def main():
parser = getBasicOptionParser()
parser = addBasicProvisionerOptions(parser)
parser.add_argument("--nodeType", dest='nodeType', required=True,
help="Node type for {non-|}preemptable nodes. The syntax 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'.")
parser.add_argument("--keyPairName", dest='keyPairName', required=True,
help="The name of the AWS key pair to include on the instance")
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: "
" -t key1=value1 --tag key2=value2 "
"Multiple tags are allowed and each tag needs its own flag. By "
"default the cluster is tagged with "
" {"
" \"Name\": clusterName,"
" \"Owner\": IAM username"
" }. ")
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("-w", "--workers", dest='workers', default=0, type=int,
help="Specify a number of workers 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")
config = parseBasicOptions(parser)
setLoggingFromOptions(config)
tagsDict = None if config.tags is None else createTagsDict(config.tags)
spotBid = None
if config.provisioner == 'aws':
logger.info('Using aws provisioner.')
try:
from toil.provisioners.aws.awsProvisioner import AWSProvisioner
except ImportError:
raise RuntimeError('The aws extra must be installed to use this provisioner')
provisioner = AWSProvisioner()
parsedBid = config.nodeType.split(':', 1)
if len(config.nodeType) != len(parsedBid[0]):
# there is a bid
spotBid = float(parsedBid[1])
config.nodeType = parsedBid[0]
else:
assert False
provisioner.launchCluster(instanceType=config.nodeType,
keyName=config.keyPairName,
clusterName=config.clusterName,
workers=config.workers,
spotBid=spotBid,
userTags=tagsDict,
zone=config.zone,
vpcSubnet=config.vpcSubnet)
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)
def main():
parser = getBasicOptionParser()
parser = addBasicProvisionerOptions(parser)
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', required=True,
help="The name of the AWS or ssh key pair to include on the instance")
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.")
config = parseBasicOptions(parser)
tagsDict = None if config.tags is None else createTagsDict(config.tags)
spotBids = []
nodeTypes = []
preemptableNodeTypes = []
numNodes = []
numPreemptableNodes = []
leaderSpotBid = None
if config.provisioner == 'aws':
logger.info('Using aws provisioner.')
try:
from toil.provisioners.aws.awsProvisioner import AWSProvisioner
except ImportError:
logger.error('The aws extra must be installed to use this provisioner')
raise
provisioner = AWSProvisioner()
elif config.provisioner == 'gce':
logger.info('Using a gce provisioner.')
try:
from toil.provisioners.gceProvisioner import GCEProvisioner
except ImportError:
logger.error('The google extra must be installed to use this provisioner')
raise
provisioner = GCEProvisioner()
else:
assert False
#Parse leader node type and spot bid
parsedBid = config.leaderNodeType.split(':', 1)
if len(config.leaderNodeType) != len(parsedBid[0]):
leaderSpotBid = float(parsedBid[1])
config.leaderNodeType = parsedBid[0]
if (config.nodeTypes or config.workers) and not (config.nodeTypes and config.workers):
raise RuntimeError("The --nodeTypes and --workers options must be specified together,")
if config.nodeTypes:
nodeTypesList = config.nodeTypes.split(",")
numWorkersList = config.workers.split(",")
if not len(nodeTypesList) == len(numWorkersList):
raise RuntimeError("List of node types must be same length as list of numbers of workers.")
for nodeTypeStr, num in zip(nodeTypesList, numWorkersList):
parsedBid = nodeTypeStr.split(':', 1)
if len(nodeTypeStr) != len(parsedBid[0]):
#Is a preemptable node
preemptableNodeTypes.append(parsedBid[0])
spotBids.append(float(parsedBid[1]))
numPreemptableNodes.append(int(num))
else:
nodeTypes.append(nodeTypeStr)
numNodes.append(int(num))
provisioner.launchCluster(leaderNodeType=config.leaderNodeType,
leaderSpotBid=leaderSpotBid,
nodeTypes=nodeTypes,
preemptableNodeTypes=preemptableNodeTypes,
numWorkers=numNodes,
numPreemptableWorkers = numPreemptableNodes,
keyName=config.keyPairName,
botoPath=config.botoPath,
clusterName=config.clusterName,
spotBids=spotBids,
userTags=tagsDict,
zone=config.zone,
leaderStorage=config.leaderStorage,
nodeStorage=config.nodeStorage,
vpcSubnet=config.vpcSubnet)
def main():
parser = getBasicOptionParser()
parser = addBasicProvisionerOptions(parser)
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',
required=True,
help="On AWS, the name of the AWS key pair to include on the instance."
" On Google/GCE, this is the ssh key pair."
" On Azure, this will be used as the owner tag.")
parser.add_argument(
"--publicKeyFile",
dest='publicKeyFile',
default="~/.ssh/id_rsa.pub",
help="On Azure, the file"
" containing the key pairs (the first key pair will be used).")
