import math
import pathlib
import shlex
from typing import List
from dargs import Argument
from dpdispatcher import dlog
from dpdispatcher.JobStatus import JobStatus
from dpdispatcher.machine import Machine, script_command_template
from dpdispatcher.utils import RetrySignal, retry
# from dpdispatcher.submission import Resources
slurm_script_header_template = """\
#!/bin/bash -l
#SBATCH --parsable
{slurm_nodes_line}
{slurm_ntasks_per_node_line}
{slurm_number_gpu_line}
{slurm_partition_line}"""
[docs]class Slurm(Machine):
[docs] def gen_script(self, job):
slurm_script = super().gen_script(job)
return slurm_script
@retry()
def do_submit(self, job):
script_file_name = job.script_file_name
script_str = self.gen_script(job)
job_id_name = job.job_hash + "_job_id"
# script_str = self.sub_script(job_dirs, cmd, args=args, resources=resources, outlog=outlog, errlog=errlog)
self.context.write_file(fname=script_file_name, write_str=script_str)
# self.context.write_file(fname=os.path.join(self.context.submission.work_base, script_file_name), write_str=script_str)
ret, stdin, stdout, stderr = self.context.block_call(
"cd {} && {} {}".format(
shlex.quote(self.context.remote_root),
"sbatch",
shlex.quote(script_file_name),
)
)
if ret != 0:
err_str = stderr.read().decode("utf-8")
if (
"Socket timed out on send/recv operation" in err_str
or "Unable to contact slurm controller" in err_str
):
# server network error, retry 3 times
raise RetrySignal(
"Get error code %d in submitting through ssh with job: %s . message: %s"
% (ret, job.job_hash, err_str)
)
elif (
"Job violates accounting/QOS policy" in err_str
# the number of jobs exceeds DEFAULT_MAX_JOB_COUNT (by default 10000)
or "Slurm temporarily unable to accept job, sleeping and retrying"
in err_str
):
# job number exceeds, skip the submitting
return ""
raise RuntimeError(
"status command squeue fails to execute\nerror message:%s\nreturn code %d\n"
% (err_str, ret)
)
subret = stdout.readlines()
# --parsable
# Outputs only the job id number and the cluster name if present.
# The values are separated by a semicolon. Errors will still be displayed.
job_id = subret[0].split(";")[0].strip()
self.context.write_file(job_id_name, job_id)
return job_id
[docs] def default_resources(self, resources):
pass
@retry()
def check_status(self, job):
job_id = job.job_id
if job_id == "":
return JobStatus.unsubmitted
ret, stdin, stdout, stderr = self.context.block_call(
'squeue -o "%.18i %.2t" -j ' + job_id
)
if ret != 0:
err_str = stderr.read().decode("utf-8")
if "Invalid job id specified" in err_str:
if self.check_finish_tag(job):
dlog.info(f"job: {job.job_hash} {job.job_id} finished")
return JobStatus.finished
else:
return JobStatus.terminated
elif (
"Socket timed out on send/recv operation" in err_str
or "Unable to contact slurm controller" in err_str
or "Invalid user for SlurmUser" in err_str
):
# retry 3 times
raise RetrySignal(
"Get error code %d in checking status through ssh with job: %s . message: %s"
% (ret, job.job_hash, err_str)
)
raise RuntimeError(
"status command squeue fails to execute."
"job_id:%s \n error message:%s\n return code %d\n"
% (job_id, err_str, ret)
)
status_line = stdout.read().decode("utf-8").split("\n")[-2]
status_word = status_line.split()[-1]
if not (len(status_line.split()) == 2 and status_word.isupper()):
raise RuntimeError(
"Error in getting job status, "
+ f"status_line = {status_line}, "
+ f"parsed status_word = {status_word}"
)
if status_word in ["PD", "CF", "S"]:
return JobStatus.waiting
elif status_word in ["R"]:
return JobStatus.running
elif status_word in ["CG"]:
return JobStatus.completing
elif status_word in [
"C",
"E",
"K",
"BF",
"CA",
"CD",
"F",
"NF",
"PR",
"SE",
"ST",
"TO",
]:
if self.check_finish_tag(job):
dlog.info(f"job: {job.job_hash} {job.job_id} finished")
return JobStatus.finished
else:
return JobStatus.terminated
else:
return JobStatus.unknown
[docs] def check_finish_tag(self, job):
job_tag_finished = job.job_hash + "_job_tag_finished"
return self.context.check_file_exists(job_tag_finished)
[docs] @classmethod
def resources_subfields(cls) -> List[Argument]:
"""Generate the resources subfields.
Returns
-------
list[Argument]
resources subfields
"""
doc_custom_gpu_line = "Custom GPU configuration, starting with #SBATCH"
return [
Argument(
"kwargs",
dict,
[
Argument(
"custom_gpu_line",
str,
optional=True,
default=None,
doc=doc_custom_gpu_line,
)
],
optional=True,
doc="Extra arguments.",
)
]
[docs] def kill(self, job):
"""Kill the job.
