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########################################################################################
# #
# Author: Bertrand Neron, #
# Organization:'Biological Software and Databases' Group, Institut Pasteur, Paris. #
# Distributed under GPLv2 Licence. Please refer to the COPYING.LIB document. #
# #
########################################################################################
"""
Classes executing the command and managing the results
"""
import os
import imp
from logging import getLogger, shutdown as logging_shutdown
_log = getLogger(__name__)
from Mobyle.MobyleLogger import MLogger
from Mobyle.Status import Status
from Mobyle.Admin import Admin
from Mobyle.Execution.ExecutionSystem import ExecutionSystem
from Mobyle.MobyleError import MobyleError
__extra_epydoc_fields__ = [('call', 'Called by','Called by')]
class DRMAA(ExecutionSystem):
"""
Run the commandline with batch system DRMAA bindings
"""
def __init__( self, drmaa_config ):
super( DRMAA , self ).__init__( drmaa_config )
self.drmaa_library_path = drmaa_config.drmaa_library_path
os.environ[ 'DRMAA_LIBRARY_PATH' ] = self.drmaa_library_path
fp , pathname , description = imp.find_module("drmaa")
self.drmaa = imp.load_module( "drmaa" , fp , pathname , description )
self.contactString = drmaa_config.contactString
def _drmaaStatus2mobyleStatus( self , drmaaStatus ):
if drmaaStatus == self.drmaa.JobState.RUNNING:
return Status( 3 ) #running
elif drmaaStatus == self.drmaa.JobState.UNDETERMINED:
return Status( -1 ) #unknown
elif drmaaStatus == self.drmaa.JobState.QUEUED_ACTIVE:
return Status( 2 ) #pending
elif drmaaStatus == self.drmaa.JobState.DONE:
return Status( 4 ) #finished
elif drmaaStatus == self.drmaa.JobState.FAILED:
return Status( 5 ) # error
elif drmaaStatus == self.drmaa.JobState.SYSTEM_ON_HOLD:
return Status( 7 ) # hold
elif drmaaStatus == self.drmaa.JobState.USER_ON_HOLD:
return Status( 7 ) # hold
elif drmaaStatus == self.drmaa.JobState.USER_SYSTEM_ON_HOLD:
return Status( 7 ) # hold
elif drmaaStatus == self.drmaa.JobState.SYSTEM_SUSPENDED:
return Status( 7 ) # hold
elif drmaaStatus == self.drmaa.JobState.USER_SUSPENDED:
return Status( 7 ) # hold
elif drmaaStatus == self.drmaa.JobState.USER_SYSTEM_SUSPENDED:
return Status( 7 ) # hold
else:
return Status( -1 )
def _run( self , commandLine , dirPath , serviceName , jobKey , jobState , queue , xmlEnv ):
"""
Run the commandLine
redirect the standard error and output on service.name.out and service.name.err, then restore the sys.stderr and sys.stdout
@param execution_config: a configuration object for this execution system
@type execution_config: a L{DRMAAConfig} instance
@return: the L{Status} of this job and a message
@rtype: Status
"""
if (os.getcwd() != os.path.abspath(dirPath) ):
msg = "the process is not in the working directory"
self._logError( dirPath , serviceName , jobKey ,
userMsg = "Mobyle internal server error" ,
logMsg = msg )
raise MobyleError , msg
else:
fout = open( serviceName + ".out" , 'w' )
ferr = open( serviceName + ".err" , 'w' )
try:
drmaaSession = self.drmaa.Session( contactString = self.contactString )
try:
drmaaSession.initialize()
except self.drmaa.errors.AlreadyActiveSessionException:
pass
except Exception, err:
self._logError( dirPath , serviceName , jobKey ,
userMsg = "Mobyle internal server error" ,
logMsg = None )
import sys
_log.critical( "error during drmaa intitialization for job %s/%s: %s (call by %s pid= %d)" %(serviceName, jobKey , err, sys.argv[0] , os.getpid() ) , exc_info= True )
jt = drmaaSession.createJobTemplate()
jt.workingDirectory = dirPath
jt.jobName = jobKey
jt.outputPath = ":" + os.path.join( dirPath , fout.name )
jt.errorPath = ":" + os.path.join( dirPath , ferr.name )
jt.joinFiles = False
jt.jobEnvironment = xmlEnv
jt.remoteCommand = "sh"
jt.args = [ os.path.join( dirPath , ".command" ) ]
nativeSpecification = ''
if self.execution_config.nativeSpecification:
nativeSpecification = self.execution_config.nativeSpecification
if queue:
nativeSpecification = "%s -q %s" % ( nativeSpecification , queue )
jt.nativeSpecification = nativeSpecification
jt.blockEmail = True
drmJobid = drmaaSession.runJob( jt )
except self.drmaa.errors , err :
_log.error( "cannot exit from drmaa properly try to deleting JobTemplate: " + str( err ) )
try:
drmaaSession.deleteJobTemplate( jt )
drmaaSession.exit()
except Exception , err :
_log.error( "cannot exit from drmaa properly : " + str( err ) )
msg= "System execution failed: " +str( err )
self._logError( dirPath , serviceName , jobKey ,
userMsg = "Mobyle internal server error" ,
logMsg = None )
_log.critical( "%s/%s : %s" %(serviceName, jobKey, msg ), exc_info= True )
raise MobyleError , msg
except Exception , err :
msg= "System execution failed: " +str( err )
_log.critical("%s/%s : %s" %(serviceName, jobKey, msg ), exc_info= True )
raise MobyleError( "Internal Server Error")
adm = Admin( dirPath )
adm.setExecutionAlias( self.execution_config_alias )
adm.setNumber( drmJobid )
