def kill(self, obj):
"""
Kill the job instance
"""
if type(obj) == Job:
jobList = [obj]
elif type(obj) == Task:
jobList = obj.jobs
else:
raise SchedulerError('wrong argument type', str(type(obj)))
jobsFile, arcId2job = self.createJobsFile(jobList, "Will kill")
cmd = self.pre_arcCmd + "arckill -i " + jobsFile.name
output, stat = self.ExecuteCommand(cmd)
if stat != 0:
raise SchedulerError('arckill returned %i' % stat, output, cmd)
for line in output.split('\n'):
# If a job URL ("arcId") occurs on a line of output, it tends
# to be en error message:
errorMatch = re.match(".*: *(gsiftp://[a-zA-Z0-9.-]+\S*/\w*)",
line)
if errorMatch:
arcId = errorMatch.group(1)
job = arcId2job[arcId]
job.runningJob.errors.append("Killing job %s failed: %s" %
(job['name'], line))
def getOutput(self, obj, outdir=''):
"""
Retrieve (move) job output from cache directory to outdir
User files from CondorG appear asynchronously in the cache directory
"""
if type(obj) == RunningJob: # The object passed is a RunningJob
raise SchedulerError(
'Operation not possible',
'CondorG cannot retrieve files when passed RunningJob')
elif type(obj) == Job: # The object passed is a Job
# check for the RunningJob integrity
if not self.valid(obj.runningJob):
raise SchedulerError('invalid object', str(obj.runningJob))
# retrieve output
self.getCondorOutput(obj, outdir)
# the object passed is a Task
elif type(obj) == Task:
if outdir == '':
outdir = obj['outputDirectory']
for job in obj.jobs:
if self.valid(job.runningJob):
self.getCondorOutput(job, outdir)
# unknown object type
else:
raise SchedulerError('wrong argument type', str(type(obj)))
def kill(self, obj):
"""
kill job
"""
jobsToKill = []
# the object passed is a job
if type(obj) == Job and self.valid(obj.runningJob):
# check for the RunningJob integrity
schedIdList = str(obj.runningJob['schedulerId']).strip()
command = "glite-wms-job-cancel --json --noint " + schedIdList
out, ret = self.ExecuteCommand(self.proxyString + command)
if ret != 0:
raise SchedulerError('error executing glite-wms-job-cancel',
out)
elif ret == 0:
try:
## try to see if we got a real json
result = eval(out)
except SyntaxError, ex:
## not possible to evaluate json - try as string
if out.find("result: success") == -1:
raise SchedulerError('error', out)
else:
## if was a json...
if 'result' in result:
if not result['result'] == "success":
raise SchedulerError('error', result)
else:
raise SchedulerError('Missing result', result)
def checkUserProxy(self):
"""
Retrieve the user proxy for the task
If the proxy is valid pass, otherwise raise an axception
"""
if self.validProxy is not None:
return self.validProxy
command = 'voms-proxy-info'
if self.cert != '':
command += ' --file ' + self.cert
output, ret = self.ExecuteCommand(command)
try:
output = output.split("timeleft :")[1].strip()
except IndexError:
self.validProxy = False
raise SchedulerError("Missing Proxy", output.strip())
if output == "0:00:00":
self.validProxy = False
raise SchedulerError("Proxy Expired", output.strip())
self.validProxy = True
return self.validProxy
def purgeService(self, obj):
"""
purge the service used by the scheduler from job files
not available for every scheduler
"""
# check the proxy
self.schedObj.checkUserProxy()
# perform action
self.schedObj.purgeService(obj)
timestamp = int(time.time())
# the object passed is a runningJob
if type(obj) == RunningJob and self.schedObj.valid(obj):
obj['status'] = 'E'
obj['closed'] = 'Y'
obj['getOutputTime'] = timestamp
obj['statusScheduler'] = "Cleared"
# the object passed is a job
elif type(obj) == Job and self.schedObj.valid(obj.runningJob):
obj.runningJob['status'] = 'E'
obj.runningJob['closed'] = 'Y'
obj.runningJob['getOutputTime'] = timestamp
obj.runningJob['statusScheduler'] = "Cleared"
# the object passed is a Task
elif type(obj) == Task:
# error messages collector
errors = ''
# update objects
for job in obj.jobs:
# skip jobs not requested for action
if not self.schedObj.valid(job.runningJob):
continue
# evaluate errors: if not, update
if job.runningJob.isError():
errors += str(job.runningJob.errors)
else:
job.runningJob['status'] = 'E'
job.runningJob['closed'] = 'Y'
job.runningJob['getOutputTime'] = timestamp
job.runningJob['statusScheduler'] = "Cleared"
# handle errors
if errors != '':
raise SchedulerError('interaction failed for some jobs', \
errors )
# unknown object type
else:
raise SchedulerError('wrong argument type', str(type(obj)))
def __init__(self, **args):
# call super class init method
super(SchedulerGLite, self).__init__(**args)
# some initializations
self.warnings = []
# typical options
self.vo = args.get("vo", "cms")
self.service = args.get("service", "")
self.config = args.get("config", "")
self.delegationId = args.get("proxyname", "bossproxy")
# rename output files with submission number
self.renameOutputFiles = args.get("renameOutputFiles", 0)
self.renameOutputFiles = int(self.renameOutputFiles)
# x509 string & hackEnv for CLI commands
if self.cert != '':
self.proxyString = "env X509_USER_PROXY=" + self.cert + ' '
self.hackEnv = hackTheEnv()
else:
self.proxyString = ''
self.hackEnv = hackTheEnv('env')
# this section requires an improvement....
if os.environ.get('CRABDIR'):
self.commandQueryPath = os.environ.get('CRABDIR') + \
'/external/ProdCommon/BossLite/Scheduler/'
elif os.environ.get('PRODCOMMON_ROOT'):
self.commandQueryPath = os.environ.get('PRODCOMMON_ROOT') + \
'/lib/ProdCommon/BossLite/Scheduler/'
else:
# Impossible to locate GLiteQueryStatus.py ...
raise SchedulerError('Impossible to locate GLiteQueryStatus.py ')
# cache pattern to optimize reg-exp substitution
self.pathPattern = re.compile('location:([\S]+)$', re.M)
self.patternCE = re.compile('(?<= - ).*(?=:)', re.M)
# init BossliteJsonDecoder specialized class
self.myJSONDecoder = BossliteJsonDecoder()
# Raise an error if UI is old than 3.2 ...
version, ret = self.ExecuteCommand('glite-version')
version = version.strip()
if version.find('3.2') != 0:
version1, ret1 = self.ExecuteCommand(
'glite-version -n glite-UI -v')
version1 = version1.strip()
if version1.find('3.2') != 0:
raise SchedulerError('SchedulerGLite is allowed on UI >3.2')
# job killed per CLI call (tunable value)
self.killThreshold = 100
def getOutput(self, obj, outdir):
"""
retrieve output or just put it in the destination directory
"""
# check the proxy
self.schedObj.checkUserProxy()
# perform action
self.schedObj.getOutput(obj, outdir)
timestamp = int(time.time())
# the object passed is a runningJob
if type(obj) == RunningJob and self.schedObj.valid(obj):
obj['status'] = 'E'
obj['closed'] = 'Y'
obj['getOutputTime'] = timestamp
obj['statusScheduler'] = "Retrieved"
# the object passed is a job
elif type(obj) == Job and self.schedObj.valid(obj.runningJob):
obj.runningJob['status'] = 'E'
obj.runningJob['closed'] = 'Y'
obj.runningJob['getOutputTime'] = timestamp
obj.runningJob['statusScheduler'] = "Retrieved"
# the object passed is a Task
elif type(obj) == Task:
# error messages collector
errors = ''
# update objects
for job in obj.jobs:
# skip jobs not requested for action
if not self.schedObj.valid(job.runningJob):
continue
# evaluate errors: if not, update
if job.runningJob.isError():
errors += str(job.runningJob.errors)
else:
job.runningJob['status'] = 'E'
job.runningJob['closed'] = 'Y'
job.runningJob['getOutputTime'] = timestamp
job.runningJob['statusScheduler'] = "Retrieved"
# handle errors
if errors != '':
raise SchedulerError('interaction failed for some jobs', \
errors )
# unknown object type
else:
raise SchedulerError('wrong argument type', str(type(obj)))
def postMortem(self, obj, schedulerId, outfile, service):
"""
Get detailed postMortem job info
"""
if not type(obj) == Task:
raise SchedulerError('Wrong argument type or object type',
str(type(obj)) + ' ' + str(objType))
if not outfile:
