def getjobexitcode(lsfJobID):
job, task = lsfJobID
# first try bjobs to find out job state
args = ["bjobs", "-l", str(job)]
logger.debug("Checking job exit code for job via bjobs: " + str(job))
process = subprocess.Popen(" ".join(args),
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
started = 0
for line in process.stdout:
if line.find("Done successfully") > -1:
logger.debug("bjobs detected job completed for job: " + str(job))
return 0
elif line.find("Completed <exit>") > -1:
logger.debug("bjobs detected job failed for job: " + str(job))
return 1
elif line.find("New job is waiting for scheduling") > -1:
logger.debug("bjobs detected job pending scheduling for job: " +
str(job))
return None
elif line.find("PENDING REASONS") > -1:
logger.debug("bjobs detected job pending for job: " + str(job))
return None
elif line.find("Started on ") > -1:
started = 1
if started == 1:
logger.debug("bjobs detected job started but not completed: " +
str(job))
return None
# if not found in bjobs, then try bacct (slower than bjobs)
logger.debug("bjobs failed to detect job - trying bacct: " + str(job))
args = ["bacct", "-l", str(job)]
logger.debug("Checking job exit code for job via bacct:" + str(job))
process = subprocess.Popen(" ".join(args),
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
for line in process.stdout:
if line.find("Completed <done>") > -1:
logger.debug("Detected job completed for job: " + str(job))
return 0
elif line.find("Completed <exit>") > -1:
logger.debug("Detected job failed for job: " + str(job))
return 1
logger.debug("Cant determine exit code for job or job still running: " +
str(job))
return None
def test_cwl_toil_kill(self):
"""Test "toil kill" on a CWL workflow with a 100 second sleep."""
run_cmd = [
'toil-cwl-runner', '--jobStore', self.jobstore, self.cwl, self.yaml
]
kill_cmd = ['toil', 'kill', self.jobstore]
cwl_process = subprocess.Popen(run_cmd)
time.sleep(2)
subprocess.Popen(kill_cmd, stderr=subprocess.PIPE)
assert cwl_process.poll() == None
def getRunningJobIDs(self):
times = {}
with self.runningJobsLock:
currentjobs = dict((str(self.batchJobIDs[x][0].strip()), x)
for x in self.runningJobs)
logger.debug("getRunningJobIDs current jobs are: " +
str(currentjobs))
# Skip running qstat if we don't have any current jobs
if not currentjobs:
return times
# Only query for job IDs to avoid clogging the batch system on heavily loaded clusters
# PBS plain qstat will return every running job on the system.
jobids = sorted(currentjobs.keys())
if self._version == "pro":
process = subprocess.Popen(['qstat', '-x'] + jobids,
stdout=subprocess.PIPE)
elif self._version == "oss":
process = subprocess.Popen(['qstat'] + jobids,
stdout=subprocess.PIPE)
stdout, stderr = process.communicate()
# qstat supports XML output which is more comprehensive, but PBSPro does not support it
# so instead we stick with plain commandline qstat tabular outputs
for currline in stdout.split('\n'):
items = currline.strip().split()
if items:
jobid = items[0].strip()
if jobid in currentjobs:
logger.debug("getRunningJobIDs job status for is: " +
items[4])
if jobid in currentjobs and items[4] == 'R':
walltime = items[3]
logger.debug(
"getRunningJobIDs qstat reported walltime is: " +
walltime)
# normal qstat has a quirk with job time where it reports '0'
# when initially running; this catches this case
if walltime == '0':
walltime = time.mktime(
time.strptime(walltime, "%S"))
else:
walltime = time.mktime(
time.strptime(walltime, "%H:%M:%S"))
times[currentjobs[jobid]] = walltime
logger.debug("Job times from qstat are: " + str(times))
return times
def _getJobDetailsFromSacct(self, slurmJobID):
