Source code for pyjob.pbs
import logging
import re
import uuid
from pyjob.cexec import cexec
from pyjob.exception import PyJobError, PyJobExecutableNotFoundError
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__.__qualname__,
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 + f" -N {self.name}")
if self.directory:
cmd = f"-w {self.directory}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.priority:
cmd = f"-p {self.priority}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.queue:
cmd = f"-q {self.queue}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.runtime:
cmd = f"-l walltime={self.get_time(self.runtime)}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.shell:
cmd = f"-S {self.shell}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
if self.nprocesses:
cmd = f"-n {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 = f"-t 1-{len(self.script)}%{self.max_array_size}"
runscript.append(self.__class__.SCRIPT_DIRECTIVE + " " + cmd)
runscript.append(self.__class__.SCRIPT_DIRECTIVE + f" -o {logf}")
runscript.append(self.__class__.SCRIPT_DIRECTIVE + f" -e {logf}")
runscript.extend(self.get_array_bash_extension(jobsf, 0))
else:
runscript.append(self.__class__.SCRIPT_DIRECTIVE + f" -o {self.log[0]}")
runscript.append(self.__class__.SCRIPT_DIRECTIVE + f" -e {self.log[0]}")
runscript.append(self.script[0])
return runscript