'
make[1]: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest/secondarystructure'
scripts/check
+++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Test session ended at Fri Oct  7 14:09:05 UTC 2016
+ ERROR in test analysis/rt-mds/
+ check file analysis/rt-mds/report.txt for more information
+ ERROR in test analysis/rt0/
+ check file analysis/rt0/report.txt for more information
+ ERROR in test mapping/rt-pca-multi/
+ check file mapping/rt-pca-multi/report.txt for more information
+ ERROR in test mapping/rt-pca/
+ check file mapping/rt-pca/report.txt for more information
+ ERROR in test mapping/rt39-mpi/
+ check file mapping/rt39-mpi/report.txt for more information
+ ERROR in test mapping/rt39/
+ check file mapping/rt39/report.txt for more information
+ ERROR in test mapping/rt40-mpi/
+ check file mapping/rt40-mpi/report.txt for more information
+ ERROR in test mapping/rt40/
+ check file mapping/rt40/report.txt for more information
+ ERROR in test multicolvar/rt-cavity/
+ check file multicolvar/rt-cavity/report.txt for more information
+ ERROR in test multicolvar/rt-dihcor/
+ check file multicolvar/rt-dihcor/report.txt for more information
+ ERROR in test multicolvar/rt-filters/
+ check file multicolvar/rt-filters/report.txt for more information
+ ERROR in test multicolvar/rt-link/
+ check file multicolvar/rt-link/report.txt for more information
+ ERROR in test multicolvar/rt-sprint/
+ check file multicolvar/rt-sprint/report.txt for more information
+ ERROR in test multicolvar/rt-waterbridge/
+ check file multicolvar/rt-waterbridge/report.txt for more information
+ ERROR in test multicolvar/rt15/
+ check file multicolvar/rt15/report.txt for more information
+ ERROR in test multicolvar/rt19-mpi/
+ check file multicolvar/rt19-mpi/report.txt for more information
+ ERROR in test multicolvar/rt19/
+ check file multicolvar/rt19/report.txt for more information
+ ERROR in test multicolvar/rt20-mpi/
+ check file multicolvar/rt20-mpi/report.txt for more information
+ ERROR in test multicolvar/rt20/
+ check file multicolvar/rt20/report.txt for more information
+ ERROR in test multicolvar/rt21/
+ check file multicolvar/rt21/report.txt for more information
+ ERROR in test multicolvar/rt22/
+ check file multicolvar/rt22/report.txt for more information
+ ERROR in test multicolvar/rt23/
+ check file multicolvar/rt23/report.txt for more information
+ ERROR in test multicolvar/rt24-lowmem/
+ check file multicolvar/rt24-lowmem/report.txt for more information
+ ERROR in test multicolvar/rt24/
+ check file multicolvar/rt24/report.txt for more information
+ ERROR in test multicolvar/rt25/
+ check file multicolvar/rt25/report.txt for more information
+ ERROR in test multicolvar/rt45/
+ check file multicolvar/rt45/report.txt for more information
+ ERROR in test secondarystructure/rt32/
+ check file secondarystructure/rt32/report.txt for more information
+ ERROR in test secondarystructure/rt33/
+ check file secondarystructure/rt33/report.txt for more information
+ ERROR in test basic/rt-combine-periodic/
+ check file basic/rt-combine-periodic/report.txt for more information
+ ERROR in test basic/rt-dhenergy/
+ check file basic/rt-dhenergy/report.txt for more information
+ ERROR in test basic/rt-ghost-1/
+ check file basic/rt-ghost-1/report.txt for more information
+ ERROR in test basic/rt-ghost-2/
+ check file basic/rt-ghost-2/report.txt for more information
+ ERROR in test basic/rt-make-0/
+ check file basic/rt-make-0/report.txt for more information
+ ERROR in test basic/rt-make-1/
+ check file basic/rt-make-1/report.txt for more information
+ ERROR in test basic/rt-make-2/
+ check file basic/rt-make-2/report.txt for more information
+ ERROR in test basic/rt-make-3/
+ check file basic/rt-make-3/report.txt for more information
+ ERROR in test basic/rt-make-4/
+ check file basic/rt-make-4/report.txt for more information
+ ERROR in test basic/rt-molfile-1/
+ check file basic/rt-molfile-1/report.txt for more information
+ ERROR in test basic/rt-molfile-2/
+ check file basic/rt-molfile-2/report.txt for more information
+ ERROR in test basic/rt-molfile-3/
+ check file basic/rt-molfile-3/report.txt for more information
+ ERROR in test basic/rt-molfile-4/
+ check file basic/rt-molfile-4/report.txt for more information
+ ERROR in test basic/rt-molfile-5/
+ check file basic/rt-molfile-5/report.txt for more information
+ ERROR in test basic/rt-molfile-6/
+ check file basic/rt-molfile-6/report.txt for more information
