Dear all,
I would like to run atomate in offline mode on a cluster with LSF job managing system. I have attached all the relevant files of running a test job in a zip file.
The error I got in “Si-structure_optimiz-41419.error” is :
/home1/xiaoh/miniconda3/lib/python3.7/site-packages/pymatgen/io/cif.py:44: UserWarning: Please install optional dependency pybtex if youwant to extract references from CIF files.
warnings.warn(“Please install optional dependency pybtex if you”
Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x2b94f8d449b0>
Traceback (most recent call last):
File “/home1/xiaoh/miniconda3/lib/python3.7/site-packages/custodian/custodian.py”, line 320, in run
self._run_job(job_n, job)
File “/home1/xiaoh/miniconda3/lib/python3.7/site-packages/custodian/custodian.py”, line 428, in _run_job
raise CustodianError(s, True, v)
custodian.custodian.CustodianError: (CustodianError(…), ‘Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x2b94f8d449b0>’)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home1/xiaoh/miniconda3/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run
m_action = t.run_task(my_spec)
File “/home1/xiaoh/miniconda3/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 204, in run_task
c.run()
File “/home1/xiaoh/miniconda3/lib/python3.7/site-packages/custodian/custodian.py”, line 330, in run
.format(self.total_errors, ex))
RuntimeError: 0 errors reached: (CustodianError(…), ‘Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x2b94f8d449b0>’). Exited…
The error I got in “std_err.txt” is:
[mpiexec@n0114] HYDU_parse_hostfile (…/…/utils/args/args.c:535): unable to open host file: $CURDIR/nodelist.41419
[mpiexec@n0114] machine_file_fn (…/…/ui/mpich/utils.c:509): error parsing machine file
[mpiexec@n0114] match_arg (…/…/utils/args/args.c:243): match handler returned error
[mpiexec@n0114] HYDU_parse_array (…/…/utils/args/args.c:269): argument matching returned error
[mpiexec@n0114] parse_args (…/…/ui/mpich/utils.c:4009): error parsing input array
[mpiexec@n0114] HYD_uii_mpx_get_parameters (…/…/ui/mpich/utils.c:4339): unable to parse user arguments
My impression is that atomate didn’t run vasp properly with lsf system. Note that I have modified the LoadSharingFacility_template.txt file, which is included in the zip file attached.
I also included my_fworker.yaml in the offline folder in the zip file attached. I am kind of confused how to define vasp_cmd in my_fworker.yaml.
I attached the lsf script I often used to submit vasp jobs in this cluster as reference.
If I define vasp_cmd as “mpirun -np 16 vasp”, the jobs will not be conducted in the computing nodes. If I define vasp_cmd as “mpirun -np $NPROCS -machinefile $CURDIR/nodelist.$LSB_JOBID /home1/xiaoh/vasp/vasp.5.3-vtst/vasp > log”, then the variables NPROCS, CURDIR and LSB_JOBID are not defined, which leads to the error in std_err.txt shown above.
Could you guys guide me to run atomate in offline mode on a cluster with LSF job managing system?
Thank you very much!
Hang Xiao
Postdoc
Columbia Univeristy
launcher_2019-02-05-19-53-01-178809.zip (129 KB)
vaspvtstTail.lsf (1.76 KB)