raise SchedulerError('Empty filename',
'postMortem called with empty logfile name')
taskId = obj['name']
condorId = schedulerId.split('//')[-1]
header = '========= LOGGING INFO FOR %s =========\n' % schedulerId
horsep = '\n' + 80 * '=' + '\n'
sep1 = '\n========= OUTPUT OF : Condor_history -match 1 -l %s =========\n' % condorId
sep2 = '\n========= OUTPUT OF : Condor_q -l %s =========\n' % condorId
self.initializeGsissh(obj)
fp = open(outfile, 'w')
fp.write(header)
fp.write(horsep)
fp.write(sep1)
command = '%s %s %s %s ' \
% (self.unsetenvScram, self.remoteCommand, self.gsisshOptions, self.remoteUserHost)
command += ' "condor_history -match 1 -userlog %s/condor.log -l %s"' % \
(taskId, condorId)
(status, output) = commands.getstatusoutput(command)
if (status):
if "already exists" in output:
self.removeGsisshSocket()
fp.write(output)
fp.write(horsep)
# the following condor_q only makes sense if job status
# is 1(Idle), 2(Run) or 5(Held) but may cost little to do always
fp.write(sep2)
command = '%s %s %s %s ' \
% (self.unsetenvScram, self.remoteCommand, self.gsisshOptions, self.remoteUserHost)
command += ' "condor_q -l %s"' % condorId
(status, output) = commands.getstatusoutput(command)
fp.write(output)
fp.write('\n')
fp.write(horsep)
fp.close()
return
def getOutput(self, obj, outdir=''):
"""
Retrieve (move) job output from cache directory to outdir
"""
self.initializeGsissh(obj)
filesToGet = []
if type(obj) == RunningJob: # The object passed is a RunningJob
raise SchedulerError(
'Operation not possible',
'Condor cannot retrieve files when passed RunningJob')
elif type(obj) == Job: # The object passed is a Job
# check for the RunningJob integrity
if not self.valid(obj.runningJob):
raise SchedulerError('Invalid object', \
str( obj.runningJob ))
filesToGet = obj['outputFiles']
# the object passed is a Task
elif type(obj) == Task:
taskId = obj['name']
self.taskId = taskId
if outdir == '':
outdir = obj['outputDirectory']
for job in obj.jobs:
if self.valid(job.runningJob):
filesToGet.extend(job['outputFiles'])
# unknown object type
else:
raise SchedulerError('Wrong argument type', str(type(obj)))
retval, stdout = \
self.rsyncFromRemoteHost(self.remoteUserHost, outdir, filesToGet )
if retval:
# uh oh
if type(obj) == Job:
jobList = [obj]
else:
jobList = obj.jobs
for job in jobList:
for fileName in job['outputFiles']:
if not os.access(outdir + '/' + fileName, os.F_OK):
msg = "Could not retrieve file %s." % fileName
self.logging.error(msg)
msg += " Rsync failed with status,output=\n%d\n%s" % \
(retval,stdout)
job.runningJob.errors.append(msg)
if "already exists" in stdout:
self.removeGsisshSocket()
def query(self, obj, service='', objType='node'):
"""
query status and eventually other scheduler related information
It may use single 'node' scheduler id or bulk id for association
"""
if type(obj) != Task:
raise SchedulerError('wrong argument type', str(type(obj)))
jobids = []
for job in obj.jobs:
if not self.valid(job.runningJob): continue
id = str(job.runningJob['schedulerId']).strip()
#p = subprocess.Popen( ['qstat', '-x', id], stdout=subprocess.PIPE,
p = subprocess.Popen([
'squeue', '-h', '-o',
'<jobid>%i</jobid><exec_host>%B</exec_host><job_state>%t</job_state>',
'-j', id
],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
qstat_output, \
qstat_error = p.communicate()
qstat_return = p.returncode
if qstat_return:
#if qstat_return != 153: # 153 means the job isn't there
if qstat_return != 1: # 153 means the job isn't there
self.logging.error('Error in job query for ' + id)
self.logging.error('SLURM stdout: \n %s' % qstat_output)
self.logging.error('SLURM stderr: \n %s' % qstat_error)
raise SchedulerError(
'SLURM error', '%s: %s' % (qstat_error, qstat_return))
host = ''
if len(qstat_output) == 0:
pbs_stat = 'Done'
else:
if qstat_output.find('</exec_host>') >= 0:
host = qstat_output[qstat_output.find('<exec_host>') +
len('<exec_host>'):qstat_output.
