custodian.custodian.ValidationError during launching calculations

Sandeep · August 2, 2019, 5:03pm

Hi,

I am a new user for atomate. After installation, I tried to launch calculations (example of MgO band structure) using atomate. I follow the instruction (https://atomate.org/running_workflows.html#prerequisites). But after running some time, I found the “FIZZLED” state instead of running. To Add workflow to LaunchPad and running the workflow, I used below step:

lpad reset

python mgo_bandstructure.py

rlaunch singleshot

Below are mongodb functioning of fireworks:

_id

:
5d4348845d924746e1f79dd0

spec

:
Object

fw_id

:
1

created_on

:
“2019-08-01T20:16:03.198678”

updated_on

:
“2019-08-01T20:16:03.198679”

name

:
“MgO-nscf line”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd1

spec

:
Object

fw_id

:
2

created_on

:
“2019-08-01T20:16:03.198584”

updated_on

:
“2019-08-01T20:16:03.198585”

name

:
“MgO-nscf uniform”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd2

spec

:
Object

fw_id

:
3

created_on

:
“2019-08-01T20:16:03.198475”

updated_on

:
“2019-08-01T20:16:03.198476”

name

:
“MgO-static”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

  _id : 5d4348845d924746e1f79dd3

 spec : Object

```
  fw_id : 4
```

  created_on : "2019-08-01T20:16:03.198222"

 updated_on : "2019-08-01T20:17:49.993173"

   name : "MgO-structure optimization"

    launches : Array

 archived_launches : Array

0 : 1

6.         state : "FIZZLED"

And at last I got an error below when I used “rlaunch singleshot”.

2019-08-01 22:16:21,937 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-01 22:16:21,938 INFO Launching Rocket

2019-08-01 22:16:26,720 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO

2019-08-01 22:16:27,945 INFO Task started: FileWriteTask.

2019-08-01 22:16:27,946 INFO Task completed: FileWriteTask

2019-08-01 22:16:28,191 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-01 22:16:28,212 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-01 22:16:28,455 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x7fd530602400>

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 205, in run_task

c.run()

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/custodian/custodian.py”, line 328, in run

self._run_job(job_n, job)

File “/home/users/skumar/anaconda3/envs/atomate_opt/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 0x7fd530602400>

2019-08-01 22:17:50,731 INFO Rocket finished

Please suggest me what should I do to remove this error? I would be thankful.

Many thanks and regards

Sandeep

Anubhav_Jain · August 6, 2019, 4:42pm

Hi Sandeep

If you run “rlaunch singleshot”, it will run the workflow on your local system. This means that VASP will also be executed on your local system. I’d first make sure VASP is properly installed on your system.

If you feel that is the case, can you provide more details? For example, does the VASP run start at all? If so, what are the contents of the OUTCAR? Also, what does FW_job.error and FW_job.out say?

Best,

Anubhav

···

On Friday, August 2, 2019 at 10:03:39 AM UTC-7, Sandeep wrote:

Hi,

I am a new user for atomate. After installation, I tried to launch calculations (example of MgO band structure) using atomate. I follow the instruction (https://atomate.org/running_workflows.html#prerequisites). But after running some time, I found the “FIZZLED” state instead of running. To Add workflow to LaunchPad and running the workflow, I used below step:

lpad reset

python mgo_bandstructure.py

rlaunch singleshot

Below are mongodb functioning of fireworks:

_id

:
5d4348845d924746e1f79dd0

spec

:
Object

fw_id

:
1

created_on

:
“2019-08-01T20:16:03.198678”

updated_on

:
“2019-08-01T20:16:03.198679”

name

:
“MgO-nscf line”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd1

spec

:
Object

fw_id

:
2

created_on

:
“2019-08-01T20:16:03.198584”

updated_on

:
“2019-08-01T20:16:03.198585”

name

:
“MgO-nscf uniform”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd2

spec

:
Object

fw_id

:
3

created_on

:
“2019-08-01T20:16:03.198475”

updated_on

:
“2019-08-01T20:16:03.198476”

name

:
“MgO-static”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

```
  _id : 5d4348845d924746e1f79dd3
```

       spec : Object

```
  fw_id : 4
```

  created_on : "2019-08-01T20:16:03.198222"

 updated_on : "2019-08-01T20:17:49.993173"

```
   name : "MgO-structure optimization"
```

          launches : Array

       archived_launches : Array

0 : 1

6.         state : "FIZZLED"

And at last I got an error below when I used “rlaunch singleshot”.

2019-08-01 22:16:21,937 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-01 22:16:21,938 INFO Launching Rocket

2019-08-01 22:16:26,720 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO

2019-08-01 22:16:27,945 INFO Task started: FileWriteTask.

2019-08-01 22:16:27,946 INFO Task completed: FileWriteTask

2019-08-01 22:16:28,191 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-01 22:16:28,212 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-01 22:16:28,455 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x7fd530602400>

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 205, in run_task

c.run()

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/custodian/custodian.py”, line 328, in run

self._run_job(job_n, job)

File “/home/users/skumar/anaconda3/envs/atomate_opt/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 0x7fd530602400>

2019-08-01 22:17:50,731 INFO Rocket finished

Please suggest me what should I do to remove this error? I would be thankful.

Many thanks and regards

Sandeep

Sandeep · August 6, 2019, 5:28pm

Dear Anubhav,

Thank you very much for your reply. Actually, VASP run through a job scheduler like SLURM . So I think I should use qlaunch instead of rlaunch and for this, I set up my_qadapter.yaml file and the contain inside are below:

my_qadapter.yaml

fw_name: CommonAdapter

_fw_q_type: SLURM

_fw_template_file: /scratch/users/skumar/atomate_opt/job_ht.sh

rocket_launch: qlaunch -c /scratch/users/skumar/atomate_opt/config rapidfire

nodes: 2

walltime: 24:00:00

queue: batch

account: null

job_name: null

pre_rocket: null

post_rocket: null

logdir: /scratch/users/skumar/atomate_opt/logs

db.json

{

"host": "mongodb+srv://cluster0-aagd1.mongodb.net/",

"port": 27017,

"database": "test",

"collection": "test",

"admin_user": "test",

"admin_password": "12345",

"authsource": "admin"

"aliases": {}

}

But when I used qlaunch singleshot, I got an error below:

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/bin/qlaunch”, line 10, in

sys.exit(qlaunch())

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/scripts/qlaunch_run.py”, line 222, in qlaunch

do_launch(args)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/scripts/qlaunch_run.py”, line 61, in do_launch

queueadapter = load_object_from_file(args.queueadapter_file)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/utilities/fw_serializers.py”, line 394, in load_object_from_file

return load_object(m_dict)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/utilities/fw_serializers.py”, line 323, in load_object

fw_name = FW_NAME_UPDATES.get(obj_dict['_fw_name'], obj_dict['_fw_name'])

KeyError: ‘_fw_name’

However, I got VASP input files like INCAR, POTCAR, KPOINTS and POSCAR when I used rlaunch singleshot with an error. And it was like below:

2019-08-06 19:07:47,701 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-06 19:07:47,702 INFO Launching Rocket

2019-08-06 19:07:52,654 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO

2019-08-06 19:07:53,886 INFO Task started: FileWriteTask.