# SLURM job exit codes are obtained by running sacct.
args = ['sacct',
'-n', # no header
'-j', str(slurmJobID), # job
'--format', 'State,ExitCode', # specify output columns
'-P', # separate columns with pipes
'-S', '1970-01-01'] # override start time limit
process = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
rc = process.returncode
if rc != 0:
# no accounting system or some other error
return (None, -999)
for line in process.stdout:
values = line.strip().split('|')
if len(values) < 2:
continue
state, exitcode = values
logger.debug("sacct job state is %s", state)
# If Job is in a running state, return None to indicate we don't have an update
status, _ = exitcode.split(':')
logger.debug("sacct exit code is %s, returning status %s", exitcode, status)
return (state, int(status))
logger.debug("Did not find exit code for job in sacct output")
return None
def getJobExitCode(self, torqueJobID):
if self._version == "pro":
args = ["qstat", "-x", "-f", str(torqueJobID).split('.')[0]]
elif self._version == "oss":
args = ["qstat", "-f", str(torqueJobID).split('.')[0]]
process = subprocess.Popen(args,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
for line in process.stdout:
line = line.strip()
#logger.debug("getJobExitCode exit status: " + line)
# Case differences due to PBSPro vs OSS Torque qstat outputs
if line.startswith("failed") or line.startswith(
"FAILED") and int(line.split()[1]) == 1:
return 1
if line.startswith("exit_status") or line.startswith(
"Exit_status"):
status = line.split(' = ')[1]
logger.debug('Exit Status: ' + status)
return int(status)
if 'unknown job id' in line.lower():
# some clusters configure Torque to forget everything about just
# finished jobs instantly, apparently for performance reasons
logger.debug(
'Batch system no longer remembers about job {}'.format(
torqueJobID))
# return assumed success; status files should reveal failure
return 0
return None
def _runParasol(self, command, autoRetry=True):
"""
Issues a parasol command using popen to capture the output. If the command fails then it
will try pinging parasol until it gets a response. When it gets a response it will
recursively call the issue parasol command, repeating this pattern for a maximum of N
times. The final exit value will reflect this.
"""
command = list(concat(self.parasolCommand, command))
while True:
logger.debug('Running %r', command)
process = subprocess.Popen(command,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
bufsize=-1)
stdout, stderr = process.communicate()
status = process.wait()
for line in stderr.split('\n'):
if line: logger.warn(line)
if status == 0:
return 0, stdout.split('\n')
message = 'Command %r failed with exit status %i' % (command,
status)
if autoRetry:
logger.warn(message)
else:
logger.error(message)
return status, None
logger.warn('Waiting for a 10s, before trying again')
time.sleep(10)
def killBatchJobs(self, jobIDs):
self.killLocalJobs(jobIDs)
"""Kills the given job IDs.
"""
for jobID in jobIDs:
try:
lsfID = self.getLsfID(jobID)
logger.debug("DEL: " + str(lsfID))
self.currentjobs.remove(jobID)
subprocess.Popen(["bkill", lsfID])
del self.jobIDs[self.lsfJobIDs[jobID]]
del self.lsfJobIDs[jobID]
except RuntimeError:
jobIDs.remove(jobID)
toKill = set(jobIDs)
while len(toKill) > 0:
for jobID in list(toKill):
if getjobexitcode(self.lsfJobIDs[jobID]) is not None:
toKill.remove(jobID)
if len(toKill) > 0:
logger.warn(
"Tried to kill some jobs, but something happened and they are still going, "
"so I'll try again")
time.sleep(5)
def coreSSH(self, *args, **kwargs):
"""
If strict=False, strict host key checking will be temporarily disabled.
This is provided as a convenience for internal/automated functions and
ought to be set to True whenever feasible, or whenever the user is directly
interacting with a resource (e.g. rsync-cluster or ssh-cluster). Assumed
to be False by default.
kwargs: input, tty, appliance, collectStdout, sshOptions, strict
"""
commandTokens = ['ssh', '-t']
strict = kwargs.pop('strict', False)
if not strict:
kwargs['sshOptions'] = ['-oUserKnownHostsFile=/dev/null', '-oStrictHostKeyChecking=no'] \
+ kwargs.get('sshOptions', [])
sshOptions = kwargs.pop('sshOptions', None)
# Forward ports:
# 3000 for Grafana dashboard
# 9090 for Prometheus dashboard
# 5050 for Mesos dashboard (although to talk to agents you will need a proxy)
commandTokens.extend(['-L', '3000:localhost:3000', \
'-L', '9090:localhost:9090', \
'-L', '5050:localhost:5050'])
if sshOptions:
# add specified options to ssh command
assert isinstance(sshOptions, list)
commandTokens.extend(sshOptions)
# specify host
user = kwargs.pop('user', 'core') # CHANGED: Is this needed?
