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

# 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

try:
    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 = {
    'time': '-t',
    'ncpus': '-c',
    'partition': '-p'
}


[docs]class Slurm(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 not k.startswith('-'):
                    k = argmap[k]
                scriptargs[k] = v
            except Exception:
                log.warning('Unrecognized long argument passed to Slurm CLI plugin: %s' % k)

        # Generated template.
        template_scriptargs = ''
        for k, v in scriptargs.items():
            template_scriptargs += '#SBATCH {} {}\n'.format(k, v)
        return dict(headers=template_scriptargs)

[docs]    def submit(self, script_file):
        return 'sbatch %s' % script_file

[docs]    def delete(self, job_id):
        return 'scancel %s' % job_id

[docs]    def get_status(self, job_ids=None):
        return "squeue -a -o '%A %t'"

[docs]    def get_single_status(self, job_id):
        return "squeue -a -o '%A %t' -j " + job_id

[docs]    def parse_status(self, status, job_ids):
        # Get status for each job, skipping header.
        rval = {}
        for line in status.splitlines()[1:]:
            id, state = line.split()
            if id in job_ids:
                # map job states to Galaxy job states.
                rval[id] = self._get_job_state(state)
        return rval

[docs]    def parse_single_status(self, status, job_id):
        status = status.splitlines()
        if len(status) > 1:
            # Job still on cluster and has state.
            id, state = status[1].split()
            return self._get_job_state(state)
        # else line like "slurm_load_jobs error: Invalid job id specified"
        return job_states.OK

    def _get_job_state(self, state):
        try:
            return {
                'F': job_states.ERROR,
                'R': job_states.RUNNING,
                'CG': job_states.RUNNING,
                'PD': job_states.QUEUED,
                'CD': job_states.OK
            }.get(state)
        except KeyError:
            raise KeyError("Failed to map slurm status code [%s] to job state." % state)


__all__ = ('Slurm',)