def main():
parser = getBasicOptionParser()
parser.add_argument(
"jobStore",
type=str,
help=
"The location of the job store used by the workflow whose jobs should "
"be killed." + jobStoreLocatorHelp)
parser.add_argument("--version", action='version', version=version)
options = parseBasicOptions(parser)
config = Config()
config.setOptions(options)
jobStore = Toil.resumeJobStore(config.jobStore)
logger.info(
"Starting routine to kill running jobs in the toil workflow: %s",
config.jobStore)
####This behaviour is now broken
batchSystem = Toil.createBatchSystem(
jobStore.config
) #This should automatically kill the existing jobs.. so we're good.
for jobID in batchSystem.getIssuedBatchJobIDs(
): #Just in case we do it again.
batchSystem.killBatchJobs(jobID)
logger.info("All jobs SHOULD have been killed")
def main():
parser = parser_with_common_options()
options = parser.parse_args()
set_logging_from_options(options)
config = Config()
config.setOptions(options)
config.jobStore = config.jobStore[5:] if config.jobStore.startswith('file:') else config.jobStore
# ':' means an aws/google jobstore; use the old (broken?) method
if ':' in config.jobStore:
jobStore = Toil.resumeJobStore(config.jobStore)
logger.info("Starting routine to kill running jobs in the toil workflow: %s", config.jobStore)
# TODO: This behaviour is now broken: https://github.com/DataBiosphere/toil/commit/a3d65fc8925712221e4cda116d1825d4a1e963a1
batchSystem = Toil.createBatchSystem(jobStore.config) # Should automatically kill existing jobs, so we're good.
for jobID in batchSystem.getIssuedBatchJobIDs(): # Just in case we do it again.
batchSystem.killBatchJobs(jobID)
logger.info("All jobs SHOULD have been killed")
# otherwise, kill the pid recorded in the jobstore
else:
pid_log = os.path.join(os.path.abspath(config.jobStore), 'pid.log')
with open(pid_log, 'r') as f:
pid2kill = f.read().strip()
try:
os.kill(int(pid2kill), signal.SIGKILL)
logger.info("Toil process %s successfully terminated." % str(pid2kill))
except OSError:
logger.error("Toil process %s could not be terminated." % str(pid2kill))
raise
def main():
parser = parser_with_common_options(jobstore_option=True)
parser.add_argument(
"jobID",
nargs=1,
help=
"The job store id of a job within the provided jobstore to run by itself."
)
parser.add_argument(
"--printJobInfo",
nargs=1,
help=
"Return information about this job to the user including preceding jobs, "
"inputs, outputs, and runtime from the last known run.")
options = parser.parse_args()
set_logging_from_options(options)
config = Config()
config.setOptions(options)
jobStore = Toil.resumeJobStore(config.jobStore)
if options.printJobInfo:
printContentsOfJobStore(jobStorePath=config.jobStore,
nameOfJob=options.printJobInfo)
# TODO: Option to print list of successor jobs
# TODO: Option to run job within python debugger, allowing step through of arguments
# idea would be to have option to import pdb and set breakpoint at the start of the user's code
jobID = options.jobID[0]
logger.debug(f"Running the following job locally: {jobID}")
workerScript(jobStore, config, jobID, jobID, redirectOutputToLogFile=False)
logger.debug(f"Finished running: {jobID}")
def main():
parser = getBasicOptionParser()
parser.add_argument("jobStore", type=str,
help="The location of the job store to delete. " + jobStoreLocatorHelp)
parser.add_argument("--version", action='version', version=version)
config = Config()
config.setOptions(parseBasicOptions(parser))
logger.info("Attempting to delete the job store")
jobStore = Toil.getJobStore(config.jobStore)
jobStore.destroy()
logger.info("Successfully deleted the job store")
def _createDummyConfig():
"""
Returns a dummy config for the batch system tests. We need a workflowID to be set up
since we are running tests without setting up a jobstore.
:rtype: toil.common.Config
"""
config = Config()
from uuid import uuid4
config.workflowID = str(uuid4())
return config
def _createDummyConfig():
"""
Returns a dummy config for the batch system tests. We need a workflowID to be set up
since we are running tests without setting up a jobstore.
:rtype: toil.common.Config
"""
config = Config()
from uuid import uuid4
config.workflowID = str(uuid4())
return config
def createConfig(cls):
"""
Returns a dummy config for the batch system tests. We need a workflowID to be set up
since we are running tests without setting up a jobstore. This is the class version
to be used when an instance is not available.
:rtype: toil.common.Config
"""
config = Config()
from uuid import uuid4
config.workflowID = str(uuid4())
return config
def createConfig(cls):
"""
Returns a dummy config for the batch system tests. We need a workflowID to be set up
since we are running tests without setting up a jobstore. This is the class version
to be used when an instance is not available.
:rtype: toil.common.Config
"""
config = Config()
from uuid import uuid4
config.workflowID = str(uuid4())
return config
def main():
""" Reports stats on the workflow, use with --stats option to toil.
"""
parser = getBasicOptionParser()
initializeOptions(parser)
options = parseBasicOptions(parser)
checkOptions(options, parser)
config = Config()
config.setOptions(options)
jobStore = Toil.resumeJobStore(config.jobStore)
stats = getStats(jobStore)
collatedStatsTag = processData(jobStore.config, stats)
reportData(collatedStatsTag, options)
def main():
""" Reports stats on the workflow, use with --stats option to toil.
"""
parser = getBasicOptionParser()
initializeOptions(parser)
options = parseBasicOptions(parser)
checkOptions(options, parser)
config = Config()
config.setOptions(options)
jobStore = Toil.resumeJobStore(config.jobStore)
stats = getStats(jobStore)
collatedStatsTag = processData(jobStore.config, stats)
reportData(collatedStatsTag, options)
def main():
parser = getBasicOptionParser()
parser.add_argument(
"jobStore",
type=str,
help="The location of the job store used by the workflow." +
jobStoreLocatorHelp)
parser.add_argument("--localFilePath",
nargs=1,
help="Location to which to copy job store files.")
parser.add_argument("--fetch",
nargs="+",
help="List of job-store files to be copied locally."
