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(provisioner_options=True, jobstore_option=False)
options = parser.parse_args()
set_logging_from_options(options)
cluster = cluster_factory(provisioner=options.provisioner,
clusterName=options.clusterName,
zone=options.zone)
cluster.destroyCluster()
def main() -> None:
parser = parser_with_common_options(provisioner_options=True, jobstore_option=False)
options = parser.parse_args()
set_logging_from_options(options)
logger.info('Destroying cluster %s', options.clusterName)
cluster = cluster_factory(provisioner=options.provisioner,
clusterName=options.clusterName,
zone=options.zone)
cluster.destroyCluster()
logger.info('Cluster %s is now gone.', options.clusterName)
def main() -> None:
parser = parser_with_common_options(jobstore_option=True)
options = parser.parse_args()
set_logging_from_options(options)
try:
jobstore = Toil.getJobStore(options.jobStore)
jobstore.resume()
jobstore.destroy()
logger.info(f"Successfully deleted the job store: {options.jobStore}")
except NoSuchJobStoreException:
logger.info(f"Failed to delete the job store: {options.jobStore} is non-existent.")
except:
logger.info(f"Failed to delete the job store: {options.jobStore}")
raise
def main() -> None:
parser = parser_with_common_options(provisioner_options=True,
jobstore_option=False)
parser.add_argument("--insecure",
action='store_true',
help="Temporarily disable strict host key checking.")
parser.add_argument("--sshOption",
dest='sshOptions',
default=[],
action='append',
help="Pass an additional option to the SSH command.")
parser.add_argument(
"--grafana_port",
dest='grafana_port',
default=3000,
help="Assign a local port to be used for the Grafana dashboard.")
parser.add_argument('args', nargs=argparse.REMAINDER)
options = parser.parse_args()
set_logging_from_options(options)
# Since we collect all the remaining arguments at the end for a command to
# run, it's easy to lose options.
if len(options.args) > 0 and options.args[0].startswith('-'):
logger.warning(
'Argument \'%s\' interpreted as a command to run '
'despite looking like an option.', options.args[0])
cluster = cluster_factory(provisioner=options.provisioner,
clusterName=options.clusterName,
zone=options.zone)
command = options.args if options.args else ['bash']
sshOptions: List[str] = options.sshOptions
# Forward ports:
# 3000 for Grafana dashboard
# 9090 for Prometheus dashboard
sshOptions.extend([
'-L', f'{options.grafana_port}:localhost:3000', '-L',
'9090:localhost:9090'
])
cluster.getLeader().sshAppliance(*command,
strict=not options.insecure,
tty=sys.stdin.isatty(),
sshOptions=sshOptions)
def main() -> None:
parser = parser_with_common_options(jobstore_option=True)
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()).")
# Load the jobStore
options = parser.parse_args()
set_logging_from_options(options)
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 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 = parser_with_common_options(provisioner_options=True,
jobstore_option=False)
parser.add_argument("--insecure",
action='store_true',
help="Temporarily disable strict host key checking.")
parser.add_argument("--sshOption",
dest='sshOptions',
default=[],
action='append',
help="Pass an additional option to the SSH command.")
parser.add_argument('args', nargs=argparse.REMAINDER)
options = parser.parse_args()
set_logging_from_options(options)
cluster = cluster_factory(provisioner=options.provisioner,
clusterName=options.clusterName,
zone=options.zone)
command = options.args if options.args else ['bash']
cluster.getLeader().sshAppliance(*command,
strict=not options.insecure,
tty=sys.stdin.isatty(),
sshOptions=options.sshOptions)
def main():
parser = parser_with_common_options(provisioner_options=True, jobstore_option=False)
parser.add_argument("--insecure", action='store_true',
help="Temporarily disable strict host key checking.")
parser.add_argument("--sshOption", dest='sshOptions', default=[], action='append',
help="Pass an additional option to the SSH command.")
