IndexError: list index out of range #992

quantumhugh · 2022-10-10T05:23:10Z

quantumhugh
Oct 10, 2022

Hello! I am a new user of dpgen. When I repeat the example of CH4 with PBS operating system in the “init_bulk” step, there are some errors in the output file, like this:

Description

2022-10-10 10:48:28,702 - INFO : info:check_all_finished: False
2022-10-10 10:48:28,769 - INFO : job: 45187ce8d3f56b858aa65af964fb9a7c3ee0e0ca submit; job_id is 120379
Traceback (most recent call last):
File "MyPrefix/.local/bin/dpgen", line 8, in
sys.exit(main())
File "MyPrefix/.local/lib/python3.10/site-packages/dpgen/main.py", line 185, in main
args.func(args)
File "MyPrefix/.local/lib/python3.10/site-packages/dpgen/data/gen.py", line 1425, in gen_init_bulk
run_vasp_relax(jdata, mdata)
File "MyPrefix/.local/lib/python3.10/site-packages/dpgen/data/gen.py", line 1056, in run_vasp_relax
submission.run_submission()
File "MyPrefix/anaconda3/envs/deepmd/lib/python3.10/site-packages/dpdispatcher/submission.py", line 187, in run_submission
self.update_submission_state()
File "MyPrefix/anaconda3/envs/deepmd/lib/python3.10/site-packages/dpdispatcher/submission.py", line 233, in update_submission_state
job.get_job_state()
File "MyPrefix/anaconda3/envs/deepmd/lib/python3.10/site-packages/dpdispatcher/submission.py", line 595, in get_job_state
job_state = self.machine.check_status(self)
File "MyPrefix/anaconda3/envs/deepmd/lib/python3.10/site-packages/dpdispatcher/pbs.py", line 67, in check_status
status_word = status_line.split ()[-2]
IndexError: list index out of range

And, the machine.json file is like this:

{
"api_version": "1.0",
"fp":[
{
"command": "/opt/intel2016/compilers_and_libraries_2016.2.181/linux/mpi/intel64/bin/mpirun -np 16 MyPrefix/soft/vasp6.3.0/vasp.6.3.0/bin/vasp_std",
"machine": {
"batch_type": "PBS",
"context_type": "local",
"local_root" : "./",
"remote_root": "MyPrefix/soft/dpgen/dpgen_example/init/work"
},
"resources": {
"number_node": 1,
"cpu_per_node": 16,
"gpu_per_node": 0,
"group_size": 1,
"queue_name": "normal",
"source_list": []
}
}
]
}

There is no change in the other input files. In each computational node, there are 16 CPU cores.
However, when I do the same thing with Slurm operating system, it works well.