find('</exec_host>')]
if qstat_output.find('</job_state>') >= 0:
pbs_stat = qstat_output[qstat_output.find('<job_state>') +
len('<job_state>'):qstat_output.
find('</job_state>')]
job.runningJob['statusScheduler'] = pbs_stat
job.runningJob['status'] = self.status_map[pbs_stat]
job.runningJob['destination'] = host
def kill(self, obj):
"""
kill the job instance
does not return
"""
r = re.compile("Job <(\d+)> is being terminated")
rFinished = re.compile("Job <(\d+)>: Job has already finished")
# for jobid in schedIdList:
for job in obj.jobs:
if not self.valid(job.runningJob):
continue
jobid = str(job.runningJob['schedulerId']).strip()
command = 'bkill ' + str(jobid)
if self.ksuCmd:
# write a ksu tmpFile
cmd = '%s\n' % command
command, fname = self.createCommand(cmd, obj)
out, ret = self.executeCommandWrapper(command)
if self.ksuCmd: os.unlink(fname)
mFailed = rFinished.search(out)
if mFailed:
raise SchedulerError(
"Unable to kill job " + jobid + " . Reason: ", out,
command)
pass
pass
def kill(self, obj):
"""
kill the job instance
does not return
"""
r = re.compile("has registered the job (\d+) for deletion")
rFinished = re.compile("Job <(\d+)>: Job has already finished")
r2 = re.compile("has deleted job (\d+)") #by Leo
# for jobid in schedIdList:
for job in obj.jobs:
if not self.valid(job.runningJob):
continue
jobid = str(job.runningJob['schedulerId']).strip()
cmd = 'qdel ' + str(jobid)
out, ret = self.ExecuteCommand(cmd)
#print "kill:"+out
mKilled = r.search(out)
mKilled2 = r2.search(out)
if not mKilled and not mKilled2:
raise SchedulerError(
"Unable to kill job #" + str(job['jobId']) + " (SGE id:" +
jobid + ") . Reason: ", out)
pass
pass
def postMortem(self, obj, outfile):
"""
execute any post mortem command such as logging-info
"""
# check the proxy
self.schedObj.checkUserProxy()
# the object passed is a runningJob
if type(obj) == RunningJob:
self.schedObj.postMortem(obj, obj['schedulerId'], outfile,
self.parameters['service'])
# the object passed is a job
elif type(obj) == Job:
self.schedObj.postMortem( obj, obj.runningJob['schedulerId'], \
outfile, self.parameters['service']
)
# the object passed is a Task
elif type(obj) == Task:
for job in obj.jobs:
if job.runningJob is None:
continue
self.schedObj.postMortem( obj, job.runningJob['schedulerId'], \
outfile, self.parameters['service'] )
# unknown object type
else:
raise SchedulerError('wrong argument type', str(type(obj)))
def getOutput(self, obj, outdir=''):
"""
retrieve output or just put it in the destination directory
"""
# obj can be a task, a job or even a running job
# several possibilities:
# 1) connect to a service and perform a remote copy
# 2) just eventually copy the local output to the destination dir
# 3) wrap a CLI command like glite-wms-job-output
errorList = []
if outdir == '' and obj['outputDirectory'] is not None:
outdir = obj['outputDirectory']
if outdir != '' and not os.path.exists(outdir):
raise SchedulerError( 'Permission denied', \
'Unable to write files in ' + outdir )
# retrieve scheduler id list
schedIdList = {}
for job in obj.jobs:
if self.valid(job.runningJob):
# retrieve output
# if error: job.runningJob.errors.append( error )
pass
def getOutput(self, obj, outdir):
"""
retrieve output or just put it in the destination directory
does not return
"""
#output ends up in the wrong location with a user defined
#output directory...Thus we have to move it to the correct
#directory here....