+ ERROR in test basic/rt-mpi0/
+ check file basic/rt-mpi0/report.txt for more information
+ ERROR in test basic/rt-mpi1/
+ check file basic/rt-mpi1/report.txt for more information
+ ERROR in test basic/rt-mpi2/
+ check file basic/rt-mpi2/report.txt for more information
+ ERROR in test basic/rt-mpi3/
+ check file basic/rt-mpi3/report.txt for more information
+ ERROR in test basic/rt-mpi4/
+ check file basic/rt-mpi4/report.txt for more information
+ ERROR in test basic/rt-mpi6/
+ check file basic/rt-mpi6/report.txt for more information
+ ERROR in test basic/rt-mpi6b/
+ check file basic/rt-mpi6b/report.txt for more information
+ ERROR in test basic/rt-mpi7/
+ check file basic/rt-mpi7/report.txt for more information
+ ERROR in test basic/rt-mpi7b/
+ check file basic/rt-mpi7b/report.txt for more information
+ ERROR in test basic/rt-mpi8/
+ check file basic/rt-mpi8/report.txt for more information
+ ERROR in test basic/rt-mpi9/
+ check file basic/rt-mpi9/report.txt for more information
+ ERROR in test basic/rt-multirmsd/
+ check file basic/rt-multirmsd/report.txt for more information
+ ERROR in test basic/rt-newline/
+ check file basic/rt-newline/report.txt for more information
+ ERROR in test basic/rt-simplemd0/
+ check file basic/rt-simplemd0/report.txt for more information
+ ERROR in test basic/rt-simplemd1/
+ check file basic/rt-simplemd1/report.txt for more information
+ ERROR in test basic/rt-simplemd2/
+ check file basic/rt-simplemd2/report.txt for more information
+ ERROR in test basic/rt-tg1/
+ check file basic/rt-tg1/report.txt for more information
+ ERROR in test basic/rt-xdrfile-1/
+ check file basic/rt-xdrfile-1/report.txt for more information
+ ERROR in test basic/rt-xdrfile-2/
+ check file basic/rt-xdrfile-2/report.txt for more information
+ ERROR in test basic/rt0/
+ check file basic/rt0/report.txt for more information
+ ERROR in test basic/rt1/
+ check file basic/rt1/report.txt for more information
+ ERROR in test basic/rt10-mpi/
+ check file basic/rt10-mpi/report.txt for more information
+ ERROR in test basic/rt10-restart/
+ check file basic/rt10-restart/report.txt for more information
+ ERROR in test basic/rt10/
+ check file basic/rt10/report.txt for more information
+ ERROR in test basic/rt11-mpi/
+ check file basic/rt11-mpi/report.txt for more information
+ ERROR in test basic/rt11/
+ check file basic/rt11/report.txt for more information
+ ERROR in test basic/rt12/
+ check file basic/rt12/report.txt for more information
+ ERROR in test basic/rt13/
+ check file basic/rt13/report.txt for more information
+ ERROR in test basic/rt14/
+ check file basic/rt14/report.txt for more information
+ ERROR in test basic/rt15/
+ check file basic/rt15/report.txt for more information
+ ERROR in test basic/rt16/
+ check file basic/rt16/report.txt for more information
+ ERROR in test basic/rt16b/
+ check file basic/rt16b/report.txt for more information
+ ERROR in test basic/rt17/
+ check file basic/rt17/report.txt for more information
+ ERROR in test basic/rt18/
+ check file basic/rt18/report.txt for more information
+ ERROR in test basic/rt19-mpi/
+ check file basic/rt19-mpi/report.txt for more information
+ ERROR in test basic/rt19/
+ check file basic/rt19/report.txt for more information
+ ERROR in test basic/rt2/
+ check file basic/rt2/report.txt for more information
+ ERROR in test basic/rt20/
+ check file basic/rt20/report.txt for more information
+ ERROR in test basic/rt21/
+ check file basic/rt21/report.txt for more information
+ ERROR in test basic/rt22-mpi/
+ check file basic/rt22-mpi/report.txt for more information
+ ERROR in test basic/rt22/
+ check file basic/rt22/report.txt for more information
+ ERROR in test basic/rt23/
+ check file basic/rt23/report.txt for more information
+ ERROR in test basic/rt24/
+ check file basic/rt24/report.txt for more information
+ ERROR in test basic/rt25/
+ check file basic/rt25/report.txt for more information
+ ERROR in test basic/rt26/
+ check file basic/rt26/report.txt for more information
+ ERROR in test basic/rt27/
+ check file basic/rt27/report.txt for more information
+ ERROR in test basic/rt28/
+ check file basic/rt28/report.txt for more information
+ ERROR in test basic/rt3/
+ check file basic/rt3/report.txt for more information
+ ERROR in test basic/rt30/
+ check file basic/rt30/report.txt for more information
+ ERROR in test basic/rt31/
+ check file basic/rt31/report.txt for more information