2019-08-06 19:07:53,891 INFO Task completed: FileWriteTask

2019-08-06 19:07:54,137 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-06 19:07:54,211 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-06 19:07:54,456 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x7f58d1ededa0>

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 205, in run_task

c.run()

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/custodian/custodian.py”, line 328, in run

self._run_job(job_n, job)

File “/home/users/skumar/anaconda3/envs/atomate_opt/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 0x7f58d1ededa0>

2019-08-06 19:08:16,703 INFO Rocket finished

Could you please suggest me what should I do ? I need your valuable suggestion to resolve this error.

Thanks and regards

Sandeep

···

On Tuesday, August 6, 2019 at 6:42:36 PM UTC+2, Anubhav Jain wrote:

Hi Sandeep

If you run “rlaunch singleshot”, it will run the workflow on your local system. This means that VASP will also be executed on your local system. I’d first make sure VASP is properly installed on your system.

If you feel that is the case, can you provide more details? For example, does the VASP run start at all? If so, what are the contents of the OUTCAR? Also, what does FW_job.error and FW_job.out say?

Best,

Anubhav

On Friday, August 2, 2019 at 10:03:39 AM UTC-7, Sandeep wrote:

Hi,

I am a new user for atomate. After installation, I tried to launch calculations (example of MgO band structure) using atomate. I follow the instruction (https://atomate.org/running_workflows.html#prerequisites). But after running some time, I found the “FIZZLED” state instead of running. To Add workflow to LaunchPad and running the workflow, I used below step:

lpad reset

python mgo_bandstructure.py

rlaunch singleshot

Below are mongodb functioning of fireworks:

_id

:
5d4348845d924746e1f79dd0

spec

:
Object

fw_id

:
1

created_on

:
“2019-08-01T20:16:03.198678”

updated_on

:
“2019-08-01T20:16:03.198679”

name

:
“MgO-nscf line”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd1

spec

:
Object

fw_id

:
2

created_on

:
“2019-08-01T20:16:03.198584”

updated_on

:
“2019-08-01T20:16:03.198585”

name

:
“MgO-nscf uniform”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd2

spec

:
Object

fw_id

:
3

created_on

:
“2019-08-01T20:16:03.198475”

updated_on

:
“2019-08-01T20:16:03.198476”

name

:
“MgO-static”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

```
  _id : 5d4348845d924746e1f79dd3
```

       spec : Object

```
  fw_id : 4
```

  created_on : "2019-08-01T20:16:03.198222"

 updated_on : "2019-08-01T20:17:49.993173"

```
   name : "MgO-structure optimization"
```

          launches : Array

       archived_launches : Array

0 : 1

6.         state : "FIZZLED"

And at last I got an error below when I used “rlaunch singleshot”.

2019-08-01 22:16:21,937 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-01 22:16:21,938 INFO Launching Rocket

2019-08-01 22:16:26,720 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO

2019-08-01 22:16:27,945 INFO Task started: FileWriteTask.

2019-08-01 22:16:27,946 INFO Task completed: FileWriteTask

2019-08-01 22:16:28,191 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-01 22:16:28,212 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-01 22:16:28,455 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x7fd530602400>

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 205, in run_task

c.run()

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/custodian/custodian.py”, line 328, in run

self._run_job(job_n, job)

File “/home/users/skumar/anaconda3/envs/atomate_opt/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 0x7fd530602400>

2019-08-01 22:17:50,731 INFO Rocket finished

Please suggest me what should I do to remove this error? I would be thankful.

Many thanks and regards

Sandeep

Anubhav_Jain · August 9, 2019, 10:54pm

Your my_qadapter.yaml should say “_fw_name: CommonAdapter” not “fw_name: CommonAdapter”

···

On Tuesday, August 6, 2019 at 10:28:35 AM UTC-7, Sandeep wrote:

Dear Anubhav,

Thank you very much for your reply. Actually, VASP run through a job scheduler like SLURM . So I think I should use qlaunch instead of rlaunch and for this, I set up my_qadapter.yaml file and the contain inside are below:

my_qadapter.yaml

fw_name: CommonAdapter

_fw_q_type: SLURM

_fw_template_file: /scratch/users/skumar/atomate_opt/job_ht.sh

rocket_launch: qlaunch -c /scratch/users/skumar/atomate_opt/config rapidfire

nodes: 2

walltime: 24:00:00

queue: batch

account: null

job_name: null

pre_rocket: null

post_rocket: null

logdir: /scratch/users/skumar/atomate_opt/logs

db.json

{

"host": "mongodb+srv://[cluster0-aagd1.mongodb.net/](http://cluster0-aagd1.mongodb.net/)",

"port": 27017,

"database": "test",

"collection": "test",

"admin_user": "test",

"admin_password": "12345",

"authsource": "admin"

"aliases": {}

}

But when I used qlaunch singleshot, I got an error below:

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/bin/qlaunch”, line 10, in

sys.exit(qlaunch())

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/scripts/qlaunch_run.py”, line 222, in qlaunch

do_launch(args)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/scripts/qlaunch_run.py”, line 61, in do_launch

queueadapter = load_object_from_file(args.queueadapter_file)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/utilities/fw_serializers.py”, line 394, in load_object_from_file

return load_object(m_dict)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/utilities/fw_serializers.py”, line 323, in load_object

fw_name = FW_NAME_UPDATES.get(obj_dict['_fw_name'], obj_dict['_fw_name'])

KeyError: ‘_fw_name’

However, I got VASP input files like INCAR, POTCAR, KPOINTS and POSCAR when I used rlaunch singleshot with an error. And it was like below:

2019-08-06 19:07:47,701 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-06 19:07:47,702 INFO Launching Rocket

2019-08-06 19:07:52,654 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO

2019-08-06 19:07:53,886 INFO Task started: FileWriteTask.

