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()
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")
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))