commandTokens.append('%s@%s' % (user,str(self.effectiveIP)))
appliance = kwargs.pop('appliance', None)
if appliance:
# run the args in the appliance
tty = kwargs.pop('tty', None)
ttyFlag = '-t' if tty else ''
commandTokens += ['docker', 'exec', '-i', ttyFlag, 'toil_leader']
inputString = kwargs.pop('input', None)
if inputString is not None:
kwargs['stdin'] = subprocess.PIPE
collectStdout = kwargs.pop('collectStdout', None)
if collectStdout:
kwargs['stdout'] = subprocess.PIPE
kwargs['stderr'] = subprocess.PIPE
logger.debug('Node %s: %s', self.effectiveIP, ' '.join(args))
args = list(map(pipes.quote, args))
commandTokens += args
logger.debug('Full command %s', ' '.join(commandTokens))
popen = subprocess.Popen(commandTokens, **kwargs)
stdout, stderr = popen.communicate(input=inputString)
# at this point the process has already exited, no need for a timeout
resultValue = popen.wait()
# ssh has been throwing random 255 errors - why?
if resultValue != 0:
logger.debug('SSH Error (%s) %s' % (resultValue, stderr))
raise RuntimeError('Executing the command "%s" on the appliance returned a non-zero '
'exit code %s with stdout %s and stderr %s'
% (' '.join(args), resultValue, stdout, stderr))
return stdout
def getRunningBatchJobIDs(self):
"""Gets a map of jobs (as jobIDs) currently running (not just waiting)
and a how long they have been running for (in seconds).
"""
times = {}
currentjobs = set()
for x in self.getIssuedBatchJobIDs():
if x in self.lsfJobIDs:
currentjobs.add(self.lsfJobIDs[x])
else:
# not yet started
pass
process = subprocess.Popen(["bjobs"], stdout=subprocess.PIPE)
for curline in process.stdout:
items = curline.strip().split()
if (len(items) > 9 and
(items[0]) in currentjobs) and items[2] == 'RUN':
jobstart = "/".join(items[7:9]) + '/' + str(date.today().year)
jobstart = jobstart + ' ' + items[9]
jobstart = time.mktime(
time.strptime(jobstart, "%b/%d/%Y %H:%M"))
jobstart = time.mktime(
time.strptime(jobstart, "%m/%d/%Y %H:%M:%S"))
times[self.jobIDs[(items[0])]] = time.time() - jobstart
times.update(self.getRunningLocalJobIDs())
return times
def needs_appliance(test_item):
"""
Use as a decorator before test classes or methods to only run them if
the Toil appliance Docker image is downloaded.
"""
test_item = _mark_test('appliance', test_item)
if os.getenv('TOIL_SKIP_DOCKER', '').lower() == 'true':
return unittest.skip('Skipping docker test.')(test_item)
if not which('docker'):
return unittest.skip("Install docker to include this test.")(test_item)
try:
image = applianceSelf()
stdout, stderr = subprocess.Popen(
['docker', 'inspect', '--format="{{json .RepoTags}}"', image],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE).communicate()
if image in stdout.decode("utf-8"):
return test_item
except:
pass
return unittest.skip(
f"Cannot find appliance {image}. Use 'make test' target to automatically build appliance, or "
f"just run 'make push_docker' prior to running this test.")(test_item)
def writeA(job, mkFile):
'''Runs a program, and writes a string 'A' into A.txt using mkFile.py.'''
job.fileStore.logToMaster('''writeA''')
# temp folder for the run
tempDir = job.fileStore.getLocalTempDir()
# import files
try:
mkFile_fs = job.fileStore.readGlobalFile(mkFile[0],
userPath=os.path.join(
tempDir, mkFile[1]))
except:
mkFile_fs = os.path.join(tempDir, mkFile[1])
# make a file (A.txt) and writes a string 'A' into it using 'mkFile.py'
content = 'A'
cmd = 'python' + ' ' + mkFile_fs + ' ' + 'A.txt' + ' ' + content
this_process = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
this_process.wait()
# get the output file and return it as a tuple of location + name
output_filename = 'A.txt'
output_file = job.fileStore.writeGlobalFile(output_filename)
A1 = (output_file, output_filename)
rvDict = {"A1": A1}
return rvDict
def getJobExitCode(self, sgeJobID):
# the task is set as part of the job ID if using getBatchSystemID()
job, task = (sgeJobID, None)
if '.' in sgeJobID:
job, task = sgeJobID.split('.', 1)
args = ["qacct", "-j", str(job)]
if task is not None:
args.extend(["-t", str(task)])
logger.debug("Running %r", args)
process = subprocess.Popen(args,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
toil = False
for line in process.stdout:
if line.startswith("failed") and int(line.split()[1]) == 1:
return 1
####start####
if line.startswith("jobname") and line.find("toil_job") != -1:
toil = True
if toil and line.startswith("exit_status"):
logger.debug('Exit Status: %r', line.split()[1])
return int(line.split()[1])
####end####
#elif line.startswith("exit_status"):
# logger.debug('Exit Status: %r', line.split()[1])
# return int(line.split()[1])
return None
def _run(cls, command, *args, **kwargs):
"""
Run a command. Convenience wrapper for subprocess.check_call and subprocess.check_output.