2019-08-06 19:07:53,891 INFO Task completed: FileWriteTask

2019-08-06 19:07:54,137 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-06 19:07:54,211 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-06 19:07:54,456 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x7f58d1ededa0>

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 205, in run_task

c.run()

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/custodian/custodian.py”, line 328, in run

self._run_job(job_n, job)

File “/home/users/skumar/anaconda3/envs/atomate_opt/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 0x7f58d1ededa0>

2019-08-06 19:08:16,703 INFO Rocket finished

Could you please suggest me what should I do ? I need your valuable suggestion to resolve this error.

Thanks and regards

Sandeep

On Tuesday, August 6, 2019 at 6:42:36 PM UTC+2, Anubhav Jain wrote:

Hi Sandeep

If you run “rlaunch singleshot”, it will run the workflow on your local system. This means that VASP will also be executed on your local system. I’d first make sure VASP is properly installed on your system.

If you feel that is the case, can you provide more details? For example, does the VASP run start at all? If so, what are the contents of the OUTCAR? Also, what does FW_job.error and FW_job.out say?

Best,

Anubhav

On Friday, August 2, 2019 at 10:03:39 AM UTC-7, Sandeep wrote:

Hi,

I am a new user for atomate. After installation, I tried to launch calculations (example of MgO band structure) using atomate. I follow the instruction (https://atomate.org/running_workflows.html#prerequisites). But after running some time, I found the “FIZZLED” state instead of running. To Add workflow to LaunchPad and running the workflow, I used below step:

lpad reset

python mgo_bandstructure.py

rlaunch singleshot

Below are mongodb functioning of fireworks:

_id

:
5d4348845d924746e1f79dd0

spec

:
Object

fw_id

:
1

created_on

:
“2019-08-01T20:16:03.198678”

updated_on

:
“2019-08-01T20:16:03.198679”

name

:
“MgO-nscf line”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd1

spec

:
Object

fw_id

:
2

created_on

:
“2019-08-01T20:16:03.198584”

updated_on

:
“2019-08-01T20:16:03.198585”

name

:
“MgO-nscf uniform”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd2

spec

:
Object

fw_id

:
3

created_on

:
“2019-08-01T20:16:03.198475”

updated_on

:
“2019-08-01T20:16:03.198476”

name

:
“MgO-static”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

```
  _id : 5d4348845d924746e1f79dd3
```

       spec : Object

```
  fw_id : 4
```

  created_on : "2019-08-01T20:16:03.198222"

 updated_on : "2019-08-01T20:17:49.993173"

```
   name : "MgO-structure optimization"
```

          launches : Array

       archived_launches : Array

0 : 1

6.         state : "FIZZLED"

And at last I got an error below when I used “rlaunch singleshot”.

2019-08-01 22:16:21,937 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-01 22:16:21,938 INFO Launching Rocket

2019-08-01 22:16:26,720 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO

2019-08-01 22:16:27,945 INFO Task started: FileWriteTask.

2019-08-01 22:16:27,946 INFO Task completed: FileWriteTask

2019-08-01 22:16:28,191 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-01 22:16:28,212 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-01 22:16:28,455 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x7fd530602400>

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 205, in run_task

c.run()

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/custodian/custodian.py”, line 328, in run

self._run_job(job_n, job)

File “/home/users/skumar/anaconda3/envs/atomate_opt/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 0x7fd530602400>

2019-08-01 22:17:50,731 INFO Rocket finished

Please suggest me what should I do to remove this error? I would be thankful.

Many thanks and regards

Sandeep

Sandeep · August 10, 2019, 10:16am

Dear Anubhav,

Thanks a lot! Now qlaunch is working and relaxation step is done but it stops after optimization. When I used qlaunch rapidfire , I also got these warning below:

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key rocket_launch has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key nodes has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key ntasks_per_node has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key walltime has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

################### slurm.out##############################

== Starting run at Sat Aug 10 11:46:06 CEST 2019

== Job ID: 682351

== Node list: iris-131

== Submit dir. : /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357

Error reading item ‘VCAIMAGES’ from file INCAR.

2019-08-10 11:46:09,017 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-10 11:46:12,788 INFO Created new dir /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:12,789 INFO Launching Rocket

2019-08-10 11:46:14,744 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:15,970 INFO Task started: FileWriteTask.

2019-08-10 11:46:15,971 INFO Task completed: FileWriteTask

2019-08-10 11:46:16,214 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-10 11:46:16,297 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-10 11:46:16,539 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

2019-08-10 11:46:48,138 INFO Task completed: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}

2019-08-10 11:46:48,386 INFO Task started: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}.

2019-08-10 11:46:48,388 INFO Task completed: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}

2019-08-10 11:46:48,633 INFO Task started: {{atomate.vasp.firetasks.parse_outputs.VaspToDb}}.

2019-08-10 11:46:48,633 INFO atomate.vasp.firetasks.parse_outputs PARSING DIRECTORY: /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:48,633 INFO atomate.vasp.drones Getting task doc for base dir :/mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:48,942 INFO atomate.vasp.drones Post-processing dir:/mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:48,943 WARNING atomate.vasp.drones Transformations file does not exist.

2019-08-10 11:46:48,984 INFO atomate.vasp.drones Post-processed /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:51,067 INFO Rocket finished

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/atomate/vasp/firetasks/parse_outputs.py”, line 113, in run_task

mmdb = VaspCalcDb.from_db_file(db_file, admin=True)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/atomate/utils/database.py”, line 114, in from_db_file

creds = loadfn(db_file)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/monty/serialization.py”, line 83, in loadfn

return json.load(fp, *args, **kwargs)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/init.py”, line 296, in load

parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/init.py”, line 361, in loads

return cls(**kw).decode(s)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/monty/json.py”, line 255, in decode

d = json.JSONDecoder.decode(self, s)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/decoder.py”, line 337, in decode

obj, end = self.raw_decode(s, idx=_w(s, 0).end())

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/decoder.py”, line 353, in raw_decode

obj, end = self.scan_once(s, idx)

json.decoder.JSONDecodeError: Expecting ‘,’ delimiter: line 9 column 3 (char 219)

···

######################################################

For your kind information, below are my_qadapter.yaml and job_ht.sh file:

my_qadapter.yaml::::::::::::::::::

_fw_name: CommonAdapter

_fw_q_type: SLURM

_fw_template_file: /scratch/users/skumar/atomate_opt/config/job_ht.sh

rocket_launch: rlaunch -c /scratch/users/skumar/atomate_opt/config rapidfire

nodes: 1

ntasks_per_node: 28

walltime: 05:00:00

queue: null

account: null

job_name: null

pre_rocket: null

post_rocket: null

logdir: /scratch/users/skumar/atomate_opt/logs

job_ht.sh

#!/bin/bash -l

Submission script for Iris

#SBATCH -J HTS

#SBATCH --mail-type=end,fail

#SBATCH [email protected]