#print "SchedulerSGE:getOutput called!"
if type(obj) == Task:
# oldoutdir=obj[ 'outputDirectory' ]
oldoutdir = obj[
'outputDirectory'] + '/temp' ## copy new output files from temp"
if (outdir != oldoutdir):
for job in obj.jobs:
jobid = job['id']
#print "job:"+str(jobid)
if self.valid(job.runningJob):
#print "is valid"
for outFile in job['outputFiles']:
#print "outputFile:"+outFile
command = "mv " + oldoutdir + "/" + outFile + " " + outdir + "/. \n"
#print command
out, ret = self.ExecuteCommand(command)
if (out != ""):
raise SchedulerError('unable to move file',
out)
#raise SchedulerError("unable to move file "+oldoutdir+"/"+outFile+" ",out)
pass
pass
pass
pass
pass
def query(self, obj, objType='node'):
"""
query status and eventually other scheduler related information
"""
# check the proxy
self.schedObj.checkUserProxy()
# error messages collector
errors = ''
# delegate query to scheduler plugin
self.schedObj.query(obj, self.parameters['service'], objType)
# handle errors
for job in obj.jobs:
# evaluate errors:
if job.runningJob.isError():
errors += str(job.runningJob.errors)
continue
# handle errors
if errors != '':
raise SchedulerError('interaction failed for some jobs', errors)
class Scheduler(object):
"""
Upper layer for scheduler interaction
"""
def __init__(self, scheduler, parameters=None):
"""
initialization
"""
# define scheduler parameters
self.scheduler = scheduler
defaults = {'user_proxy': '', 'service': '', 'config': ''}
if parameters is not None:
defaults.update(parameters)
self.parameters = defaults
# load scheduler plugin
try:
module = __import__(
'ProdCommon.BossLite.Scheduler.' + self.scheduler, \
globals(), locals(), [self.scheduler]
)
schedClass = vars(module)[self.scheduler]
self.schedObj = schedClass(**self.parameters)
except KeyError, e:
msg = 'Scheduler interface' + self.scheduler + 'not found'
raise SchedulerError(msg, str(e))
except Exception, e:
raise SchedulerError(e.__class__.__name__, str(e))
def submitJob(self, job, task=None, requirements=''):
"""Need to copy the inputsandbox to WN before submitting a job"""
arg = self.decode(job, task, requirements)
command = "qsub " + arg
self.logging.debug(command)
out, ret = self.ExecuteCommand(command)
self.logging.debug("crab: %s" % out)
r = re.compile("Your job (\d+) .* has been submitted")
m = r.search(out)
if m is not None:
jobId = m.group(1)
command = "qstat -j " + jobId
#out, ret = self.ExecuteCommand(command)
#print "out:" + out + "\n"
#queue = m.group(2)
queue = "all"
else:
#rNot = re.compile("Job not submitted.*<(\w+)>")
#m= rNot.search(out)
#if m is not None:
# print m
# print "Job NOT submitted"
# print out
raise SchedulerError('error', out)
taskId = None
#print "Your job identifier is: ", taskId, queue
map = {job['name']: jobId}
return map, taskId, queue
def pbs_conn(self):
conn = pbs.pbs_connect(pbs.pbs_default())
if (conn < 0):
err, err_text = pbs.error()
self.logging.error('Error in PBS server conncet')
self.logging.error('PBS error code ' + str(err) + ': ' + err_text)
raise SchedulerError('PBS error', str(err) + ': ' + err_text)
return conn
def getOutput(self, obj, outdir=''):
"""
Get output files from jobs in 'obj' and put them in 'outdir', and
remove the job from the CE.