+ ERROR in test basic/rt32/
+ check file basic/rt32/report.txt for more information
+ ERROR in test basic/rt34/
+ check file basic/rt34/report.txt for more information
+ ERROR in test basic/rt35/
+ check file basic/rt35/report.txt for more information
+ ERROR in test basic/rt36/
+ check file basic/rt36/report.txt for more information
+ ERROR in test basic/rt37/
+ check file basic/rt37/report.txt for more information
+ ERROR in test basic/rt38/
+ check file basic/rt38/report.txt for more information
+ ERROR in test basic/rt39-mpi/
+ check file basic/rt39-mpi/report.txt for more information
+ ERROR in test basic/rt39/
+ check file basic/rt39/report.txt for more information
+ ERROR in test basic/rt4/
+ check file basic/rt4/report.txt for more information
+ ERROR in test basic/rt40-mpi/
+ check file basic/rt40-mpi/report.txt for more information
+ ERROR in test basic/rt40/
+ check file basic/rt40/report.txt for more information
+ ERROR in test basic/rt41/
+ check file basic/rt41/report.txt for more information
+ ERROR in test basic/rt42/
+ check file basic/rt42/report.txt for more information
+ ERROR in test basic/rt42b/
+ check file basic/rt42b/report.txt for more information
+ ERROR in test basic/rt42c/
+ check file basic/rt42c/report.txt for more information
+ ERROR in test basic/rt44/
+ check file basic/rt44/report.txt for more information
+ ERROR in test basic/rt44b/
+ check file basic/rt44b/report.txt for more information
+ ERROR in test basic/rt46/
+ check file basic/rt46/report.txt for more information
+ ERROR in test basic/rt47/
+ check file basic/rt47/report.txt for more information
+ ERROR in test basic/rt48/
+ check file basic/rt48/report.txt for more information
+ ERROR in test basic/rt49/
+ check file basic/rt49/report.txt for more information
+ ERROR in test basic/rt5/
+ check file basic/rt5/report.txt for more information
+ ERROR in test basic/rt50/
+ check file basic/rt50/report.txt for more information
+ ERROR in test basic/rt51/
+ check file basic/rt51/report.txt for more information
+ ERROR in test basic/rt52/
+ check file basic/rt52/report.txt for more information
+ ERROR in test basic/rt54-xdrfile/
+ check file basic/rt54-xdrfile/report.txt for more information
+ ERROR in test basic/rt54/
+ check file basic/rt54/report.txt for more information
+ ERROR in test basic/rt55/
+ check file basic/rt55/report.txt for more information
+ ERROR in test basic/rt56/
+ check file basic/rt56/report.txt for more information
+ ERROR in test basic/rt57/
+ check file basic/rt57/report.txt for more information
+ ERROR in test basic/rt58/
+ check file basic/rt58/report.txt for more information
+ ERROR in test basic/rt59/
+ check file basic/rt59/report.txt for more information
+ ERROR in test basic/rt6/
+ check file basic/rt6/report.txt for more information
+ ERROR in test basic/rt60-cregex/
+ check file basic/rt60-cregex/report.txt for more information
+ ERROR in test basic/rt61-cregex/
+ check file basic/rt61-cregex/report.txt for more information
+ ERROR in test basic/rt62-cregex/
+ check file basic/rt62-cregex/report.txt for more information
+ ERROR in test basic/rt63/
+ check file basic/rt63/report.txt for more information
+ ERROR in test basic/rt63b/
+ check file basic/rt63b/report.txt for more information
+ ERROR in test basic/rt64-mpi/
+ check file basic/rt64-mpi/report.txt for more information
+ ERROR in test basic/rt64-pca/
+ check file basic/rt64-pca/report.txt for more information
+ ERROR in test basic/rt64/
+ check file basic/rt64/report.txt for more information
+ ERROR in test basic/rt65-mpi/
+ check file basic/rt65-mpi/report.txt for more information
+ ERROR in test basic/rt65-rmsd2/
+ check file basic/rt65-rmsd2/report.txt for more information
+ ERROR in test basic/rt66/
+ check file basic/rt66/report.txt for more information
+ ERROR in test basic/rt66b/
+ check file basic/rt66b/report.txt for more information
+ ERROR in test basic/rt67-mpi/
+ check file basic/rt67-mpi/report.txt for more information
+ ERROR in test basic/rt67/
+ check file basic/rt67/report.txt for more information
+ ERROR in test basic/rt7/
+ check file basic/rt7/report.txt for more information
+ ERROR in test basic/rt8/
+ check file basic/rt8/report.txt for more information
+ ERROR in test basic/rt9/
+ check file basic/rt9/report.txt for more information
+++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Final report:
+ 143 tests performed, 0 tests not appliable
+ 143 errors found
+ Find the bug!
