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Source code for galaxy.jobs.runners.slurm

"""
SLURM job control via the DRMAA API.
"""
import logging
import os
import subprocess
import time

from galaxy import model
from galaxy.jobs.runners.drmaa import DRMAAJobRunner

log = logging.getLogger(__name__)

__all__ = ('SlurmJobRunner', )

# Error message printed to job stderr when SLURM itself kills a job.
# See src/common/slurm_jobacct_gather.c and src/slurmd/slurmd/req.c in
# https://github.com/SchedMD/slurm/
SLURM_MEMORY_LIMIT_EXCEEDED_MSG = 'slurmstepd: error: Exceeded job memory limit'
# Warning messages which may be printed to job stderr by SLURM after termination
# of a job step when using the cgroup task plugin. The exceeded memory is not
# always the cause of the step termination, which can be successful.
# See src/plugins/task/cgroup/task_cgroup_memory.c in
# https://github.com/SchedMD/slurm/
SLURM_MEMORY_LIMIT_EXCEEDED_PARTIAL_WARNINGS = [': Exceeded job memory limit at some point.',
                                                ': Exceeded step memory limit at some point.']
SLURM_MEMORY_LIMIT_SCAN_SIZE = 16 * 1024 * 1024  # 16MB


[docs]class SlurmJobRunner(DRMAAJobRunner): runner_name = "SlurmRunner" restrict_job_name_length = False def _complete_terminal_job(self, ajs, drmaa_state, **kwargs): def _get_slurm_state_with_sacct(job_id, cluster): cmd = ['sacct', '-n', '-o state'] if cluster: cmd.extend(['-M', cluster]) cmd.extend(['-j', job_id]) p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) stdout, stderr = p.communicate() if p.returncode != 0: stderr = stderr.strip() if stderr == 'SLURM accounting storage is disabled': log.warning('SLURM accounting storage is not properly configured, unable to run sacct') return raise Exception('`%s` returned %s, stderr: %s' % (' '.join(cmd), p.returncode, stderr)) # First line is for 'job_id' # Second line is for 'job_id.batch' (only available after the batch job is complete) # Following lines are for the steps 'job_id.0', 'job_id.1', ... (but Galaxy does not use steps) first_line = stdout.splitlines()[0] # Strip whitespaces and the final '+' (if present) return first_line.strip().rstrip('+') def _get_slurm_state(): cmd = ['scontrol', '-o'] if '.' in ajs.job_id: # custom slurm-drmaa-with-cluster-support job id syntax job_id, cluster = ajs.job_id.split('.', 1) cmd.extend(['-M', cluster]) else: job_id = ajs.job_id cluster = None cmd.extend(['show', 'job', job_id]) p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) stdout, stderr = p.communicate() if p.returncode != 0: # Will need to be more clever here if this message is not consistent if stderr == 'slurm_load_jobs error: Invalid job id specified\n': # The job may be old, try to get its state with sacct job_state = _get_slurm_state_with_sacct(job_id, cluster) if job_state: return job_state return 'NOT_FOUND' raise Exception('`%s` returned %s, stderr: %s' % (' '.join(cmd), p.returncode, stderr)) job_info_dict = dict([out_param.split('=', 1) for out_param in stdout.split()]) return job_info_dict['JobState'] try: if drmaa_state == self.drmaa_job_states.FAILED: slurm_state = _get_slurm_state() sleep = 1 while slurm_state == 'COMPLETING': log.debug('(%s/%s) Waiting %s seconds for failed job to exit COMPLETING state for post-mortem', ajs.job_wrapper.get_id_tag(), ajs.job_id, sleep) time.sleep(sleep) sleep *= 2 if sleep > 64: ajs.fail_message = "This job failed and the system timed out while trying to determine the cause of the failure." break slurm_state = _get_slurm_state() if slurm_state == 'NOT_FOUND': log.warning('(%s/%s) Job not found, assuming job check exceeded MinJobAge and completing as successful', ajs.job_wrapper.get_id_tag(), ajs.job_id) drmaa_state = self.drmaa_job_states.DONE elif slurm_state == 