У меня есть сценарий задания PBS с исполняемым файлом, который записывает результаты в файл out.
### some lines
PBS_O_EXEDIR="path/to/software"
EXECUTABLE="executablefile"
OUTFILE="out"
### Copy application directory on compute node
[ -d $PBS_O_EXEDIR ] || mkdir -p $PBS_O_EXEDIR
[ -w $PBS_O_EXEDIR ] && \
rsync -Cavz --rsh=$SSH $HOST:$PBS_O_EXEDIR `dirname $PBS_O_EXEDIR`
[ -d $PBS_O_WORKDIR ] || mkdir -p $PBS_O_WORKDIR
rsync -Cavz --rsh=$SSH $HOST:$PBS_O_WORKDIR `dirname $PBS_O_WORKDIR`
# Change into the working directory
cd $PBS_O_WORKDIR
# Save the jobid in the outfile
echo "PBS-JOB-ID was $PBS_JOBID" > $OUTFILE
# Run the executable
$PBS_O_EXEDIR/$EXECUTABLE >> $OUTFILE
В моем проекте я должен использовать Dask для отправки этого задания и для их мониторинга. Поэтому я настроил файл jobqueue.yaml следующим образом.
jobqueue:
pbs:
name: htc_calc
# Dask worker options
cores: 4 # Total number of cores per job
memory: 50GB # Total amount of memory per job
# PBS resource manager options
shebang: "#!/usr/bin/env bash"
walltime: '00:30:00'
exe_dir: "/home/r/rb11/softwares/FPLO/bin"
excutable: "fplo18.00-57-x86_64"
outfile: "out"
job-extra: "exe_dir/executable >> outfile"
Однако я получил эту ошибку при отправке заданий через Dask.
qsub: directive error: e
tornado.application - ERROR - Exception in callback functools.partial(<function wrap.<locals>.null_wrapper at 0x7f3d8c4a56a8>, <Task finished coro=<SpecCluster._correct_state_internal() done, defined at /home/r/rb11/anaconda3/envs/htc/lib/python3.5/site-packages/distributed/deploy/spec.py:284> exception=RuntimeError('Command exited with non-zero exit code.\nExit code: 1\nCommand:\nqsub /tmp/tmpwyvkfcmi.sh\nstdout:\n\nstderr:\nqsub: directive error: e \n\n',)>)
Traceback (most recent call last):
File "/home/r/rb11/anaconda3/envs/htc/lib/python3.5/site-packages/tornado/ioloop.py", line 758, in _run_callback
ret = callback()
File "/home/r/rb11/anaconda3/envs/htc/lib/python3.5/site-packages/tornado/stack_context.py", line 300, in null_wrapper
return fn(*args, **kwargs)
File "/home/r/rb11/anaconda3/envs/htc/lib/python3.5/site-packages/tornado/ioloop.py", line 779, in _discard_future_result
future.result()
File "/home/r/rb11/anaconda3/envs/htc/lib/python3.5/asyncio/futures.py", line 294, in result
raise self._exception
File "/home/r/rb11/anaconda3/envs/htc/lib/python3.5/asyncio/tasks.py", line 240, in _step
result = coro.send(None)
File "/home/r/rb11/anaconda3/envs/htc/lib/python3.5/site-packages/distributed/deploy/spec.py", line 317, in _correct_state_internal
await w # for tornado gen.coroutine support
File "/home/r/rb11/anaconda3/envs/htc/lib/python3.5/site-packages/distributed/deploy/spec.py", line 41, in _
await self.start()
File "/home/r/rb11/anaconda3/envs/htc/lib/python3.5/site-packages/dask_jobqueue/core.py", line 285, in start
out = await self._submit_job(fn)
File "/home/r/rb11/anaconda3/envs/htc/lib/python3.5/site-packages/dask_jobqueue/core.py", line 268, in _submit_job
return self._call(shlex.split(self.submit_command) + [script_filename])
File "/home/r/rb11/anaconda3/envs/htc/lib/python3.5/site-packages/dask_jobqueue/core.py", line 368, in _call
"stderr:\n{}\n".format(proc.returncode, cmd_str, out, err)
RuntimeError: Command exited with non-zero exit code.
Exit code: 1
Command:
qsub /tmp/tmpwyvkfcmi.sh
stdout:
stderr:
qsub: directive error: e
Как указать собственный скрипт bash в Dask?