#SBATCH -N 1

#SBATCH --ntasks-per-node=28

#SBATCH -c 1

#SBATCH --time=0-05:00:00

#SBATCH -p batch

#SBATCH --qos=qos-batch

####SBATCH --qos=qos-besteffort

#print

echo “== Starting run at $(date)”

echo “== Job ID: ${SLURM_JOBID}”

echo “== Node list: ${SLURM_NODELIST}”

echo “== Submit dir. : ${SLURM_SUBMIT_DIR}”

Set up the python environment

Set up the linux environment, i.e. load the modules you need to run VASP

#module load swenv/default-env/devel

module load phys/VASP/5.4.4-intel-2018a

####srun -n $SLURM_NTASKS vasp_ncl

srun -n $SLURM_NTASKS vasp_std

####srun -n $SLURM_NTASKS vasp_ncl

Run the rlaunch command

rlaunch -c /scratch/users/skumar/atomate_opt/config rapidfire

Could you please tell me where I did a mistake ? I would be very thankful to you.

Thanks and regards

Sandeep

On Saturday, August 10, 2019 at 12:54:22 AM UTC+2, Anubhav Jain wrote:

Your my_qadapter.yaml should say “_fw_name: CommonAdapter” not “fw_name: CommonAdapter”

On Tuesday, August 6, 2019 at 10:28:35 AM UTC-7, Sandeep wrote:

Dear Anubhav,

Thank you very much for your reply. Actually, VASP run through a job scheduler like SLURM . So I think I should use qlaunch instead of rlaunch and for this, I set up my_qadapter.yaml file and the contain inside are below:

my_qadapter.yaml

fw_name: CommonAdapter

_fw_q_type: SLURM

_fw_template_file: /scratch/users/skumar/atomate_opt/job_ht.sh

rocket_launch: qlaunch -c /scratch/users/skumar/atomate_opt/config rapidfire

nodes: 2

walltime: 24:00:00

queue: batch

account: null

job_name: null

pre_rocket: null

post_rocket: null

logdir: /scratch/users/skumar/atomate_opt/logs

db.json

{

"host": "mongodb+srv://[cluster0-aagd1.mongodb.net/](http://cluster0-aagd1.mongodb.net/)",

"port": 27017,

"database": "test",

"collection": "test",

"admin_user": "test",

"admin_password": "12345",

"authsource": "admin"

"aliases": {}

}

But when I used qlaunch singleshot, I got an error below:

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/bin/qlaunch”, line 10, in

sys.exit(qlaunch())

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/scripts/qlaunch_run.py”, line 222, in qlaunch

do_launch(args)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/scripts/qlaunch_run.py”, line 61, in do_launch

queueadapter = load_object_from_file(args.queueadapter_file)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/utilities/fw_serializers.py”, line 394, in load_object_from_file

return load_object(m_dict)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/utilities/fw_serializers.py”, line 323, in load_object

fw_name = FW_NAME_UPDATES.get(obj_dict['_fw_name'], obj_dict['_fw_name'])

KeyError: ‘_fw_name’

However, I got VASP input files like INCAR, POTCAR, KPOINTS and POSCAR when I used rlaunch singleshot with an error. And it was like below:

2019-08-06 19:07:47,701 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-06 19:07:47,702 INFO Launching Rocket

2019-08-06 19:07:52,654 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO

2019-08-06 19:07:53,886 INFO Task started: FileWriteTask.

2019-08-06 19:07:53,891 INFO Task completed: FileWriteTask

2019-08-06 19:07:54,137 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-06 19:07:54,211 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-06 19:07:54,456 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x7f58d1ededa0>

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 205, in run_task

c.run()

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/custodian/custodian.py”, line 328, in run

self._run_job(job_n, job)

File “/home/users/skumar/anaconda3/envs/atomate_opt/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 0x7f58d1ededa0>

2019-08-06 19:08:16,703 INFO Rocket finished

Could you please suggest me what should I do ? I need your valuable suggestion to resolve this error.

Thanks and regards

Sandeep

On Tuesday, August 6, 2019 at 6:42:36 PM UTC+2, Anubhav Jain wrote:

Hi Sandeep

If you run “rlaunch singleshot”, it will run the workflow on your local system. This means that VASP will also be executed on your local system. I’d first make sure VASP is properly installed on your system.

If you feel that is the case, can you provide more details? For example, does the VASP run start at all? If so, what are the contents of the OUTCAR? Also, what does FW_job.error and FW_job.out say?

Best,

Anubhav

On Friday, August 2, 2019 at 10:03:39 AM UTC-7, Sandeep wrote:

Hi,

I am a new user for atomate. After installation, I tried to launch calculations (example of MgO band structure) using atomate. I follow the instruction (https://atomate.org/running_workflows.html#prerequisites). But after running some time, I found the “FIZZLED” state instead of running. To Add workflow to LaunchPad and running the workflow, I used below step:

lpad reset

python mgo_bandstructure.py

rlaunch singleshot

Below are mongodb functioning of fireworks:

_id

:
5d4348845d924746e1f79dd0

spec

:
Object

fw_id

:
1

created_on

:
“2019-08-01T20:16:03.198678”

updated_on

:
“2019-08-01T20:16:03.198679”

name

:
“MgO-nscf line”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd1

spec

:
Object

fw_id

:
2

created_on

:
“2019-08-01T20:16:03.198584”

updated_on

:
“2019-08-01T20:16:03.198585”

name

:
“MgO-nscf uniform”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd2

spec

:
Object

fw_id

:
3

created_on

:
“2019-08-01T20:16:03.198475”

updated_on

:
“2019-08-01T20:16:03.198476”

name

:
“MgO-static”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

```
  _id : 5d4348845d924746e1f79dd3
```

       spec : Object

```
  fw_id : 4
```

  created_on : "2019-08-01T20:16:03.198222"

 updated_on : "2019-08-01T20:17:49.993173"

```
   name : "MgO-structure optimization"
```

          launches : Array

       archived_launches : Array

0 : 1

6.         state : "FIZZLED"

And at last I got an error below when I used “rlaunch singleshot”.

2019-08-01 22:16:21,937 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-01 22:16:21,938 INFO Launching Rocket

2019-08-01 22:16:26,720 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO

2019-08-01 22:16:27,945 INFO Task started: FileWriteTask.