parser.add_argument('args', nargs=argparse.REMAINDER)
options = parser.parse_args()
set_logging_from_options(options)
# Since we collect all the remaining arguments at the end for a command to
# run, it's easy to lose options.
if len(options.args) > 0 and options.args[0].startswith('-'):
logger.warning('Argument \'%s\' interpreted as a command to run '
'despite looking like an option.', options.args[0])
cluster = cluster_factory(provisioner=options.provisioner,
clusterName=options.clusterName,
zone=options.zone)
command = options.args if options.args else ['bash']
cluster.getLeader().sshAppliance(*command, strict=not options.insecure, tty=sys.stdin.isatty(),
sshOptions=options.sshOptions)
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 main() -> None:
parser = parser_with_common_options(provisioner_options=True,
jobstore_option=False)
parser.add_argument("--insecure",
dest='insecure',
action='store_true',
required=False,
help="Temporarily disable strict host key checking.")
parser.add_argument(
"args",
nargs=argparse.REMAINDER,
help="Arguments to pass to"
"`rsync`. Takes any arguments that rsync accepts. Specify the"
" remote with a colon. For example, to upload `example.py`,"
" specify `toil rsync-cluster -p aws test-cluster example.py :`."
"\nOr, to download a file from the remote:, `toil rsync-cluster"
" -p aws test-cluster :example.py .`")
options = parser.parse_args()
set_logging_from_options(options)
cluster = cluster_factory(provisioner=options.provisioner,
clusterName=options.clusterName,
zone=options.zone)
cluster.getLeader().coreRsync(args=options.args,
strict=not options.insecure)
def main():
parser = parser_with_common_options(provisioner_options=True, jobstore_option=False)
parser.add_argument("-T", "--clusterType", dest="clusterType",
choices=['mesos', 'kubernetes'], default='mesos',
help="Cluster scheduler to use.")
parser.add_argument("--leaderNodeType", dest="leaderNodeType", required=True,
help="Non-preemptable node type to use for the cluster leader.")
parser.add_argument("--keyPairName", dest='keyPairName',
help="On AWS, the name of the AWS key pair to include on the instance."
" On Google/GCE, this is the ssh key pair.")
parser.add_argument("--owner", dest='owner',
help="The owner tag for all instances. If not given, the value in"
" --keyPairName will be used if given.")
parser.add_argument("--boto", dest='botoPath',
help="The path to the boto credentials directory. This is transferred "
"to all nodes in order to access the AWS jobStore from non-AWS instances.")
parser.add_argument("-t", "--tag", metavar='NAME=VALUE', dest='tags',
default=[], action='append',
help="Tags are added to the AWS cluster for this node and all of its "
"children. Tags are of the form:\n"
" -t key1=value1 --tag key2=value2\n"
"Multiple tags are allowed and each tag needs its own flag. By "
"default the cluster is tagged with "
" {\n"
" \"Name\": clusterName,\n"
" \"Owner\": IAM username\n"
" }. ")
parser.add_argument("--vpcSubnet",
help="VPC subnet ID to launch cluster in. Uses default subnet if not "
"specified. This subnet needs to have auto assign IPs turned on.")
parser.add_argument("--nodeTypes", dest='nodeTypes', default=None, type=str,
help="Specifies a list of comma-separated node types, each of which is "
"composed of slash-separated instance types, and an optional spot "
"bid set off by a colon, making the node type preemptable. Instance "
"types may appear in multiple node types, and the same node type "
"may appear as both preemptable and non-preemptable.\n"
"Valid argument specifying two node types:\n"
"\tc5.4xlarge/c5a.4xlarge:0.42,t2.large\n"
"Node types:\n"
"\tc5.4xlarge/c5a.4xlarge:0.42 and t2.large\n"
"Instance types:\n"
"\tc5.4xlarge, c5a.4xlarge, and t2.large\n"
"Semantics:\n"
"\tBid $0.42/hour for either c5.4xlarge or c5a.4xlarge instances,\n"
"\ttreated interchangeably, while they are available at that price,\n"
"\tand buy t2.large instances at full price\n"
"Must also provide the --workers argument to specify how many "
"workers of each node type to create.")
