# MIT License
#
# Copyright (c) 2017-18 Felix Simkovic
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
__author__ = 'Felix Simkovic'
__version__ = '1.0'
import logging
import re
import uuid
from pyjob.cexec import cexec
from pyjob.exception import PyJobExecutableNotFoundError, PyJobError
from pyjob.script import Script
from pyjob.task import ClusterTask
logger = logging.getLogger(__name__)
RE_LINE_SPLIT_1 = re.compile(r":\\s+")
RE_LINE_SPLIT_2 = re.compile(r"\\s+=\\s+")
[docs]class PortableBatchSystemTask(ClusterTask):
"""PortableBatchSystem executable :obj:`~pyjob.task.Task`"""
JOB_ARRAY_INDEX = '$PBS_ARRAYID'
SCRIPT_DIRECTIVE = '#PBS'
@property
def info(self):
""":obj:`~pyjob.pbs.PortableBatchSystemTask` information"""
if self.pid is None:
return {}
try:
stdout = cexec(['qstat', '-f', str(self.pid)], permit_nonzero=True)
except PyJobExecutableNotFoundError:
return {}
all_lines = stdout.splitlines()
data = {}
key, job_id = RE_LINE_SPLIT_1.split(all_lines[0], 1)
data[key] = job_id
for line in all_lines[1:]:
line = line.strip()
if 'Unknown queue destination' in line:
return data
else:
kv = RE_LINE_SPLIT_2.split(line, 1)
if len(kv) == 2:
data[kv[0]] = kv[1]
return data
def _check_requirements(self):
"""Check if the requirements for task execution are met"""
self._ensure_exec_available('qstat')
[docs] def kill(self):
"""Immediately terminate the :obj:`~pyjob.pbs.PortableBatchSystemTask`"""
if self.pid is None:
return
cexec(['qdel', str(self.pid)])
logger.debug("Terminated task: %d", self.pid)
def _run(self):
"""Method to initialise :obj:`~pyjob.pbs.PortableBatchSystemTask` execution"""
self.runscript = self._create_runscript()
self.runscript.write()
self.pid = cexec(['qsub', self.runscript.path], cwd=self.directory)
logger.debug('%s [%d] submission script is %s', self.__class__.__name__, self.pid, self.runscript.path)
def _create_runscript(self):
"""Utility method to create runscript"""
runscript = Script(directory=self.directory, prefix='pbs_', suffix='.script', stem=str(uuid.uuid1().int))
runscript.append(self.__class__.SCRIPT_DIRECTIVE + ' -V')
runscript.append(self.__class__.SCRIPT_DIRECTIVE + ' -N {}'.format(self.name))
if self.directory:
cmd = '-w {}'.format(self.directory)
runscript.append(self.__class__.SCRIPT_DIRECTIVE + ' ' + cmd)
if self.priority:
cmd = '-p {}'.format(self.priority)
runscript.append(self.__class__.SCRIPT_DIRECTIVE + ' ' + cmd)
if self.queue:
cmd = '-q {}'.format(self.queue)
runscript.append(self.__class__.SCRIPT_DIRECTIVE + ' ' + cmd)
if self.runtime:
cmd = '-l walltime={}'.format(self.get_time(self.runtime))
runscript.append(self.__class__.SCRIPT_DIRECTIVE + ' ' + cmd)
if self.shell:
cmd = '-S {}'.format(self.shell)
runscript.append(self.__class__.SCRIPT_DIRECTIVE + ' ' + cmd)
if self.nprocesses:
cmd = '-n {}'.format(self.nprocesses)
runscript.append(self.__class__.SCRIPT_DIRECTIVE + ' ' + cmd)
if self.extra:
cmd = ' '.join(map(str, self.extra))
runscript.append(self.__class__.SCRIPT_DIRECTIVE + ' ' + cmd)
if len(self.script) > 1:
logf = runscript.path.replace('.script', '.log')
jobsf = runscript.path.replace('.script', '.jobs')
with open(jobsf, 'w') as f_out:
f_out.write('\n'.join(self.script))
cmd = '-t {}-{}%{}'.format(1, len(self.script), self.max_array_size)
runscript.append(self.__class__.SCRIPT_DIRECTIVE + ' ' + cmd)
runscript.append(self.__class__.SCRIPT_DIRECTIVE + ' -o {}'.format(logf))
runscript.append(self.__class__.SCRIPT_DIRECTIVE + ' -e {}'.format(logf))
runscript.extend(self.get_array_bash_extension(jobsf, 0))
else:
runscript.append(self.__class__.SCRIPT_DIRECTIVE + ' -o {}'.format(self.log[0]))
runscript.append(self.__class__.SCRIPT_DIRECTIVE + ' -e {}'.format(self.log[0]))
runscript.append(self.script[0])
return runscript