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WIP: Initial LSF support, based on hacked LSF in original qbatch, untested #51

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WIP: Initial LSF support, based on hacked LSF in original qbatch, untested #51

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Initial LSF support, based on hacked LSF in original qbatch, untested…
gdevenyi Mar 22, 2016
739f164
Fix assignemnt of array ID variable
gdevenyi Mar 29, 2016
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47 changes: 44 additions & 3 deletions bin/qbatch
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Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,22 @@ SGE_HEADER_TEMPLATE = """
ARRAY_IND=$SGE_TASK_ID
""".strip()

LSF_HEADER_TEMPLATE = """
{shebang}
#BSUB {o_ppn}
#BSUB {o_log}
#BSUB -cwd {workdir}
#BSUB {o_memopts}
#BSUB {o_array}
#BSUB {o_walltime}
#BSUB {o_dependencies}
#BSUB {o_options}
{env}
{header_commands}
ARRAY_IND=$LSB_JOBINDEX
""".strip()


LOCAL_TEMPLATE = """
#!{shell}
{env}
Expand Down Expand Up @@ -327,10 +343,10 @@ if __name__ == "__main__":
"-i", action="store_true",
help="Submit individual jobs instead of an array job")
group.add_argument(
"-b", default=SYSTEM, choices=['pbs', 'sge', 'local'],
"-b", default=SYSTEM, choices=['pbs', 'sge', 'lsf', 'local'],
help="""The type of queueing system to use. 'pbs' and 'sge' both make
calls to qsub to submit jobs. 'local' runs the entire command list
(without chunking) locally.""")
calls to qsub to submit jobs. 'lsf' makes calls to bsub. 'local' runs
the entire command list (without chunking) locally.""")
group.add_argument(
"--env", choices=['copied', 'batch', 'none'], default='copied',
help="""Determines how your environment is propagated when your
Expand Down Expand Up @@ -379,6 +395,9 @@ if __name__ == "__main__":
if system == 'sge' or system == 'pbs':
if not which("qsub"):
sys.exit("qsub command not found")
elif system == 'lsf':
if not which("bsub"):
sys.exit("bsub command not found")

if not which("parallel"):
sys.exit("parallel command not found")
Expand Down Expand Up @@ -466,6 +485,18 @@ if __name__ == "__main__":
o_queue = queue and '-q {0}'.format(queue) or ''

header = SGE_HEADER_TEMPLATE.format(**vars())
elif system == 'lsf':
o_ppn = (ppn > 1) and '-n {0}'.format(ppn) or ''
o_array = (use_array and num_jobs > 1) and \
'\"-J {0}[1-{1}]\"'.format(job_name, num_jobs) \
or '-J {0}'.format(job_name)
o_dependencies = afterok_pattern and \
'-w \'done("' + '") && done("'.join(afterok_pattern) + '")\'' or ''
o_log = '-o {0}/{1}.%J.%I'.format(logdir, job_name)
o_memopts = mem and '-M {0}'.format(mem) or ''
o_walltime = walltime and '-W {0}'.format(walltime) or ''
o_options = '\n#BSUB '.join(options)
header = LSF_HEADER_TEMPLATE.format(**vars())

elif system == 'local':
header = LOCAL_TEMPLATE.format(**vars())
Expand Down Expand Up @@ -536,6 +567,16 @@ if __name__ == "__main__":
if return_code:
sys.exit("qsub call " +
"returned error code {0}".format(return_code))
elif system == 'lsf':
if verbose:
print("Running: bsub < {0}".format(script))
if dry_run:
continue
return_code = subprocess.call("bsub < {0}".format(script),
shell=True)
if return_code:
sys.exit("bsub call " +
"returned error code {0}".format(return_code))
else:
logfile = "{0}/{1}.log".format(logdir, job_name)
if verbose:
Expand Down