2019-08-01 22:16:27,946 INFO Task completed: FileWriteTask

2019-08-01 22:16:28,191 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-01 22:16:28,212 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-01 22:16:28,455 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x7fd530602400>

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 205, in run_task

c.run()

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/custodian/custodian.py”, line 328, in run

self._run_job(job_n, job)

File “/home/users/skumar/anaconda3/envs/atomate_opt/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 0x7fd530602400>

2019-08-01 22:17:50,731 INFO Rocket finished

Please suggest me what should I do to remove this error? I would be thankful.

Many thanks and regards

Sandeep

Anubhav_Jain · August 22, 2019, 8:03pm

hi Sandeep

As for the warnings, it looks like you did not specify the correct queue adapter file. For some reason your queue adapter file is being specified as /scratch/users/skumar/atomate_opt/config/job_ht.sh. It should instead be your path/to/my_qadapter.yaml

i.e.

qlaunch -q path/to/my_qadapter.yaml rapidfire

Since I don’t know the exact command you are typing or your exact set up, I don’t know why /scratch/users/skumar/atomate_opt/config/job_ht.sh is being read in as the my_qadapter.yaml file.

As for the error below that, first I’d fix the above error. Then let’s see if you continue getting the second error

···

On Saturday, August 10, 2019 at 3:16:58 AM UTC-7, Sandeep wrote:

Dear Anubhav,

Thanks a lot! Now qlaunch is working and relaxation step is done but it stops after optimization. When I used qlaunch rapidfire , I also got these warning below:

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key rocket_launch has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key nodes has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key ntasks_per_node has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key walltime has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

################### slurm.out##############################

== Starting run at Sat Aug 10 11:46:06 CEST 2019

== Job ID: 682351

== Node list: iris-131

== Submit dir. : /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357

Error reading item ‘VCAIMAGES’ from file INCAR.

2019-08-10 11:46:09,017 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-10 11:46:12,788 INFO Created new dir /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:12,789 INFO Launching Rocket

2019-08-10 11:46:14,744 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:15,970 INFO Task started: FileWriteTask.

2019-08-10 11:46:15,971 INFO Task completed: FileWriteTask

2019-08-10 11:46:16,214 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-10 11:46:16,297 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-10 11:46:16,539 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

2019-08-10 11:46:48,138 INFO Task completed: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}

2019-08-10 11:46:48,386 INFO Task started: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}.

2019-08-10 11:46:48,388 INFO Task completed: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}

2019-08-10 11:46:48,633 INFO Task started: {{atomate.vasp.firetasks.parse_outputs.VaspToDb}}.

2019-08-10 11:46:48,633 INFO atomate.vasp.firetasks.parse_outputs PARSING DIRECTORY: /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:48,633 INFO atomate.vasp.drones Getting task doc for base dir :/mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:48,942 INFO atomate.vasp.drones Post-processing dir:/mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:48,943 WARNING atomate.vasp.drones Transformations file does not exist.

2019-08-10 11:46:48,984 INFO atomate.vasp.drones Post-processed /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:51,067 INFO Rocket finished

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/atomate/vasp/firetasks/parse_outputs.py”, line 113, in run_task

mmdb = VaspCalcDb.from_db_file(db_file, admin=True)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/atomate/utils/database.py”, line 114, in from_db_file

creds = loadfn(db_file)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/monty/serialization.py”, line 83, in loadfn

return json.load(fp, *args, **kwargs)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/init.py”, line 296, in load

parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/init.py”, line 361, in loads

return cls(**kw).decode(s)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/monty/json.py”, line 255, in decode

d = json.JSONDecoder.decode(self, s)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/decoder.py”, line 337, in decode

obj, end = self.raw_decode(s, idx=_w(s, 0).end())

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/decoder.py”, line 353, in raw_decode

obj, end = self.scan_once(s, idx)

json.decoder.JSONDecodeError: Expecting ‘,’ delimiter: line 9 column 3 (char 219)

######################################################

For your kind information, below are my_qadapter.yaml and job_ht.sh file:

my_qadapter.yaml::::::::::::::::::

_fw_name: CommonAdapter

_fw_q_type: SLURM

_fw_template_file: /scratch/users/skumar/atomate_opt/config/job_ht.sh

rocket_launch: rlaunch -c /scratch/users/skumar/atomate_opt/config rapidfire

nodes: 1

ntasks_per_node: 28

walltime: 05:00:00

queue: null

account: null

job_name: null

pre_rocket: null

post_rocket: null

logdir: /scratch/users/skumar/atomate_opt/logs

job_ht.sh

#!/bin/bash -l

Submission script for Iris

#SBATCH -J HTS

#SBATCH --mail-type=end,fail

#SBATCH [email protected]

#SBATCH -N 1

#SBATCH --ntasks-per-node=28

#SBATCH -c 1

#SBATCH --time=0-05:00:00

#SBATCH -p batch

#SBATCH --qos=qos-batch

####SBATCH --qos=qos-besteffort

#print

echo “== Starting run at $(date)”

echo “== Job ID: ${SLURM_JOBID}”

echo “== Node list: ${SLURM_NODELIST}”

echo “== Submit dir. : ${SLURM_SUBMIT_DIR}”

Set up the python environment

Set up the linux environment, i.e. load the modules you need to run VASP

#module load swenv/default-env/devel

module load phys/VASP/5.4.4-intel-2018a

####srun -n $SLURM_NTASKS vasp_ncl

srun -n $SLURM_NTASKS vasp_std

####srun -n $SLURM_NTASKS vasp_ncl

Run the rlaunch command

rlaunch -c /scratch/users/skumar/atomate_opt/config rapidfire

Could you please tell me where I did a mistake ? I would be very thankful to you.

Thanks and regards

Sandeep

On Saturday, August 10, 2019 at 12:54:22 AM UTC+2, Anubhav Jain wrote:

Your my_qadapter.yaml should say “_fw_name: CommonAdapter” not “fw_name: CommonAdapter”

On Tuesday, August 6, 2019 at 10:28:35 AM UTC-7, Sandeep wrote:

Dear Anubhav,

Thank you very much for your reply. Actually, VASP run through a job scheduler like SLURM . So I think I should use qlaunch instead of rlaunch and for this, I set up my_qadapter.yaml file and the contain inside are below:

my_qadapter.yaml

fw_name: CommonAdapter

_fw_q_type: SLURM

_fw_template_file: /scratch/users/skumar/atomate_opt/job_ht.sh

rocket_launch: qlaunch -c /scratch/users/skumar/atomate_opt/config rapidfire

nodes: 2

walltime: 24:00:00

queue: batch

account: null

job_name: null

pre_rocket: null

post_rocket: null

logdir: /scratch/users/skumar/atomate_opt/logs

db.json

{

"host": "mongodb+srv://[cluster0-aagd1.mongodb.net/](http://cluster0-aagd1.mongodb.net/)",

