pyDarwinOptionsGridAdapter {Certara.RDarwin} | R Documentation |
Grid Adapter Options for pyDarwin
Description
This function creates a list of grid adapter options for pyDarwin, which are used to configure the interaction between pyDarwin and grid computing environments.
Usage
pyDarwinOptionsGridAdapter(
python_path = "~/darwin/venv/bin/python",
submit_search_command = paste("qsub -b y -cwd -o {project_stem}_out.txt",
"-e {project_stem}_err.txt -N '{project_name}'"),
submit_command = paste("qsub -b y -o {results_dir}/{run_name}.out",
"-e {results_dir}/{run_name}.err -N {job_name}"),
submit_job_id_re = "Your job (\\w+) \\(\".+?\"\\) has been submitted",
poll_command = "qstat -s z",
poll_job_id_re = "^\\s+(\\w+)",
poll_interval = 10,
delete_command = "qdel {project_stem}-*"
)
Arguments
python_path |
Required. Path to Python interpreter, preferably to the instance of the interpreter located in the virtual environment where pyDarwin is deployed. The path must be available to all grid nodes that run jobs. |
submit_search_command |
Required. A command that submits a search job to the grid queue. This command is used for the entire search. |
submit_command |
Required. A command that submits individual runs to the
grid queue. The actual command submitted to the queue is constructed by
pyDarwin. It should not include |
submit_job_id_re |
Required. A regular expression pattern to extract the job ID after submission. The job ID must be captured with the first capturing group. |
poll_command |
Required. A command that retrieves finished jobs from the
grid controller. If the controller/setup allows to specify ids/patterns in
polling commands, do it. Otherwise, all finished jobs should be polled
using commands |
poll_job_id_re |
Required. A regular expression pattern to find a job ID in every line of the poll_command output. Similar to submit_job_id_re. |
poll_interval |
Optional. How often to poll jobs (in seconds). Default is 10 seconds. |
delete_command |
Optional. A command that deletes all unfinished jobs
related to the search when you stop it. It may delete all of them by ID
(e.g., |
Value
A list containing the configured grid adapter options.
Examples
grid_options <- pyDarwinOptionsGridAdapter(
python_path = "~/darwin/venv/bin/python",
submit_search_command =
"qsub -b y -cwd -o {project_stem}_out.txt -e {project_stem}_err.txt -N '{project_name}'",
submit_command =
"qsub -b y -o {results_dir}/{run_name}.out -e {results_dir}/{run_name}.err -N {job_name}",
submit_job_id_re = "Your job (\\w+) \\(\".+?\"\\) has been submitted",
poll_command = "qstat -s z",
poll_job_id_re = "^\\s+(\\w+)",
poll_interval = 10,
delete_command = "qdel {project_stem}-*"
)