def getCEStatus(self):
""" Method to return information on running and pending jobs.
"""
result = S_OK()
result['SubmittedJobs'] = self.submittedJobs
ssh = SSH(parameters=self.ceParameters)
cmd = ["qstat", "-Q", self.execQueue]
ret = ssh.sshCall(10, cmd)
if not ret['OK']:
self.log.error('Timeout', ret['Message'])
return ret
status = ret['Value'][0]
stdout = ret['Value'][1]
stderr = ret['Value'][2]
self.log.debug("status:", status)
self.log.debug("stdout:", stdout)
self.log.debug("stderr:", stderr)
if status:
self.log.error('Failed qstat execution:', stderr)
return S_ERROR(stderr)
matched = re.search(
self.queue +
"\D+(\d+)\D+(\d+)\W+(\w+)\W+(\w+)\D+(\d+)\D+(\d+)\D+(\d+)\D+(\d+)\D+(\d+)\D+(\d+)\W+(\w+)",
stdout)
if matched.groups < 6:
return S_ERROR("Error retrieving information from qstat:" +
stdout + stderr)
try:
waitingJobs = int(matched.group(5))
runningJobs = int(matched.group(6))
except:
return S_ERROR("Error retrieving information from qstat:" +
stdout + stderr)
result['WaitingJobs'] = waitingJobs
result['RunningJobs'] = runningJobs
self.log.verbose('Waiting Jobs: ', waitingJobs)
self.log.verbose('Running Jobs: ', runningJobs)
return result
def getJobStatus( self, jobIDList ):
""" Get the status information for the given list of jobs
"""
resultDict = {}
ssh = SSH( parameters = self.ceParameters )
for jobList in breakListIntoChunks( jobIDList, 100 ):
jobDict = {}
for job in jobList:
result = pfnparse( job )
if result['OK']:
stamp = result['Value']['FileName'].split('.')[0]
else:
self.log.error( 'Invalid job id', job )
continue
jobDict[stamp] = job
stampList = jobDict.keys()
cmd = [ 'qstat', ' '.join( stampList ) ]
result = ssh.sshCall( 10, cmd )
if not result['OK']:
return result
status = result['Value'][0]
if status == -1:
return S_ERROR( 'Timeout while SSH call' )
elif status != 0:
return S_ERROR( 'Error while SSH call' )
output = result['Value'][1].replace( '\r', '' )
lines = output.split( '\n' )
for job in jobDict:
resultDict[jobDict[job]] = 'Unknown'
for line in lines:
if line.find( job ) != -1:
if line.find( 'Unknown' ) != -1:
resultDict[jobDict[job]] = 'Unknown'
else:
torqueStatus = line.split()[4]
if torqueStatus in ['E', 'C']:
resultDict[jobDict[job]] = 'Done'
elif torqueStatus in ['R']:
resultDict[jobDict[job]] = 'Running'
elif torqueStatus in ['S', 'W', 'Q', 'H', 'T']:
resultDict[jobDict[job]] = 'Waiting'
return S_OK( resultDict )
def getJobStatus(self, jobIDList):
""" Get the status information for the given list of jobs
"""
resultDict = {}
ssh = SSH(parameters=self.ceParameters)
for jobList in breakListIntoChunks(jobIDList, 100):
jobDict = {}
for job in jobList:
result = pfnparse(job)
if result['OK']:
stamp = result['Value']['FileName'].split('.')[0]
else:
self.log.error('Invalid job id', job)
continue
jobDict[stamp] = job
stampList = jobDict.keys()
cmd = ['qstat', ' '.join(stampList)]
result = ssh.sshCall(10, cmd)
if not result['OK']:
return result
status = result['Value'][0]
if status == -1:
return S_ERROR('Timeout while SSH call')
elif status != 0:
return S_ERROR('Error while SSH call')
output = result['Value'][1].replace('\r', '')
lines = output.split('\n')
for job in jobDict:
resultDict[jobDict[job]] = 'Unknown'
for line in lines:
if line.find(job) != -1:
if line.find('Unknown') != -1:
resultDict[jobDict[job]] = 'Unknown'
else:
torqueStatus = line.split()[4]
if torqueStatus in ['E', 'C']:
resultDict[jobDict[job]] = 'Done'
elif torqueStatus in ['R']:
resultDict[jobDict[job]] = 'Running'
elif torqueStatus in ['S', 'W', 'Q', 'H', 'T']:
resultDict[jobDict[job]] = 'Waiting'
return S_OK(resultDict)
def getCEStatus( self ):
""" Method to return information on running and pending jobs.