"port": 27017,

"database": "test",

"collection": "test",

"admin_user": "test",

"admin_password": "12345",

"authsource": "admin"

"aliases": {}

}

But when I used qlaunch singleshot, I got an error below:

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/bin/qlaunch”, line 10, in

sys.exit(qlaunch())

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/scripts/qlaunch_run.py”, line 222, in qlaunch

do_launch(args)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/scripts/qlaunch_run.py”, line 61, in do_launch

queueadapter = load_object_from_file(args.queueadapter_file)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/utilities/fw_serializers.py”, line 394, in load_object_from_file

return load_object(m_dict)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/utilities/fw_serializers.py”, line 323, in load_object

fw_name = FW_NAME_UPDATES.get(obj_dict['_fw_name'], obj_dict['_fw_name'])

KeyError: ‘_fw_name’

However, I got VASP input files like INCAR, POTCAR, KPOINTS and POSCAR when I used rlaunch singleshot with an error. And it was like below:

2019-08-06 19:07:47,701 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-06 19:07:47,702 INFO Launching Rocket

2019-08-06 19:07:52,654 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO

2019-08-06 19:07:53,886 INFO Task started: FileWriteTask.

2019-08-06 19:07:53,891 INFO Task completed: FileWriteTask

2019-08-06 19:07:54,137 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-06 19:07:54,211 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-06 19:07:54,456 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x7f58d1ededa0>

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 205, in run_task

c.run()

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/custodian/custodian.py”, line 328, in run

self._run_job(job_n, job)

File “/home/users/skumar/anaconda3/envs/atomate_opt/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 0x7f58d1ededa0>

2019-08-06 19:08:16,703 INFO Rocket finished

Could you please suggest me what should I do ? I need your valuable suggestion to resolve this error.

Thanks and regards

Sandeep

On Tuesday, August 6, 2019 at 6:42:36 PM UTC+2, Anubhav Jain wrote:

Hi Sandeep

If you run “rlaunch singleshot”, it will run the workflow on your local system. This means that VASP will also be executed on your local system. I’d first make sure VASP is properly installed on your system.

If you feel that is the case, can you provide more details? For example, does the VASP run start at all? If so, what are the contents of the OUTCAR? Also, what does FW_job.error and FW_job.out say?

Best,

Anubhav

On Friday, August 2, 2019 at 10:03:39 AM UTC-7, Sandeep wrote:

Hi,

I am a new user for atomate. After installation, I tried to launch calculations (example of MgO band structure) using atomate. I follow the instruction (https://atomate.org/running_workflows.html#prerequisites). But after running some time, I found the “FIZZLED” state instead of running. To Add workflow to LaunchPad and running the workflow, I used below step:

lpad reset

python mgo_bandstructure.py

rlaunch singleshot

Below are mongodb functioning of fireworks:

_id

:
5d4348845d924746e1f79dd0

spec

:
Object

fw_id

:
1

created_on

:
“2019-08-01T20:16:03.198678”

updated_on

:
“2019-08-01T20:16:03.198679”

name

:
“MgO-nscf line”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd1

spec

:
Object

fw_id

:
2

created_on

:
“2019-08-01T20:16:03.198584”

updated_on

:
“2019-08-01T20:16:03.198585”

name

:
“MgO-nscf uniform”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd2

spec

:
Object

fw_id

:
3

created_on

:
“2019-08-01T20:16:03.198475”

updated_on

:
“2019-08-01T20:16:03.198476”

name

:
“MgO-static”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

```
  _id : 5d4348845d924746e1f79dd3
```

       spec : Object

```
  fw_id : 4
```

  created_on : "2019-08-01T20:16:03.198222"

 updated_on : "2019-08-01T20:17:49.993173"

```
   name : "MgO-structure optimization"
```

          launches : Array

       archived_launches : Array

0 : 1

6.         state : "FIZZLED"

And at last I got an error below when I used “rlaunch singleshot”.

2019-08-01 22:16:21,937 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-01 22:16:21,938 INFO Launching Rocket

2019-08-01 22:16:26,720 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO

2019-08-01 22:16:27,945 INFO Task started: FileWriteTask.

2019-08-01 22:16:27,946 INFO Task completed: FileWriteTask

2019-08-01 22:16:28,191 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-01 22:16:28,212 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-01 22:16:28,455 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x7fd530602400>

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 205, in run_task

c.run()

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/custodian/custodian.py”, line 328, in run

self._run_job(job_n, job)

File “/home/users/skumar/anaconda3/envs/atomate_opt/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 0x7fd530602400>

2019-08-01 22:17:50,731 INFO Rocket finished

Please suggest me what should I do to remove this error? I would be thankful.

Many thanks and regards

Sandeep

Sandeep · September 17, 2019, 9:11am

Dear Anubhav,

Thank you for your response. Now the first problem is solved but now I am getting VASP output files in gzipped format and my job is fizzled:

id

:
5d7f5d4cff9ad99e63961a80

spec

:
Object

fw_id

:
4

created_on

:
“2019-09-16T10:00:42.524125”

updated_on

:
“2019-09-17T07:54:32.558292”

launches

:
Array

state

:
“FIZZLED”

name

:
“MgO-structure optimization”

archived_launches

:
Array

Please suggest what should I do.

Thanks

Sandeep

···

On Thursday, August 22, 2019 at 10:03:12 PM UTC+2, Anubhav Jain wrote:

hi Sandeep

As for the warnings, it looks like you did not specify the correct queue adapter file. For some reason your queue adapter file is being specified as /scratch/users/skumar/atomate_opt/config/job_ht.sh. It should instead be your path/to/my_qadapter.yaml

i.e.

qlaunch -q path/to/my_qadapter.yaml rapidfire

Since I don’t know the exact command you are typing or your exact set up, I don’t know why /scratch/users/skumar/atomate_opt/config/job_ht.sh is being read in as the my_qadapter.yaml file.

As for the error below that, first I’d fix the above error. Then let’s see if you continue getting the second error

On Saturday, August 10, 2019 at 3:16:58 AM UTC-7, Sandeep wrote:

Dear Anubhav,

Thanks a lot! Now qlaunch is working and relaxation step is done but it stops after optimization. When I used qlaunch rapidfire , I also got these warning below:

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key rocket_launch has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key nodes has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key ntasks_per_node has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key walltime has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

################### slurm.out##############################

== Starting run at Sat Aug 10 11:46:06 CEST 2019

== Job ID: 682351

== Node list: iris-131

== Submit dir. : /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357

Error reading item ‘VCAIMAGES’ from file INCAR.

