About the machine.json for the PBS system

[maverick422]

First of all, thanks for taking the time to read my question!
here is version of the modules i used
DeepModeling

Version: 0.10.2
Date: Aug-28-2021
DeePMD-kit v2.0.3

for the test, i had two jobs and two machine.json files
for the first one here is my input file

param.json.txt
machine.json.txt
and PBS script
dpgen-init.pbs.txt
the log file is

`DeepModeling

Version: 0.10.2
Date: Aug-28-2021
Path: /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen

Dependency

 numpy     1.20.3   /public/home/huangan21/dpgen/lib/python3.8/site-packages/numpy
dpdata      0.2.1   /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpdata

pymatgen unknown version or path
monty 2021.8.17 /public/home/huangan21/dpgen/lib/python3.8/site-packages/monty
ase 3.22.0 /public/home/huangan21/dpgen/lib/python3.8/site-packages/ase
paramiko 2.7.2 /public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko
custodian Not Found

Reference

Please cite:
Yuzhi Zhang, Haidi Wang, Weijie Chen, Jinzhe Zeng, Linfeng Zhang, Han Wang, and Weinan E,
DP-GEN: A concurrent learning platform for the generation of reliable deep learning
based potential energy models, Computer Physics Communications, 2020, 107206.

Description

Traceback (most recent call last):
File "/public/home/huangan21/dpgen/bin/dpgen", line 10, in
sys.exit(main())
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/main.py", line 175, in main
args.func(args)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/data/gen.py", line 777, in gen_init_bulk
make_vasp_relax(jdata, mdata)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/data/gen.py", line 311, in make_vasp_relax
os.remove(os.path.join(work_dir, 'INCAR' ))
FileNotFoundError: [Errno 2] No such file or directory: '/public/home/huangan21/SiC/dpgen/init/POSCAR.01x01x01/00.place_ele/INCAR'
DeepModeling

Version: 0.10.2
Date: Aug-28-2021
Path: /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen

Dependency

 numpy     1.20.3   /public/home/huangan21/dpgen/lib/python3.8/site-packages/numpy
dpdata      0.2.1   /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpdata

pymatgen unknown version or path
monty 2021.8.17 /public/home/huangan21/dpgen/lib/python3.8/site-packages/monty
ase 3.22.0 /public/home/huangan21/dpgen/lib/python3.8/site-packages/ase
paramiko 2.7.2 /public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko
custodian Not Found

Reference

Please cite:
Yuzhi Zhang, Haidi Wang, Weijie Chen, Jinzhe Zeng, Linfeng Zhang, Han Wang, and Weinan E,
DP-GEN: A concurrent learning platform for the generation of reliable deep learning
based potential energy models, Computer Physics Communications, 2020, 107206.

Description

DeepModeling

Version: 0.10.2
Date: Aug-28-2021
Path: /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen

Dependency

 numpy     1.20.3   /public/home/huangan21/dpgen/lib/python3.8/site-packages/numpy
dpdata      0.2.1   /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpdata

pymatgen unknown version or path
monty 2021.8.17 /public/home/huangan21/dpgen/lib/python3.8/site-packages/monty
ase 3.22.0 /public/home/huangan21/dpgen/lib/python3.8/site-packages/ase
paramiko 2.7.2 /public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko
custodian Not Found

Reference

Please cite:
Yuzhi Zhang, Haidi Wang, Weijie Chen, Jinzhe Zeng, Linfeng Zhang, Han Wang, and Weinan E,
DP-GEN: A concurrent learning platform for the generation of reliable deep learning
based potential energy models, Computer Physics Communications, 2020, 107206.

Description

Traceback (most recent call last):
File "/public/home/huangan21/dpgen/bin/dpgen", line 10, in
sys.exit(main())
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/main.py", line 175, in main
args.func(args)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/data/gen.py", line 777, in gen_init_bulk
make_vasp_relax(jdata, mdata)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/data/gen.py", line 313, in make_vasp_relax
os.remove(os.path.join(work_dir, 'POTCAR'))
FileNotFoundError: [Errno 2] No such file or directory: '/public/home/huangan21/SiC/dpgen/init/POSCAR.01x01x01/00.place_ele/POTCAR'
Traceback (most recent call last):
File "/public/home/huangan21/dpgen/bin/dpgen", line 10, in
sys.exit(main())
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/main.py", line 175, in main
args.func(args)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/data/gen.py", line 777, in gen_init_bulk
make_vasp_relax(jdata, mdata)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/data/gen.py", line 313, in make_vasp_relax
os.remove(os.path.join(work_dir, 'POTCAR'))
FileNotFoundError: [Errno 2] No such file or directory: '/public/home/huangan21/SiC/dpgen/init/POSCAR.01x01x01/00.place_ele/POTCAR'
DeepModeling

