Source code for pyworkflow.protocol.launch

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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# * the Free Software Foundation; either version 3 of the License, or
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This module is responsible for launching protocol executions.
There are two main scenarios: local execution and remote execution.

A. Local execution: 
This will depend on the 'localhost' configuration
1- Check if the protocol will be launched with MPI or not (using MPI template from config)
2- Check if the protocol will be submitted to a queue (using Queue template from config)
3- Build the command that will be launched.

B. Remote execution:
1- Establish a connection with remote host for protocol execution
2- Copy necessary files to remote host.
3- Run a local process (for local execution, see case A) in the remote host
4- Get the result back after launching remotely

import os
import re
from subprocess import Popen, PIPE
import pyworkflow as pw
from pyworkflow.utils import (redStr, greenStr, makeFilePath, join, process,
from pyworkflow.protocol.constants import UNKNOWN_JOBID

LOCALHOST = 'localhost'

# ******************************************************************
# *         Public functions provided by the module
# ******************************************************************

[docs]def launch(protocol, wait=False, stdin=None, stdout=None, stderr=None): """ This function should be used to launch a protocol This function will decide which case, A or B will be used. """ if _isLocal(protocol): jobId = _launchLocal(protocol, wait, stdin, stdout, stderr) else: jobId = _launchRemote(protocol, wait) protocol.setJobId(jobId) return jobId
[docs]def stop(protocol): """ """ if _isLocal(protocol): return _stopLocal(protocol) else: return _stopRemote(protocol)
[docs]def schedule(protocol, wait=False): """ Use this function to schedule protocols that are not ready to run yet. Right now it only make sense to schedule jobs locally. """ cmd = '%s %s' % (pw.PYTHON, pw.getScheduleScript()) cmd += ' "%s" "%s" %s' % (protocol.getProject().path, protocol.getDbPath(), protocol.strId()) jobId = _run(cmd, wait) protocol.setJobId(jobId) return jobId
# ****************************************************************** # * Internal utility functions # ****************************************************************** def _isLocal(protocol): return protocol.getHostName() == LOCALHOST def _runsLocally(protocol): """ Return True if this protocol is running in this machine, where the PID makes sense. """ return protocol.getHostFullName() == getHostFullName() # ****************************************************************** # * Function related to LAUNCH # ****************************************************************** def _getAppsProgram(prog): """ Get a command to launch a program under the apps folder. """ return "%s %s" % (pw.PYTHON, pw.join(pw.APPS, prog)) def _launchLocal(protocol, wait, stdin=None, stdout=None, stderr=None): # Check first if we need to launch with MPI or not command = ('%s %s "%s" "%s" %s' % (pw.PYTHON, pw.join(pw.APPS, ''), protocol.getProject().path, protocol.getDbPath(), protocol.strId())) hostConfig = protocol.getHostConfig() useQueue = protocol.useQueue() # Check if need to submit to queue if useQueue and (protocol.getSubmitDict()["QUEUE_FOR_JOBS"] == "N"): submitDict = dict(hostConfig.getQueuesDefault()) submitDict.update(protocol.getSubmitDict()) submitDict['JOB_COMMAND'] = command jobId = _submit(hostConfig, submitDict) else: jobId = _run(command, wait, stdin, stdout, stderr) return jobId def _runRemote(protocol, mode): """ Launch remotely '' script to run or stop a protocol. Params: protocol: the protocol to be ran or stopped. mode: should be either 'run' or 'stop' """ host = protocol.getHostConfig() tpl = "ssh %(address)s '%(scipion)s/scipion " if host.getScipionConfig() is not None: tpl += "--config %(config)s " tpl += "runprotocol %(mode)s " tpl += "%(project)s %(protDb)s %(protId)s' " # Use project base name, # in remote SCIPION_USER_DATA/projects should be prepended projectPath = os.path.basename(protocol.getProject().path) args = {'address': host.getAddress(), 'mode': mode, 'scipion': host.getScipionHome(), 'config': host.getScipionConfig(), 'project': projectPath, 'protDb': protocol.getDbPath(), 'protId': protocol.getObjId() } cmd = tpl % args print("** Running remote: %s" % greenStr(cmd)) p = Popen(cmd, shell=True, stdout=PIPE) return p def _launchRemote(protocol, wait): p = _runRemote(protocol, 'run') jobId = UNKNOWN_JOBID out, err = p.communicate() if err: raise Exception(err) s ='Scipion remote jobid: (\d+)', out) if s: jobId = int( else: raise Exception("** Couldn't parse ouput: %s" % redStr(out)) return jobId def _copyFiles(protocol, rpath): """ Copy all required files for protocol to run in a remote execution host. NOTE: this function should always be execute with the current working dir pointing to the project dir. And the remotePath is assumed to be in protocol.getHostConfig().getHostPath() Params: protocol: protocol to copy files ssh: an ssh connection to copy the files. """ remotePath = protocol.getHostConfig().getHostPath() for f in protocol.getFiles(): remoteFile = join(remotePath, f) rpath.putFile(f, remoteFile) def _submit(hostConfig, submitDict, cwd=None, env=None): """ Submit a protocol to a queue system. Return its job id. """ # Create first the submission script to be launched # formatting using the template template = hostConfig.getSubmitTemplate() % submitDict # FIXME: CREATE THE PATH FIRST scripPath = submitDict['JOB_SCRIPT'] f = open(scripPath, 'w') # Ensure the path exists makeFilePath(scripPath) # Add some line ends because in some clusters it fails # to submit jobs if the submit script does not have end of line f.write(template + '\n\n') f.close() # This should format the command using a template like: # "qsub %(JOB_SCRIPT)s" command = hostConfig.getSubmitCommand() % submitDict gcmd = greenStr(command) print("** Submitting to queue: '%s'" % gcmd) p = Popen(command, shell=True, stdout=PIPE, cwd=cwd, env=env) out = p.communicate()[0] # Try to parse the result of qsub, searching for a number (jobId) # Review this, seems to exclusive to torque batch system s ='(\d+)', str(out)) if p.returncode == 0 and s: job = int( print("Launched job with id %s" % job) return job else: print("Couldn't submit to queue for reason: %s " % redStr(out.decode())) return UNKNOWN_JOBID def _run(command, wait, stdin=None, stdout=None, stderr=None): """ Execute a command in a subprocess and return the pid. """ gcmd = greenStr(command) print("** Running command: '%s'" % gcmd) p = Popen(command, shell=True, stdout=stdout, stderr=stderr) jobId = if wait: p.wait() return jobId # ****************************************************************** # * Function related to STOP # ****************************************************************** def _stopLocal(protocol): if protocol.useQueue() and not protocol.isScheduled(): jobId = protocol.getJobId() host = protocol.getHostConfig() cancelCmd = host.getCancelCommand() % {'JOB_ID': jobId} _run(cancelCmd, wait=True) else: process.killWithChilds(protocol.getPid()) def _stopRemote(protocol): _runRemote(protocol, 'stop')