2019-08-10 11:46:09,017 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-10 11:46:12,788 INFO Created new dir /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:12,789 INFO Launching Rocket

2019-08-10 11:46:14,744 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:15,970 INFO Task started: FileWriteTask.

2019-08-10 11:46:15,971 INFO Task completed: FileWriteTask

2019-08-10 11:46:16,214 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-10 11:46:16,297 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-10 11:46:16,539 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

2019-08-10 11:46:48,138 INFO Task completed: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}

2019-08-10 11:46:48,386 INFO Task started: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}.

2019-08-10 11:46:48,388 INFO Task completed: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}

2019-08-10 11:46:48,633 INFO Task started: {{atomate.vasp.firetasks.parse_outputs.VaspToDb}}.

2019-08-10 11:46:48,633 INFO atomate.vasp.firetasks.parse_outputs PARSING DIRECTORY: /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:48,633 INFO atomate.vasp.drones Getting task doc for base dir :/mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:48,942 INFO atomate.vasp.drones Post-processing dir:/mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:48,943 WARNING atomate.vasp.drones Transformations file does not exist.

2019-08-10 11:46:48,984 INFO atomate.vasp.drones Post-processed /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:51,067 INFO Rocket finished

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/atomate/vasp/firetasks/parse_outputs.py”, line 113, in run_task

mmdb = VaspCalcDb.from_db_file(db_file, admin=True)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/atomate/utils/database.py”, line 114, in from_db_file

creds = loadfn(db_file)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/monty/serialization.py”, line 83, in loadfn

return json.load(fp, *args, **kwargs)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/init.py”, line 296, in load

parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/init.py”, line 361, in loads

return cls(**kw).decode(s)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/monty/json.py”, line 255, in decode

d = json.JSONDecoder.decode(self, s)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/decoder.py”, line 337, in decode

obj, end = self.raw_decode(s, idx=_w(s, 0).end())

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/decoder.py”, line 353, in raw_decode

obj, end = self.scan_once(s, idx)

json.decoder.JSONDecodeError: Expecting ‘,’ delimiter: line 9 column 3 (char 219)

######################################################

For your kind information, below are my_qadapter.yaml and job_ht.sh file:

my_qadapter.yaml::::::::::::::::::

_fw_name: CommonAdapter

_fw_q_type: SLURM

_fw_template_file: /scratch/users/skumar/atomate_opt/config/job_ht.sh

rocket_launch: rlaunch -c /scratch/users/skumar/atomate_opt/config rapidfire

nodes: 1

ntasks_per_node: 28

walltime: 05:00:00

queue: null

account: null

job_name: null

pre_rocket: null

post_rocket: null

logdir: /scratch/users/skumar/atomate_opt/logs

job_ht.sh

#!/bin/bash -l

Submission script for Iris

#SBATCH -J HTS

#SBATCH --mail-type=end,fail

#SBATCH [email protected]

#SBATCH -N 1

#SBATCH --ntasks-per-node=28

#SBATCH -c 1

#SBATCH --time=0-05:00:00

#SBATCH -p batch

#SBATCH --qos=qos-batch

####SBATCH --qos=qos-besteffort

#print

echo “== Starting run at $(date)”

echo “== Job ID: ${SLURM_JOBID}”

echo “== Node list: ${SLURM_NODELIST}”

echo “== Submit dir. : ${SLURM_SUBMIT_DIR}”

Set up the python environment

Set up the linux environment, i.e. load the modules you need to run VASP

#module load swenv/default-env/devel

module load phys/VASP/5.4.4-intel-2018a

####srun -n $SLURM_NTASKS vasp_ncl

srun -n $SLURM_NTASKS vasp_std

####srun -n $SLURM_NTASKS vasp_ncl

Run the rlaunch command

rlaunch -c /scratch/users/skumar/atomate_opt/config rapidfire

Could you please tell me where I did a mistake ? I would be very thankful to you.

Thanks and regards

Sandeep

On Saturday, August 10, 2019 at 12:54:22 AM UTC+2, Anubhav Jain wrote:

Your my_qadapter.yaml should say “_fw_name: CommonAdapter” not “fw_name: CommonAdapter”

On Tuesday, August 6, 2019 at 10:28:35 AM UTC-7, Sandeep wrote:

Dear Anubhav,

Thank you very much for your reply. Actually, VASP run through a job scheduler like SLURM . So I think I should use qlaunch instead of rlaunch and for this, I set up my_qadapter.yaml file and the contain inside are below:

my_qadapter.yaml

fw_name: CommonAdapter

_fw_q_type: SLURM

_fw_template_file: /scratch/users/skumar/atomate_opt/job_ht.sh

rocket_launch: qlaunch -c /scratch/users/skumar/atomate_opt/config rapidfire

nodes: 2

walltime: 24:00:00

queue: batch

account: null

job_name: null

pre_rocket: null

post_rocket: null

logdir: /scratch/users/skumar/atomate_opt/logs

db.json

{

"host": "mongodb+srv://[cluster0-aagd1.mongodb.net/](http://cluster0-aagd1.mongodb.net/)",

"port": 27017,

"database": "test",

"collection": "test",

"admin_user": "test",

"admin_password": "12345",

"authsource": "admin"

"aliases": {}

}

But when I used qlaunch singleshot, I got an error below:

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/bin/qlaunch”, line 10, in

sys.exit(qlaunch())

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/scripts/qlaunch_run.py”, line 222, in qlaunch

do_launch(args)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/scripts/qlaunch_run.py”, line 61, in do_launch

queueadapter = load_object_from_file(args.queueadapter_file)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/utilities/fw_serializers.py”, line 394, in load_object_from_file

return load_object(m_dict)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/utilities/fw_serializers.py”, line 323, in load_object

fw_name = FW_NAME_UPDATES.get(obj_dict['_fw_name'], obj_dict['_fw_name'])

KeyError: ‘_fw_name’

However, I got VASP input files like INCAR, POTCAR, KPOINTS and POSCAR when I used rlaunch singleshot with an error. And it was like below:

2019-08-06 19:07:47,701 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-06 19:07:47,702 INFO Launching Rocket

2019-08-06 19:07:52,654 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO

2019-08-06 19:07:53,886 INFO Task started: FileWriteTask.

2019-08-06 19:07:53,891 INFO Task completed: FileWriteTask

2019-08-06 19:07:54,137 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-06 19:07:54,211 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-06 19:07:54,456 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x7f58d1ededa0>

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 205, in run_task

c.run()

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/custodian/custodian.py”, line 328, in run

self._run_job(job_n, job)

File “/home/users/skumar/anaconda3/envs/atomate_opt/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 0x7f58d1ededa0>

2019-08-06 19:08:16,703 INFO Rocket finished

Could you please suggest me what should I do ? I need your valuable suggestion to resolve this error.

