def submit(self):
self._create_logdir()
self._remove_previous_logs()
try:
external_job_id = self._submit_cmd_and_get_external_job_id()
parameters_to_status_script = self._get_parameters_to_status_script(
external_job_id)
OSLayer.print(parameters_to_status_script)
except subprocess.CalledProcessError as error:
raise BsubInvocationError(error)
except AttributeError as error:
raise JobidNotFoundError(error)
def _query_status_using_bjobs(self) -> str:
output_stream, error_stream = OSLayer.run_process(self.bjobs_query_cmd)
stdout_is_empty = not output_stream.strip()
if stdout_is_empty:
raise BjobsError(
"bjobs error.\nstdout is empty.\nstderr = {stderr}".format(
stderr=error_stream
)
)
return self.STATUS_TABLE[output_stream]
def __init__(
self,
jobscript: PathLike,
cluster_cmds: List[str] = None,
memory_units: Unit = Unit.MEGA,
lsf_config: Optional[Config] = None,
):
if cluster_cmds is None:
cluster_cmds = []
if lsf_config is None:
lsf_config = Config()
self._jobscript = jobscript
self._cluster_cmd = " ".join(cluster_cmds)
self._job_properties = read_job_properties(self._jobscript)
self.random_string = OSLayer.get_uuid4_string()
self._memory_units = memory_units
self.lsf_config = lsf_config
def _query_status_using_bjobs(self) -> str:
output_stream, error_stream = OSLayer.run_process(self.bjobs_query_cmd)
stdout_is_empty = not output_stream.strip()
if stdout_is_empty:
raise BjobsError(
"bjobs error.\nstdout is empty.\nstderr = {stderr}".format(
stderr=error_stream
)
)
if output_stream == UNKNOWN:
return self._handle_unknown_job()
if output_stream == ZOMBIE:
return self._handle_zombie_job()
return self.STATUS_TABLE[output_stream]
def _kill_job(self):
kill_cmd = "bkill -r {}".format(self.jobid)
_ = OSLayer.run_process(kill_cmd)
def _get_tail_of_log_file(self) -> List[str]:
# 30 lines gives us the whole LSF completion summary
tail = OSLayer.tail(self.outlog, num_lines=30)
return [line.decode().strip() for line in tail]
def _submit_cmd_and_get_external_job_id(self) -> int:
output_stream, error_stream = OSLayer.run_process(self.submit_cmd)
match = re.search(r"Job <(\d+)> is submitted", output_stream)
jobid = match.group(1)
return int(jobid)
def _remove_previous_logs(self):
OSLayer.remove_file(self.outlog)
OSLayer.remove_file(self.errlog)
def _create_logdir(self):
OSLayer.mkdir(self.logdir)