parser.add_argument("-w", "--workers", dest='workers', default=None, type=str,
help="Comma-separated list of the ranges of numbers of workers of each "
"node type to launch, such as '0-2,5,1-3'. If a range is given, "
"workers will automatically be launched and terminated by the cluster "
"to auto-scale to the workload.")
parser.add_argument("--leaderStorage", dest='leaderStorage', type=int, default=50,
help="Specify the size (in gigabytes) of the root volume for the leader "
"instance. This is an EBS volume.")
parser.add_argument("--nodeStorage", dest='nodeStorage', type=int, default=50,
help="Specify the size (in gigabytes) of the root volume for any worker "
"instances created when using the -w flag. This is an EBS volume.")
parser.add_argument('--forceDockerAppliance', dest='forceDockerAppliance', action='store_true',
default=False,
help="Disables sanity checking the existence of the docker image specified "
"by TOIL_APPLIANCE_SELF, which Toil uses to provision mesos for "
"autoscaling.")
parser.add_argument('--awsEc2ProfileArn', dest='awsEc2ProfileArn', default=None, type=str,
help="If provided, the specified ARN is used as the instance profile for EC2 instances."
"Useful for setting custom IAM profiles. If not specified, a new IAM role is created "
"by default with sufficient access to perform basic cluster operations.")
parser.add_argument('--awsEc2ExtraSecurityGroupId', dest='awsEc2ExtraSecurityGroupIds', default=[], action='append',
help="Any additional security groups to attach to EC2 instances. Note that a security group "
"with its name equal to the cluster name will always be created, thus ensure that "
"the extra security groups do not have the same name as the cluster name.")
options = parser.parse_args()
set_logging_from_options(options)
tags = create_tags_dict(options.tags) if options.tags else dict()
# Get worker node types
worker_node_types = parse_node_types(options.nodeTypes)
check_valid_node_types(options.provisioner, worker_node_types + [({options.leaderNodeType}, None)])
# Holds string ranges, like "5", or "3-10"
worker_node_ranges = options.workers.split(',') if options.workers else []
# checks the validity of TOIL_APPLIANCE_SELF before proceeding
applianceSelf(forceDockerAppliance=options.forceDockerAppliance)
# This holds either ints to launch static nodes, or tuples of ints
# specifying ranges to launch managed auto-scaling nodes, for each type.
nodeCounts = []
if ((worker_node_types != [] or worker_node_ranges != []) and not
(worker_node_types != [] and worker_node_ranges != [])):
raise RuntimeError("The --nodeTypes option requires --workers, and visa versa.")
if worker_node_types and worker_node_ranges:
if not len(worker_node_types) == len(worker_node_ranges):
raise RuntimeError("List of worker count ranges must be the same length as the list of node types.")
for spec in worker_node_ranges:
if '-' in spec:
# Provision via autoscaling
parts = spec.split('-')
if len(parts) != 2:
raise RuntimeError("Unacceptable range: " + spec)
nodeCounts.append((int(parts[0]), int(parts[1])))
else:
# Provision fixed nodes
nodeCounts.append(int(spec))
owner = options.owner or options.keyPairName or 'toil'
# Check to see if the user specified a zone. If not, see if one is stored in an environment variable.
options.zone = options.zone or os.environ.get(f'TOIL_{options.provisioner.upper()}_ZONE')
if not options.zone:
raise RuntimeError(f'Please provide a value for --zone or set a default in the '
f'TOIL_{options.provisioner.upper()}_ZONE environment variable.')
