def update(self):
try:
process = subprocess.Popen(
self.command,
stdout = subprocess.PIPE,
stderr = subprocess.PIPE
)
except OSError as e:
raise errors.ExecutableError("'%s': %s" % ( " ".join( self.command ), e ))
( out, err ) = process.communicate()
if process.poll():
message = "Poll error: '%s' exited abnormally (code %s, message %s)" % (
" ".join( self.command ),
process.poll(),
err,
)
raise errors.AbnormalExitError(message)
self.running.clear()
self.completed.clear()
self.evaluate( out = out, running = self.running, completed = self.completed )
self.polltime = time.time()
def __call__(self, name, executable, script, include, cleanup):
(process, outfile, errfile) = self.create(name=name)
(out, err) = process.communicate(
input=self.handler.script(include=include,
executable=executable,
script=script,
cwd=self.cwd))
if process.poll():
message = "Submission error: '%s' exited abnormally (code %s, message %s)" % (
" ".join(self.cmds),
process.poll(),
err,
)
raise errors.AbnormalExitError(message)
return self.handler(
jobid=self.extract(output=out),
poller=self.poller,
outfile=outfile,
errfile=errfile,
additional=cleanup,
qdel=self.qdel,
)
def sge_single_evaluate(out, err):
"Evaluates SGE text output in single mode"
if err:
if SGE_REGEX().search( err ):
return True
else:
raise errors.AbnormalExitError("SGE error:\n%s" % err)
else:
return False
def outcome(self, timeout, polltime):
exitcode = self.exit_code()
assert exitcode is not None
stdout = self.get_stdout(timeout=timeout, polltime=polltime)
stderr = self.get_stderr(timeout=timeout, polltime=polltime)
if stdout is None or stderr is None:
stdout = self.process.stdout.read()
stderr = self.process.stderr.read()
raise errors.AbnormalExitError("Queue error:%s\n%s" %
(stdout, stderr))
return Finished(stdout=stdout, stderr=stderr, exitcode=exitcode)
def slurm_single_evaluate(out, err):
"Evaluates Slurm text output in single mode"
if err:
if SLURM_SEARCH_REGEX().search( err ):
return True
else:
raise errors.AbnormalExitError("Slurm error:\n%s" % err)
state = out.strip()
if state not in SLURM_CODES:
raise errors.ExtractionError("Unexpected response from Slurm: %r" % out)
return state == "CD"
def pbs_single_evaluate(out, err):
"Evaluates PBS text output in single mode"
if err:
if PBS_SEARCH_REGEX().search( err ):
return True
else:
raise errors.AbnormalExitError("PBS error:\n%s" % err)
state = PBS_EVAL_REGEX().search( out )
if not state:
raise errors.ExtractionError("Unexpected response from PBS: %r" % out)
return state.group(1) == "C"
def __call__(self, name, executable, script, include, cleanup):
outfile = "%s.out" % name
errfile = "%s.err" % name
scriptfile = "%s.condor.script" % name
logfile = "%s.condor.xml" % name
with open(scriptfile, "w") as ofile:
ofile.write(
self.handler.script(include=include,
executable=executable,
script=script))
import os
import stat
os.chmod(scriptfile, stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR)
process = self.create()
(out,
err) = process.communicate(input=self.script %
(scriptfile, outfile, errfile, logfile))
if process.poll():
message = "Submission error: '%s' exited abnormally (code %s, message %s)" % (
" ".join(self.cmds),
process.poll(),
err,
)
raise errors.AbnormalExitError(message)
return self.handler(
jobid=self.extract(output=out),
poller=self.poller,
outfile=outfile,
errfile=errfile,
logfile=logfile,
additional=cleanup + [scriptfile],
qdel=self.qdel,
)
def outcome(self, timeout, polltime):
# Use accounting file to return exit code
try:
process = subprocess.Popen(["qacct", "-j", self.jobid],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
except OSError as e:
raise errors.ExecutableError("'qacct -j %s': %s" % (self.jobid, e))
(out, err) = process.communicate()
if process.poll():
raise errors.AbnormalExitError("Accounting error:\n%s" % err)
exit_code = extract_exit_code_text(output=out)
return Finished(
stdout=self.get_stdout(timeout=timeout, polltime=polltime),
stderr=self.get_stderr(timeout=timeout, polltime=polltime),
exitcode=exit_code,
)