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Source code for galaxy.jobs.runners.slurm
"""
SLURM job control via the DRMAA API.
"""
import os
import time
from galaxy import model
from galaxy.jobs.runners.drmaa import DRMAAJobRunner
from galaxy.util import (
commands,
unicodify,
)
from galaxy.util.custom_logging import get_logger
log = get_logger(__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.",
]
# 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])
try:
stdout = commands.execute(cmd)
except commands.CommandLineException as e:
if e.stderr.strip() == "SLURM accounting storage is disabled":
log.warning("SLURM accounting storage is not properly configured, unable to run sacct")
return
raise e
# 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])
try:
stdout = commands.execute(cmd).strip()
except commands.CommandLineException as e:
if e.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 e
# 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] += f" {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":
if ajs.job_wrapper.get_state() == model.Job.states.STOPPED:
# User requested to stop job, this isn't an error, just finish as normal
return super()._complete_terminal_job(ajs, drmaa_state=drmaa_state)
# 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
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()._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, "rb") as f:
if os.path.getsize(efile_path) > 2048:
f.seek(-2048, os.SEEK_END)
f.readline()
for line in f.readlines():
stripped_line = unicodify(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 FileNotFoundError:
# Entirely expected, as __check_memory_limit is only called if the job state is CANCELLED
return False
except Exception:
log.exception("Error reading end of %s:", efile_path)
return False