The Virtual Brain Project

Source code for

# -*- coding: utf-8 -*-
# TheVirtualBrain-Framework Package. This package holds all Data Management, and 
# Web-UI helpful to run brain-simulations. To use it, you also need do download
# TheVirtualBrain-Scientific Package (for simulators). See content of the
# documentation-folder for more details. See also
# (c) 2012-2017, Baycrest Centre for Geriatric Care ("Baycrest") and others
# This program is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software Foundation,
# either version 3 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.  See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with this
# program.  If not, see <>.
# When using The Virtual Brain for scientific publications, please cite it as follows:
#   Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
#   Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
#       The Virtual Brain: a simulator of primate brain network dynamics.
#   Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)

.. moduleauthor:: Lia Domide <>
.. moduleauthor:: Bogdan Neacsa <>
.. moduleauthor:: Yann Gordon <yann@invalid.tvb>

import os
import sys
import signal
import Queue as queue
import threading
from subprocess import Popen, PIPE
from tvb.basic.profile import TvbProfile
from tvb.basic.logger.builder import get_logger
from tvb.core.utils import parse_json_parameters
from tvb.core.entities import model
from import dao
from import WorkflowService

LOGGER = get_logger(__name__)


LOCKS_QUEUE = queue.Queue(0)
for i in range(TvbProfile.current.MAX_THREADS_NUMBER):