"Use either explicit names (i.e. 'data.txt'), or "
"specify glob patterns (i.e. '*.txt')")
parser.add_argument(
"--listFilesInJobStore",
help="Prints a list of the current files in the jobStore.")
parser.add_argument(
"--fetchEntireJobStore",
help="Copy all job store files into a local directory.")
parser.add_argument(
"--useSymlinks",
help="Creates symlink 'shortcuts' of files in the localFilePath"
" instead of hardlinking or copying, where possible. If this is"
" not possible, it will copy the files (shutil.copyfile()).")
parser.add_argument("--version", action='version', version=version)
# Load the jobStore
options = parseBasicOptions(parser)
config = Config()
config.setOptions(options)
jobStore = Toil.resumeJobStore(config.jobStore)
logger.debug("Connected to job store: %s", config.jobStore)
if options.fetch:
# Copy only the listed files locally
logger.debug("Fetching local files: %s", options.fetch)
fetchJobStoreFiles(jobStore=jobStore, options=options)
elif options.fetchEntireJobStore:
# Copy all jobStore files locally
logger.debug("Fetching all local files.")
options.fetch = "*"
fetchJobStoreFiles(jobStore=jobStore, options=options)
if options.listFilesInJobStore:
# Log filenames and create a file containing these names in cwd
printContentsOfJobStore(jobStorePath=options.jobStore)
def testMultipleJobsPerWorkerStats(self):
"""
Tests case where multiple jobs are run on 1 worker to insure that all jobs report back their data
"""
options = Job.Runner.getDefaultOptions(self._getTestJobStorePath())
options.clean = 'never'
options.stats = True
Job.Runner.startToil(RunTwoJobsPerWorker(), options)
config = Config()
config.setOptions(options)
jobStore = Toil.resumeJobStore(config.jobStore)
stats = getStats(jobStore)
collatedStats = processData(jobStore.config, stats)
self.assertTrue(len(collatedStats.job_types) == 2,
"Some jobs are not represented in the stats")
def testMultipleJobsPerWorkerStats(self):
"""
Tests case where multiple jobs are run on 1 worker to insure that all jobs report back their data
"""
options = Job.Runner.getDefaultOptions(self._getTestJobStorePath())
options.clean = 'never'
options.stats = True
Job.Runner.startToil(RunTwoJobsPerWorker(), options)
config = Config()
config.setOptions(options)
jobStore = Toil.resumeJobStore(config.jobStore)
stats = getStats(jobStore)
collatedStats = processData(jobStore.config, stats)
self.assertTrue(len(collatedStats.job_types) == 2,
"Some jobs are not represented in the stats")
def main():
"""
This is a Toil pipeline to transfer TCGA data into an S3 Bucket
Data is pulled down with Genetorrent and transferred to S3 via S3AM.
"""
# Define Parser object and add to toil
def existing_file(fname):
"""
Argparse type for an existing file
"""
if not os.path.isfile(fname):
raise ValueError("Invalid file: " + str(fname))
return fname
parser = argparse.ArgumentParser(
description=main.__doc__,
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument(
'--sudo',
dest='sudo',
default=None,
action='store_true',
help=
'Docker usually needs sudo to execute locally, but not when running Mesos or when '
'the user is a member of a Docker group.')
Job.Runner.addToilOptions(parser)
parser.add_argument('datafiles',
nargs='+',
help='FASTA input',
type=existing_file)
args = parser.parse_args()
assert args.jobStore is not None
config = Config()
config.setOptions(args)
# Store inputs from argparse
inputs = {'sudo': args.sudo}
datafiles = [os.path.abspath(d) for d in args.datafiles]
# Start Pipeline
options = Job.Runner.getDefaultOptions("./toilWorkflow")
Job.Runner.startToil(Job.wrapJobFn(start_batch, datafiles, inputs),
options)
def setUp(self):
super(WorkerTests, self).setUp()
path = self._getTestJobStorePath()
self.jobStore = FileJobStore(path)
self.config = Config()
self.config.jobStore = 'file:%s' % path
self.jobStore.initialize(self.config)
self.jobNumber = 0
def main():
parser = getBasicOptionParser()
parser.add_argument("jobStore", type=str,
help="The location of the job store used by the workflow whose jobs should "
"be killed." + jobStoreLocatorHelp)
parser.add_argument("--version", action='version', version=version)
options = parseBasicOptions(parser)
config = Config()
config.setOptions(options)
jobStore = Toil.resumeJobStore(config.jobStore)
logger.info("Starting routine to kill running jobs in the toil workflow: %s", config.jobStore)
####This behaviour is now broken
batchSystem = Toil.createBatchSystem(jobStore.config) #This should automatically kill the existing jobs.. so we're good.
for jobID in batchSystem.getIssuedBatchJobIDs(): #Just in case we do it again.
batchSystem.killBatchJobs(jobID)
logger.info("All jobs SHOULD have been killed")
def main():
parser = getBasicOptionParser()
parser.add_argument("jobStore",
type=str,
help="The location of the job store to delete. " +
jobStoreLocatorHelp)
parser.add_argument("--version", action='version', version=version)
config = Config()
config.setOptions(parseBasicOptions(parser))
try:
jobStore = Toil.getJobStore(config.jobStore)
jobStore.resume()
jobStore.destroy()
logger.info("Successfully deleted the job store: %s" % config.jobStore)
except NoSuchJobStoreException:
logger.info("Failed to delete the job store: %s is non-existent" %
config.jobStore)
except:
logger.info("Failed to delete the job store: %s" % config.jobStore)
raise
def main() -> None:
"""Reports stats on the workflow, use with --stats option to toil."""
parser = parser_with_common_options()
add_stats_options(parser)
options = parser.parse_args()
for c in options.categories.split(","):
if c.strip() not in category_choices:
raise ValueError(f'{c} not in {category_choices}!')
options.categories = [
x.strip().lower() for x in options.categories.split(",")
]
set_logging_from_options(options)
config = Config()
config.setOptions(options)
jobStore = Toil.resumeJobStore(config.jobStore)
stats = getStats(jobStore)
collatedStatsTag = processData(jobStore.config, stats)
reportData(collatedStatsTag, options)
def main():
parser = getBasicOptionParser()
parser.add_argument(
"jobStore",
type=str,
help="The location of the job store used by the workflow." +
jobStoreLocatorHelp)
parser.add_argument("jobID",
nargs=1,
help="The job store id of a job "
"within the provided jobstore to run by itself.")
parser.add_argument(
"--printJobInfo",
nargs=1,
help="Return information about this job to the user"
" including preceding jobs, inputs, outputs, and runtime"
" from the last known run.")