"""
result = S_OK()
result['SubmittedJobs'] = self.submittedJobs
ssh = SSH( parameters = self.ceParameters )
cmd = ["qstat", "-Q" , self.execQueue ]
ret = ssh.sshCall( 10, cmd )
if not ret['OK']:
self.log.error( 'Timeout', ret['Message'] )
return ret
status = ret['Value'][0]
stdout = ret['Value'][1]
stderr = ret['Value'][2]
self.log.debug( "status:", status )
self.log.debug( "stdout:", stdout )
self.log.debug( "stderr:", stderr )
if status:
self.log.error( 'Failed qstat execution:', stderr )
return S_ERROR( stderr )
matched = re.search( self.queue + "\D+(\d+)\D+(\d+)\W+(\w+)\W+(\w+)\D+(\d+)\D+(\d+)\D+(\d+)\D+(\d+)\D+(\d+)\D+(\d+)\W+(\w+)", stdout )
if matched.groups < 6:
return S_ERROR( "Error retrieving information from qstat:" + stdout + stderr )
try:
waitingJobs = int( matched.group( 5 ) )
runningJobs = int( matched.group( 6 ) )
except:
return S_ERROR( "Error retrieving information from qstat:" + stdout + stderr )
result['WaitingJobs'] = waitingJobs
result['RunningJobs'] = runningJobs
self.log.verbose( 'Waiting Jobs: ', waitingJobs )
self.log.verbose( 'Running Jobs: ', runningJobs )
return result
def getCEStatus(self):
""" Method to return information on running and pending jobs.
"""
result = S_OK()
result['SubmittedJobs'] = self.submittedJobs
ssh = SSH(parameters=self.ceParameters)
cmd = ["bjobs", "-q", self.execQueue, "-a"]
ret = ssh.sshCall(100, cmd)
if not ret['OK']:
self.log.error('Timeout', ret['Message'])
return ret
status = ret['Value'][0]
stdout = ret['Value'][1]
stderr = ret['Value'][2]
self.log.debug("status:", status)
self.log.debug("stdout:", stdout)
self.log.debug("stderr:", stderr)
if status:
self.log.error('Failed bjobs execution:', stderr)
return S_ERROR(stderr)
waitingJobs = 0
runningJobs = 0
lines = stdout.split("\n")
for line in lines:
if line.count("PEND") or line.count('PSUSP'):
waitingJobs += 1
if line.count("RUN") or line.count('USUSP'):
runningJobs += 1
result['WaitingJobs'] = waitingJobs
result['RunningJobs'] = runningJobs
self.log.verbose('Waiting Jobs: ', waitingJobs)
self.log.verbose('Running Jobs: ', runningJobs)
return result
def getCEStatus( self ):
""" Method to return information on running and pending jobs.
"""
result = S_OK()
result['SubmittedJobs'] = self.submittedJobs
ssh = SSH( parameters = self.ceParameters )
cmd = ["bjobs", "-q" , self.execQueue , "-a" ]
ret = ssh.sshCall( 100, cmd )
if not ret['OK']:
self.log.error( 'Timeout', ret['Message'] )
return ret
status = ret['Value'][0]
stdout = ret['Value'][1]
stderr = ret['Value'][2]
self.log.debug( "status:", status )
self.log.debug( "stdout:", stdout )
self.log.debug( "stderr:", stderr )
if status:
self.log.error( 'Failed bjobs execution:', stderr )
return S_ERROR( stderr )
waitingJobs = 0
runningJobs = 0
lines = stdout.split( "\n" )
for line in lines:
if line.count( "PEND" ) or line.count( 'PSUSP' ):
waitingJobs += 1
if line.count( "RUN" ) or line.count( 'USUSP' ):
runningJobs += 1
result['WaitingJobs'] = waitingJobs
result['RunningJobs'] = runningJobs
self.log.verbose( 'Waiting Jobs: ', waitingJobs )
self.log.verbose( 'Running Jobs: ', runningJobs )
return result
def getJobStatus(self, jobIDList):
""" Get the status information for the given list of jobs
"""
resultDict = {}
ssh = SSH(parameters=self.ceParameters)
for jobList in breakListIntoChunks(jobIDList, 100):
jobDict = {}
for job in jobList:
result = pfnparse(job)
jobNumber = result['Value']['FileName']
if jobNumber:
jobDict[jobNumber] = job
jobStamps = jobDict.keys()
cmd = ['bjobs', ' '.join(jobStamps)]
result = ssh.sshCall(100, cmd)
if not result['OK']:
return result
output = result['Value'][1].replace('\r', '')
lines = output.split('\n')
for job in jobDict:
resultDict[jobDict[job]] = 'Unknown'
for line in lines:
if line.find(job) != -1:
if line.find('UNKWN') != -1:
resultDict[jobDict[job]] = 'Unknown'
else:
lsfStatus = line.split()[2]
if lsfStatus in ['DONE', 'EXIT']:
resultDict[jobDict[job]] = 'Done'
elif lsfStatus in ['RUN', 'SSUSP']:
resultDict[jobDict[job]] = 'Running'
elif lsfStatus in ['PEND', 'PSUSP']:
resultDict[jobDict[job]] = 'Waiting'
return S_OK(resultDict)
def getJobStatus( self, jobIDList ):
""" Get the status information for the given list of jobs
"""
resultDict = {}
