def get_run_options(workflowClassName):
from optparse import OptionGroup, SUPPRESS_HELP
from configBuildTimeInfo import workflowVersion
from configureUtil import EpilogOptionParser
from estimateHardware import EstException, getNodeHyperthreadCoreCount, getNodeMemMb
sgeDefaultCores = workflowClassName.runModeDefaultCores('sge')
epilog = """Note this script can be re-run to continue the workflow run in case of interruption.
Also note that dryRun option has limited utility when task definition depends on upstream task
results -- in this case the dry run will not cover the full 'live' run task set."""
parser = EpilogOptionParser(description="Version: %s" % (workflowVersion),
epilog=epilog,
version=workflowVersion)
parser.add_option("-m",
"--mode",
type="string",
dest="mode",
help="select run mode (local|sge)")
parser.add_option("-q",
"--queue",
type="string",
dest="queue",
help="specify scheduler queue name")
parser.add_option(
"-j",
"--jobs",
type="string",
dest="jobs",
help=
"number of jobs, must be an integer or 'unlimited' (default: Estimate total cores on this node for local mode, %s for sge mode)"
% (sgeDefaultCores))
parser.add_option(
"-g",
"--memGb",
type="string",
dest="memGb",
help=
"gigabytes of memory available to run workflow -- only meaningful in local mode, must be an integer (default: Estimate the total memory for this node for local mode, 'unlimited' for sge mode)"
)
parser.add_option(
"-d",
"--dryRun",
dest="isDryRun",
action="store_true",
default=False,
help="dryRun workflow code without actually running command-tasks")
parser.add_option(
"--quiet",
dest="isQuiet",
action="store_true",
default=False,
help=
"Don't write any log output to stderr (but still write to workspace/pyflow.data/logs/pyflow_log.txt)"
)
def isLocalSmtp():
import smtplib
try:
smtplib.SMTP('localhost')
except:
return False
return True
isEmail = isLocalSmtp()
emailHelp = SUPPRESS_HELP
if isEmail:
emailHelp = "send email notification of job completion status to this address (may be provided multiple times for more than one email address)"
parser.add_option("-e",
"--mailTo",
type="string",
dest="mailTo",
action="append",
help=emailHelp)
debug_group = OptionGroup(parser, "development debug options")
debug_group.add_option(
"--rescore",
dest="isRescore",
action="store_true",
default=False,
help=
"Reset task list to re-run hypothesis generation and scoring without resetting graph generation."
)
parser.add_option_group(debug_group)
ext_group = OptionGroup(
parser,
"extended portability options (should not be needed by most users)")
ext_group.add_option(
"--maxTaskRuntime",
type="string",
metavar="hh:mm:ss",
help=
"Specify scheduler max runtime per task, argument is provided to the 'h_rt' resource limit if using SGE (no default)"
)
parser.add_option_group(ext_group)
(options, args) = parser.parse_args()
if not isEmail: options.mailTo = None
if len(args):
parser.print_help()
sys.exit(2)
if options.mode is None:
parser.print_help()
sys.exit(2)
elif options.mode not in ["local", "sge"]:
parser.error("Invalid mode. Available modes are: local, sge")
if options.jobs is None:
if options.mode == "sge":
options.jobs = sgeDefaultCores
else:
try:
options.jobs = getNodeHyperthreadCoreCount()
except EstException:
parser.error(
"Failed to estimate cores on this node. Please provide job count argument (-j)."
)
if options.jobs != "unlimited":
options.jobs = int(options.jobs)
if options.jobs <= 0:
parser.error(
"Jobs must be 'unlimited' or an integer greater than 1")
# note that the user sees gigs, but we set megs
if options.memGb is None:
if options.mode == "sge":
options.memMb = "unlimited"
else:
try:
options.memMb = getNodeMemMb()
except EstException:
parser.error(
"Failed to estimate available memory on this node. Please provide available gigabyte argument (-g)."
)
elif options.memGb != "unlimited":
options.memGb = int(options.memGb)
if options.memGb <= 0:
parser.error(
"memGb must be 'unlimited' or an integer greater than 1")
options.memMb = 1024 * options.memGb
else:
options.memMb = options.memGb
options.schedulerArgList = []
if options.queue is not None:
options.schedulerArgList.extend(["-q", options.queue])
if options.maxTaskRuntime is not None:
options.schedulerArgList.extend(
["-l", "h_rt=" + options.maxTaskRuntime])
options.resetTasks = []
if options.isRescore:
options.resetTasks.append("makeHyGenDir")
return options
def get_run_options(workflowClassName) :
from configureUtil import EpilogOptionParser
from estimateHardware import EstException, getNodeHyperthreadCoreCount, getNodeMemMb
sgeDefaultCores=workflowClassName.runModeDefaultCores('sge')
epilog="""Note this script can be re-run to continue the workflow run in case of interruption.
Also note that dryRun option has limited utility when task definition depends on upstream task
results -- in this case the dry run will not cover the full 'live' run task set."""
parser = EpilogOptionParser(epilog=epilog)
parser.add_option("-m", "--mode", type="string",dest="mode",
help="select run mode (local|sge)")
parser.add_option("-q", "--queue", type="string",dest="queue",
help="specify sge queue name")
parser.add_option("-j", "--jobs", type="string",dest="jobs",
help="number of jobs, must be an integer or 'unlimited' (default: Estimate total cores on this node for local mode, %s for sge mode)" % (sgeDefaultCores))
parser.add_option("-g","--memGb", type="string",dest="memGb",
help="gigabytes of memory available to run workflow -- only meaningful in local mode, must be an integer (default: Estimate the total memory for this node for local mode, 'unlimited' for sge mode)")
parser.add_option("-e","--mailTo", type="string",dest="mailTo",action="append",
help="send email notification of job completion status to this address (may be provided multiple times for more than one email address)")
parser.add_option("-d","--dryRun", dest="isDryRun",action="store_true",default=False,
help="dryRun workflow code without actually running command-tasks")
(options,args) = parser.parse_args()
if len(args) :
parser.print_help()
sys.exit(2)
if options.mode is None :
parser.print_help()
sys.exit(2)
elif options.mode not in ["local","sge"] :
parser.error("Invalid mode. Available modes are: local, sge")
if options.jobs is None :
if options.mode == "sge" :
options.jobs = sgeDefaultCores
else :
try :
options.jobs = getNodeHyperthreadCoreCount()
except EstException:
parser.error("Failed to estimate cores on this node. Please provide job count argument (-j).")
if options.jobs != "unlimited" :
options.jobs=int(options.jobs)
if options.jobs <= 0 :
parser.error("Jobs must be 'unlimited' or an integer greater than 1")
# note that the user sees gigs, but we set megs
if options.memGb is None :
if options.mode == "sge" :
options.memMb = "unlimited"
else :
try :
options.memMb = getNodeMemMb()
except EstException:
parser.error("Failed to estimate available memory on this node. Please provide available gigabyte argument (-g).")
elif options.memGb != "unlimited" :
options.memGb=int(options.memGb)
if options.memGb <= 0 :
parser.error("memGb must be 'unlimited' or an integer greater than 1")
options.memMb = 1024*options.memGb
else :
options.memMb = options.memGb
options.schedulerArgList=[]
if options.queue is not None :
options.schedulerArgList=["-q",options.queue]
return options