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Source code for galaxy.jobs.runners.util.cli.job.lsf

# A simple CLI runner for slurm that can be used when running Galaxy from a
# non-submit host and using a Slurm cluster.
from logging import getLogger

from galaxy.jobs import JobState
    from galaxy.model import Job
    job_states = Job.states
except ImportError:
    # Not in Galaxy, map Galaxy job states to Pulsar ones.
    from pulsar.util import enum
    job_states = enum(RUNNING='running', OK='complete', QUEUED='queued', ERROR="failed")
from ..job import BaseJobExec

log = getLogger(__name__)

argmap = {
    'memory': '-M',  # There is code in job_script_kwargs relying on this name's setting
    'cores': '-n',
    'queue': '-q',
    'working_dir': '-cwd',
    'project': '-P'

[docs]class LSF(BaseJobExec):
[docs] def __init__(self, **params): self.params = {} for k, v in params.items(): self.params[k] = v
[docs] def job_script_kwargs(self, ofile, efile, job_name): scriptargs = {'-o': ofile, '-e': efile, '-J': job_name} # Map arguments using argmap. for k, v in self.params.items(): if k == 'plugin': continue try: if k == 'memory': # Memory requires both -m and -R rusage[mem=v] request scriptargs['-R'] = "\"rusage[mem=%s]\"" % v if not k.startswith('-'): k = argmap[k] scriptargs[k] = v except Exception: log.warning('Unrecognized long argument passed to LSF CLI plugin: %s' % k) # Generated template. template_scriptargs = '' for k, v in scriptargs.items(): template_scriptargs += '#BSUB {} {}\n'.format(k, v) return dict(headers=template_scriptargs)
[docs] def submit(self, script_file): # bsub returns Job <9147983> is submitted to default queue <research-rh7>. # This should be really handled outside with something like # parse_external. Currently CLI runner expect this to just send it in the last position # of the string. return "bsub <%s | awk '{ print $2}' | sed 's/[<>]//g'" % script_file
[docs] def delete(self, job_id): return 'bkill %s' % job_id
[docs] def get_status(self, job_ids=None): return "bjobs -a -o \"id stat\" -noheader" # check this
[docs] def get_single_status(self, job_id): return "bjobs -o stat -noheader " + job_id
[docs] def parse_status(self, status, job_ids): # Get status for each job, skipping header. rval = {} for line in status.splitlines(): job_id, state = line.split() if job_id in job_ids: # map job states to Galaxy job states. rval[job_id] = self._get_job_state(state) return rval
[docs] def parse_single_status(self, status, job_id): if not status: # Job not found in LSF, most probably finished and forgotten. # lsf outputs: Job <num> is not found -- but that is on the stderr # Note: a very old failed job job will not be shown here either, # which would be badly handled here. So this only works well when Galaxy # is constantly monitoring the jobs. The logic here is that DONE jobs get forgotten # faster than failed jobs. log.warning("Job id '%s' not found LSF status check" % job_id) return job_states.OK return self._get_job_state(status)
[docs] def get_failure_reason(self, job_id): return "bjobs -l " + job_id
[docs] def parse_failure_reason(self, reason, job_id): # LSF will produce the following in the job output file: # TERM_MEMLIMIT: job killed after reaching LSF memory usage limit. # Exited with exit code 143. for line in reason.splitlines(): if "TERM_MEMLIMIT" in line: return JobState.runner_states.MEMORY_LIMIT_REACHED return None
def _get_job_state(self, state): # based on: # https://www.ibm.com/support/knowledgecenter/en/SSETD4_9.1.3/lsf_admin/job_state_lsf.html # https://www.ibm.com/support/knowledgecenter/en/SSETD4_9.1.2/lsf_command_ref/bjobs.1.html try: return { 'EXIT': job_states.ERROR, 'RUN': job_states.RUNNING, 'PEND': job_states.QUEUED, 'DONE': job_states.OK, 'PSUSP': job_states.ERROR, 'USUSP': job_states.ERROR, 'SSUSP': job_states.ERROR, 'UNKWN': job_states.ERROR, 'WAIT': job_states.QUEUED, 'ZOMBI': job_states.ERROR }.get(state) except KeyError: raise KeyError("Failed to map LSF status code [%s] to job state." % state)
__all__ = ('LSF',)