Parameters
----------
job : Job
job
"""
job_id = job.job_id
# -Q Do not report an error if the specified job is already completed.
ret, stdin, stdout, stderr = self.context.block_call(
"scancel -Q " + str(job_id)
)
# we do not need to stop here if scancel failed; just continue
[docs]class SlurmJobArray(Slurm):
"""Slurm with job array enabled for multiple tasks in a job."""
[docs] def gen_script_command(self, job):
resources = job.resources
slurm_job_size = resources.kwargs.get("slurm_job_size", 1)
# SLURM_ARRAY_TASK_ID: 0 ~ n_jobs-1
script_command = "case $SLURM_ARRAY_TASK_ID in\n"
for ii, task in enumerate(job.job_task_list):
command_env = ""
command_env += self.gen_command_env_cuda_devices(resources=resources)
task_tag_finished = task.task_hash + "_task_tag_finished"
log_err_part = ""
if task.outlog is not None:
log_err_part += f"1>>{shlex.quote(task.outlog)} "
if task.errlog is not None:
log_err_part += f"2>>{shlex.quote(task.errlog)} "
flag_if_job_task_fail = job.job_hash + "_flag_if_job_task_fail"
single_script_command = script_command_template.format(
flag_if_job_task_fail=flag_if_job_task_fail,
command_env=command_env,
task_work_path=shlex.quote(
pathlib.PurePath(task.task_work_path).as_posix()
),
command=task.command,
task_tag_finished=task_tag_finished,
log_err_part=log_err_part,
)
if ii % slurm_job_size == 0:
script_command += f"{ii // slurm_job_size})\n"
script_command += single_script_command
script_command += self.gen_script_wait(resources=resources)
script_command += "\n"
if (
ii % slurm_job_size == slurm_job_size - 1
or ii == len(job.job_task_list) - 1
):
script_command += ";;\n"
script_command += "*)\nexit 1\n;;\nesac\n"
return script_command
[docs] def gen_script_end(self, job):
# We cannot have a end script for job array
# we may check task tag instead
return ""
@retry()
def check_status(self, job):
job_id = job.job_id
if job_id == "":
return JobStatus.unsubmitted
ret, stdin, stdout, stderr = self.context.block_call(
'squeue -h -o "%.18i %.2t" -j ' + job_id
)
if ret != 0:
err_str = stderr.read().decode("utf-8")
if "Invalid job id specified" in err_str:
if self.check_finish_tag(job):
dlog.info(f"job: {job.job_hash} {job.job_id} finished")
return JobStatus.finished
else:
return JobStatus.terminated
elif (
"Socket timed out on send/recv operation" in err_str
or "Unable to contact slurm controller" in err_str
):
# retry 3 times
raise RetrySignal(
"Get error code %d in checking status through ssh with job: %s . message: %s"
% (ret, job.job_hash, err_str)
)
raise RuntimeError(
"status command squeue fails to execute."
"job_id:%s \n error message:%s\n return code %d\n"
% (job_id, err_str, ret)
)
status_lines = stdout.read().decode("utf-8").split("\n")[:-1]
status = []
for status_line in status_lines:
status_word = status_line.split()[-1]
if not (len(status_line.split()) == 2 and status_word.isupper()):
raise RuntimeError(
"Error in getting job status, "
+ f"status_line = {status_line}, "
+ f"parsed status_word = {status_word}"
)
if status_word in ["PD", "CF", "S"]:
status.append(JobStatus.waiting)
elif status_word in ["R"]:
status.append(JobStatus.running)
elif status_word in ["CG"]:
status.append(JobStatus.completing)
elif status_word in [
"C",
"E",
"K",
"BF",
"CA",
"CD",
"F",
"NF",
"PR",
"SE",
"ST",
"TO",
]:
status.append(JobStatus.finished)
else:
status.append(JobStatus.unknown)
# running if any job is running
if JobStatus.running in status:
return JobStatus.running
elif JobStatus.waiting in status:
return JobStatus.waiting
elif JobStatus.completing in status:
return JobStatus.completing
elif JobStatus.unknown in status:
return JobStatus.unknown
else:
if self.check_finish_tag(job):
dlog.info(f"job: {job.job_hash} {job.job_id} finished")
return JobStatus.finished
else:
return JobStatus.terminated
[docs] def check_finish_tag(self, job):
results = []
for task in job.job_task_list:
task.get_task_state(self.context)
results.append(task.task_state == JobStatus.finished)
return all(results)
[docs] @classmethod
def resources_subfields(cls) -> List[Argument]:
"""Generate the resources subfields.
Returns
-------
list[Argument]
resources subfields
"""
doc_slurm_job_size = "Number of tasks in a Slurm job"
arg = super().resources_subfields()[0]
arg.extend_subfields(
[
Argument(
"slurm_job_size",
int,
optional=True,
default=1,
doc=doc_slurm_job_size,
),
]
)
return [arg]