def _getScript(self):
def userScript():
from toil.job import Job
from toil.common import Toil
# Because this is the only job in the pipeline and because it is preemptable,
# there will be no non-preemptable jobs. The non-preemptable scaler will therefore
# not request any nodes initially. And since we made it impossible for the
# preemptable scaler to allocate any nodes (using an abnormally low spot bid),
# we will observe a deficit of preemptable nodes that the non-preemptable scaler will
# compensate for by spinning up non-preemptable nodes instead.
#
def job(job, disk='10M', cores=1, memory='10M', preemptable=True):
pass
if __name__ == '__main__':
options = Job.Runner.getDefaultArgumentParser().parse_args()
with Toil(options) as toil:
if toil.config.restart:
toil.restart()
else:
toil.start(Job.wrapJobFn(job))
script = dedent('\n'.join(getsource(userScript).split('\n')[1:]))
# use appliance ssh method instead of sshutil so we can specify input param
AWSProvisioner._sshAppliance(self.leader.ip_address, 'tee', '/home/userScript.py', input=script)
def _getScript(self):
def restartScript():
from toil.job import Job
import argparse
import os
def f0(job):
if 'FAIL' in os.environ:
raise RuntimeError('failed on purpose')
if __name__ == '__main__':
parser = argparse.ArgumentParser()
Job.Runner.addToilOptions(parser)
options = parser.parse_args()
rootJob = Job.wrapJobFn(f0,
cores=0.5,
memory='50 M',
disk='50 M')
Job.Runner.startToil(rootJob, options)
script = dedent('\n'.join(getsource(restartScript).split('\n')[1:]))
# use appliance ssh method instead of sshutil so we can specify input param
AWSProvisioner._sshAppliance(self.leader.ip_address,
'tee',
self.scriptName,
input=script)
def _getScript(self):
def userScript():
from toil.job import Job
from toil.common import Toil
# Because this is the only job in the pipeline and because it is preemptable,
# there will be no non-preemptable jobs. The non-preemptable scaler will therefore
# not request any nodes initially. And since we made it impossible for the
# preemptable scaler to allocate any nodes (using an abnormally low spot bid),
# we will observe a deficit of preemptable nodes that the non-preemptable scaler will
# compensate for by spinning up non-preemptable nodes instead.
#
def job(job, disk='10M', cores=1, memory='10M', preemptable=True):
pass
if __name__ == '__main__':
options = Job.Runner.getDefaultArgumentParser().parse_args()
with Toil(options) as toil:
if toil.config.restart:
toil.restart()
else:
toil.start(Job.wrapJobFn(job))
script = dedent('\n'.join(getsource(userScript).split('\n')[1:]))
# use appliance ssh method instead of sshutil so we can specify input param
AWSProvisioner._sshAppliance(self.leader.ip_address,
'tee',
'/home/userScript.py',
input=script)
def _getScript(self):
def restartScript():
from toil.job import Job
import argparse
import os
def f0(job):
if 'FAIL' in os.environ:
raise RuntimeError('failed on purpose')
if __name__ == '__main__':
parser = argparse.ArgumentParser()
Job.Runner.addToilOptions(parser)
options = parser.parse_args()
rootJob = Job.wrapJobFn(f0, cores=0.5, memory='50 M', disk='50 M')
Job.Runner.startToil(rootJob, options)
script = dedent('\n'.join(getsource(restartScript).split('\n')[1:]))
# use appliance ssh method instead of sshutil so we can specify input param
AWSProvisioner._sshAppliance(self.leader.ip_address, 'tee', self.scriptName, input=script)
def _test(self, spotInstances=False):
from toil.provisioners.aws.awsProvisioner import AWSProvisioner
leader = AWSProvisioner.launchCluster(instanceType=self.instanceType,
keyName=self.keyName,
clusterName=self.clusterName)
# --never-download prevents silent upgrades to pip, wheel and setuptools
venv_command = 'virtualenv --system-site-packages --never-download /home/venv'
AWSProvisioner._sshAppliance(leader.ip_address, command=venv_command)
upgrade_command = '/home/venv/bin/pip install setuptools==28.7.1'
AWSProvisioner._sshAppliance(leader.ip_address,
command=upgrade_command)
yaml_command = '/home/venv/bin/pip install pyyaml==3.12'
AWSProvisioner._sshAppliance(leader.ip_address, command=yaml_command)
# install toil scripts
install_command = ('/home/venv/bin/pip install toil-scripts==%s' %
self.toilScripts)
AWSProvisioner._sshAppliance(leader.ip_address,
command=install_command)
# install curl
install_command = 'sudo apt-get -y install curl'
AWSProvisioner._sshAppliance(leader.ip_address,
command=install_command)
toilOptions = [
'--batchSystem=mesos', '--workDir=/var/lib/toil',
'--mesosMaster=%s:5050' % leader.private_ip_address,
'--clean=always', '--retryCount=0'
]
toilOptions.extend([
'--provisioner=aws', '--nodeType=' + self.instanceType,
'--maxNodes=%s' % self.numWorkers, '--logDebug'
])
if spotInstances:
toilOptions.extend([
'--preemptableNodeType=%s:%s' %
(self.instanceType, self.spotBid),
# The RNASeq pipeline does not specify a preemptability requirement so we
# need to specify a default, otherwise jobs would never get scheduled.
'--defaultPreemptable',
'--maxPreemptableNodes=%s' % self.numWorkers
])
toilOptions = ' '.join(toilOptions)
runCommand = 'bash -c \\"export PATH=/home/venv/bin/:$PATH;export TOIL_SCRIPTS_TEST_NUM_SAMPLES=%i; export TOIL_SCRIPTS_TEST_TOIL_OPTIONS=' + pipes.quote(toilOptions) + \
'; export TOIL_SCRIPTS_TEST_JOBSTORE=' + self.jobStore + \
'; /home/venv/bin/python -m unittest -v' + \
' toil_scripts.rnaseq_cgl.test.test_rnaseq_cgl.RNASeqCGLTest.test_manifest\\"'
runCommand %= self.numSamples
AWSProvisioner._sshAppliance(leader.ip_address, runCommand)