Version: 0.10.2
Date: Aug-28-2021
Path: /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen

Dependency

 numpy     1.20.3   /public/home/huangan21/dpgen/lib/python3.8/site-packages/numpy
dpdata      0.2.1   /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpdata

pymatgen unknown version or path
monty 2021.8.17 /public/home/huangan21/dpgen/lib/python3.8/site-packages/monty
ase 3.22.0 /public/home/huangan21/dpgen/lib/python3.8/site-packages/ase
paramiko 2.7.2 /public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko
custodian Not Found

Reference

Please cite:
Yuzhi Zhang, Haidi Wang, Weijie Chen, Jinzhe Zeng, Linfeng Zhang, Han Wang, and Weinan E,
DP-GEN: A concurrent learning platform for the generation of reliable deep learning
based potential energy models, Computer Physics Communications, 2020, 107206.

Description

/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/data/gen.py:612: UserWarning: the dpdispatcher will be updated to new version.And the interface may be changed. Please check the documents for more details
warnings.warn(f"the dpdispatcher will be updated to new version."
Traceback (most recent call last):
File "/public/home/huangan21/dpgen/bin/dpgen", line 10, in
sys.exit(main())
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/main.py", line 175, in main
args.func(args)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/data/gen.py", line 778, in gen_init_bulk
run_vasp_relax(jdata, mdata)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/data/gen.py", line 614, in run_vasp_relax
dispatcher = make_dispatcher(mdata['fp_machine'], mdata['fp_resources'], work_dir, run_tasks, fp_group_size)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Dispatcher.py", line 343, in make_dispatcher
disp = Dispatcher(mdata, context_type=context_type, batch_type=batch_type)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Dispatcher.py", line 52, in init
self.session = SSHSession(remote_profile)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/SSHContext.py", line 22, in init
self._setup_ssh(hostname=self.remote_host,
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/SSHContext.py", line 70, in _setup_ssh
self.ssh.connect(hostname=hostname, port=port,
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko/client.py", line 349, in connect
retry_on_signal(lambda: sock.connect(addr))
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko/util.py", line 283, in retry_on_signal
return function()
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko/client.py", line 349, in
retry_on_signal(lambda: sock.connect(addr))
OSError: [Errno 101] Network is unreachable`

the second one use a diffierent machine.json
machine2.json.txt
the PBS script
dpgen.pbs.txt
the log file

`/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py:580: UserWarning: the dpdispatcher will be updated to new version.And the interface may be changed. Please check the documents for more details
warnings.warn(f"the dpdispatcher will be updated to new version."
INFO:dpgen:cannot find key "batch" in machine file, try to use deprecated key "machine_type"
/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py:580: UserWarning: the dpdispatcher will be updated to new version.And the interface may be changed. Please check the documents for more details
warnings.warn(f"the dpdispatcher will be updated to new version."
INFO:dpgen:cannot find key "batch" in machine file, try to use deprecated key "machine_type"
/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py:580: UserWarning: the dpdispatcher will be updated to new version.And the interface may be changed. Please check the documents for more details
warnings.warn(f"the dpdispatcher will be updated to new version."
INFO:dpgen:cannot find key "batch" in machine file, try to use deprecated key "machine_type"
/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py:580: UserWarning: the dpdispatcher will be updated to new version.And the interface may be changed. Please check the documents for more details
warnings.warn(f"the dpdispatcher will be updated to new version."
INFO:dpgen:cannot find key "batch" in machine file, try to use deprecated key "machine_type"
/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py:580: UserWarning: the dpdispatcher will be updated to new version.And the interface may be changed. Please check the documents for more details
warnings.warn(f"the dpdispatcher will be updated to new version."
INFO:dpgen:cannot find key "batch" in machine file, try to use deprecated key "machine_type"
/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py:580: UserWarning: the dpdispatcher will be updated to new version.And the interface may be changed. Please check the documents for more details
warnings.warn(f"the dpdispatcher will be updated to new version."
INFO:dpgen:cannot find key "batch" in machine file, try to use deprecated key "machine_type"
/public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko/client.py:835: UserWarning: Unknown ssh-ed25519 host key for localhost: b'edbf351dbd64d98b54cc2ddf358eed1b'
warnings.warn(
DeepModeling