'COMPLETED': log.debug("(%s/%s) SLURM reported job success, assuming job check exceeded MinJobAge and completing as successful", ajs.job_wrapper.get_id_tag(), ajs.job_id) drmaa_state = self.drmaa_job_states.DONE elif slurm_state == 'TIMEOUT': log.info('(%s/%s) Job hit walltime', ajs.job_wrapper.get_id_tag(), ajs.job_id) ajs.fail_message = "This job was terminated because it ran longer than the maximum allowed job run time." ajs.runner_state = ajs.runner_states.WALLTIME_REACHED elif slurm_state == 'NODE_FAIL': log.warning('(%s/%s) Job failed due to node failure, attempting resubmission', ajs.job_wrapper.get_id_tag(), ajs.job_id) ajs.job_wrapper.change_state(model.Job.states.QUEUED, info='Job was resubmitted due to node failure') try: self.queue_job(ajs.job_wrapper) return except: ajs.fail_message = "This job failed due to a cluster node failure, and an attempt to resubmit the job failed." elif slurm_state == 'CANCELLED': # Check to see if the job was killed for exceeding memory consumption check_memory_limit_msg = self.__check_memory_limit(ajs.error_file) if check_memory_limit_msg: log.info('(%s/%s) Job hit memory limit', ajs.job_wrapper.get_id_tag(), ajs.job_id) ajs.fail_message = check_memory_limit_msg ajs.runner_state = ajs.runner_states.MEMORY_LIMIT_REACHED else: log.info('(%s/%s) Job was cancelled via SLURM (e.g. with scancel(1))', ajs.job_wrapper.get_id_tag(), ajs.job_id) ajs.fail_message = "This job failed because it was cancelled by an administrator." elif slurm_state in ('PENDING', 'RUNNING'): log.warning('(%s/%s) Job was reported by drmaa as terminal but job state in SLURM is: %s, returning to monitor queue', ajs.job_wrapper.get_id_tag(), ajs.job_id, slurm_state) return True else: log.warning('(%s/%s) Job failed due to unknown reasons, job state in SLURM was: %s', ajs.job_wrapper.get_id_tag(), ajs.job_id, slurm_state) ajs.fail_message = "This job failed for reasons that could not be determined." if drmaa_state == self.drmaa_job_states.FAILED: ajs.fail_message += '\nPlease click the bug icon to report this problem if you need help.' ajs.stop_job = False self.work_queue.put((self.fail_job, ajs)) return if drmaa_state == self.drmaa_job_states.DONE: with open(ajs.error_file, 'r+') as f: if os.path.getsize(ajs.error_file) > SLURM_MEMORY_LIMIT_SCAN_SIZE: f.seek(-SLURM_MEMORY_LIMIT_SCAN_SIZE, os.SEEK_END) f.readline() pos = f.tell() lines = f.readlines() f.seek(pos) for line in lines: stripped_line = line.strip() if any(_ in stripped_line for _ in SLURM_MEMORY_LIMIT_EXCEEDED_PARTIAL_WARNINGS): log.debug('(%s/%s) Job completed, removing SLURM exceeded memory warning: "%s"', ajs.job_wrapper.get_id_tag(), ajs.job_id, stripped_line) else: f.write(line) f.truncate() except Exception: log.exception('(%s/%s) Failure in SLURM _complete_terminal_job(), job final state will be: %s', ajs.job_wrapper.get_id_tag(), ajs.job_id, drmaa_state) # by default, finish the job with the state from drmaa return super(SlurmJobRunner, self)._complete_terminal_job(ajs, drmaa_state=drmaa_state) def __check_memory_limit(self, efile_path): """ A very poor implementation of tail, but it doesn't need to be fancy since we are only searching the last 2K """ try: log.debug('Checking %s for exceeded memory message from SLURM', efile_path) with open(efile_path) as f: if os.path.getsize(efile_path) > 2048: f.seek(-2048, os.SEEK_END) f.readline() for line in f.readlines(): stripped_line = line.strip() if stripped_line == SLURM_MEMORY_LIMIT_EXCEEDED_MSG: return 'This job was terminated because it used more memory than it was allocated.' elif any(_ in stripped_line for _ in SLURM_MEMORY_LIMIT_EXCEEDED_PARTIAL_WARNINGS): return 'This job was cancelled probably because it used more memory than it was allocated.' except: log.exception('Error reading end of %s:', efile_path) return False