Hello.
I'm Japanese student. If there is something wrong in my question , please let me know that.
I'm trying "Installing atomate", and finished "Submit the workflow" . However, the error in "FW_job-***.error" occurred like:
Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x150f6451eb70>
Traceback (most recent call last):
File "/home/kamatani/.pyenv/versions/3.7.3/lib/python3.7/site-packages/fireworks/core/rocket.py", line 262, in run
m_action = t.run_task(my_spec)
File "/home/kamatani/.pyenv/versions/3.7.3/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py", line 205, in run_task
c.run()
File "/home/kamatani/.pyenv/versions/3.7.3/lib/python3.7/site-packages/custodian/custodian.py", line 328, in run
self._run_job(job_n, job)
File "/home/kamatani/.pyenv/versions/3.7.3/lib/python3.7/site-packages/custodian/custodian.py", line 452, in _run_job
raise ValidationError(s, True, v)
custodian.custodian.ValidationError: Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x150f6451eb70>
In "Add a workflow", I used the command that atwf add -l vasp -s optimize_only.yaml -m mp-149 -c '{"vasp_cmd": "sbatch /home/kamatani/atomate/config/slurm_mpi_job.sh", "db_file": "/home/kamatani/atomate/config/db.json"}'
I don't know what the cause was.
please help me.
custodian.custodian.ValidationError: Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x150f6451eb70>
"sbatch /home/kamatani/atomate/config/slurm_mpi_job.sh"
_fw_name : CommonAdapter
_fw_q_type : SLURM
rocket_launch : rlaunch -c /home/kamatani/atomate/config rapidfire
nodes : 2
walltime : 24:00:00
queue : null
account : null
job_name : null
pre_rocket : null
post_rocket : null
logdir : /home/kamatani/atomate/logs
(atomate_env) kamatani@valkyrie01 $ lpad reset [~/calc/vasp/mgo]
Are you sure? This will RESET 1 workflows and all data. (Y/N)Y
2019-06-10 17:48:59,453 INFO Performing db tune-up
2019-06-10 17:48:59,659 INFO LaunchPad was RESET.
(atomate_env) kamatani@valkyrie01 $ atwf add -l vasp -s optimize_only.yaml -m mp-149 -c '{"vasp_cmd": "mpirun vasp_std", "db_file": "/home/kamatani/atomate/config/db.json"}'
2019-06-10 17:49:12,322 INFO Added a workflow. id_map: {-1: 1}
(atomate_env) kamatani@valkyrie01 $ qlaunch singleshot [~/calc/vasp/mgo]
2019-06-10 17:49:19,543 INFO moving to launch_dir /home/kamatani/calc/vasp/mgo
2019-06-10 17:49:19,544 INFO submitting queue script
2019-06-10 17:49:19,561 INFO Job submission was successful and job_id is 735
(atomate_env) kamatani@valkyrie01 $ lpad get_wflows [~/calc/vasp/mgo]
{
"state": "FIZZLED",
"name": "Si--1",
"created_on": "2019-06-10T08:49:12.293000",
"states_list": "F"
}
lpad get_fws -i 1 -d more
(atomate_env) kamatani@valkyrie01 $ lpad get_fws -i 1 -d more [~/calc/vasp/mgo]
{
"fw_id": 1,
"created_on": "2019-06-10T08:49:12.292858",
"updated_on": "2019-06-10T08:49:35.686104",
"launches": [
{
"fworker": {
"name": "kamatani",
"category": "",
"query": "{}",
"env": {
"db_file": "/home/kamatani/atomate/config/db.json",
"vasp_cmd": "sbatch /home/kamatani/atomate/config/slurm_mpi_job.sh",
"scratch_dir": null
}
},
"fw_id": 1,
"launch_dir": "/home/kamatani/calc/vasp/mgo/launcher_2019-06-10-08-49-25-373963",
"host": "valkyrie16",
"ip": "192.168.114.95",
"trackers": [],
"action": {
"stored_data": {
"_message": "runtime error during task",
"_task": {
"vasp_cmd": "mpirun vasp_std",
"job_type": "double_relaxation_run",
"max_force_threshold": 0.25,
"ediffg": null,
"auto_npar": ">>auto_npar<<",
"half_kpts_first_relax": false,
"_fw_name": "{{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}"
},
"_exception": {
"_stacktrace": "Traceback (most recent call last):\n File \"/home/kamatani/.pyenv/versions/3.7.3/lib/python3.7/site-packages/fireworks/core/rocket.py\", line 262, in run\n m_action = t.run_task(my_spec)\n File \"/home/kamatani/.pyenv/versions/3.7.3/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py\", line 205, in run_task\n c.run()\n File \"/home/kamatani/.pyenv/versions/3.7.3/lib/python3.7/site-packages/custodian/custodian.py\", line 328, in run\n self._run_job(job_n, job)\n File \"/home/kamatani/.pyenv/versions/3.7.3/lib/python3.7/site-packages/custodian/custodian.py\", line 452, in _run_job\n raise ValidationError(s, True, v)\ncustodian.custodian.ValidationError: Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x1540dfedcd30>\n",
"_details": null
}
},
"exit": true,
"update_spec": {},
"mod_spec": [],
"additions": [],
"detours": [],
"defuse_children": false,
"defuse_workflow": false
},
"state": "FIZZLED",
"state_history": [
{
"state": "RUNNING",
"created_on": "2019-06-10T08:49:25.420923",
"updated_on": "2019-06-10T08:49:35.670536",
"checkpoint": {
"_task_n": 1,
"_all_stored_data": {},
"_all_update_spec": {},
"_all_mod_spec": []
}
},
{
"state": "FIZZLED",
"created_on": "2019-06-10T08:49:35.674017",
"checkpoint": {
"_task_n": 1,
"_all_stored_data": {},
"_all_update_spec": {},
"_all_mod_spec": []
}
}
],
"launch_id": 1
}
],
"state": "FIZZLED",
"name": "Si-structure optimization"
}
(atomate_env) kamatani@valkyrie01 $ mpirun vasp_std [~/calc/vasp/mgo]
--------------------------------------------------------------------------
mpirun was unable to find the specified executable file, and therefore
did not launch the job. This error was first reported for process
rank 0; it may have occurred for other processes as well.
NOTE: A common cause for this error is misspelling a mpirun command
line parameter option (remember that mpirun interprets the first
unrecognized command line token as the executable).
Node: valkyrie01
Executable: vasp_std
--------------------------------------------------------------------------
16 total processes failed to start
(atomate_env) kamatani@valkyrie01 $ cd launcher_2019-06-10-08-49-25-373963 [~/calc/vasp/mgo]
(atomate_env) kamatani@valkyrie01 $ mpirun vasp_std [~/calc/vasp/mgo/launcher_2019-06-10-08-49-25-373963]
--------------------------------------------------------------------------
mpirun was unable to find the specified executable file, and therefore
did not launch the job. This error was first reported for process
rank 0; it may have occurred for other processes as well.
NOTE: A common cause for this error is misspelling a mpirun command
line parameter option (remember that mpirun interprets the first
unrecognized command line token as the executable).
Node: valkyrie01
Executable: vasp_std
--------------------------------------------------------------------------
16 total processes failed to start