ssh = SSH( parameters = self.ceParameters )
for jobList in breakListIntoChunks( jobIDList, 100 ):
jobDict = {}
for job in jobList:
result = pfnparse( job )
jobNumber = result['Value']['FileName']
if jobNumber:
jobDict[jobNumber] = job
jobStamps = jobDict.keys()
cmd = [ 'bjobs', ' '.join( jobStamps ) ]
result = ssh.sshCall( 100, cmd )
if not result['OK']:
return result
output = result['Value'][1].replace( '\r', '' )
lines = output.split( '\n' )
for job in jobDict:
resultDict[jobDict[job]] = 'Unknown'
for line in lines:
if line.find( job ) != -1:
if line.find( 'UNKWN' ) != -1:
resultDict[jobDict[job]] = 'Unknown'
else:
lsfStatus = line.split()[2]
if lsfStatus in ['DONE', 'EXIT']:
resultDict[jobDict[job]] = 'Done'
elif lsfStatus in ['RUN', 'SSUSP']:
resultDict[jobDict[job]] = 'Running'
elif lsfStatus in ['PEND', 'PSUSP']:
resultDict[jobDict[job]] = 'Waiting'
return S_OK( resultDict )
def submitJob_old(self, executableFile, proxy, numberOfJobs=1):
""" Method to submit job
"""
self.log.verbose("Executable file path: %s" % executableFile)
if not os.access(executableFile, 5):
os.chmod(executableFile, 0755)
# if no proxy is supplied, the executable can be submitted directly
# otherwise a wrapper script is needed to get the proxy to the execution node
# The wrapper script makes debugging more complicated and thus it is
# recommended to transfer a proxy inside the executable if possible.
if proxy:
self.log.verbose('Setting up proxy for payload')
compressedAndEncodedProxy = base64.encodestring(
bz2.compress(proxy.dumpAllToString()['Value'])).replace(
'\n', '')
compressedAndEncodedExecutable = base64.encodestring(
bz2.compress(open(executableFile, "rb").read(),
9)).replace('\n', '')
wrapperContent = """#!/usr/bin/env python
# Wrapper script for executable and proxy
import os, tempfile, sys, base64, bz2, shutil
try:
workingDirectory = tempfile.mkdtemp( suffix = '_wrapper', prefix= 'TORQUE_' )
os.chdir( workingDirectory )
open( 'proxy', "w" ).write(bz2.decompress( base64.decodestring( "%(compressedAndEncodedProxy)s" ) ) )
open( '%(executable)s', "w" ).write(bz2.decompress( base64.decodestring( "%(compressedAndEncodedExecutable)s" ) ) )
os.chmod('proxy',0600)
os.chmod('%(executable)s',0700)
os.environ["X509_USER_PROXY"]=os.path.join(workingDirectory, 'proxy')
except Exception, x:
print >> sys.stderr, x
sys.exit(-1)
cmd = "./%(executable)s"
print 'Executing: ', cmd
sys.stdout.flush()
os.system( cmd )
shutil.rmtree( workingDirectory )
""" % { 'compressedAndEncodedProxy': compressedAndEncodedProxy, \
'compressedAndEncodedExecutable': compressedAndEncodedExecutable, \
'executable': os.path.basename( executableFile ) }
fd, name = tempfile.mkstemp(suffix='_wrapper.py',
prefix='TORQUE_',
dir=os.getcwd())
wrapper = os.fdopen(fd, 'w')
wrapper.write(wrapperContent)
wrapper.close()
submitFile = name
else: # no proxy
submitFile = executableFile
ssh = SSH(parameters=self.ceParameters)
# Copy the executable
os.chmod(submitFile, stat.S_IRUSR | stat.S_IXUSR)
sFile = os.path.basename(submitFile)
result = ssh.scpCall(
10, submitFile,
'%s/%s' % (self.executableArea, os.path.basename(submitFile)))
# submit submitFile to the batch system
cmd = "i=0; while [ $i -lt %(numberOfJobs)d ]; do qsub -o %(output)s -e %(error)s -q %(queue)s -N DIRACPilot %(submitOptions)s %(executable)s; let i=i+1; done; rm -f %(executable)s" % \
{'numberOfJobs': numberOfJobs, \
'output': self.batchOutput, \
'error': self.batchError, \
'queue': self.queue, \
'submitOptions': self.submitOptions, \
'executable': '%s/%s' % ( self.executableArea, os.path.basename( submitFile ) ) }
self.log.verbose('CE submission command: %s' % (cmd))
result = ssh.sshCall(10, cmd)
if not result['OK'] or result['Value'][0] != 0:
self.log.warn('===========> SSHTorque CE result NOT OK')
self.log.debug(result)
return S_ERROR(result['Value'])
else:
self.log.debug('Torque CE result OK')
batchIDList = result['Value'][1].strip().replace('\r', '').split('\n')
self.submittedJobs += 1
return S_OK(batchIDList)
def submitJob_old( self, executableFile, proxy, numberOfJobs = 1 ):
""" Method to submit job
"""
self.log.verbose( "Executable file path: %s" % executableFile )
if not os.access( executableFile, 5 ):
os.chmod( executableFile, 0755 )