parser.add_argument("--version", action='version', version=version)
# Parse options
options = parseBasicOptions(parser)
config = Config()
config.setOptions(options)
# Load the job store
jobStore = Toil.resumeJobStore(config.jobStore)
if options.printJobInfo:
printContentsOfJobStore(jobStorePath=options.jobStore,
nameOfJob=options.printJobInfo)
# TODO: Option to print list of successor jobs
# TODO: Option to run job within python debugger, allowing step through of arguments
# idea would be to have option to import pdb and set breakpoint at the start of the user's code
# Run the job locally
jobID = options.jobID[0]
logger.debug("Going to run the following job locally: %s", jobID)
workerScript(jobStore, config, jobID, jobID, redirectOutputToLogFile=False)
logger.debug("Ran the following job locally: %s", jobID)
def setUp(self):
super(ClusterScalerTest, self).setUp()
self.config = Config()
self.config.targetTime = 1800
self.config.nodeTypes = ['r3.8xlarge', 'c4.8xlarge:0.6']
# Set up a stub provisioner with some nodeTypes and nodeShapes.
self.provisioner = object()
self.provisioner.nodeTypes = ['r3.8xlarge', 'c4.8xlarge']
self.provisioner.nodeShapes = [r3_8xlarge, c4_8xlarge_preemptable]
self.provisioner.setStaticNodes = lambda _, __: None
self.provisioner.retryPredicate = lambda _: False
self.leader = MockBatchSystemAndProvisioner(self.config, 1)
def setUp(self):
super(ClusterScalerTest, self).setUp()
self.config = Config()
self.config.targetTime = 1800
self.config.nodeTypes = [r3_8xlarge, c4_8xlarge_preemptable]
# Set up the mock leader
self.leader = MockBatchSystemAndProvisioner(self.config, 1)
# It is also a full mock provisioner, so configure it to be that as well
self.provisioner = self.leader
# Pretend that Shapes are actually strings we can use for instance type names.
self.provisioner.setAutoscaledNodeTypes([
({t}, None) for t in self.config.nodeTypes
])
def main() -> None:
parser = parser_with_common_options()
options = parser.parse_args()
set_logging_from_options(options)
config = Config()
config.setOptions(options)
job_store_type, _ = Toil.parseLocator(config.jobStore)
if job_store_type != 'file':
# Remote (aws/google) jobstore; use the old (broken?) method
job_store = Toil.resumeJobStore(config.jobStore)
logger.info("Starting routine to kill running jobs in the toil workflow: %s", config.jobStore)
# TODO: This behaviour is now broken: https://github.com/DataBiosphere/toil/commit/a3d65fc8925712221e4cda116d1825d4a1e963a1
# There's no guarantee that the batch system in use can enumerate
# running jobs belonging to the job store we've attached to. And
# moreover we don't even bother trying to kill the leader at its
# recorded PID, even if it is a local process.
batch_system = Toil.createBatchSystem(job_store.config) # Should automatically kill existing jobs, so we're good.
for job_id in batch_system.getIssuedBatchJobIDs(): # Just in case we do it again.
batch_system.killBatchJobs([job_id])
logger.info("All jobs SHOULD have been killed")
else:
# otherwise, kill the pid recorded in the jobstore.
# TODO: We assume thnis is a local PID.
job_store = Toil.resumeJobStore(config.jobStore)
assert isinstance(job_store, FileJobStore), "Need a FileJobStore which has a sharedFilesDir"
pid_log = os.path.join(job_store.sharedFilesDir, 'pid.log')
with open(pid_log) as f:
pid_to_kill = f.read().strip()
try:
os.kill(int(pid_to_kill), signal.SIGTERM)
logger.info("Toil process %s successfully terminated." % str(pid_to_kill))
except OSError:
logger.error("Toil process %s could not be terminated." % str(pid_to_kill))
raise
def test(self):
# We'll use fractions to avoid rounding errors. Remember that not every fraction can be
# represented as a floating point number.
F = Fraction
# This test isn't general enough to cover every possible value of minCores in
# SingleMachineBatchSystem. Instead we hard-code a value and assert it.
minCores = F(1, 10)
self.assertEquals(float(minCores), SingleMachineBatchSystem.minCores)
for maxCores in {F(minCores), minCores * 10, F(1), F(numCores, 2), F(numCores)}:
for coresPerJob in {F(minCores), F(minCores * 10), F(1), F(maxCores, 2), F(maxCores)}:
for load in (F(1, 10), F(1), F(10)):
jobs = int(maxCores / coresPerJob * load)
if jobs >= 1 and minCores <= coresPerJob < maxCores:
self.assertEquals(maxCores, float(maxCores))
bs = SingleMachineBatchSystem(config=Config(),
maxCores=float(maxCores),
# Ensure that memory or disk requirements
# don't get in the way.
maxMemory=jobs * 10,
maxDisk=jobs * 10)
try:
jobIds = set()
for i in range(0, int(jobs)):
jobIds.add(bs.issueBatchJob(command=self.scriptCommand(),
cores=float(coresPerJob),
memory=1,
disk=1,
preemptable=preemptable))
self.assertEquals(len(jobIds), jobs)
while jobIds:
job = bs.getUpdatedBatchJob(maxWait=10)
self.assertIsNotNone(job)
jobId, status, wallTime = job
self.assertEquals(status, 0)
# would raise KeyError on absence
jobIds.remove(jobId)
finally:
bs.shutdown()
concurrentTasks, maxConcurrentTasks = getCounters(self.counterPath)
self.assertEquals(concurrentTasks, 0)
log.info('maxCores: {maxCores}, '
'coresPerJob: {coresPerJob}, '
'load: {load}'.format(**locals()))
# This is the key assertion:
expectedMaxConcurrentTasks = min(maxCores / coresPerJob, jobs)
self.assertEquals(maxConcurrentTasks, expectedMaxConcurrentTasks)
resetCounters(self.counterPath)
def _createDummyConfig():
config = Config()
"""
config = ElementTree.Element("config")
config.attrib["log_level"] = 'DEBUG'
config.attrib["job_store"] = '.'
config.attrib["parasol_command"] = None
config.attrib["try_count"] = str(2)
config.attrib["max_job_duration"] = str(1)
config.attrib["batch_system"] = None
config.attrib["max_log_file_size"] = str(1)
config.attrib["default_memory"] = str(1)
config.attrib["default_cores"] = str(1)
config.attrib["max_cores"] = str(1)
config.attrib["max_memory"] = str(1)
config.attrib["scale"] = str(1)
"""
return config
def setUp(self):
super(ClusterScalerTest, self).setUp()
self.config = Config()
self.config.targetTime = 1800
self.config.nodeTypes = ['r3.8xlarge', 'c4.8xlarge:0.6']
# Set up a stub provisioner with some nodeTypes and nodeShapes.
try:
# In Python 3 we can use a SimpleNamespace as a mock provisioner
self.provisioner = types.SimpleNamespace()
except:
# In Python 2 we can just tack fields onto an object
self.provisioner = object()
setattr(self.provisioner, 'nodeTypes', ['r3.8xlarge', 'c4.8xlarge'])
setattr(self.provisioner, 'nodeShapes',
[r3_8xlarge, c4_8xlarge_preemptable])
setattr(self.provisioner, 'setStaticNodes', lambda _, __: None)
setattr(self.provisioner, 'retryPredicate', lambda _: False)
self.leader = MockBatchSystemAndProvisioner(self.config, 1)
def setUp(self):
super(ClusterScalerTest, self).setUp()
self.config = Config()
self.config.targetTime = 1800
self.config.nodeTypes = ['r3.8xlarge', 'c4.8xlarge:0.6']
# Set up a stub provisioner with some nodeTypes and nodeShapes.
try:
# In Python 3 we can use a SimpleNamespace as a mock provisioner
self.provisioner = types.SimpleNamespace()
except:
# In Python 2 we should just be able to tack fields onto an object.
# But this has been known to produce:
# AttributeError: 'newobject' object has no attribute 'nodeTypes'
# So we use an Argparse Namespace instead.
import argparse
self.provisioner = argparse.Namespace()
setattr(self.provisioner, 'nodeTypes', ['r3.8xlarge', 'c4.8xlarge'])
setattr(self.provisioner, 'nodeShapes',
[r3_8xlarge, c4_8xlarge_preemptable])
setattr(self.provisioner, 'setStaticNodes', lambda _, __: None)
setattr(self.provisioner, 'retryPredicate', lambda _: False)
self.leader = MockBatchSystemAndProvisioner(self.config, 1)
def _createDummyConfig(self):
return Config()
def testClusterScalingMultipleNodeTypes(self):
smallNode = Shape(20, 5, 10, 10, False)
mediumNode = Shape(20, 10, 10, 10, False)
largeNode = Shape(20, 20, 10, 10, False)
numJobs = 100
config = Config()
# Make defaults dummy values
config.defaultMemory = 1
config.defaultCores = 1
config.defaultDisk = 1
# No preemptable nodes/jobs
config.preemptableNodeTypes = []
config.minPreemptableNodes = []
config.maxPreemptableNodes = [] # No preemptable nodes
# Make sure the node types don't have to be ordered
config.nodeTypes = [largeNode, smallNode, mediumNode]
config.minNodes = [0, 0, 0]
config.maxNodes = [10, 10] # test expansion of this list
# Algorithm parameters
config.targetTime = defaultTargetTime
config.betaInertia = 0.1
config.scaleInterval = 3
mock = MockBatchSystemAndProvisioner(config, secondsPerJob=2.0)
clusterScaler = ScalerThread(mock, mock, config)
clusterScaler.start()
mock.start()
try:
# Add small jobs
list(
map(lambda x: mock.addJob(jobShape=smallNode),
list(range(numJobs))))
list(
map(lambda x: mock.addJob(jobShape=mediumNode),
list(range(numJobs))))
# Add medium completed jobs
for i in range(1000):
iJ = JobNode(jobStoreID=1,
requirements=dict(memory=random.choice(
range(smallNode.memory, mediumNode.memory)),
cores=mediumNode.cores,
disk=largeNode.cores,
preemptable=False),
command=None,
jobName='testClusterScaling',
unitName='')
clusterScaler.addCompletedJob(iJ, random.choice(range(1, 10)))
while mock.getNumberOfJobsIssued() > 0 or mock.getNumberOfNodes(
) > 0:
logger.debug("%i nodes currently provisioned" %
mock.getNumberOfNodes())
# Make sure there are no large nodes
self.assertEqual(mock.getNumberOfNodes(nodeType=largeNode), 0)
clusterScaler.check()
time.sleep(0.5)
finally:
clusterScaler.shutdown()
mock.shutDown()
# Make sure jobs ran on both the small and medium node types
self.assertTrue(mock.totalJobs > 0)
self.assertTrue(mock.maxWorkers[smallNode] > 0)
self.assertTrue(mock.maxWorkers[mediumNode] > 0)
self.assertEqual(mock.maxWorkers[largeNode], 0)
def main():
"""Reports the state of a Toil workflow."""
parser = getBasicOptionParser()
parser.add_argument("jobStore", type=str,
help="The location of a job store that holds the information about the "
"workflow whose status is to be reported on." + jobStoreLocatorHelp)
parser.add_argument("--failIfNotComplete", action="store_true",
help="Return exit value of 1 if toil jobs not all completed. default=%(default)s",
default=False)
parser.add_argument("--noAggStats", dest="stats", action="store_false",
help="Do not print overall, aggregate status of workflow.",
default=True)
parser.add_argument("--printDot", action="store_true",
help="Print dot formatted description of the graph. If using --jobs will "
"restrict to subgraph including only those jobs. default=%(default)s",
default=False)
parser.add_argument("--jobs", nargs='+',
help="Restrict reporting to the following jobs (allows subsetting of the report).",
default=None)
parser.add_argument("--printPerJobStats", action="store_true",
help="Print info about each job. default=%(default)s",
default=False)
parser.add_argument("--printLogs", action="store_true",
help="Print the log files of jobs (if they exist). default=%(default)s",
default=False)
parser.add_argument("--printChildren", action="store_true",
help="Print children of each job. default=%(default)s",
default=False)
parser.add_argument("--version", action='version', version=version)
options = parseBasicOptions(parser)
logger.info("Parsed arguments")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
config = Config()
config.setOptions(options)
jobStore = Toil.resumeJobStore(config.jobStore)
##########################################
# Gather the jobs to report
##########################################
# Gather all jobs in the workflow in jobsToReport
if options.jobs == None:
rootJob = fetchRootJob(jobStore)
logger.info('Traversing the job graph gathering jobs. This may take a couple of minutes.')
jobsToReport = traverseJobGraph(rootJob, jobStore)
# Only gather jobs specified in options.jobs
else:
jobsToReport = fetchUserJobs(jobStore, jobs=options.jobs)
##########################################
# Report on the jobs
##########################################
jobStats = report_on_jobs(jobsToReport, jobStore, options)
hasChildren = jobStats['hasChildren']
readyToRun = jobStats['readyToRun']
zombies = jobStats['zombies']
hasServices = jobStats['hasServices']
services = jobStats['services']
hasLogFile = jobStats['hasLogFile']
properties = jobStats['properties']
childNumber = jobStats['childNumber']
if options.printPerJobStats:
printAggregateJobStats(jobsToReport, properties, childNumber)
if options.printLogs:
printJobLog(jobsToReport, jobStore)
if options.printChildren:
printJobChildren(jobsToReport)
if options.printDot:
print_dot_chart(jobsToReport, jobStore_name=config.jobStore)
if options.stats:
print('Of the %i jobs considered, '
'there are %i jobs with children, '
'%i jobs ready to run, '
'%i zombie jobs, '
'%i jobs with services, '
'%i services, '
'and %i jobs with log files currently in %s.' %
(len(jobsToReport), len(hasChildren), len(readyToRun), len(zombies),
len(hasServices), len(services), len(hasLogFile), config.jobStore))
if len(jobsToReport) > 0 and options.failIfNotComplete:
# Upon workflow completion, all jobs will have been removed from job store
exit(1)
def testClusterScalingWithPreemptableJobs(self):
"""
Test scaling simultaneously for a batch of preemptable and non-preemptable jobs.
