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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
from subprocess import Popen, PIPE
from logging import getLogger, shutdown as logging_shutdown
_log = getLogger(__name__)
from Mobyle.MobyleLogger import MLogger
from Mobyle.Admin import Admin
from Mobyle.Execution.ExecutionSystem import ExecutionSystem
from Mobyle.MobyleError import MobyleError
from Mobyle.Status import Status
__extra_epydoc_fields__ = [('call', 'Called by','Called by')]
class SGE (ExecutionSystem):
"""
Run the commandline with Sun GridEngine commands
"""
def __init__( self, sge_config ):
super( SGE , self ).__init__( sge_config )
arch_path= os.path.join( sge_config.root , 'util' , 'arch' )
try:
arch_pipe = Popen(arch_path ,
shell = False ,
stdout = PIPE ,
stdin = None ,
stderr = None ,
close_fds = True )
arch_pipe.wait()
arch_rc = arch_pipe.returncode
except OSError , err:
#this error is log by calling method because I can't access to jobKey , adm status ... from static method
msg = "SGE: I can't determined the system arch:"+str(err)
raise MobyleError( msg )
if arch_rc != 0 :
msg = "I can't determined the system arch (return code = " + str( arch_rc ) + " )"
raise MobyleError( msg )
arch = ''.join( arch_pipe.stdout.readlines() ).strip()
self.sge_prefix = os.path.join( sge_config.root , 'bin' , arch )
self.sge_env = {'SGE_CELL': sge_config.cell , 'SGE_ROOT': sge_config.root }
def _run( self , commandLine , dirPath , serviceName , jobKey , jobState , queue , xmlEnv ):
"""
@param execution_config: the configuration of the Execution
@type execution_config: ExecutionConfig instance
@param commandLine: the command to be executed
@type commandLine: String
@param dirPath: the absolute path to directory where the job will be executed (normaly we are already in)
@type dirPath: String
@param serviceName: the name of the service
@type serviceName: string
@param jobState:
@type jobState: a L{JobState} instance
"""
options = { '-cwd': '' , #set the working dir to current dir
'-now': 'n' , #the job is not executed immediately
'-N' : jobKey , #the id of the job
'-V' : '' #job inherits of the whole environment
}
if queue:
options[ '-q' ] = queue
sge_opts = ''
for opt in options.keys():
sge_opts += opt + ' ' + options[opt]+' '
sge_cmd = os.path.join( self.sge_prefix , 'qrsh' ) + ' ' + sge_opts
cmd = sge_cmd + " " + commandLine
try:
fout = open( serviceName + ".out" , 'w' )
ferr = open( serviceName + ".err" , 'w' )
except IOError , err:
msg= "SGE: can't open file for standard job output: "+ str(err)
self._logError( dirPath , serviceName , jobKey ,
admMsg = msg ,
userMsg = "Mobyle internal server error" ,
logMsg = msg )
raise MobyleError , msg
xmlEnv.update( self.sge_env )
try:
pipe = Popen( cmd ,
shell = True ,
stdout = fout ,
stdin = None ,
stderr = ferr ,
close_fds = True ,
env = xmlEnv
)
except OSError, err:
msg= "SGE execution failed: "+ str(err)
self._logError( dirPath , serviceName , jobKey ,
admMsg = msg ,
userMsg = "Mobyle internal server error" ,
logMsg = None )
_log.critical( "%s/%s : %s" %( serviceName ,
jobKey ,
msg
) ,
exc_info = True
)
raise MobyleError , msg
adm = Admin( dirPath )
adm.setExecutionAlias( self.execution_config_alias )
adm.setNumber( jobKey )
adm.commit()
linkName = ( "%s/%s.%s" %( self._cfg.admindir() ,
serviceName ,
jobKey
)
)
try:
os.symlink(
os.path.join( dirPath , '.admin') ,
linkName
)
