Exemplo n.º 1
0
def killMasterAndParasol():
    """Method to destroy master process
    """
    tempFile = getTempFile()
    popen("ps -a", tempFile)
    fileHandle = open(tempFile, 'r')
    line = fileHandle.readline()
    #Example parasol state lines:
    #67401 ttys002    0:00.06 /Users/benedictpaten/kent/src/parasol/bin/paraNode start -hub=localhost -log=/tmp/node.2009-07-08.log -umask=002 -userPath=bin:bin/x86_64:bin/i
    #67403 ttys002    0:00.65 /Users/benedictpaten/kent/src/parasol/bin/paraHub -log=/tmp/hub.2009-07-08.log machineList subnet=127.0.0
    #68573 ttys002    0:00.00 /Users/benedictpaten/kent/src/parasol/bin/paraNode start -hub=localhost -log=/tmp/node.2009-07-08.log -umask=002 -userPath=bin:bin/x86_64:bin/i
    while line != '':
        tokens = line.split()
        if 'paraNode' in line or 'paraHub' in line:
            if random.random() > 0.5:
                i = os.system("kill %i" % int(tokens[0]))
                logger.info("Tried to kill parasol process: %i, line: %s, exit value: %i" % (int(tokens[0]), line, i))
                break
        elif 'jobTreeMaster.py' in line:
            logger.info("Have job tree master line")
            if random.random() > 0.5:
                i = os.system("kill %i" % int(tokens[0]))
                logger.info("Tried to kill master process: %i, line: %s, exit value: %i" % (int(tokens[0]), line, i))
                break
        line = fileHandle.readline()
    fileHandle.close()
    os.remove(tempFile)
    parasolRestart()
Exemplo n.º 2
0
def parasolRestart():
    """Function starts the parasol hub and node.
    """
    parasolStop()
    while True:
        machineList = os.path.join(workflowRootPath(), "jobTree", "machineList")
        #pathEnvVar = os.environ["PATH"]
        os.system("paraNode start -hub=localhost") 
        #-umask=002 -userPath=%s -sysPath=%s" % (pathEnvVar, pathEnvVar))
        os.system("paraHub %s subnet=127.0.0 &" % (machineList,))
        tempFile = getTempFile()
        dead = True
        try:
            popen("parasol status", tempFile)
            fileHandle = open(tempFile, 'r')
            line = fileHandle.readline()
            while line != '':
                if "Nodes dead" in line:
                    print line
                    if int(line.split()[-1]) == 0:
                        dead = False
                line = fileHandle.readline()
            fileHandle.close()
        except RuntimeError:
            pass
        os.remove(tempFile)
        if not dead:
            break
        else:
            logger.info("Tried to restart the parasol process, but failed, will try again")
            parasolStop()
            time.sleep(5)
    logger.info("Restarted the parasol process")
Exemplo n.º 3
0
    def _run_evolver_decomposed_wdl(self, name):
        """ Run the full evolver test, putting the jobstore and output in tempDir
        but instead of doing in in one shot, use cactus-prepare to make a wdl
        script and run that locally through cromwell """

        # hack to use docker to remove filetree in teardown, as cromwell
        # can leave root files hanging around there
        self.cromwell = True

        out_seqfile = os.path.join(self.tempDir, 'evolverMammalsOut.txt')
        in_seqfile = './examples/evolverMammals.txt'
        out_wdl = os.path.join(self.tempDir, 'prepared.wdl')
        cmd = [
            'cactus-prepare', in_seqfile, '--outHal',
            self._out_hal(name), '--jobStore',
            self._job_store(name), '--wdl', '--dockerImage',
            'evolvertestdocker/cactus:latest', '--preprocessCores', '2',
            '--blastCores', '4', '--alignCores', '4'
        ]

        # specify an output directory
        cw_optionsfile = os.path.join(self.tempDir, 'options.json')
        cw_output = os.path.join(self.tempDir, 'cromwell-output')
        with open(cw_optionsfile, 'w') as cw_opts:
            cw_opts.write('{\n')
            cw_opts.write(
                '    \"final_workflow_outputs_dir\": \"{}\",\n'.format(
                    cw_output))
            cw_opts.write('    \"use_relative_output_paths\": true\n')
            cw_opts.write('}\n')

        # download cromwell
        subprocess.check_call([
            'wget', '-q',
            'https://github.com/broadinstitute/cromwell/releases/download/49/cromwell-49.jar'
        ],
                              cwd=self.tempDir)

        # run cactus-prepare and write the output to a wdl file
        popen(' '.join(cmd), out_wdl)

        # run the wdl script in cromwell
        subprocess.check_call([
            'java', '-jar', './cromwell-49.jar', 'run', out_wdl, '-o',
            cw_optionsfile
        ],
                              cwd=self.tempDir)

        # fish the file out of cromwell
        shutil.copyfile(
            os.path.join(cw_output, os.path.basename(self._out_hal(name))),
            self._out_hal(name))