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import logging
import os
import time
from parsl.jobs.states import JobState, JobStatus
from parsl.launchers import SingleNodeLauncher
from parsl.providers.cluster_provider import ClusterProvider
from parsl.providers.grid_engine.template import template_string
from parsl.utils import RepresentationMixin
logger = logging.getLogger(__name__)
translate_table = {
'qw': JobState.PENDING,
'hqw': JobState.PENDING,
'hrwq': JobState.PENDING,
'r': JobState.RUNNING,
's': JobState.FAILED, # obsuspended
'ts': JobState.FAILED,
't': JobState.FAILED, # Suspended by alarm
'eqw': JobState.FAILED, # Error states
'ehqw': JobState.FAILED, # ..
'ehrqw': JobState.FAILED, # ..
'd': JobState.COMPLETED,
'dr': JobState.COMPLETED,
'dt': JobState.COMPLETED,
'drt': JobState.COMPLETED,
'ds': JobState.COMPLETED,
'drs': JobState.COMPLETED,
}
class GridEngineProvider(ClusterProvider, RepresentationMixin):
"""A provider for the Grid Engine scheduler.
Parameters
----------
nodes_per_block : int
Nodes to provision per block.
min_blocks : int
Minimum number of blocks to maintain.
max_blocks : int
Maximum number of blocks to maintain.
parallelism : float
Ratio of provisioned task slots to active tasks. A parallelism value of 1 represents aggressive
scaling where as many resources as possible are used; parallelism close to 0 represents
the opposite situation in which as few resources as possible (i.e., min_blocks) are used.
walltime : str
Walltime requested per block in HH:MM:SS.
scheduler_options : str
String to prepend to the #$$ blocks in the submit script to the scheduler.
worker_init : str
Command to be run before starting a worker, such as 'module load Anaconda; source activate env'.
launcher : Launcher
Launcher for this provider. Possible launchers include
:class:`~parsl.launchers.SingleNodeLauncher` (the default),
cmd_timeout : int
Timeout for commands made to the scheduler in seconds
"""
def __init__(self,
nodes_per_block=1,
init_blocks=1,
min_blocks=0,
max_blocks=1,
parallelism=1,
walltime="00:10:00",
scheduler_options='',
worker_init='',
launcher=SingleNodeLauncher(),
cmd_timeout: int = 60,
queue=None):
label = 'grid_engine'
super().__init__(label,
nodes_per_block,
init_blocks,
min_blocks,
max_blocks,
parallelism,
walltime,
launcher,
cmd_timeout=cmd_timeout)
self.scheduler_options = scheduler_options
self.worker_init = worker_init
self.queue = queue
if launcher in ['srun', 'srun_mpi']:
logger.warning("Use of {} launcher is usually appropriate for Slurm providers. "
"Recommended options include 'single_node' or 'aprun'.".format(launcher))
def get_configs(self, command, tasks_per_node):
"""Compose a dictionary with information for writing the submit script."""
logger.debug("Requesting one block with {} nodes per block and {} tasks per node".format(
self.nodes_per_block, tasks_per_node))
job_config = {}
job_config["submit_script_dir"] = self.script_dir
job_config["nodes"] = self.nodes_per_block
job_config["walltime"] = self.walltime
job_config["scheduler_options"] = self.scheduler_options
job_config["worker_init"] = self.worker_init
job_config["user_script"] = command
job_config["user_script"] = self.launcher(command,
tasks_per_node,
self.nodes_per_block)
return job_config
def submit(self, command, tasks_per_node, job_name="parsl.sge"):
''' The submit method takes the command string to be executed upon
instantiation of a resource most often to start a pilot.
Args :
- command (str) : The bash command string to be executed.
- tasks_per_node (int) : command invocations to be launched per node
KWargs:
- job_name (str) : Human friendly name to be assigned to the job request
Returns:
- A job identifier, this could be an integer, string etc
Raises:
- ExecutionProviderException or its subclasses
'''
# Set job name
job_name = "{0}.{1}".format(job_name, time.time())
# Set script path
script_path = "{0}/{1}.submit".format(self.script_dir, job_name)
script_path = os.path.abspath(script_path)
job_config = self.get_configs(command, tasks_per_node)
logger.debug("Writing submit script")
self._write_submit_script(template_string, script_path, job_name, job_config)
if self.queue is not None:
cmd = "qsub -q {0} -terse {1}".format(self.queue, script_path)
else:
cmd = "qsub -terse {0}".format(script_path)
retcode, stdout, stderr = self.execute_wait(cmd)
if retcode == 0:
for line in stdout.split('\n'):
job_id = line.strip()
if not job_id:
continue
self.resources[job_id] = {'job_id': job_id, 'status': JobStatus(JobState.PENDING)}
return job_id
else:
logger.error("Submit command failed")
logger.error("Retcode:%s STDOUT:%s STDERR:%s", retcode, stdout.strip(), stderr.strip())
def _status(self):
''' Get the status of a list of jobs identified by the job identifiers
returned from the submit request.
Returns:
- A list of JobStatus objects corresponding to each job_id in the job_ids list.
Raises:
- ExecutionProviderException or its subclasses
'''
cmd = "qstat"
retcode, stdout, stderr = self.execute_wait(cmd)
# Execute_wait failed. Do no update
if retcode != 0:
return
jobs_missing = list(self.resources.keys())
for line in stdout.split('\n'):
parts = line.split()
if parts and parts[0].lower().lower() != 'job-id' \
and not parts[0].startswith('----'):
job_id = parts[0]
state = translate_table.get(parts[4].lower(), JobState.UNKNOWN)
if job_id in self.resources:
self.resources[job_id]['status'] = JobStatus(state)
jobs_missing.remove(job_id)
# Filling in missing blanks for jobs that might have gone missing
# we might lose some information about why the jobs failed.
for missing_job in jobs_missing:
self.resources[missing_job]['status'] = JobStatus(JobState.COMPLETED)
def cancel(self, job_ids):
''' Cancels the resources identified by the job_ids provided by the user.
Args:
- job_ids (list): A list of job identifiers
Returns:
- A list of status from cancelling the job which can be True, False
Raises:
- ExecutionProviderException or its subclasses
'''
job_id_list = ' '.join(job_ids)
cmd = "qdel {}".format(job_id_list)
retcode, stdout, stderr = self.execute_wait(cmd)
rets = None
if retcode == 0:
for jid in job_ids:
self.resources[jid]['status'] = JobStatus(JobState.COMPLETED)
rets = [True for i in job_ids]
else:
rets = [False for i in job_ids]
return rets
@property
def status_polling_interval(self):
return 60
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