logger.info('Creating cluster %s...', options.clusterName)
cluster = cluster_factory(provisioner=options.provisioner,
clusterName=options.clusterName,
clusterType=options.clusterType,
zone=options.zone,
nodeStorage=options.nodeStorage)
cluster.launchCluster(leaderNodeType=options.leaderNodeType,
leaderStorage=options.leaderStorage,
owner=owner,
keyName=options.keyPairName,
botoPath=options.botoPath,
userTags=tags,
vpcSubnet=options.vpcSubnet,
awsEc2ProfileArn=options.awsEc2ProfileArn,
awsEc2ExtraSecurityGroupIds=options.awsEc2ExtraSecurityGroupIds)
for typeNum, spec in enumerate(nodeCounts):
# For each batch of workers to make
wanted = worker_node_types[typeNum]
if isinstance(spec, int):
# Make static nodes
if spec == 0:
# Don't make anything
continue
if wanted[1] is None:
# Make non-spot instances
cluster.addNodes(nodeTypes=wanted[0], numNodes=spec, preemptable=False)
else:
# We have a spot bid
cluster.addNodes(nodeTypes=wanted[0], numNodes=spec, preemptable=True,
spotBid=wanted[1])
elif isinstance(spec, tuple):
# Make a range of auto-scaling nodes
max_count, min_count = spec
if max_count < min_count:
# Flip them around
min_count, max_count = max_count, min_count
if max_count == 0:
# Don't want any
continue
if wanted[1] is None:
# Make non-spot instances
cluster.addManagedNodes(nodeTypes=wanted[0], minNodes=min_count, maxNodes=max_count,
preemptable=False)
else:
# Bid at the given price.
cluster.addManagedNodes(nodeTypes=wanted[0], minNodes=min_count, maxNodes=max_count,
preemptable=True, spotBid=wanted[1])
logger.info('Cluster created successfully.')
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 setLoggingFromOptions(options):
logger.warning(
'Deprecated toil method. Please use "toil.statsAndLogging.set_logging_from_options()" instead."'
)
set_logging_from_options(options)
def main():
parser = parser_with_common_options(provisioner_options=True,
jobstore_option=False)
parser.add_argument(
"--leaderNodeType",
dest="leaderNodeType",
required=True,
help="Non-preemptable node type to use for the cluster leader.")
parser.add_argument(
"--keyPairName",
dest='keyPairName',
help="On AWS, the name of the AWS key pair to include on the instance."
" On Google/GCE, this is the ssh key pair.")
parser.add_argument(
"--owner",
dest='owner',
help="The owner tag for all instances. If not given, the value in"
" --keyPairName will be used if given.")
parser.add_argument(
"--boto",
dest='botoPath',
help="The path to the boto credentials directory. This is transferred "
"to all nodes in order to access the AWS jobStore from non-AWS instances."
)
parser.add_argument(
"-t",
"--tag",
metavar='NAME=VALUE',
dest='tags',
default=[],
action='append',
help="Tags are added to the AWS cluster for this node and all of its "
"children. Tags are of the form:\n"
" -t key1=value1 --tag key2=value2\n"
"Multiple tags are allowed and each tag needs its own flag. By "
"default the cluster is tagged with "
" {\n"
" \"Name\": clusterName,\n"
" \"Owner\": IAM username\n"
" }. ")
parser.add_argument(
"--vpcSubnet",
help="VPC subnet ID to launch cluster in. Uses default subnet if not "
"specified. This subnet needs to have auto assign IPs turned on.")
parser.add_argument(
"--nodeTypes",
dest='nodeTypes',
default=None,
type=str,
help="Comma-separated list of node types to create while launching the "
"leader. The syntax for each node type depends on the provisioner "
"used. For the aws provisioner this is the name of an EC2 instance "
"type followed by a colon and the price in dollar to bid for a spot "
"instance, for example 'c3.8xlarge:0.42'. Must also provide the "
"--workers argument to specify how many workers of each node type "
"to create.")