Version: 0.10.2
Date: Aug-28-2021
Path: /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen

Dependency

 numpy     1.20.3   /public/home/huangan21/dpgen/lib/python3.8/site-packages/numpy
dpdata      0.2.1   /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpdata

pymatgen unknown version or path
monty 2021.8.17 /public/home/huangan21/dpgen/lib/python3.8/site-packages/monty
ase 3.22.0 /public/home/huangan21/dpgen/lib/python3.8/site-packages/ase
paramiko 2.7.2 /public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko
custodian Not Found

Reference

Please cite:
Yuzhi Zhang, Haidi Wang, Weijie Chen, Jinzhe Zeng, Linfeng Zhang, Han Wang, and Weinan E,
DP-GEN: A concurrent learning platform for the generation of reliable deep learning
based potential energy models, Computer Physics Communications, 2020, 107206.

Description

/public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko/client.py:835: UserWarning: Unknown ssh-ed25519 host key for localhost: b'edbf351dbd64d98b54cc2ddf358eed1b'
warnings.warn(
DeepModeling

Version: 0.10.2
Date: Aug-28-2021
Path: /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen

Dependency

 numpy     1.20.3   /public/home/huangan21/dpgen/lib/python3.8/site-packages/numpy
dpdata      0.2.1   /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpdata

pymatgen unknown version or path
monty 2021.8.17 /public/home/huangan21/dpgen/lib/python3.8/site-packages/monty
ase 3.22.0 /public/home/huangan21/dpgen/lib/python3.8/site-packages/ase
paramiko 2.7.2 /public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko
custodian Not Found

Reference

Please cite:
Yuzhi Zhang, Haidi Wang, Weijie Chen, Jinzhe Zeng, Linfeng Zhang, Han Wang, and Weinan E,
DP-GEN: A concurrent learning platform for the generation of reliable deep learning
based potential energy models, Computer Physics Communications, 2020, 107206.

Description

/public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko/client.py:835: UserWarning: Unknown ssh-ed25519 host key for localhost: b'edbf351dbd64d98b54cc2ddf358eed1b'
warnings.warn(
DeepModeling

Version: 0.10.2
Date: Aug-28-2021
Path: /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen

Dependency

 numpy     1.20.3   /public/home/huangan21/dpgen/lib/python3.8/site-packages/numpy
dpdata      0.2.1   /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpdata

pymatgen unknown version or path
monty 2021.8.17 /public/home/huangan21/dpgen/lib/python3.8/site-packages/monty
ase 3.22.0 /public/home/huangan21/dpgen/lib/python3.8/site-packages/ase
paramiko 2.7.2 /public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko
custodian Not Found

Reference

Please cite:
Yuzhi Zhang, Haidi Wang, Weijie Chen, Jinzhe Zeng, Linfeng Zhang, Han Wang, and Weinan E,
DP-GEN: A concurrent learning platform for the generation of reliable deep learning
based potential energy models, Computer Physics Communications, 2020, 107206.

Description

/public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko/client.py:835: UserWarning: Unknown ssh-ed25519 host key for localhost: b'edbf351dbd64d98b54cc2ddf358eed1b'
warnings.warn(
DeepModeling

Version: 0.10.2
Date: Aug-28-2021
Path: /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen

Dependency

 numpy     1.20.3   /public/home/huangan21/dpgen/lib/python3.8/site-packages/numpy
dpdata      0.2.1   /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpdata

pymatgen unknown version or path
monty 2021.8.17 /public/home/huangan21/dpgen/lib/python3.8/site-packages/monty
ase 3.22.0 /public/home/huangan21/dpgen/lib/python3.8/site-packages/ase
paramiko 2.7.2 /public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko
custodian Not Found

Reference

Please cite:
Yuzhi Zhang, Haidi Wang, Weijie Chen, Jinzhe Zeng, Linfeng Zhang, Han Wang, and Weinan E,
DP-GEN: A concurrent learning platform for the generation of reliable deep learning
based potential energy models, Computer Physics Communications, 2020, 107206.

Description

DeepModeling

Version: 0.10.2
Date: Aug-28-2021
Path: /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen

Dependency

 numpy     1.20.3   /public/home/huangan21/dpgen/lib/python3.8/site-packages/numpy
dpdata      0.2.1   /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpdata

pymatgen unknown version or path
monty 2021.8.17 /public/home/huangan21/dpgen/lib/python3.8/site-packages/monty
ase 3.22.0 /public/home/huangan21/dpgen/lib/python3.8/site-packages/ase
paramiko 2.7.2 /public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko
custodian Not Found

Reference

Please cite:
Yuzhi Zhang, Haidi Wang, Weijie Chen, Jinzhe Zeng, Linfeng Zhang, Han Wang, and Weinan E,
DP-GEN: A concurrent learning platform for the generation of reliable deep learning
based potential energy models, Computer Physics Communications, 2020, 107206.