adm.commit()
linkName = ( "%s/%s.%s" %( self._cfg.admindir() ,
serviceName ,
jobKey
)
)
try:
os.symlink(
os.path.join( dirPath , '.admin') ,
linkName
)
except OSError , err:
try:
drmaaSession.deleteJobTemplate( jt )
drmaaSession.exit()
except Exception , err :
_log.error( "cannot exit from drmaa properly : " + str( err ) )
msg = "can't create symbolic link %s in ADMINDIR: %s" %( linkName , err )
self._logError( dirPath , serviceName , jobKey ,
userMsg = "Mobyle internal server error" ,
logMsg = None )
_log.critical( "%s/%s : %s" %(serviceName, jobKey, msg ), exc_info= True )
raise MobyleError , msg
logging_shutdown() #close all loggers
#JobInfo =( jobId , hasExited , hasSignal , terminatedSignal, hasCoreDump, wasAborted, exitStatus, resourceUsage)
# 0 1 2 3 4 5 6 7
try:
jobInfos = drmaaSession.wait( drmJobid , self.drmaa.Session.TIMEOUT_WAIT_FOREVER )
except Exception , err :
MLogger(child = True )
self._logError( dirPath , serviceName , jobKey ,
userMsg = "Mobyle internal server error" ,
logMsg = None )
_log.critical( "%s/%s : %s" %( serviceName ,
jobKey ,
"cannot wait the completion of job : %s" % err
)
)
finally:
MLogger(child = True )
try:
drmaaSession.deleteJobTemplate( jt )
drmaaSession.exit()
except Exception , err :
MLogger(child = True )
_log.error( "cannot exit from drmaa properly : " + str( err ) )
try:
os.unlink( linkName )
except Exception , err:
msg = "cannot remove symbolic link %s in ADMINDIR: %s" %( linkName , err )
self._logError( dirPath , serviceName , jobKey ,
userMsg = "Mobyle internal server error" ,
logMsg = None )
_log.critical( "%s/%s : %s" %(serviceName, jobKey, msg ), exc_info= True )
try:
fout.close()
except Exception , err:
msg = "cannot close file: %s" %( fout.name , err )
self._logError( dirPath , serviceName , jobKey ,
userMsg = "Mobyle internal server error" ,
logMsg = None )
_log.critical( "%s/%s : %s" %(serviceName, jobKey, msg ), exc_info= True )
try:
ferr.close()
except Exception , err:
msg = "cannot close file: %s" %( ferr.name , err )
self._logError( dirPath , serviceName , jobKey ,
userMsg = "Mobyle internal server error" ,
logMsg = None )
_log.critical( "%s/%s : %s" %(serviceName, jobKey, msg ), exc_info= True )
status = self.status_manager.getStatus( dirPath )
if not status.isEnded():
if jobInfos[ 5 ] :#wasAborted
status = Status( code = 6 , message = "Your job has been cancelled" ) #killed
else:
if jobInfos[ 1 ]:#hasExited
if jobInfos[ 6 ] == 0:#exitStatus
status = Status( code = 4 ) #finished
elif jobInfos[ 6 ] < 0 or jobInfos[ 6 ] > 128:
#all the signals that we don't know where they come from
status = Status( code = 5 , message = "Your job execution failed ( %s )" %jobInfos[ 6 ] )
else:
status = Status( code = 4 , message = "Your job finished with an unusual status code ( %d ), check your results carefully." % jobInfos[ 6 ] )
else:
status = Status( code = 6 , message = "Your job execution failed ( %d )" %jobInfos[ 6 ] )
return status
def getStatus( self , key ):
"""
@param execution_config: a configuration object for this execution system
@type execution_config: a L{DRMAAConfig} instance
@param key: the value associate to the key "NUMBER" in Admin object (and .admin file )
@type key: string
@return: the status of the job corresponding to the key
@rtype: Status instance
@call: by L{Utils.getStatus}
"""
try:
s = self.drmaa.Session( contactString = self.contactString )
except Exception , err:
_log.error( "getStatus(%s) cannot open drmma session : %s " %( key , err ) )
return Status( -1 ) #unknown
try:
s.initialize()
except self.drmaa.errors.AlreadyActiveSessionException:
pass
except Exception, err:
s.exit()
import sys
_log.critical( "error during drmaa intitialization for getStatus job %s: %s (call by %s pid=%d)" %(key , err,sys.argv[0], os.getpid()) , exc_info= True )
return Status( -1 )
try:
drmaaStatus = s.jobStatus( key )
except :
s.exit()
return Status( -1 ) #unknown
s.exit()
return self._drmaaStatus2mobyleStatus( drmaaStatus )
def kill( self , key ):
"""
kill a job
@param execution_config: a configuration object for this execution system
@type execution_config: a L{DRMAAConfig} instance
@param key : the value associate to the key "NUMBER" in Admin object (and .admin file )
@type key: string
@raise MobyleError: if can't kill the job
@call: by L{Utils.Mkill}
"""
try:
s = self.drmaa.Session( contactString = self.contactString )
except Exception , err:
_log.error( "kill( %s ) cannot open drmma session : %s " %( key , err ) )
return
try:
s.initialize()
except self.drmaa.errors.AlreadyActiveSessionException:
pass
except Exception, err:
import sys
_log.critical( "error during drmaa intitialization for kill job %s: %s (call by %s)" %(key , err,sys.argv[0]) , exc_info= True )
return
try:
s.control( key , self.drmaa.JobControlAction.TERMINATE )
except Exception , err :
msg = "error when trying to kill job %s : %s" %( key , err )
_log.error( msg )
raise MobyleError( msg )
finally:
s.exit()
return
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