except OSError , err:
msg = "can't create symbolic link %s in ADMINDIR: %s" %( linkName , err )
self._logError( dirPath , serviceName , jobKey ,
admMsg = msg ,
userMsg = "Mobyle internal server error" ,
logMsg = None )
_log.critical( "%s/%s : %s" %( serviceName ,
jobKey ,
msg
)
)
raise MobyleError , msg
logging_shutdown() #close all loggers
pipe.wait()
MLogger(child = True )
try:
os.unlink( linkName )
except OSError , err:
msg = "can't remove symbolic link %s in ADMINDIR: %s" %( linkName , err )
self._logError( dirPath , serviceName , jobKey ,
admMsg = msg ,
userMsg = "Mobyle internal server error" ,
logMsg = None )
_log.critical( "%s/%s : %s" %( serviceName ,
jobKey ,
msg
)
)
raise MobyleError , msg
fout.close()
ferr.close()
#self._returncode = pipe.returncode
oldStatus = self.status_manager.getStatus( dirPath )
if oldStatus.isEnded():
return oldStatus
else:
if pipe.returncode == 0 :# finished
status = Status( code = 4 ) #finished
elif pipe.returncode in ( 137 , 143 , 153 ): #killed
## 137 = 9 ( SIGKILL ) + 128 ( python add 128 )
## 143 = 15 ( SIGTERM )
## 153 = 25 ( SIGXFSZ ) + 128 (file size exceeded )
## be careful if a job exit with a 137 or 153 exit status it will be labelled as killed
status = Status( code = 6 , message = "Your job has been cancelled" )
elif pipe.returncode > 128 :
status = Status( code = 6 , message = "Your job execution failed ( %s )" %pipe.returncode )
## if return code > 128 it's a signal
## the 9 , 15 25 signal are send by administrator
## the other are self aborting signal see signal(7)
else:
status = Status( code = 4 , message = "Your job finished with an unusual status code ( %s ), check your results carefully." % pipe.returncode )
return status
def getStatus( self ,jobNum ):
"""
@param sge_config: the configuration of this Execution engine
@type sge_config: a L{SGEConfig} instance
@param jobNum:
@type jobNum:
@return: the status of job with number jobNum
@rtype: a Mobyle.Status.Status instance
@todo: for best performance, restrict the sge querying to one queue
"""
sge_cmd = [ os.path.join( self.sge_prefix , 'qstat' ) , '-r' ]
try:
pipe = Popen( sge_cmd,
executable = sge_cmd[0] ,
shell = False ,
stdout = PIPE ,
stdin = None ,
stderr= None ,
close_fds = True ,
env= self.sge_env
)
except OSError , err:
raise MobyleError , "can't querying sge : %s :%s "%( sge_cmd , err )
sge2mobyleStatus = { 'r' : 3 , # running
't' : 3 ,
'R' : 3 ,
's' : 7 , #hold
'S' : 7 ,
'T' : 7 ,
'h' : 7 ,
'w' : 2 , #pending
'd' : 6 , #killed
'E' : 5 , #error
}
for job in pipe.stdout :
job_sge_status = job.split()
try:
status = job_sge_status[ 4 ][ -1 ]
continue
except ( ValueError , IndexError ):
pass #it's not the fisrt line
try:
if not ( jobNum == job_sge_status[2] and 'Full' == job_sge_status[0] ):
continue #it's not the right jobNum
except IndexError :
continue #it's not the 2nde line
pipe.stdout.close()
pipe.wait()
if pipe.returncode == 0 :
try:
return Status( code = sge2mobyleStatus[ status ] )
except MobyleError , err :
raise MobyleError , "unexpected sge status: " +str( status )
else:
raise MobyleError , "cannot get status " + str( pipe.returncode )
return Status( code = -1 ) #unknown
def kill( self, job_number ):
"""
@todo: kill the Job
"""
sge_cmd = "%s %s 1>&2" %( os.path.join( self.sge_prefix , 'qdel' ) , job_number )
os.environ.update( self.sge_env )
os.system( sge_cmd )
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