:param str command: The command to be run.
:param str args: Any arguments to be passed to the command.
:param Any kwargs: keyword arguments for subprocess.Popen constructor. Pass capture=True
to have the process' stdout returned. Pass input='some string' to feed input to the
process' stdin.
:rtype: None|str
:return: The output of the process' stdout if capture=True was passed, None otherwise.
"""
args = list(concat(command, args))
log.info('Running %r', args)
capture = kwargs.pop('capture', False)
_input = kwargs.pop('input', None)
if capture:
kwargs['stdout'] = subprocess.PIPE
if _input is not None:
kwargs['stdin'] = subprocess.PIPE
popen = subprocess.Popen(args, **kwargs)
stdout, stderr = popen.communicate(input=_input)
assert stderr is None
if popen.returncode != 0:
raise subprocess.CalledProcessError(popen.returncode, args)
if capture:
return stdout
def testGetPIDStatus(self):
"""Test that ToilStatus.getPIDStatus() behaves as expected."""
wf = subprocess.Popen(self.sort_workflow_cmd)
self.check_status('RUNNING', status_fn=ToilStatus.getPIDStatus)
wf.wait()
self.check_status('COMPLETED', status_fn=ToilStatus.getPIDStatus)
os.remove(os.path.join(self.toilDir, 'pid.log'))
self.check_status('QUEUED', status_fn=ToilStatus.getPIDStatus)
def run(self):
command = self.parasolCommand()
with self.lock:
self.popen = subprocess.Popen(command)
status = self.popen.wait()
if status != 0 and status != -signal.SIGKILL:
log.error("Command '%s' failed with %i.", command, status)
raise subprocess.CalledProcessError(status, command)
log.info('Exiting %s', self.__class__.__name__)
def checkExitCode(self, script):
program = os.path.join(self.directory, "scripts", script)
process = subprocess.Popen(["python", program, "file:my-jobstore", "--clean=always"],
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stdout, stderr = process.communicate()
assert process.returncode == 0, stderr
if isinstance(stdout, bytes):
return stdout.decode('utf-8') + ' ' + stderr.decode('utf-8')
return stdout + ' ' + stderr
def bsub(bsubline):
process = subprocess.Popen(" ".join(bsubline),
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
liney = process.stdout.readline()
logger.debug("BSUB: " + liney)
result = int(liney.strip().split()[1].strip('<>'))
logger.debug("Got the job id: %s" % (str(result)))
return result
def submitJob(self, subLine):
combinedEnv = self.boss.environment
combinedEnv.update(os.environ)
process = subprocess.Popen(subLine, stdout=subprocess.PIPE,
env=combinedEnv)
line = process.stdout.readline()
logger.debug("BSUB: " + line)
result = int(line.strip().split()[1].strip('<>'))
logger.debug("Got the job id: {}".format(result))
return result
def _addToHosts(self, node, destinationIP=None):
"""
Add an "privateIP hostname" line to the /etc/hosts file. If destinationIP is given,
do this on the remote machine.
Azure VMs sometimes fail to initialize, causing the appliance to fail.
This error is given:
Failed to obtain the IP address for 'l7d41a19b-15a6-442c-8ba1-9678a951d824';
the DNS service may not be able to resolve it: Name or service not known.
This method is a fix.
:param node: Node to add to /etc/hosts.