"""
config = Config()
jobShape = Shape(20, 10, 10, 10, False)
preemptableJobShape = Shape(20, 10, 10, 10, True)
# Make defaults dummy values
config.defaultMemory = 1
config.defaultCores = 1
config.defaultDisk = 1
# non-preemptable node parameters
config.nodeTypes = [jobShape, preemptableJobShape]
config.minNodes = [0, 0]
config.maxNodes = [10, 10]
# Algorithm parameters
config.targetTime = defaultTargetTime
config.betaInertia = 0.9
config.scaleInterval = 3
self._testClusterScaling(config,
numJobs=100,
numPreemptableJobs=100,
jobShape=jobShape)
def main(args=None, stdout=sys.stdout):
config = Config()
config.cwl = True
parser = argparse.ArgumentParser()
addOptions(parser, config)
parser.add_argument("cwltool", type=str)
parser.add_argument("cwljob", nargs=argparse.REMAINDER)
# Will override the "jobStore" positional argument, enables
# user to select jobStore or get a default from logic one below.
parser.add_argument("--jobStore", type=str)
parser.add_argument("--not-strict", action="store_true")
parser.add_argument("--no-container", action="store_true")
parser.add_argument("--quiet", dest="logLevel", action="store_const", const="ERROR")
parser.add_argument("--basedir", type=str)
parser.add_argument("--outdir", type=str, default=os.getcwd())
parser.add_argument("--version", action='version', version=baseVersion)
parser.add_argument("--user-space-docker-cmd",
help="(Linux/OS X only) Specify a user space docker "
"command (like udocker or dx-docker) that will be "
"used to call 'pull' and 'run'")
parser.add_argument("--preserve-environment", type=str, nargs='+',
help="Preserve specified environment variables when running CommandLineTools",
metavar=("VAR1 VAR2"),
default=("PATH",),
dest="preserve_environment")
# help="Dependency resolver configuration file describing how to adapt 'SoftwareRequirement' packages to current system."
parser.add_argument("--beta-dependency-resolvers-configuration", default=None)
# help="Defaut root directory used by dependency resolvers configuration."
parser.add_argument("--beta-dependencies-directory", default=None)
# help="Use biocontainers for tools without an explicitly annotated Docker container."
parser.add_argument("--beta-use-biocontainers", default=None, action="store_true")
# help="Short cut to use Conda to resolve 'SoftwareRequirement' packages."
parser.add_argument("--beta-conda-dependencies", default=None, action="store_true")
parser.add_argument("--tmpdir-prefix", type=Text,
help="Path prefix for temporary directories",
default="tmp")
parser.add_argument("--tmp-outdir-prefix", type=Text,
help="Path prefix for intermediate output directories",
default="tmp")
# mkdtemp actually creates the directory, but
# toil requires that the directory not exist,
# so make it and delete it and allow
# toil to create it again (!)
workdir = tempfile.mkdtemp()
os.rmdir(workdir)
if args is None:
args = sys.argv[1:]
options = parser.parse_args([workdir] + args)
use_container = not options.no_container
if options.logLevel:
cwllogger.setLevel(options.logLevel)
outdir = os.path.abspath(options.outdir)
fileindex = {}
existing = {}
make_tool_kwargs = {}
conf_file = getattr(options, "beta_dependency_resolvers_configuration", None) # Text
use_conda_dependencies = getattr(options, "beta_conda_dependencies", None) # Text
job_script_provider = None
if conf_file or use_conda_dependencies:
dependencies_configuration = DependenciesConfiguration(options) # type: DependenciesConfiguration
job_script_provider = dependencies_configuration
options.default_container = None
make_tool_kwargs["find_default_container"] = functools.partial(find_default_container, options)
with Toil(options) as toil:
if options.restart:
outobj = toil.restart()
else:
useStrict = not options.not_strict
make_tool_kwargs["hints"] = [{
"class": "ResourceRequirement",
"coresMin": toil.config.defaultCores,
"ramMin": toil.config.defaultMemory / (2**20),
"outdirMin": toil.config.defaultDisk / (2**20),
"tmpdirMin": 0
}]
try:
t = cwltool.load_tool.load_tool(options.cwltool, toilMakeTool,
kwargs=make_tool_kwargs,
resolver=cwltool.resolver.tool_resolver,
strict=useStrict)
unsupportedRequirementsCheck(t.requirements)
except cwltool.process.UnsupportedRequirement as e:
logging.error(e)
return 33
if type(t) == int:
return t
options.workflow = options.cwltool
options.job_order = options.cwljob
options.tool_help = None
options.debug = options.logLevel == "DEBUG"
job, options.basedir, loader = cwltool.main.load_job_order(
options, sys.stdin, None, [], options.job_order)
job = cwltool.main.init_job_order(job, options, t, loader=loader)
fillInDefaults(t.tool["inputs"], job)
def pathToLoc(p):
if "location" not in p and "path" in p:
p["location"] = p["path"]
del p["path"]
def importFiles(tool):
visit_class(tool, ("File", "Directory"), pathToLoc)
normalizeFilesDirs(tool)
adjustDirObjs(tool, functools.partial(get_listing,
cwltool.stdfsaccess.StdFsAccess(""),
recursive=True))
adjustFileObjs(tool, functools.partial(uploadFile,
toil.importFile,
fileindex, existing, skip_broken=True))
t.visit(importFiles)
for inp in t.tool["inputs"]:
def setSecondary(fileobj):
if isinstance(fileobj, dict) and fileobj.get("class") == "File":
if "secondaryFiles" not in fileobj:
fileobj["secondaryFiles"] = [{
"location": cwltool.builder.substitute(fileobj["location"], sf), "class": "File"}
for sf in inp["secondaryFiles"]]
if isinstance(fileobj, list):
for e in fileobj:
setSecondary(e)
if shortname(inp["id"]) in job and inp.get("secondaryFiles"):
setSecondary(job[shortname(inp["id"])])
importFiles(job)
visitSteps(t, importFiles)
try:
make_opts = copy.deepcopy(vars(options))
make_opts.update({'tool': t, 'jobobj': {},
'use_container': use_container,
'tmpdir': os.path.realpath(outdir),
'job_script_provider': job_script_provider})
(wf1, wf2) = makeJob(**make_opts)
except cwltool.process.UnsupportedRequirement as e:
logging.error(e)
return 33
wf1.cwljob = job
outobj = toil.start(wf1)
outobj = resolve_indirect(outobj)
toilStageFiles(toil, outobj, outdir, fileindex, existing, True)
visit_class(outobj, ("File",), functools.partial(compute_checksums, cwltool.stdfsaccess.StdFsAccess("")))
stdout.write(json.dumps(outobj, indent=4))
return 0
def main() -> None:
"""Reports the state of a Toil workflow."""