# if no proxy is supplied, the executable can be submitted directly
# otherwise a wrapper script is needed to get the proxy to the execution node
# The wrapper script makes debugging more complicated and thus it is
# recommended to transfer a proxy inside the executable if possible.
if proxy:
self.log.verbose( 'Setting up proxy for payload' )
compressedAndEncodedProxy = base64.encodestring( bz2.compress( proxy.dumpAllToString()['Value'] ) ).replace( '\n', '' )
compressedAndEncodedExecutable = base64.encodestring( bz2.compress( open( executableFile, "rb" ).read(), 9 ) ).replace( '\n', '' )
wrapperContent = """#!/usr/bin/env python
# Wrapper script for executable and proxy
import os, tempfile, sys, base64, bz2, shutil
try:
workingDirectory = tempfile.mkdtemp( suffix = '_wrapper', prefix= 'TORQUE_' )
os.chdir( workingDirectory )
open( 'proxy', "w" ).write(bz2.decompress( base64.decodestring( "%(compressedAndEncodedProxy)s" ) ) )
open( '%(executable)s', "w" ).write(bz2.decompress( base64.decodestring( "%(compressedAndEncodedExecutable)s" ) ) )
os.chmod('proxy',0600)
os.chmod('%(executable)s',0700)
os.environ["X509_USER_PROXY"]=os.path.join(workingDirectory, 'proxy')
except Exception, x:
print >> sys.stderr, x
sys.exit(-1)
cmd = "./%(executable)s"
print 'Executing: ', cmd
sys.stdout.flush()
os.system( cmd )
shutil.rmtree( workingDirectory )
""" % { 'compressedAndEncodedProxy': compressedAndEncodedProxy, \
'compressedAndEncodedExecutable': compressedAndEncodedExecutable, \
'executable': os.path.basename( executableFile ) }
fd, name = tempfile.mkstemp( suffix = '_wrapper.py', prefix = 'TORQUE_', dir = os.getcwd() )
wrapper = os.fdopen( fd, 'w' )
wrapper.write( wrapperContent )
wrapper.close()
submitFile = name
else: # no proxy
submitFile = executableFile
ssh = SSH( parameters = self.ceParameters )
# Copy the executable
os.chmod( submitFile, stat.S_IRUSR | stat.S_IXUSR )
sFile = os.path.basename( submitFile )
result = ssh.scpCall( 10, submitFile, '%s/%s' % ( self.executableArea, os.path.basename( submitFile ) ) )
# submit submitFile to the batch system
cmd = "i=0; while [ $i -lt %(numberOfJobs)d ]; do qsub -o %(output)s -e %(error)s -q %(queue)s -N DIRACPilot %(submitOptions)s %(executable)s; let i=i+1; done; rm -f %(executable)s" % \
{'numberOfJobs': numberOfJobs, \
'output': self.batchOutput, \
'error': self.batchError, \
'queue': self.queue, \
'submitOptions': self.submitOptions, \
'executable': '%s/%s' % ( self.executableArea, os.path.basename( submitFile ) ) }
self.log.verbose( 'CE submission command: %s' % ( cmd ) )
result = ssh.sshCall( 10, cmd )
if not result['OK'] or result['Value'][0] != 0:
self.log.warn( '===========> SSHTorque CE result NOT OK' )
self.log.debug( result )
return S_ERROR( result['Value'] )
else:
self.log.debug( 'Torque CE result OK' )
batchIDList = result['Value'][1].strip().replace( '\r', '' ).split( '\n' )
self.submittedJobs += 1
return S_OK( batchIDList )