Description

/public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko/client.py:835: UserWarning: Unknown ssh-ed25519 host key for localhost: b'edbf351dbd64d98b54cc2ddf358eed1b'
warnings.warn(
Traceback (most recent call last):
File "/public/home/huangan21/dpgen/bin/dpgen", line 10, in
sys.exit(main())
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/main.py", line 175, in main
args.func(args)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 2944, in gen_run
run_iter (args.PARAM, args.MACHINE)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 2909, in run_iter
run_train (ii, jdata, mdata)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 583, in run_train
dispatcher.run_jobs(mdata['train_resources'],
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Dispatcher.py", line 84, in run_jobs
job_handler = self.submit_jobs(resources,
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Dispatcher.py", line 159, in submit_jobs
rjob['batch'].submit(cur_chunk, command, res = resources, outlog=outlog, errlog=errlog, restart = True)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Batch.py", line 109, in submit
status = self.check_status()
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/PBS.py", line 25, in check_status
raise RuntimeError ("status command qstat fails to execute. erro info: %s return code %d"
RuntimeError: status command qstat fails to execute. erro info: bash: qstat: command not found
return code 127
Traceback (most recent call last):
File "/public/home/huangan21/dpgen/bin/dpgen", line 10, in
sys.exit(main())
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/main.py", line 175, in main
args.func(args)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 2944, in gen_run
run_iter (args.PARAM, args.MACHINE)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 2909, in run_iter
run_train (ii, jdata, mdata)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 583, in run_train
dispatcher.run_jobs(mdata['train_resources'],
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Dispatcher.py", line 84, in run_jobs
job_handler = self.submit_jobs(resources,
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Dispatcher.py", line 159, in submit_jobs
rjob['batch'].submit(cur_chunk, command, res = resources, outlog=outlog, errlog=errlog, restart = True)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Batch.py", line 109, in submit
status = self.check_status()
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/PBS.py", line 25, in check_status
raise RuntimeError ("status command qstat fails to execute. erro info: %s return code %d"
RuntimeError: status command qstat fails to execute. erro info: bash: qstat: command not found
return code 127
Traceback (most recent call last):
File "/public/home/huangan21/dpgen/bin/dpgen", line 10, in
sys.exit(main())
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/main.py", line 175, in main
args.func(args)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 2944, in gen_run
run_iter (args.PARAM, args.MACHINE)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 2909, in run_iter
run_train (ii, jdata, mdata)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 583, in run_train
dispatcher.run_jobs(mdata['train_resources'],
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Dispatcher.py", line 84, in run_jobs
job_handler = self.submit_jobs(resources,
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Dispatcher.py", line 159, in submit_jobs
rjob['batch'].submit(cur_chunk, command, res = resources, outlog=outlog, errlog=errlog, restart = True)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Batch.py", line 109, in submit
status = self.check_status()
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/PBS.py", line 25, in check_status
raise RuntimeError ("status command qstat fails to execute. erro info: %s return code %d"
RuntimeError: status command qstat fails to execute. erro info: bash: qstat: command not found
return code 127
Traceback (most recent call last):
File "/public/home/huangan21/dpgen/bin/dpgen", line 10, in
sys.exit(main())
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/main.py", line 175, in main
args.func(args)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 2944, in gen_run
run_iter (args.PARAM, args.MACHINE)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 2909, in run_iter
run_train (ii, jdata, mdata)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 583, in run_train
dispatcher.run_jobs(mdata['train_resources'],
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Dispatcher.py", line 84, in run_jobs
job_handler = self.submit_jobs(resources,
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Dispatcher.py", line 159, in submit_jobs
rjob['batch'].submit(cur_chunk, command, res = resources, outlog=outlog, errlog=errlog, restart = True)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Batch.py", line 109, in submit
status = self.check_status()
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/PBS.py", line 25, in check_status
raise RuntimeError ("status command qstat fails to execute. erro info: %s return code %d"
RuntimeError: status command qstat fails to execute. erro info: bash: qstat: command not found
return code 127
Traceback (most recent call last):
File "/public/home/huangan21/dpgen/bin/dpgen", line 10, in
sys.exit(main())
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/main.py", line 175, in main
args.func(args)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 2944, in gen_run
run_iter (args.PARAM, args.MACHINE)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 2909, in run_iter
run_train (ii, jdata, mdata)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 583, in run_train
dispatcher.run_jobs(mdata['train_resources'],
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Dispatcher.py", line 84, in run_jobs
job_handler = self.submit_jobs(resources,
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Dispatcher.py", line 159, in submit_jobs
rjob['batch'].submit(cur_chunk, command, res = resources, outlog=outlog, errlog=errlog, restart = True)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Batch.py", line 109, in submit
status = self.check_status()
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/PBS.py", line 25, in check_status
raise RuntimeError ("status command qstat fails to execute. erro info: %s return code %d"
RuntimeError: status command qstat fails to execute. erro info: bash: qstat: command not found
return code 127
/public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko/client.py:835: UserWarning: Unknown ssh-ed25519 host key for localhost: b'edbf351dbd64d98b54cc2ddf358eed1b'
warnings.warn(
DeepModeling

