Hi Anubhav,
Thank you so much for your response! I got the vasp to run, and it had to do with how I tunnel from my database to my localhost. However, the job still doesn’t finish. Now I am doing an elastic constant calculation.
-
The SLURM job says it’s COMPLETED, but the state of my Fireworks is FIZZLED.
-
Here is my the error message I got in my FW_job.error:
ERROR:custodian.custodian:
{ ‘actions’: [ { ‘action’: { ‘_set’: { ‘ALGO’: ‘Normal’}},
‘dict’: ‘INCAR’}],
‘errors’: [ 'Positive ’
‘energy’],
‘handler’: <custodian.vasp.handlers.PositiveEnergyErrorHandler object at 0x2b4687887780>}
ERROR:custodian.custodian:
{ ‘actions’: [ { ‘action’: { ‘_set’: { ‘IBRION’: 3,
‘SMASS’: 0.75}},
‘dict’: ‘INCAR’}],
‘errors’: [ ‘POTIM’],
‘handler’: <custodian.vasp.handlers.PotimErrorHandler object at 0x2b4687887da0>}
ERROR:custodian.custodian:
{ ‘actions’: None,
‘errors’: [ 'Positive ’
‘energy’],
‘handler’: <custodian.vasp.handlers.PositiveEnergyErrorHandler object at 0x2b4687887780>}
ERROR:custodian.custodian:Unrecoverable error for handler: <custodian.vasp.handlers.PositiveEnergyErrorHandler object at 0x2b
Traceback (most recent call last):
File “/n/home02/zzhu/.conda/envs/atomate_env/lib/python3.6/site-packages/custodian/custodian.py”, line 320, in run
self._run_job(job_n, job)
File “/n/home02/zzhu/.conda/envs/atomate_env/lib/python3.6/site-packages/custodian/custodian.py”, line 446, in _run_job
raise CustodianError(s, True, x[“handler”])
custodian.custodian.CustodianError: (CustodianError(…), 'Unrecoverable error for handler: <custodian.vasp.handlers.Positive
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/n/home02/zzhu/atomate/codes/fireworks/fireworks/core/rocket.py”, line 262, in run
m_action = t.run_task(my_spec)
File “/n/home02/zzhu/atomate/codes/atomate/atomate/vasp/firetasks/run_calc.py”, line 205, in run_task
c.run()
File “/n/home02/zzhu/.conda/envs/atomate_env/lib/python3.6/site-packages/custodian/custodian.py”, line 330, in run
.format(self.total_errors, ex))
RuntimeError: 5 errors reached: (CustodianError(…), 'Unrecoverable error for handler: <custodian.vasp.handlers.PositiveEner
INFO:rocket.launcher:Rocket finished
Here is my FW_job.out file content:
2019-04-09 16:39:04,330 INFO Hostname/IP lookup (this will take a few seconds)
2019-04-09 16:39:18,399 INFO Created new dir /n/home02/zzhu/atomate/testruns/elastic/launcher_2019-04-09-20-39-18-392015
2019-04-09 16:39:18,404 INFO Launching Rocket
2019-04-09 16:39:19,786 INFO RUNNING fw_id: 30 in directory: /n/home02/zzhu/atomate/testruns/elastic/launcher_2019-04-09-20-3
2019-04-09 16:39:20,607 INFO Task started: FileWriteTask.
2019-04-09 16:39:20,619 INFO Task completed: FileWriteTask
2019-04-09 16:39:20,791 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.
2019-04-09 16:39:20,867 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}
2019-04-09 16:39:21,039 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.
2019-04-09 19:55:16,512 INFO Rocket finished
- Here are my config files:
db.json
{
“host”: “localhost”,
“port”: 27021,
“database”: “2d_materials”,
“collection”: “tasks”,
“admin_user”: “<<admin_user>>”,
“admin_password”: “<<admin_pwd>>”,
“readonly_user”: “<<ro_user>>”,
“readonly_password”: <<ro_pwd>>",
“aliases”: {}
}
FW_config.yaml
CONFIG_FILE_DIR: <<home_directory>>/atomate/config_nersc/db.json
my_fworker.yaml
name: fwork
category: ‘’
query: ‘{}’
env:
db_file: <<home_directory>>/atomate/config_nersc/db.json
vasp_cmd: mpirun -n 2 <<vasp_directory>>/vasp.5.4.4.std
scratch_dir: null
my_launchpad.yaml
host: localhost
port: 27021
name: 2d_materials
username: <<admin_user>>
password: <<admin_pwd>>
ssl: false
logdir: null
strm_lvl: INFO
user_indices:
wf_user_indices:
I really appreciate your help!
Best.
Zoe
···
Ziyan (Zoe) Zhu
Ph.D. Candidate
Department of Physics, Harvard University
zz…@g.harvard.edu, [email protected]
(310)-210-0580
On Tue, Apr 9, 2019 at 12:36 PM Anubhav Jain [email protected] wrote:
Hi Zoe,
Congrats on getting everything set up!
When you say “the status of the job is completed”, do you mean your PBS/SLURM/etc job is completed, or that FireWorks says that your job is in the COMPLETED state?
I think the following checks / information is needed to debug more:
- What is the state of your Firework? My guess is it will be FIZZLED. If it is fizzled, what is the error message in the launch object?
- What are the contents of your FW_job.out and FW_job.error files (assuming you used standard my_qadapter.yaml names for error files) in your output directory?
- If you can send any other files in your directory (e.g. FW.json) that would also be helpful.
On Monday, April 8, 2019 at 3:12:07 PM UTC-7, [email protected] wrote:
Hi,
I followed all the documentation, configured everything, added the pseudopotential files, and got my database set up properly. I was able to add workflows and submit the job. However, even though the job submission is successful, I don’t get any output.
Here is the python file that adds the workflow:
#Calculate band structure of bilayer Graphene
from pymatgen import Structure
from fireworks import LaunchPad
from atomate.vasp.workflows.presets.core import wf_bandstructure
struct = Structure.from_file(‘POSCAR’)
wf = wf_bandstructure(struct)
lpad = LaunchPad.auto_load()
lpad.add_wf(wf)
And if I do “qlauanch singleshot”, this is the only output I get:
2019-04-08 17:56:42,376 INFO Hostname/IP lookup (this will take a few seconds)
And the status of the job is completed.
The vasp calculation doesn’t start, and it doesn’t create incar or any other files.
Any help is appreciated!
Thanks,
Zoe
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