"""
if type(obj) == Task:
joblist = obj.jobs
if outdir == '':
outdir = obj['outputDirectory']
elif type(obj) == Job:
joblist = [obj]
else:
raise SchedulerError('wrong argument type', str(type(obj)))
assert outdir != ''
if outdir[-1] != '/': outdir += '/'
jobsFile, arcId2job = self.createJobsFile(joblist, "Will fetch")
# Create a tmp dir where ngget can create its subdirs of job
# output. Use outdir as the parent dir, to keep moving of files
# afterwards within the same files system (faster!)
tmpdir = tempfile.mkdtemp(prefix="joboutputs.", dir=outdir)
cmd = self.pre_arcCmd + 'arcget -i %s -dir %s' % (jobsFile.name,
tmpdir)
self.logging.debug("Running command: %s" % cmd)
output, stat = self.ExecuteCommand(cmd)
self.logging.debug("Output of arcget: %s" % output)
jobsFile.close()
if stat != 0:
raise SchedulerError('arcget returned %i' % stat, output, cmd)
# Copy the dowlodaed files to their final destination
cmd = 'mv %s/*/* %s' % (tmpdir, outdir)
self.logging.debug("Moving files from %s/* to %s" % (tmpdir, outdir))
output, stat = self.ExecuteCommand(cmd)
if stat != 0:
raise SchedulerError('mv returned %i' % stat, output, cmd)
# Remove the tmp output dir
cmd = 'rm -r %s' % tmpdir
output, stat = self.ExecuteCommand(cmd)
if stat != 0:
raise SchedulerError('rm returned %i' % stat, output, cmd)
def submitJob(self, job, task=None, requirements=''):
""" Need to copy the inputsandbox to WN before submitting a job"""
arg = self.decode(job, task, requirements)
# command = "bsub " + arg
chDir = "pushd . > /dev/null ; "
resetDir = " ; popd > /dev/null"
command = " bsub " + arg + resetDir
if self.ksuCmd:
chDir += "cd /tmp; "
cmd = "#!/usr/bin/pagsh.krb\n"
cmd += "aklog\n"
cmd += '%s %s\n' % (chDir, command)
command, fname = self.createCommand(cmd, task)
else:
# execute bsub in the directory where files have be returned
chDir += " cd %s ;" % task['outputDirectory']
command = '%s %s' % (chDir, command)
out, ret = self.executeCommandWrapper(command)
if self.ksuCmd: os.unlink(fname)
if ret != 0:
raise SchedulerError('Error in submit', out, command)
r = re.compile("Job <(\d+)> is submitted.*<(\w+)>")
m = r.search(out)
if m is not None:
jobId = m.group(1)
queue = m.group(2)
else:
rNot = re.compile("Job not submitted.*<(\w+)>")
m = rNot.search(out)
if m is not None:
self.logging.error(m)
self.logging.error("Job NOT submitted")
self.logging.error(out)
job.runningJob.errors.append(out)
raise SchedulerError('Cannot submit ', out, command)
taskId = None
#print "Your job identifier is: ", taskId, queue
map = {job['name']: jobId}
return map, taskId, queue
def query(self, obj, service='', objType='node'):
"""
query status and eventually other scheduler related information
It may use single 'node' scheduler id or bulk id for association
"""
if type(obj) != Task:
raise SchedulerError('wrong argument type', str(type(obj)))
jobids = []
conn = self.pbs_conn()
attrl = pbs.new_attrl(2)
attrl[0].name = 'job_state'
attrl[1].name = 'exec_host'
for job in obj.jobs:
if not self.valid(job.runningJob): continue
id = str(job.runningJob['schedulerId']).strip()
jobstat = pbs.pbs_statjob(conn, id, attrl, 'Null')
if not jobstat:
err, err_text = pbs.error()
if err != 15001: # unknown job (probably finished)
self.logging.error('Error in job query for ' + id)
self.logging.error('PBS error code ' + str(err) + ': ' +
err_text)
self.pbs_disconn(conn)
raise SchedulerError('PBS error',
str(err) + ': ' + err_text)
host = ''
if len(jobstat) == 0:
pbs_stat = 'Done'
else:
pbs_stat = jobstat[0].attribs[0].value
if len(jobstat[0].attribs) > 1:
host = jobstat[0].attribs[1].value
job.runningJob['statusScheduler'] = pbs_stat
job.runningJob['status'] = self.status_map[pbs_stat]
job.runningJob['destination'] = host
self.pbs_disconn(conn)
def purgeService(self, obj):
"""
Purge job (even bulk) from service
"""
