def f_blockOnScheduledJobs(**kwargs):
'''
A simple wrapper around a stage.kwBlockOnSchedule(...)
call.
'''
str_blockUntil = "0"
str_blockProcess = ""
timepoll = 10
for key, val in kwargs.iteritems():
if key == 'obj': stage = val
if key == 'blockCondition': str_blockCondition = val
if key == 'blockProcess': str_blockProcess = val
if key == 'blockUntil': str_blockUntil = val
if key == 'timepoll': timepoll = val
str_blockMsg = '''\n
Postconditions are still running: multiple '%s' instances
detected in cluster %s (%s). Blocking until all scheduled jobs are
completed. Block interval = %s seconds.
\n''' % (str_blockProcess,
stage.shell().clusterName(),
stage.shell().clusterType(),
timepoll)
str_loopMsg = 'Waiting for scheduled jobs to complete... ' +\
'(hit <ctrl>-c to kill this script). '
stage.kwBlockOnScheduler( loopMsg = str_loopMsg,
blockMsg = str_blockMsg,
blockUntil = str_blockUntil,
blockProcess = str_blockProcess,
timeout = timepoll)
return True
def f_stage0callback(**kwargs):
for key, val in kwargs.iteritems():
if key == 'jobs': jobs = val
if key == 'obj': stage = val
if key == 'pipe': pipeline = val
# Create shell for scheduling/executing on the remote HPC
pipeline.stageShell_createRemoteInstance(args.cluster, stage=stage)
for job in range(0, int(args.jobs)):
log = stage.log()
log('Processing job: %d...\n' % job)
str_cmd = args.cmd
shell = stage.shell()
shell.echo(True)
shell(
str_cmd, waitForChild=shell.waitForChild(),
stdoutflush=True, stderrflush=True
)
if shell.exitCode():
error.fatal(hpc, 'stageExec', shell.stderr())
os.chdir(pipeline.startDir())
return True
def stageShell_createRemoteInstance(self, astr_remoteHPC, **kwargs):
'''
Returns a crun object in the passed stage object that
functions as a shell on the remote HPC.
'''
for key, val in kwargs.iteritems():
if key == 'stage': stage = val
for case in misc.switch(astr_remoteHPC):
if case('PICES'):
stage.shell(crun.crun_hpc_mosix(
remoteUser="******",
remoteHost="rc-majesty.tch.harvard.edu")
)
stage.shell().emailUser('*****@*****.**')
b_jobDetach = True
b_disassocaite = True
b_waitForChild = False
break
if case('launchpad'):
stage.shell(crun.crun_hpc_launchpad(
remoteUser="******",
remoteHost="fnndsc:7774")
)
b_jobDetach = False
b_disassocaite = False
b_waitForChild = True
break
if case('erisone'):
stage.shell(crun.crun_hpc_lsf(
remoteUser="******",
remoteHost="fnndsc:7773")
)
stage.shell().scheduleHostOnly(
"cmu058 cmu059 cmu061 cmu066 cmu067 cmu071 cmu073 cmu075 cmu077 cmu079 cmu081 cmu087 cmu090 cmu093 cmu094 cmu095 cmu096 cmu102 cmu106 cmu107 cmu108 cmu109 cmu111 cmu112 cmu114 cmu121 cmu123 cmu126 cmu149 cmu154 cmu156 cmu157 "
)
b_jobDetach = False
b_disassocaite = False
b_waitForChild = True
break
if case():
error.fatal(self, 'noClusterSpec')
shell = stage.shell()
shell.emailWhenDone(True)
if args.b_debug:
shell.echo(True)
shell.echoStdOut(True)
else:
shell.echo(False)
shell.echoStdOut(False)
shell.detach(b_jobDetach)
shell.disassociate(b_disassocaite)
shell.waitForChild(b_waitForChild)