[docs]class OperationExecutor(threading.Thread): """ Thread in charge for starting an operation, used both on cluster and with stand-alone installations. """ def __init__(self, op_id): threading.Thread.__init__(self) self.operation_id = op_id self._stop = threading.Event()
[docs] def run(self): """ Get the required data from the operation queue and launch the operation. """ # Try to get a spot to launch own operation. LOCKS_QUEUE.get(True) operation_id = self.operation_id run_params = [TvbProfile.current.PYTHON_INTERPRETER_PATH, '-m', 'tvb.core.operation_async_launcher', str(operation_id), TvbProfile.CURRENT_PROFILE_NAME] # In the exceptional case where the user pressed stop while the Thread startup is done, # We should no longer launch the operation. if self.stopped() is False: env = os.environ.copy() env['PYTHONPATH'] = os.pathsep.join(sys.path) # anything that was already in $PYTHONPATH should have been reproduced in sys.path launched_process = Popen(run_params, stdout=PIPE, stderr=PIPE, env=env) LOGGER.debug("Storing pid=%s for operation id=%s launched on local machine." % (operation_id, op_ident = model.OperationProcessIdentifier(operation_id, dao.store_entity(op_ident) if self.stopped(): # In the exceptional case where the user pressed stop while the Thread startup is done. # and stop_operation is concurrently asking about OperationProcessIdentity. self.stop_pid( subprocess_result = launched_process.communicate()"Finished with launch of operation %s" % operation_id) returned = launched_process.wait() if returned != 0 and not self.stopped(): # Process did not end as expected. (e.g. Segmentation fault) workflow_service = WorkflowService() operation = dao.get_operation_by_id(self.operation_id) LOGGER.error("Operation suffered fatal failure! Exit code: %s Exit message: %s" % (returned, subprocess_result)) workflow_service.persist_operation_state(operation, model.STATUS_ERROR, "Operation failed unexpectedly! Please check the log files.") burst_entity = dao.get_burst_for_operation_id(self.operation_id) if burst_entity: message = "Error in operation process! Possibly segmentation fault." workflow_service.mark_burst_finished(burst_entity, error_message=message) del launched_process # Give back empty spot now that you finished your operation CURRENT_ACTIVE_THREADS.remove(self) LOCKS_QUEUE.put(1)
[docs] def stop(self): """ Mark current thread for stop""" self._stop.set()
[docs] def stopped(self): """Check if current thread was marked for stop.""" return self._stop.isSet()
[docs] def stop_pid(pid): """ Stop a process specified by PID. :returns: True when specified Process was stopped in here, \ False in case of exception(e.g. process stopped in advance). """ if sys.platform == 'win32': try: import ctypes handle = ctypes.windll.kernel32.OpenProcess(1, False, int(pid)) ctypes.windll.kernel32.TerminateProcess(handle, -1) ctypes.windll.kernel32.CloseHandle(handle) except OSError: return False else: try: os.kill(int(pid), signal.SIGKILL) except OSError: return False return True
[docs]class StandAloneClient(object): """ Instead of communicating with a back-end cluster, fire locally a new thread. """ @staticmethod
[docs] def execute(operation_id, user_name_label, adapter_instance): """Start asynchronous operation locally""" thread = OperationExecutor(operation_id) CURRENT_ACTIVE_THREADS.append(thread) thread.start()
[docs] def stop_operation(operation_id): """ Stop a thread for a given operation id """ operation = dao.try_get_operation_by_id(operation_id) if not operation or operation.has_finished: LOGGER.warning("Operation already stopped or not found is given to stop job: %s" % operation_id) return True LOGGER.debug("Stopping operation: %s" % str(operation_id)) # Set the thread stop flag to true for thread in CURRENT_ACTIVE_THREADS: if int(thread.operation_id) == operation_id: thread.stop() LOGGER.debug("Found running thread for operation: %d" % operation_id) # Kill Thread stopped = True operation_process = dao.get_operation_process_for_operation(operation_id) if operation_process is not None: # Now try to kill the operation if it exists stopped = OperationExecutor.stop_pid( if not stopped: LOGGER.debug("Operation %d was probably killed from it's specific thread." % operation_id) else: LOGGER.debug("Stopped OperationExecutor process for %d" % operation_id) # Mark operation as canceled in DB and on disk WorkflowService().persist_operation_state(operation, model.STATUS_CANCELED) return stopped
[docs]class ClusterSchedulerClient(object): """ Simple class, to mimic the same behavior we are expecting from StandAloneClient, but firing behind the cluster job scheduling process.. """ @staticmethod def _run_cluster_job(operation_identifier, user_name_label, adapter_instance): """ Threaded Popen It is the function called by the ClusterSchedulerClient in a Thread. This function starts a new process. """ # Load operation so we can estimate the execution time operation = dao.get_operation_by_id(operation_identifier) kwargs = parse_json_parameters(operation.parameters) kwargs = adapter_instance.prepare_ui_inputs(kwargs) time_estimate = int(adapter_instance.get_execution_time_approximation(**kwargs)) hours = int(time_estimate / 3600) minutes = (int(time_estimate) % 3600) / 60 seconds = int(time_estimate) % 60 # Anything lower than 5 hours just use default walltime if hours < 5: walltime = "05:00:00" else: if hours < 10: hours = "0%d" % hours else: hours = str(hours) walltime = "%s:%s:%s" % (hours, str(minutes), str(seconds)) call_arg = TvbProfile.current.cluster.SCHEDULE_COMMAND % (operation_identifier, user_name_label, walltime) process_ = Popen([call_arg], stdout=PIPE, shell=True) job_id ='\n', '').split(TvbProfile.current.cluster.JOB_ID_STRING)[-1]"Got jobIdentifier = %s for CLUSTER operationID = %s" % (job_id, operation_identifier)) operation_identifier = model.OperationProcessIdentifier(operation_identifier, job_id=job_id) dao.store_entity(operation_identifier) @staticmethod
[docs] def execute(operation_id, user_name_label, adapter_instance): """Call the correct system command to submit a job to the cluster.""" thread = threading.Thread(target=ClusterSchedulerClient._run_cluster_job, kwargs={'operation_identifier': operation_id, 'user_name_label': user_name_label, 'adapter_instance': adapter_instance}) thread.start()
[docs] def stop_operation(operation_id): """ Stop a thread for a given operation id """ operation = dao.try_get_operation_by_id(operation_id) if not operation or operation.has_finished: LOGGER.warning("Operation already stopped or not found is given to stop job: %s" % operation_id) return True operation_process = dao.get_operation_process_for_operation(operation_id) result = 0 # Try to kill only if operation job process is not None if operation_process is not None: stop_command = TvbProfile.current.cluster.STOP_COMMAND % operation_process.job_id"Stopping cluster operation: %s" % stop_command) result = os.system(stop_command) if result != 0: LOGGER.error("Stopping cluster operation was unsuccessful. Try following status with '" + TvbProfile.current.cluster.STATUS_COMMAND + "'" % operation_process.job_id) WorkflowService().persist_operation_state(operation, model.STATUS_CANCELED) return result == 0
if TvbProfile.current.cluster.IS_DEPLOY: # Return an entity capable to submit jobs to the cluster. BACKEND_CLIENT = ClusterSchedulerClient() else: # Return a thread launcher. BACKEND_CLIENT = StandAloneClient()