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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fsl.utils.fslsub.
submit
(command, minutes=None, queue=None, architecture=None, priority=None, email=None, wait_for=None, job_name=None, ram=None, logdir=None, mail_options=None, output=None, flags=False, multi_threaded=None, verbose=False)[source]¶ Submits a given command to the cluster
- Parameters
command – single string 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
- 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.
_flatten_job_ids
(job_ids)[source]¶ Returns a potentially nested sequence of job ids as a single comma-separated string
- Parameters
job_ids – possibly nested sequence of job ids. The job ids themselves should be strings.
- Returns
comma-separated string of job ids
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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