:param destinationIP: A remote host's address
"""
cmd = "echo %s %s | sudo tee --append /etc/hosts > /dev/null" % (node.privateIP, node.name)
logger.debug("Running command %s on %s" % (cmd, destinationIP))
if destinationIP:
subprocess.Popen(["ssh", "-oStrictHostKeyChecking=no", "core@%s" % destinationIP, cmd])
else:
subprocess.Popen(cmd, shell=True)
def testGetPIDStatus(self):
"""Test that ToilStatus.getPIDStatus() behaves as expected."""
wf = subprocess.Popen(self.sort_workflow_cmd)
self.check_status('RUNNING', status_fn=ToilStatus.getPIDStatus)
wf.wait()
self.check_status('COMPLETED', status_fn=ToilStatus.getPIDStatus)
# TODO: we need to reach into the FileJobStore's files and
# delete this shared file. We assume we know its internal layout.
os.remove(os.path.join(self.toilDir, 'files/shared/pid.log'))
self.check_status('QUEUED', status_fn=ToilStatus.getPIDStatus)
def testGetStatusSuccessfulCWLWF(self):
"""Test that ToilStatus.getStatus() behaves as expected with a successful CWL workflow."""
cmd = [
'toil-cwl-runner', '--jobStore', self.toilDir, '--clean=never',
'src/toil/test/cwl/sorttool.cwl', '--reverse', '--input',
'src/toil/test/cwl/whale.txt'
]
wf = subprocess.Popen(cmd)
self.check_status('RUNNING', status_fn=ToilStatus.getStatus)
wf.wait()
self.check_status('COMPLETED', status_fn=ToilStatus.getStatus)
def testGetStatusFailedCWLWF(self):
"""Test that ToilStatus.getStatus() behaves as expected with a failing CWL workflow."""
# --badWorker is set to force failure.
cmd = [
'toil-cwl-runner', '--jobStore', self.toilDir, '--clean=never',
'--badWorker=1', 'src/toil/test/cwl/sorttool.cwl', '--reverse',
'--input', 'src/toil/test/cwl/whale.txt'
]
wf = subprocess.Popen(cmd)
self.check_status('RUNNING', status_fn=ToilStatus.getStatus)
wf.wait()
self.check_status('ERROR', status_fn=ToilStatus.getStatus)
def testGetStatusFailedToilWF(self):
"""
Test that ToilStatus.getStatus() behaves as expected with a failing Toil workflow.
While this workflow could be called by importing and evoking its main function, doing so would remove the
opportunity to test the 'RUNNING' functionality of getStatus().
"""
# --badWorker is set to force failure.
wf = subprocess.Popen(self.sort_workflow_cmd + ['--badWorker=1'])
self.check_status('RUNNING', status_fn=ToilStatus.getStatus)
wf.wait()
self.check_status('ERROR', status_fn=ToilStatus.getStatus)
def runJob(job):
"""
:type job: toil.batchSystems.mesos.ToilJob
:rtype: subprocess.Popen
"""
if job.userScript:
job.userScript.register()
log.debug("Invoking command: '%s'", job.command)
with self.popenLock:
return subprocess.Popen(job.command,
preexec_fn=lambda: os.setpgrp(),
shell=True, env=dict(os.environ, **job.environment))
def _runWorker(self, jobCommand, jobID, environment):
"""
Run the jobCommand using the worker and wait for it to finish.
The worker is forked unless it is a '_toil_worker' job and
debugWorker is True.