+ To replace references, go to the test directory and
+ type 'make reset'
+++++++++++++++++++++++++++++++++++++++++++++++++++++
scripts/what
scripts/what: line 15: plumed: command not found
cat: /src/*/*.cpp: No such file or directory
make: Leaving directory `/builddir/build/BUILD/plumed-2.2.1/serial/regtest'
+ popd
~/build/BUILD/plumed-2.2.1
+ exit 0
Processing files: plumed-2.2.1-2.el7.centos.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.6Ctdit
+ umask 022
+ cd /builddir/build/BUILD
+ cd plumed-2.2.1
+ DOCDIR=/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed-2.2.1
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed-2.2.1
+ cp -pr serial/COPYING.LESSER /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed-2.2.1
+ cp -pr serial/CHANGES /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed-2.2.1
+ cp -pr serial/PEOPLE /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed-2.2.1
+ exit 0
Provides: libplumed.so()(64bit) libplumedKernel.so()(64bit) plumed = 2.2.1-2.el7.centos plumed(x86-64) = 2.2.1-2.el7.centos
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libdl.so.2()(64bit) libdl.so.2(GLIBC_2.2.5)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_4.0.0)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libmatheval.so.1()(64bit) libopenblas.so.0()(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.2.5)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0.2)(64bit) rtld(GNU_HASH)
Processing files: plumed-devel-2.2.1-2.el7.centos.x86_64
Provides: libplumed.so()(64bit) libplumedKernel.so()(64bit) plumed-devel = 2.2.1-2.el7.centos plumed-devel(x86-64) = 2.2.1-2.el7.centos
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /bin/bash libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libdl.so.2()(64bit) libdl.so.2(GLIBC_2.2.5)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_4.0.0)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libmatheval.so.1()(64bit) libopenblas.so.0()(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.2.5)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0.2)(64bit) rtld(GNU_HASH)
Processing files: plumed-openmpi-2.2.1-2.el7.centos.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.2vvReV
+ umask 022
+ cd /builddir/build/BUILD
+ cd plumed-2.2.1
+ DOCDIR=/builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed-openmpi-2.2.1
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed-openmpi-2.2.1
+ cp -pr openmpi/COPYING.LESSER /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed-openmpi-2.2.1
+ cp -pr openmpi/CHANGES /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed-openmpi-2.2.1
+ cp -pr openmpi/PEOPLE /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64/usr/share/doc/plumed-openmpi-2.2.1
+ exit 0
Provides: libplumed.so()(64bit) libplumedKernel.so()(64bit) plumed-openmpi = 2.2.1-2.el7.centos plumed-openmpi(x86-64) = 2.2.1-2.el7.centos
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /bin/bash libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libdl.so.2()(64bit) libdl.so.2(GLIBC_2.2.5)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_4.0.0)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libmatheval.so.1()(64bit) libmpi.so.12()(64bit) libmpi_cxx.so.1()(64bit) libopenblas.so.0()(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.2.5)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0.2)(64bit) rtld(GNU_HASH)
Processing files: plumed-openmpi-devel-2.2.1-2.el7.centos.x86_64
Provides: plumed-openmpi-devel = 2.2.1-2.el7.centos plumed-openmpi-devel(x86-64) = 2.2.1-2.el7.centos
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /bin/bash
Processing files: plumed-debuginfo-2.2.1-2.el7.centos.x86_64
Provides: plumed-debuginfo = 2.2.1-2.el7.centos plumed-debuginfo(x86-64) = 2.2.1-2.el7.centos
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64
Wrote: /builddir/build/RPMS/plumed-2.2.1-2.el7.centos.x86_64.rpm
Wrote: /builddir/build/RPMS/plumed-devel-2.2.1-2.el7.centos.x86_64.rpm
Wrote: /builddir/build/RPMS/plumed-openmpi-2.2.1-2.el7.centos.x86_64.rpm
Wrote: /builddir/build/RPMS/plumed-openmpi-devel-2.2.1-2.el7.centos.x86_64.rpm
Wrote: /builddir/build/RPMS/plumed-debuginfo-2.2.1-2.el7.centos.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.QBbvxI
+ umask 022
+ cd /builddir/build/BUILD
+ cd plumed-2.2.1
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/plumed-2.2.1-2.el7.centos.x86_64
+ exit 0
Child return code was: 0