Version: 0.10.2
Date: Aug-28-2021
Path: /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen

Dependency

 numpy     1.20.3   /public/home/huangan21/dpgen/lib/python3.8/site-packages/numpy
dpdata      0.2.1   /public/home/huangan21/dpgen/lib/python3.8/site-packages/dpdata

pymatgen unknown version or path
monty 2021.8.17 /public/home/huangan21/dpgen/lib/python3.8/site-packages/monty
ase 3.22.0 /public/home/huangan21/dpgen/lib/python3.8/site-packages/ase
paramiko 2.7.2 /public/home/huangan21/dpgen/lib/python3.8/site-packages/paramiko
custodian Not Found

Reference

Please cite:
Yuzhi Zhang, Haidi Wang, Weijie Chen, Jinzhe Zeng, Linfeng Zhang, Han Wang, and Weinan E,
DP-GEN: A concurrent learning platform for the generation of reliable deep learning
based potential energy models, Computer Physics Communications, 2020, 107206.

Description

Traceback (most recent call last):
File "/public/home/huangan21/dpgen/bin/dpgen", line 10, in
sys.exit(main())
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/main.py", line 175, in main
args.func(args)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 2944, in gen_run
run_iter (args.PARAM, args.MACHINE)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 2909, in run_iter
run_train (ii, jdata, mdata)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/generator/run.py", line 583, in run_train
dispatcher.run_jobs(mdata['train_resources'],
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Dispatcher.py", line 84, in run_jobs
job_handler = self.submit_jobs(resources,
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Dispatcher.py", line 159, in submit_jobs
rjob['batch'].submit(cur_chunk, command, res = resources, outlog=outlog, errlog=errlog, restart = True)
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/Batch.py", line 109, in submit
status = self.check_status()
File "/public/home/huangan21/dpgen/lib/python3.8/site-packages/dpgen/dispatcher/PBS.py", line 25, in check_status
raise RuntimeError ("status command qstat fails to execute. erro info: %s return code %d"
RuntimeError: status command qstat fails to execute. erro info: bash: qstat: command not found
return code 127
`
what shuold i do to continue my job? also how should i control the used nodes for the Submitted tasks? thank you very much!

[AnguseZhang]

What's your running command? Why are there so many error logs?

[maverick422]

for prepare initial data for bulk systems

#!/bin/bash
#PBS -N dpgen
#PBS -l nodes=node008:ppn=4
#PBS -q gpu
#PBS -j oe

cd "$PBS_O_WORKDIR"
NPROCS=wc -l < $PBS_NODEFILE

OMP_NUM_THREADS=1 mpirun -machinefile $PBS_NODEFILE -np $NPROCS dpgen init_bulk param.json machine.json >|LOG.dp 2>&1

and the Main Process of Generator

#!/bin/bash
#PBS -N dpgen
#PBS -l nodes=node008:ppn=6
#PBS -q gpu
#PBS -j oe

cd "$PBS_O_WORKDIR"
NPROCS=wc -l < $PBS_NODEFILE

OMP_NUM_THREADS=1 mpirun -machinefile $PBS_NODEFILE -np $NPROCS dpgen run param_BPo.json machine.json >|LOG.dp 2>&1

[AnguseZhang]

There is no need to perform mpirun for dpgen run, otherwise there will be too many warnings like you did and stop you from locating the real problem.
Also, there is no need to submit dpgen run as a job. You can configure the parameters for machines in machine.json.

[maverick422]

Thank you very much and I will try as you said!