"""
startTime = time.time() # Time job is started
if self.debugWorker and "_toil_worker" in jobCommand:
# Run the worker without forking
jobName, jobStoreLocator, jobStoreID = jobCommand.split()[
1:] # Parse command
jobStore = Toil.resumeJobStore(jobStoreLocator)
# TODO: The following does not yet properly populate self.runningJobs so it is not possible to kill
# running jobs in forkless mode - see the "None" value in place of popen
info = Info(time.time(), None, killIntended=False)
try:
self.runningJobs[jobID] = info
try:
toil_worker.workerScript(
jobStore,
jobStore.config,
jobName,
jobStoreID,
redirectOutputToLogFile=not self.debugWorker
) # Call the worker
finally:
self.runningJobs.pop(jobID)
finally:
if not info.killIntended:
self.outputQueue.put((jobID, 0, time.time() - startTime))
else:
with self.popenLock:
popen = subprocess.Popen(jobCommand,
shell=True,
env=dict(os.environ, **environment))
info = Info(time.time(), popen, killIntended=False)
try:
self.runningJobs[jobID] = info
try:
statusCode = popen.wait()
if statusCode != 0 and not info.killIntended:
log.error(
"Got exit code %i (indicating failure) "
"from job %s.", statusCode, self.jobs[jobID])
finally:
self.runningJobs.pop(jobID)
finally:
if not info.killIntended:
self.outputQueue.put(
(jobID, statusCode, time.time() - startTime))
def getRunningJobIDs(self):
times = {}
with self.runningJobsLock:
currentjobs = dict((str(self.batchJobIDs[x][0]), x) for x in self.runningJobs)
process = subprocess.Popen(["qstat"], stdout=subprocess.PIPE)
stdout, stderr = process.communicate()
for currline in stdout.decode('utf-8').split('\n'):
items = currline.strip().split()
if items:
if items[0] in currentjobs and items[4] == 'r':
jobstart = " ".join(items[5:7])
jobstart = time.mktime(time.strptime(jobstart, "%m/%d/%Y %H:%M:%S"))
times[currentjobs[items[0]]] = time.time() - jobstart
return times
def __enter__(self):
with self.lock:
image = applianceSelf()
# Omitting --rm, it's unreliable, see https://github.com/docker/docker/issues/16575
args = list(
concat('docker', 'run',
'--entrypoint=' + self._entryPoint(), '--net=host',
'-i', '--name=' + self.containerName, [
'--volume=%s:%s' % mount
for mount in iteritems(self.mounts)
], image, self._containerCommand()))
log.info('Running %r', args)
self.popen = subprocess.Popen(args)
self.start()
self.__wait_running()
return self
def getRunningJobIDs(self):
times = {}
with self.runningJobsLock:
currentjobs = dict(
(str(self.batchJobIDs[x][0]), x) for x in self.runningJobs)
process = subprocess.Popen(
["bjobs", "-o", "jobid stat start_time delimiter='|'"],
stdout=subprocess.PIPE)
stdout, _ = process.communicate()
for curline in stdout.split('\n'):
items = curline.strip().split('|')
if items[0] in currentjobs and items[1] == 'RUN':
jobstart = parse(items[2], default=datetime.now(tzlocal()))
times[currentjobs[items[0]]] = datetime.now(tzlocal()) \
- jobstart
return times
def obtainSystemConstants(cls):
p = subprocess.Popen(["lshosts"],
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
line = p.stdout.readline().decode('utf-8')
items = line.strip().split()
num_columns = len(items)
cpu_index = None
mem_index = None
for i in range(num_columns):
if items[i] == 'ncpus':
cpu_index = i
elif items[i] == 'maxmem':
mem_index = i
if cpu_index is None or mem_index is None:
RuntimeError("lshosts command does not return ncpus or maxmem "
"columns")
# p.stdout.readline().decode('utf-8')
maxCPU = 0
maxMEM = MemoryString("0")
for line in p.stdout:
split_items = line.strip().split()
items = [
item.decode('utf-8') for item in split_items
if isinstance(item, bytes)
]
if len(items) < num_columns:
RuntimeError("lshosts output has a varying number of "
"columns")
if items[cpu_index] != '-' and int(items[cpu_index]) > int(maxCPU):
maxCPU = items[cpu_index]
if (items[mem_index] != '-'
and MemoryString(items[mem_index]) > maxMEM):
maxMEM = MemoryString(items[mem_index])
if maxCPU is 0 or maxMEM is 0:
RuntimeError("lshosts returns null ncpus or maxmem info")
logger.debug("Got the maxMEM: {}".format(maxMEM))
logger.debug("Got the maxCPU: {}".format(maxCPU))
return maxCPU, maxMEM
def testGetPIDStatus(self):
"""Test that ToilStatus.getPIDStatus() behaves as expected."""
jobstoreName = 'pidStatusTest'
jobstoreLoc = os.path.join(os.getcwd(), jobstoreName)
cmd = [
'python', '-m', 'toil.test.sort.sort', 'file:' + jobstoreName,
'--clean', 'never'
]
wf = subprocess.Popen(cmd)
time.sleep(
2) # Need to let jobstore be created before checking its contents.
self.assertEqual(ToilStatus.getPIDStatus(jobstoreLoc), 'RUNNING')
wf.wait()
self.assertEqual(ToilStatus.getPIDStatus(jobstoreLoc), 'COMPLETED')
os.remove(os.path.join(jobstoreLoc, 'pid.log'))
self.assertEqual(ToilStatus.getPIDStatus(jobstoreLoc), 'QUEUED')
shutil.rmtree(jobstoreLoc)