# not always available...
# it may be useful to connect to a remote service and purge job sandbox
out = "whatever"
if out.find('error') >= 0:
raise SchedulerError("Unable to purge job", out)
def __init__(self, **args):
super(SchedulerPbs, self).__init__(**args)
self.jobScriptDir = args['jobScriptDir']
self.jobResDir = args['jobResDir']
self.queue = args['queue']
self.workerNodeWorkDir = args.get('workDir', '')
self.res_dict = {}
for a in args['resources'].split(','):
if len(a) > 0:
if a.find("=") != -1:
res, val = a.split('=')
self.res_dict.update({res: val})
else:
raise SchedulerError("PBS error", +\
"Unkown resource format: " + a)
env = []
for v in ('HOME', 'LANG', 'LOGNAME', 'MAIL', 'PATH', 'SHELL'):
env.append('PBS_O_' + v + '=' + os.environ[v])
env.append('PBS_O_WORKDIR=' + os.getcwd())
env.append('PBS_O_HOST=' + pbs.pbs_default())
#if 'use_proxy' in args:
# if args['use_proxy'] == 1:
# proxy_location = ''
# try:
# proxy_location = os.environ['X509_USER_PROXY']
# except:
# proxy_location = '/tmp/x509up_u'+ repr(os.getuid())
# msg, ret = self.ExecuteCommand('cp ' + proxy_location + " " + self.cert)
## proxy_path = self.getUserProxy()
# env.append('X509_USER_PROXY=' + self.cert)
# env.append('X509_USER_CERT=' + self.cert)
# env.append('X509_USER_KEY=' + self.cert)
# else:
# raise SchedulerError(str(args), self.cert)
self.pbs_env = ','.join(env)
self.status_map = {
'E': 'R',
'H': 'SS',
'Q': 'SS',
'R': 'R',
'S': 'R',
'T': 'R',
'W': 'SS',
'Done': 'SD',
'C': 'SD'
}
def matchResources(self, obj, requirements='', config='', service=''):
"""
resources list match
"""
# several possibilities:
# 1) connect to a service and ask
# 2) wrap a CLI command like glite-wms-job-listmatch
# 3) nor available... skip
# 4) there is a useful lcgInfo...
out = "whatever"
if out.find('error') >= 0:
raise SchedulerError("Unable to find resources", out)
def getOutput(self, obj, outdir=''):
"""
Get output files from jobs in 'obj' and put them in 'outdir', and
remove the job from the CE.