parser = parser_with_common_options()
parser.add_argument(
"--failIfNotComplete",
action="store_true",
help=
"Return exit value of 1 if toil jobs not all completed. default=%(default)s",
default=False)
parser.add_argument(
"--noAggStats",
dest="stats",
action="store_false",
help="Do not print overall, aggregate status of workflow.",
default=True)
parser.add_argument(
"--printDot",
action="store_true",
help=
"Print dot formatted description of the graph. If using --jobs will "
"restrict to subgraph including only those jobs. default=%(default)s",
default=False)
parser.add_argument(
"--jobs",
nargs='+',
help=
"Restrict reporting to the following jobs (allows subsetting of the report).",
default=None)
parser.add_argument("--printPerJobStats",
action="store_true",
help="Print info about each job. default=%(default)s",
default=False)
parser.add_argument(
"--printLogs",
action="store_true",
help="Print the log files of jobs (if they exist). default=%(default)s",
default=False)
parser.add_argument("--printChildren",
action="store_true",
help="Print children of each job. default=%(default)s",
default=False)
options = parser.parse_args()
set_logging_from_options(options)
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
config = Config()
config.setOptions(options)
try:
status = ToilStatus(config.jobStore, options.jobs)
except NoSuchJobStoreException:
print('No job store found.')
return
except JobException: # Workflow likely complete, user informed in ToilStatus()
return
jobStats = status.report_on_jobs()
# Info to be reported.
hasChildren = jobStats['hasChildren']
readyToRun = jobStats['readyToRun']
zombies = jobStats['zombies']
hasServices = jobStats['hasServices']
services = jobStats['services']
hasLogFile = jobStats['hasLogFile']
properties = jobStats['properties']
childNumber = jobStats['childNumber']
if options.printPerJobStats:
status.printAggregateJobStats(properties, childNumber)
if options.printLogs:
status.printJobLog()
if options.printChildren:
status.printJobChildren()
if options.printDot:
status.print_dot_chart()
if options.stats:
print('Of the %i jobs considered, '
'there are %i jobs with children, '
'%i jobs ready to run, '
'%i zombie jobs, '
'%i jobs with services, '
'%i services, '
'and %i jobs with log files currently in %s.' %
(len(status.jobsToReport), len(hasChildren), len(readyToRun),
len(zombies), len(hasServices), len(services), len(hasLogFile),
status.jobStore))
if len(status.jobsToReport) > 0 and options.failIfNotComplete:
# Upon workflow completion, all jobs will have been removed from job store
exit(1)
def main(args=None, stdout=sys.stdout):
"""Main method for toil-cwl-runner."""
cwllogger.removeHandler(defaultStreamHandler)
config = Config()
config.cwl = True
parser = argparse.ArgumentParser()
addOptions(parser, config)
parser.add_argument("cwltool", type=str)
parser.add_argument("cwljob", nargs=argparse.REMAINDER)
# Will override the "jobStore" positional argument, enables
# user to select jobStore or get a default from logic one below.
parser.add_argument("--jobStore", type=str)
parser.add_argument("--not-strict", action="store_true")
parser.add_argument("--quiet", dest="logLevel", action="store_const",
const="ERROR")
parser.add_argument("--basedir", type=str)
parser.add_argument("--outdir", type=str, default=os.getcwd())
parser.add_argument("--version", action='version', version=baseVersion)
dockergroup = parser.add_mutually_exclusive_group()
dockergroup.add_argument(
"--user-space-docker-cmd",
help="(Linux/OS X only) Specify a user space docker command (like "
"udocker or dx-docker) that will be used to call 'pull' and 'run'")
dockergroup.add_argument(
"--singularity", action="store_true", default=False,
help="[experimental] Use Singularity runtime for running containers. "
"Requires Singularity v2.3.2+ and Linux with kernel version v3.18+ or "
"with overlayfs support backported.")
dockergroup.add_argument(
"--no-container", action="store_true", help="Do not execute jobs in a "
"Docker container, even when `DockerRequirement` "
"is specified under `hints`.")
parser.add_argument(
"--preserve-environment", type=str, nargs='+',
help="Preserve specified environment variables when running"
" CommandLineTools", metavar=("VAR1 VAR2"), default=("PATH",),
dest="preserve_environment")
parser.add_argument(
"--destBucket", type=str,
help="Specify a cloud bucket endpoint for output files.")
parser.add_argument(
"--beta-dependency-resolvers-configuration", default=None)
parser.add_argument("--beta-dependencies-directory", default=None)
parser.add_argument(
"--beta-use-biocontainers", default=None, action="store_true")
parser.add_argument(
"--beta-conda-dependencies", default=None, action="store_true")
parser.add_argument("--tmpdir-prefix", type=Text,
help="Path prefix for temporary directories",
default="tmp")
parser.add_argument("--tmp-outdir-prefix", type=Text,
help="Path prefix for intermediate output directories",
default="tmp")
parser.add_argument(
"--force-docker-pull", action="store_true", default=False,
dest="force_docker_pull",
help="Pull latest docker image even if it is locally present")
parser.add_argument(
"--no-match-user", action="store_true", default=False,
help="Disable passing the current uid to `docker run --user`")
# mkdtemp actually creates the directory, but
# toil requires that the directory not exist,
# so make it and delete it and allow
# toil to create it again (!)
workdir = tempfile.mkdtemp()
os.rmdir(workdir)
if args is None:
args = sys.argv[1:]
# we use workdir as jobStore:
options = parser.parse_args([workdir] + args)
# if tmpdir_prefix is not the default value, set workDir too
if options.tmpdir_prefix != 'tmp':
options.workDir = options.tmpdir_prefix
if options.provisioner and not options.jobStore:
raise NoSuchJobStoreException(
'Please specify a jobstore with the --jobStore option when specifying a provisioner.')