parser.add_argument(
"-w",
"--workers",
dest='workers',
default=None,
type=str,
help=
"Comma-separated list of the number of workers of each node type to "
"launch alongside the leader when the cluster is created. This can be "
"useful if running toil without auto-scaling but with need of more "
"hardware support")
parser.add_argument(
"--leaderStorage",
dest='leaderStorage',
type=int,
default=50,
help="Specify the size (in gigabytes) of the root volume for the leader "
"instance. This is an EBS volume.")
parser.add_argument(
"--nodeStorage",
dest='nodeStorage',
type=int,
default=50,
help="Specify the size (in gigabytes) of the root volume for any worker "
"instances created when using the -w flag. This is an EBS volume.")
parser.add_argument(
'--forceDockerAppliance',
dest='forceDockerAppliance',
action='store_true',
default=False,
help=
"Disables sanity checking the existence of the docker image specified "
"by TOIL_APPLIANCE_SELF, which Toil uses to provision mesos for "
"autoscaling.")
parser.add_argument(
'--awsEc2ProfileArn',
dest='awsEc2ProfileArn',
default=None,
type=str,
help=
"If provided, the specified ARN is used as the instance profile for EC2 instances."
"Useful for setting custom IAM profiles. If not specified, a new IAM role is created "
"by default with sufficient access to perform basic cluster operations."
)
parser.add_argument(
'--awsEc2ExtraSecurityGroupId',
dest='awsEc2ExtraSecurityGroupIds',
default=[],
action='append',
help=
"Any additional security groups to attach to EC2 instances. Note that a security group "
"with its name equal to the cluster name will always be created, thus ensure that "
"the extra security groups do not have the same name as the cluster name."
)
options = parser.parse_args()
set_logging_from_options(options)
tags = create_tags_dict(options.tags) if options.tags else dict()
worker_node_types = options.nodeTypes.split(
',') if options.nodeTypes else []
worker_quantities = options.workers.split(',') if options.workers else []
check_valid_node_types(options.provisioner,
worker_node_types + [options.leaderNodeType])
# checks the validity of TOIL_APPLIANCE_SELF before proceeding
applianceSelf(forceDockerAppliance=options.forceDockerAppliance)
owner = options.owner or options.keyPairName or 'toil'
# Check to see if the user specified a zone. If not, see if one is stored in an environment variable.
options.zone = options.zone or os.environ.get(
f'TOIL_{options.provisioner.upper()}_ZONE')
if not options.zone:
raise RuntimeError(
f'Please provide a value for --zone or set a default in the '
f'TOIL_{options.provisioner.upper()}_ZONE environment variable.')
if (options.nodeTypes or
options.workers) and not (options.nodeTypes and options.workers):
raise RuntimeError(
"The --nodeTypes and --workers options must be specified together."
)
if not len(worker_node_types) == len(worker_quantities):
raise RuntimeError(
"List of node types must be the same length as the list of workers."
)
cluster = cluster_factory(provisioner=options.provisioner,
clusterName=options.clusterName,
zone=options.zone,
nodeStorage=options.nodeStorage)
cluster.launchCluster(
leaderNodeType=options.leaderNodeType,
leaderStorage=options.leaderStorage,
owner=owner,
keyName=options.keyPairName,
botoPath=options.botoPath,
userTags=tags,
vpcSubnet=options.vpcSubnet,
awsEc2ProfileArn=options.awsEc2ProfileArn,
awsEc2ExtraSecurityGroupIds=options.awsEc2ExtraSecurityGroupIds)
for worker_node_type, num_workers in zip(worker_node_types,
worker_quantities):
if ':' in worker_node_type:
worker_node_type, bid = worker_node_type.split(':', 1)
cluster.addNodes(nodeType=worker_node_type,
numNodes=int(num_workers),
preemptable=True,
spotBid=float(bid))
else:
cluster.addNodes(nodeType=worker_node_type,
numNodes=int(num_workers),
preemptable=False)