"""
if type(obj) == Task:
self.logging.debug("getOutput called for %i jobs" % len(obj.jobs))
joblist = obj.jobs
if outdir == '':
outdir = obj['outputDirectory']
elif type(obj) == Job:
self.logging.debug("getOutput called for 1 job")
joblist = [obj]
else:
raise SchedulerError('wrong argument type', str(type(obj)))
assert outdir != ''
if outdir[-1] != '/': outdir += '/'
for job in joblist:
tmpdir = tempfile.mkdtemp(prefix="joboutputs.", dir=outdir)
cmd = self.pre_arcCmd + 'arcget --timeout=600 %s --dir %s' % (
job.runningJob['schedulerId'], tmpdir)
self.logging.debug("Running command: %s" % cmd)
output, stat = self.ExecuteCommand(cmd)
self.logging.debug("Status and output of arcget: %i, '%s'" %
(stat, output))
if stat != 0:
msg = "arcget failed with status %i: %s" % (stat, output)
self.logging.warning(msg)
else:
# Copy the dowlodaed files to their final destination
cmd = 'mv %s/*/* %s' % (tmpdir, outdir)
self.logging.debug("Moving files from %s/* to %s" %
(tmpdir, outdir))
output, stat = self.ExecuteCommand(cmd)
if stat != 0:
msg = "Moving files to final destination failed: %s" % (
output)
self.logging.warning(msg)
else:
cmd = ' rm -r %s' % (tmpdir)
self.logging.debug("Removing tempdir %s" % (tmpdir))
output, stat = self.ExecuteCommand(cmd)
if stat != 0:
msg = "Removing tempdir: %s" % (output)
self.logging.warning(msg)
def kill(self, obj):
for job in obj.jobs :
if not self.valid( job.runningJob ): continue
id=str(job.runningJob['schedulerId']).strip()
p = subprocess.Popen( ['qdel', id], stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
qdel_output, \
qdel_error = p.communicate()
qdel_return = p.returncode
if qdel_return != 0:
self.logging.error('Error in job kill for '+id)
self.logging.error('PBS Error stdout: %s' % qdel_output)
raise SchedulerError('PBS Error in kill', qdel_output)
def submit(self, task, requirements='', config='', service=''):
"""
user submission function
takes as arguments:
- a finite, dedicated jdl
- eventually a list of services to connect
- eventually a config file
the passed config file or, if not provided, a default one can be
used from eventual defaults
the function returns an eventual parent id, the service of the
successfully submission and a map associating the jobname to the
node id. If the submission is not bulk, the parent id should be the
node id of the unique entry of the map
"""
taskId = None
queue = None
retMap = {}
for job in task.jobs:
command = self.decodeJob(job, task, requirements)
out, ret = self.ExecuteCommand(command)
if ret != 0:
raise SchedulerError('Error in submit', out, command)
r = re.compile("Job <(\d+)> is submitted.*<(\w+)>")
m = r.search(out)
if m is not None:
jobId = m.group(1)
queue = m.group(2)
retMap[job['name']] = jobId
else:
rNot = re.compile("Job not submitted.*<(\w+)>")
m = rNot.search(out)
if m is not None:
self.logging.error("Job NOT submitted: %s" % out)
job.runningJob.errors.append('Cannot submit using %s: %s' %
(out, command))
return retMap, taskId, queue
def query(self, obj, service='', objType='node'):
"""
query status and eventually other scheduler related information
"""
# ask for the job informations, mainly status
# some systems allow a query job per job, others also bulk queries
#print schedIdList, service, objType
r = re.compile("(\d+)\s+\w+\s+(\w+).*")
rfull = re.compile("(\d+)\s+\w+\s+(\w+)\s+(\w+)\s+\w+\s+(\w+).*")
rnotfound = re.compile("Job <(\d+)> is not found")
for job in obj.jobs:
if not self.valid(job.runningJob):
continue
jobid = str(job.runningJob['schedulerId']).strip()
command = 'bjobs ' + str(jobid)
out, ret = self.ExecuteCommand(command)
if ret != 0:
raise SchedulerError('Error in status query', out, command)
mnotfound = rnotfound.search(out)
queue = None
host = None
sid = None
st = None
if (mnotfound):
sid = mnotfound.group(1)
st = 'DONE'
else:
mfull = rfull.search(out)
if (mfull):
sid, st, queue, host = mfull.groups()
else:
m = r.search(out)
if (m):
sid, st = m.groups()
if (st):
job.runningJob['statusScheduler'] = st
job.runningJob['status'] = self.statusMap[st]
if (host):
job.runningJob['destination'] = host
def kill(self, obj):
conn = self.pbs_conn()
for job in obj.jobs:
if not self.valid(job.runningJob): continue
id = str(job.runningJob['schedulerId']).strip()
res = pbs.pbs_deljob(conn, id, '')
if res != 0:
err, err_text = pbs.error()
self.logging.error('Error in job kill for ' + id)
self.logging.error('PBS error code ' + str(err) + ': ' +
err_text)
self.pbs_disconn(conn)
raise SchedulerError('PBS error', str(err) + ': ' + err_text)
self.pbs_disconn(conn)
