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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
# These messages are returned to the user
OUT_OF_MEMORY_MSG = 'This job was terminated because it used more memory than it was allocated.'
PROBABLY_OUT_OF_MEMORY_MSG = 'This job was cancelled probably because it used more memory than it was allocated.'
[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%-32']
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), only return the first word
return first_line.strip().rstrip('+').split()[0]
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))
stdout = stdout.strip()
# stdout is a single line in format "key1=value1 key2=value2 ..."
job_info_keys = []
job_info_values = []
for job_info in stdout.split():
try:
# Some value may contain `=` (e.g. `StdIn=StdIn=/dev/null`)
k, v = job_info.split('=', 1)
job_info_keys.append(k)
job_info_values.append(v)
except ValueError:
# Some value may contain spaces (e.g. `Comment=** time_limit (60m) min_nodes (1) **`)
job_info_values[-1] += ' ' + job_info
job_info_dict = dict(zip(job_info_keys, job_info_values))
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 Exception:
ajs.fail_message = "This job failed due to a cluster node failure, and an attempt to resubmit the job failed."
elif slurm_state == 'OUT_OF_MEMORY':
log.info('(%s/%s) Job hit memory limit (SLURM state: OUT_OF_MEMORY)', ajs.job_wrapper.get_id_tag(), ajs.job_id)
ajs.fail_message = OUT_OF_MEMORY_MSG
ajs.runner_state = ajs.runner_states.MEMORY_LIMIT_REACHED
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 (SLURM state: CANCELLED)', 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 OUT_OF_MEMORY_MSG
elif any(_ in stripped_line for _ in SLURM_MEMORY_LIMIT_EXCEEDED_PARTIAL_WARNINGS):
return PROBABLY_OUT_OF_MEMORY_MSG
except Exception:
log.exception('Error reading end of %s:', efile_path)
return False