use_container = not options.no_container
if options.logLevel:
cwllogger.setLevel(options.logLevel)
outdir = os.path.abspath(options.outdir)
tmp_outdir_prefix = os.path.abspath(options.tmp_outdir_prefix)
tmpdir_prefix = os.path.abspath(options.tmpdir_prefix)
fileindex = {}
existing = {}
conf_file = getattr(options,
"beta_dependency_resolvers_configuration", None)
use_conda_dependencies = getattr(options, "beta_conda_dependencies", None)
job_script_provider = None
if conf_file or use_conda_dependencies:
dependencies_configuration = DependenciesConfiguration(options)
job_script_provider = dependencies_configuration
options.default_container = None
runtime_context = cwltool.context.RuntimeContext(vars(options))
runtime_context.find_default_container = functools.partial(
find_default_container, options)
runtime_context.workdir = workdir
runtime_context.move_outputs = "leave"
runtime_context.rm_tmpdir = False
loading_context = cwltool.context.LoadingContext(vars(options))
with Toil(options) as toil:
if options.restart:
outobj = toil.restart()
else:
loading_context.hints = [{
"class": "ResourceRequirement",
"coresMin": toil.config.defaultCores,
"ramMin": toil.config.defaultMemory / (2**20),
"outdirMin": toil.config.defaultDisk / (2**20),
"tmpdirMin": 0
}]
loading_context.construct_tool_object = toil_make_tool
loading_context.resolver = cwltool.resolver.tool_resolver
loading_context.strict = not options.not_strict
options.workflow = options.cwltool
options.job_order = options.cwljob
uri, tool_file_uri = cwltool.load_tool.resolve_tool_uri(
options.cwltool, loading_context.resolver,
loading_context.fetcher_constructor)
options.tool_help = None
options.debug = options.logLevel == "DEBUG"
job_order_object, options.basedir, jobloader = \
cwltool.main.load_job_order(
options, sys.stdin, loading_context.fetcher_constructor,
loading_context.overrides_list, tool_file_uri)
document_loader, workflowobj, uri = \
cwltool.load_tool.fetch_document(
uri, loading_context.resolver,
loading_context.fetcher_constructor)
document_loader, avsc_names, processobj, metadata, uri = \
cwltool.load_tool.validate_document(
document_loader, workflowobj, uri,
loading_context.enable_dev, loading_context.strict, False,
loading_context.fetcher_constructor, False,
loading_context.overrides_list,
do_validate=loading_context.do_validate)
loading_context.overrides_list.extend(
metadata.get("cwltool:overrides", []))
try:
tool = cwltool.load_tool.make_tool(
document_loader, avsc_names, metadata, uri,
loading_context)
except cwltool.process.UnsupportedRequirement as err:
logging.error(err)
return 33
runtime_context.secret_store = SecretStore()
initialized_job_order = cwltool.main.init_job_order(
job_order_object, options, tool, jobloader, sys.stdout,
secret_store=runtime_context.secret_store)
fs_access = cwltool.stdfsaccess.StdFsAccess(options.basedir)
fill_in_defaults(
tool.tool["inputs"], initialized_job_order, fs_access)
def path_to_loc(obj):
if "location" not in obj and "path" in obj:
obj["location"] = obj["path"]
del obj["path"]
def import_files(tool):
visit_class(tool, ("File", "Directory"), path_to_loc)
visit_class(tool, ("File", ), functools.partial(
add_sizes, fs_access))
normalizeFilesDirs(tool)
adjustDirObjs(tool, functools.partial(
get_listing, fs_access, recursive=True))
adjustFileObjs(tool, functools.partial(
uploadFile, toil.importFile, fileindex, existing,
skip_broken=True))
tool.visit(import_files)
for inp in tool.tool["inputs"]:
def set_secondary(fileobj):
if isinstance(fileobj, Mapping) \
and fileobj.get("class") == "File":
if "secondaryFiles" not in fileobj:
fileobj["secondaryFiles"] = [
{"location": cwltool.builder.substitute(
fileobj["location"], sf), "class": "File"}
for sf in inp["secondaryFiles"]]
if isinstance(fileobj, MutableSequence):
for entry in fileobj:
set_secondary(entry)
if shortname(inp["id"]) in initialized_job_order \
and inp.get("secondaryFiles"):
set_secondary(initialized_job_order[shortname(inp["id"])])
import_files(initialized_job_order)
visitSteps(tool, import_files)
try:
runtime_context.use_container = use_container
runtime_context.tmpdir = os.path.realpath(tmpdir_prefix)
runtime_context.tmp_outdir_prefix = os.path.realpath(
tmp_outdir_prefix)
runtime_context.job_script_provider = job_script_provider
runtime_context.force_docker_pull = options.force_docker_pull
runtime_context.no_match_user = options.no_match_user
(wf1, _) = makeJob(tool, {}, None, runtime_context)
except cwltool.process.UnsupportedRequirement as err:
logging.error(err)
return 33
wf1.cwljob = initialized_job_order
if wf1 is CWLJob: # Clean up temporary directories only created with CWLJobs.
wf1.addFollowOnFn(cleanTempDirs, wf1)
outobj = toil.start(wf1)
outobj = resolve_indirect(outobj)
# Stage files. Specify destination bucket if specified in CLI
# options. If destination bucket not passed in,
# options.destBucket's value will be None.
toilStageFiles(
toil,
outobj,
outdir,
fileindex,
existing,
export=True,
destBucket=options.destBucket)
if not options.destBucket:
visit_class(outobj, ("File",), functools.partial(
compute_checksums, cwltool.stdfsaccess.StdFsAccess("")))
visit_class(outobj, ("File", ), MutationManager().unset_generation)
stdout.write(json.dumps(outobj, indent=4))
return 0
def main():
"""Reports the state of the toil.
"""
##########################################
#Construct the arguments.
##########################################
parser = getBasicOptionParser()
parser.add_argument("jobStore", type=str,
help="The location of a job store that holds the information about the "
"workflow whose status is to be reported on." + jobStoreLocatorHelp)
parser.add_argument("--verbose", dest="verbose", action="store_true",
help="Print loads of information, particularly all the log files of \
jobs that failed. default=%(default)s",
default=False)
parser.add_argument("--failIfNotComplete", dest="failIfNotComplete", action="store_true",
help="Return exit value of 1 if toil jobs not all completed. default=%(default)s",
default=False)
parser.add_argument("--version", action='version', version=version)
options = parseBasicOptions(parser)
logger.info("Parsed arguments")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
##########################################
#Do some checks.
##########################################
logger.info("Checking if we have files for Toil")
assert options.jobStore is not None
config = Config()
config.setOptions(options)
##########################################
#Survey the status of the job and report.
##########################################
jobStore = Toil.resumeJobStore(config.jobStore)
try:
rootJob = jobStore.loadRootJob()
except JobException:
print('The root job of the job store is absent, the workflow completed successfully.',
file=sys.stderr)
sys.exit(0)
def traverseGraph(jobGraph):
foundJobStoreIDs = set()
totalJobs = []
def inner(jobGraph):
if jobGraph.jobStoreID in foundJobStoreIDs:
return
foundJobStoreIDs.add(jobGraph.jobStoreID)
totalJobs.append(jobGraph)
# Traverse jobs in stack
for jobs in jobGraph.stack:
for successorJobStoreID in [x.jobStoreID for x in jobs]:
if (successorJobStoreID not in foundJobStoreIDs and jobStore.exists(successorJobStoreID)):
inner(jobStore.load(successorJobStoreID))
# Traverse service jobs
for jobs in jobGraph.services:
for serviceJobStoreID in [x.jobStoreID for x in jobs]:
if jobStore.exists(serviceJobStoreID):
assert serviceJobStoreID not in foundJobStoreIDs
foundJobStoreIDs.add(serviceJobStoreID)
totalJobs.append(jobStore.load(serviceJobStoreID))
inner(jobGraph)
return totalJobs
logger.info('Traversing the job graph. This may take a couple minutes.')
