Source code for processpoolexecution

# Copyright 2011-2014 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

import multiprocessing
import os
import subprocess
import sys
import traceback
import fastr
from fastr.core.baseplugin import PluginState
from fastr.execution.executionpluginmanager import ExecutionPlugin, JobAction
from fastr.execution.job import Job, JobState
from fastr.utils.classproperty import classproperty
from fastr.utils.multiprocesswrapper import function_wrapper


def run_job(job, job_status):
    try:
        fastr.log.debug('Running job {}'.format(job.jobid))
        job_status[job.jobid] = JobState.running

        command = [sys.executable,
                   os.path.join(fastr.config.executionscript),
                   job.commandfile]

        with open(job.stdoutfile, 'w') as fh_stdout, open(job.stderrfile, 'w') as fh_stderr:
            proc = subprocess.Popen(command, stdout=fh_stdout, stderr=fh_stderr)
            proc.wait()
            fastr.log.debug('Subprocess finished')
        fastr.log.debug('Finished {}'.format(job.jobid))
    except Exception:
        exc_type, _, trace = sys.exc_info()
        exc_info = traceback.format_exc()
        trace = traceback.extract_tb(trace, 1)[0]
        fastr.log.error('Encountered exception ({}) during execution:\n{}'.format(exc_type.__name__, exc_info))
        job.info_store['errors'].append((exc_type.__name__, exc_info, trace[0], trace[1]))
        job.status = JobState.failed

    fastr.log.debug('Finished run for {}'.format(job.jobid))

    return job


class ProcessPoolExecution(ExecutionPlugin):
    """
    A local execution plugin that uses multiprocessing to create a pool of
    worker processes. This allows fastr to execute jobs in parallel with
    true concurrency. The number of workers can be specified in the fastr
    configuration, but the default amount is the ``number of cores - 1``
    with a minimum of ``1``.

    .. warning::

        The ProcessPoolExecution does not check memory requirements of jobs
        and running many workers might lead to memory starvation and thus an
        unresponsive system.
    """
    _status = (PluginState.uninitialized, 'Please use the test() function to check DRMAA capability')

[docs] def __init__(self, finished_callback=None, cancelled_callback=None, status_callback=None, nr_of_workers=None): super(ProcessPoolExecution, self).__init__(finished_callback, cancelled_callback, status_callback) self.pool = multiprocessing.Pool(processes=fastr.config.process_pool_worker_number)
@classproperty def configuration_fields(cls): return { "process_pool_worker_number": ( int, # Default number of workers is core - 1 (to assure system # responsiveness) max(multiprocessing.cpu_count() - 1, 1), "Number of workers to use in a process pool" ) }
[docs] def cleanup(self): super(ProcessPoolExecution, self).cleanup() # Close the multiprocess pool fastr.log.debug('Stopping ProcessPool') fastr.log.debug('Terminating worker processes...') self.pool.terminate() fastr.log.debug('Joining worker processes...') self.pool.join() fastr.log.debug('ProcessPool stopped!')
@classmethod
[docs] def test(cls): try: # See if we can make a Pool and then remove it fastr.log.debug('Creating Pool') pool = multiprocessing.Pool(processes=2) fastr.log.debug('Terminating Pool') pool.terminate() del pool _status = ('Loaded', '') except OSError: _status = ('Failed', 'Multiprocessing Failed ({}):\n{}'.format(sys.exc_info()[0].__name__, traceback.format_exc())) cls._status = _status
def _job_finished(self, result): pass def _cancel_job(self, job): fastr.log.debug('Cannot remove jobs from a LinearExecution queue!') def _release_job(self, job): if not isinstance(job, Job): job = self.job_dict[job] self.queue_job(job) def _queue_job(self, job): # Check if the job is ready to run or must be held action = self.check_job_requirements(job.jobid) if action == JobAction.hold: fastr.log.debug('Holding {} until dependencies are met'.format(job.jobid)) self.job_status[job.jobid] = job.status = JobState.hold elif action == JobAction.cancel: self.cancel_job(job) else: fastr.log.debug('Queueing {}'.format(job.jobid)) self.pool.apply_async(function_wrapper, [os.path.abspath(__file__), 'run_job', job, self.job_status], callback=self.job_finished) if __name__ == '__main__': multiprocessing.freeze_support()