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(
"--azureStorageCredentials",
dest='azureStorageCredentials',
type=str,
default=credential_file_path,
help=
"The location of the file containing the Azure storage credentials. If not specified,"
" the default file is used with Azure provisioning. Use 'None' to disable"
" the transfer of credentials.")
config = parseBasicOptions(parser)
tagsDict = None if config.tags is None else createTagsDict(config.tags)
# checks the validity of TOIL_APPLIANCE_SELF before proceeding
checkToilApplianceSelf = applianceSelf(
forceDockerAppliance=config.forceDockerAppliance)
spotBids = []
nodeTypes = []
preemptableNodeTypes = []
numNodes = []
numPreemptableNodes = []
leaderSpotBid = None
if config.provisioner == 'aws':
logger.info('Using aws provisioner.')
try:
from toil.provisioners.aws.awsProvisioner import AWSProvisioner
except ImportError:
logger.error(
'The aws extra must be installed to use this provisioner')
raise
provisioner = AWSProvisioner()
elif config.provisioner == 'azure':
try:
from toil.provisioners.azure.azureProvisioner import AzureProvisioner
except ImportError:
raise RuntimeError(
'The aws extra must be installed to use this provisioner')
provisioner = AzureProvisioner()
elif config.provisioner == 'gce':
logger.info('Using a gce provisioner.')
try:
from toil.provisioners.gceProvisioner import GCEProvisioner
except ImportError:
logger.error(
'The google extra must be installed to use this provisioner')
raise
provisioner = GCEProvisioner()
else:
assert False
#Parse leader node type and spot bid
parsedBid = config.leaderNodeType.split(':', 1)
if len(config.leaderNodeType) != len(parsedBid[0]):
leaderSpotBid = float(parsedBid[1])
config.leaderNodeType = parsedBid[0]
if (config.nodeTypes
or config.workers) and not (config.nodeTypes and config.workers):
raise RuntimeError(
"The --nodeTypes and --workers options must be specified together,"
)
if config.nodeTypes:
nodeTypesList = config.nodeTypes.split(",")
numWorkersList = config.workers.split(",")
if not len(nodeTypesList) == len(numWorkersList):
raise RuntimeError(
"List of node types must be the same length as the list of workers."
)
for nodeTypeStr, num in zip(nodeTypesList, numWorkersList):
parsedBid = nodeTypeStr.split(':', 1)
if len(nodeTypeStr) != len(parsedBid[0]):
#Is a preemptable node
preemptableNodeTypes.append(parsedBid[0])
spotBids.append(float(parsedBid[1]))
numPreemptableNodes.append(int(num))
else:
nodeTypes.append(nodeTypeStr)
numNodes.append(int(num))
provisioner.launchCluster(
leaderNodeType=config.leaderNodeType,
leaderSpotBid=leaderSpotBid,
nodeTypes=nodeTypes,
preemptableNodeTypes=preemptableNodeTypes,
numWorkers=numNodes,
numPreemptableWorkers=numPreemptableNodes,
keyName=config.keyPairName,
botoPath=config.botoPath,
clusterName=config.clusterName,
spotBids=spotBids,
userTags=tagsDict,
zone=config.zone,
leaderStorage=config.leaderStorage,
nodeStorage=config.nodeStorage,
vpcSubnet=config.vpcSubnet,
publicKeyFile=config.publicKeyFile,
azureStorageCredentials=config.azureStorageCredentials)
def main():
parser = getBasicOptionParser()
parser = addBasicProvisionerOptions(parser)
parser.add_argument("--nodeType", dest='nodeType', required=True,
help="Node type for {non-|}preemptable nodes. The syntax 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'.")
parser.add_argument("--keyPairName", dest='keyPairName', required=True,
help="The name of the AWS key pair to include on the instance")
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("-w", "--workers", dest='workers', default=0, type=int,
help="Specify a number of workers 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.")
config = parseBasicOptions(parser)
tagsDict = None if config.tags is None else createTagsDict(config.tags)
spotBid = None
if config.provisioner == 'aws':
logger.info('Using aws provisioner.')
try:
from toil.provisioners.aws.awsProvisioner import AWSProvisioner
except ImportError:
raise RuntimeError('The aws extra must be installed to use this provisioner')
provisioner = AWSProvisioner()
parsedBid = config.nodeType.split(':', 1)
if len(config.nodeType) != len(parsedBid[0]):
# there is a bid
spotBid = float(parsedBid[1])
config.nodeType = parsedBid[0]
else:
assert False
provisioner.launchCluster(instanceType=config.nodeType,
keyName=config.keyPairName,
clusterName=config.clusterName,
workers=config.workers,
spotBid=spotBid,
userTags=tagsDict,
zone=config.zone,
leaderStorage=config.leaderStorage,
nodeStorage=config.nodeStorage,
vpcSubnet=config.vpcSubnet)