totalJobs = traverseGraph(rootJob)
failedJobs = []
hasChildren = []
hasServices = []
services = []
currentlyRunnning = []
for job in totalJobs:
if job.logJobStoreFileID is not None:
failedJobs.append(job)
if job.stack:
hasChildren.append(job)
elif job.remainingRetryCount != 0 and job.logJobStoreFileID != 0 and job.command:
# The job has no children, hasn't failed, and has a command to run. This indicates that the job is
# likely currently running, or at least could be run.
currentlyRunnning.append(job)
if job.services:
hasServices.append(job)
if job.startJobStoreID or job.terminateJobStoreID or job.errorJobStoreID:
# these attributes are only set in service jobs
services.append(job)
logger.info('There are %i unfinished jobs, %i parent jobs with children, %i jobs with services, %i services, '
'and %i totally failed jobs currently in %s.' %
(len(totalJobs), len(hasChildren), len(hasServices), len(services), len(failedJobs), config.jobStore))
if currentlyRunnning:
logger.info('These %i jobs are currently active: %s',
len(currentlyRunnning), ' \n'.join(map(str, currentlyRunnning)))
if options.verbose: #Verbose currently means outputting the files that have failed.
if failedJobs:
msg = "Outputting logs for the %i failed jobs" % (len(failedJobs))
msg += ": %s" % ", ".join((str(failedJob) for failedJob in failedJobs))
for jobNode in failedJobs:
job = jobStore.load(jobNode.jobStoreID)
msg += "\n=========> Failed job %s \n" % jobNode
with job.getLogFileHandle(jobStore) as fH:
msg += fH.read()
msg += "<=========\n"
print(msg)
else:
print('There are no failed jobs to report.', file=sys.stderr)
if totalJobs and options.failIfNotComplete:
exit(1) # when the workflow is complete, all jobs will have been removed from job store
def testClusterScalingWithPreemptableJobs(self):
"""
Test scaling simultaneously for a batch of preemptable and non-preemptable jobs.
"""
config = Config()
# Make defaults dummy values
config.defaultMemory = 1
config.defaultCores = 1
config.defaultDisk = 1
# Preemptable node parameters
config.nodeType = Shape(20, 10, 10, 10)
config.minNodes = 0
config.maxNodes = 10
# Preemptable node parameters
config.preemptableNodeType = Shape(20, 10, 10, 10)
config.minPreemptableNodes = 0
config.maxPreemptableNodes = 10
# Algorithm parameters
config.alphaPacking = 0.8
config.betaInertia = 1.2
config.scaleInterval = 3
self._testClusterScaling(config, numJobs=100, numPreemptableJobs=100)
def testClusterScaling(self):
"""
Test scaling for a batch of non-preemptable jobs and no preemptable jobs (makes debugging
easier).
"""
config = Config()
# Make defaults dummy values
config.defaultMemory = 1
config.defaultCores = 1
config.defaultDisk = 1
# No preemptable nodes/jobs
config.maxPreemptableNodes = 0 # No preemptable nodes
# Non-preemptable parameters
config.nodeType = Shape(20, 10, 10, 10)
config.minNodes = 0
config.maxNodes = 10
# Algorithm parameters
config.alphaPacking = 0.8
config.betaInertia = 1.2
config.scaleInterval = 3
self._testClusterScaling(config, numJobs=100, numPreemptableJobs=0)
def main():
"""Reports the state of the toil.
"""
##########################################
#Construct the arguments.
##########################################
parser = getBasicOptionParser()
parser.add_argument("jobStore", type=str,
help="The location of a job store that holds the information about the "
"workflow whose status is to be reported on." + jobStoreLocatorHelp)
parser.add_argument("--verbose", dest="verbose", action="store_true",
help="Print loads of information, particularly all the log files of \
jobs that failed. default=%(default)s",
default=False)
parser.add_argument("--failIfNotComplete", dest="failIfNotComplete", action="store_true",
help="Return exit value of 1 if toil jobs not all completed. default=%(default)s",
default=False)
parser.add_argument("--version", action='version', version=version)
options = parseBasicOptions(parser)
logger.info("Parsed arguments")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
##########################################
#Do some checks.
##########################################
logger.info("Checking if we have files for Toil")
assert options.jobStore is not None
config = Config()
config.setOptions(options)
##########################################
#Survey the status of the job and report.
##########################################
jobStore = Toil.resumeJobStore(config.jobStore)
try:
rootJob = jobStore.loadRootJob()
except JobException:
print('The root job of the job store is absent, the workflow completed successfully.',
file=sys.stderr)
sys.exit(0)
toilState = ToilState(jobStore, rootJob )
# The first element of the toilState.updatedJobs tuple is the jobGraph we want to inspect
totalJobs = set(toilState.successorCounts.keys()) | \
{jobTuple[0] for jobTuple in toilState.updatedJobs}
failedJobs = [ job for job in totalJobs if job.remainingRetryCount == 0 ]
print('There are %i active jobs, %i parent jobs with children, and %i totally failed jobs '
'currently in %s.' % (len(toilState.updatedJobs), len(toilState.successorCounts),
len(failedJobs), config.jobStore), file=sys.stderr)
if options.verbose: #Verbose currently means outputting the files that have failed.
for job in failedJobs:
if job.logJobStoreFileID is not None:
with job.getLogFileHandle(jobStore) as logFileHandle:
logStream(logFileHandle, job.jobStoreID, logger.warn)
else:
print('Log file for job %s is absent.' % job.jobStoreID, file=sys.stderr)
if len(failedJobs) == 0:
print('There are no failed jobs to report.', file=sys.stderr)
if (len(toilState.updatedJobs) + len(toilState.successorCounts)) != 0 and \
options.failIfNotComplete:
sys.exit(1)
def _createConfig(self):
return Config()
def testClusterScaling(self):
"""
Test scaling for a batch of non-preemptable jobs and no preemptable jobs (makes debugging
easier).
"""
config = Config()
# Make defaults dummy values
config.defaultMemory = 1
config.defaultCores = 1
config.defaultDisk = 1
# No preemptable nodes/jobs
config.maxPreemptableNodes = [] # No preemptable nodes
# Non-preemptable parameters
config.nodeTypes = [Shape(20, 10, 10, 10, False)]
config.minNodes = [0]
config.maxNodes = [10]
# Algorithm parameters
config.targetTime = defaultTargetTime
config.betaInertia = 0.1
config.scaleInterval = 3
self._testClusterScaling(config,
numJobs=100,
numPreemptableJobs=0,
jobShape=config.nodeTypes[0])