fsl.utils.fslsub
¶
This module submits jobs to a computing cluster using FSL’s fsl_sub command line tool. It is assumed that the computing cluster is managed by SGE.
Example usage, building a short pipeline:
from fsl.utils.fslsub import submit, wait
# submits bet to veryshort queue unless <mask_filename> already exists
bet_job = submit('bet <input_filename> -m',
queue='veryshort.q',
output='<mask_filename>')
# submits another job
other_job = submit('some other pre-processing step', queue='short.q')
# submits cuda job, that should only start after both preparatory jobs are
# finished. This will work if bet_job and other_job are single job-ids
# (i.e., strings) or a sequence of multiple job-ids
cuda_job = submit('expensive job',
wait_for=(bet_job, other_job),
queue='cuda.q')
# waits for the cuda job to finish
wait(cuda_job)
Submits a given command to the cluster |
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Gets information on a given job id |
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Returns the output of the given job. |
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Wait for one or more jobs to finish |
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Defines the command needed to run the function from the command line |
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class
fsl.utils.fslsub.
SubmitParams
(minutes: Optional[float] = None, queue: Optional[str] = None, architecture: Optional[str] = None, priority: Optional[int] = None, email: Optional[str] = None, wait_for: Union[str, None, Collection[str]] = None, job_name: Optional[str] = None, ram: Optional[int] = None, logdir: Optional[str] = None, mail_options: Optional[str] = None, flags: bool = False, multi_threaded: Optional[Tuple[str, str]] = None, verbose: bool = False, env: dict = None)[source]¶ Bases:
object
Represents the fsl_sub parameters
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minutes
: Optional[float] = None¶
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queue
: Optional[str] = None¶
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architecture
: Optional[str] = None¶
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priority
: Optional[int] = None¶
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email
: Optional[str] = None¶
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wait_for
: Union[str, None, Collection[str]] = None¶
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job_name
: Optional[str] = None¶
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ram
: Optional[int] = None¶
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logdir
: Optional[str] = None¶
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mail_options
: Optional[str] = None¶
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flags
: bool = False¶
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multi_threaded
: Optional[Tuple[str, str]] = None¶
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verbose
: bool = False¶
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env
: dict = None¶
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cmd_line_flags
= {'-M': 'email', '-N': 'job_name', '-R': 'ram', '-T': 'minutes', '-a': 'architecture', '-l': 'logdir', '-m': 'mail_options', '-p': 'priority', '-q': 'queue'}¶
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as_flags
()[source]¶ Creates flags for submission using fsl_sub
All parameters changed from their default value (typically None) will be included in the flags.
- Returns
tuple with the flags
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classmethod
add_to_parser
(parser: argparse.ArgumentParser, as_group='fsl_sub commands', include='wait_for', 'logdir', 'email', 'mail_options')[source]¶ Adds submission parameters to the parser
- Parameters
parser – parser that should understand submission commands
as_group – add as a new group
include – sequence of argument flags/names that should be added to the parser (set to None to include everything)
- Returns
the group the arguments got added to
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fsl.utils.fslsub.
submit
(*command, **kwargs)[source]¶ Submits a given command to the cluster
You can pass the command and arguments as a single string, or as a regular or unpacked sequence.
- Parameters
command – string or regular/unpacked sequence of strings with the job command
minutes – Estimated job length in minutes, used to auto-set queue name
queue – Explicitly sets the queue name
architecture – e.g., darwin or lx24-amd64
priority – Lower priority [0:-1024] default = 0
email – Who to email after job completion
wait_for – Place a hold on this task until the job-ids in this string or tuple are complete
job_name – Specify job name as it will appear on the queue
ram – Max total RAM to use for job (integer in MB)
logdir – where to output logfiles
mail_options – Change the SGE mail options, see qsub for details
output – If <output> image or file already exists, do nothing and exit
flags – If True, use flags embedded in scripts to set SGE queuing options
multi_threaded –
Submit a multi-threaded task - Set to a tuple containing two elements:
<pename>: a PE configures for the requested queues
<threads>: number of threads to run
verbose – If True, use verbose mode
env – Dict containing environment variables
- Returns
string of submitted job id
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fsl.utils.fslsub.
info
(job_id)[source]¶ Gets information on a given job id
Uses qstat -j <job_id>
- Parameters
job_id – string with job id
- Returns
dictionary with information on the submitted job (empty if job does not exist)
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fsl.utils.fslsub.
output
(job_id, logdir='.', command=None, name=None)[source]¶ Returns the output of the given job.
- Parameters
job_id – String containing job ID.
logdir – Directory containing the log - defaults to the current directory.
command – Command that was run. Not currently used.
name – Job name if it was specified. Not currently used.
- Returns
A tuple containing the standard output and standard error.
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fsl.utils.fslsub.
wait
(job_ids)[source]¶ Wait for one or more jobs to finish
- Parameters
job_ids – string or tuple of strings with jobs that should finish before continuing
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fsl.utils.fslsub.
func_to_cmd
(func, args, kwargs, tmp_dir=None, clean=False)[source]¶ Defines the command needed to run the function from the command line
WARNING: if submitting a function defined in the __main__ script, the script will be run again to retrieve this function. Make sure there is a “if __name__ == ‘__main__’” guard to prevent the full script from being rerun.
- Parameters
func – function to be run
args – positional arguments
kwargs – keyword arguments
tmp_dir – directory where to store the temporary file
clean – if True removes the submitted script after running it
- Returns
string which will run the function