Thanks and regards

Sandeep

On Tuesday, August 6, 2019 at 6:42:36 PM UTC+2, Anubhav Jain wrote:

Hi Sandeep

If you run “rlaunch singleshot”, it will run the workflow on your local system. This means that VASP will also be executed on your local system. I’d first make sure VASP is properly installed on your system.

If you feel that is the case, can you provide more details? For example, does the VASP run start at all? If so, what are the contents of the OUTCAR? Also, what does FW_job.error and FW_job.out say?

Best,

Anubhav

On Friday, August 2, 2019 at 10:03:39 AM UTC-7, Sandeep wrote:

Hi,

I am a new user for atomate. After installation, I tried to launch calculations (example of MgO band structure) using atomate. I follow the instruction (https://atomate.org/running_workflows.html#prerequisites). But after running some time, I found the “FIZZLED” state instead of running. To Add workflow to LaunchPad and running the workflow, I used below step:

lpad reset

python mgo_bandstructure.py

rlaunch singleshot

Below are mongodb functioning of fireworks:

_id

:
5d4348845d924746e1f79dd0

spec

:
Object

fw_id

:
1

created_on

:
“2019-08-01T20:16:03.198678”

updated_on

:
“2019-08-01T20:16:03.198679”

name

:
“MgO-nscf line”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd1

spec

:
Object

fw_id

:
2

created_on

:
“2019-08-01T20:16:03.198584”

updated_on

:
“2019-08-01T20:16:03.198585”

name

:
“MgO-nscf uniform”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd2

spec

:
Object

fw_id

:
3

created_on

:
“2019-08-01T20:16:03.198475”

updated_on

:
“2019-08-01T20:16:03.198476”

name

:
“MgO-static”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

```
  _id : 5d4348845d924746e1f79dd3
```

       spec : Object

```
  fw_id : 4
```

  created_on : "2019-08-01T20:16:03.198222"

 updated_on : "2019-08-01T20:17:49.993173"

```
   name : "MgO-structure optimization"
```

          launches : Array

       archived_launches : Array

0 : 1

6.         state : "FIZZLED"

And at last I got an error below when I used “rlaunch singleshot”.

2019-08-01 22:16:21,937 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-01 22:16:21,938 INFO Launching Rocket

2019-08-01 22:16:26,720 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO

2019-08-01 22:16:27,945 INFO Task started: FileWriteTask.

2019-08-01 22:16:27,946 INFO Task completed: FileWriteTask

2019-08-01 22:16:28,191 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-01 22:16:28,212 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-01 22:16:28,455 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x7fd530602400>

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 205, in run_task

c.run()

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/custodian/custodian.py”, line 328, in run

self._run_job(job_n, job)

File “/home/users/skumar/anaconda3/envs/atomate_opt/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 0x7fd530602400>

2019-08-01 22:17:50,731 INFO Rocket finished

Please suggest me what should I do to remove this error? I would be thankful.

Many thanks and regards

Sandeep

Anubhav_Jain · September 20, 2019, 10:54pm

Hi Sandeep

The gzipped is expected - there are multiple ways to turn it off if you’d like, but that would be unrelated to your error.

As for why the job failed, can you send the output directory? There are dozens of possible failures (VASP not found, VASP POTCARs not found, some setting is inconsistent, etc) and it’s not possible to guess without seeing all your logs.

···

On Tuesday, September 17, 2019 at 2:11:42 AM UTC-7, Sandeep wrote:

Dear Anubhav,

Thank you for your response. Now the first problem is solved but now I am getting VASP output files in gzipped format and my job is fizzled:

id

:
5d7f5d4cff9ad99e63961a80

spec

:
Object

fw_id

:
4

created_on

:
“2019-09-16T10:00:42.524125”

updated_on

:
“2019-09-17T07:54:32.558292”

launches

:
Array

state

:
“FIZZLED”

name

:
“MgO-structure optimization”

archived_launches

:
Array

Please suggest what should I do.

Thanks

Sandeep

On Thursday, August 22, 2019 at 10:03:12 PM UTC+2, Anubhav Jain wrote:

hi Sandeep

As for the warnings, it looks like you did not specify the correct queue adapter file. For some reason your queue adapter file is being specified as /scratch/users/skumar/atomate_opt/config/job_ht.sh. It should instead be your path/to/my_qadapter.yaml

i.e.

qlaunch -q path/to/my_qadapter.yaml rapidfire

Since I don’t know the exact command you are typing or your exact set up, I don’t know why /scratch/users/skumar/atomate_opt/config/job_ht.sh is being read in as the my_qadapter.yaml file.

As for the error below that, first I’d fix the above error. Then let’s see if you continue getting the second error

On Saturday, August 10, 2019 at 3:16:58 AM UTC-7, Sandeep wrote:

Dear Anubhav,

Thanks a lot! Now qlaunch is working and relaxation step is done but it stops after optimization. When I used qlaunch rapidfire , I also got these warning below:

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key rocket_launch has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key nodes has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key ntasks_per_node has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key walltime has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

################### slurm.out##############################

== Starting run at Sat Aug 10 11:46:06 CEST 2019

== Job ID: 682351

== Node list: iris-131

== Submit dir. : /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357

Error reading item ‘VCAIMAGES’ from file INCAR.

2019-08-10 11:46:09,017 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-10 11:46:12,788 INFO Created new dir /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:12,789 INFO Launching Rocket

2019-08-10 11:46:14,744 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:15,970 INFO Task started: FileWriteTask.

2019-08-10 11:46:15,971 INFO Task completed: FileWriteTask

2019-08-10 11:46:16,214 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-10 11:46:16,297 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-10 11:46:16,539 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

2019-08-10 11:46:48,138 INFO Task completed: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}

2019-08-10 11:46:48,386 INFO Task started: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}.

2019-08-10 11:46:48,388 INFO Task completed: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}

2019-08-10 11:46:48,633 INFO Task started: {{atomate.vasp.firetasks.parse_outputs.VaspToDb}}.

2019-08-10 11:46:48,633 INFO atomate.vasp.firetasks.parse_outputs PARSING DIRECTORY: /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:48,633 INFO atomate.vasp.drones Getting task doc for base dir :/mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:48,942 INFO atomate.vasp.drones Post-processing dir:/mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:48,943 WARNING atomate.vasp.drones Transformations file does not exist.

2019-08-10 11:46:48,984 INFO atomate.vasp.drones Post-processed /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:51,067 INFO Rocket finished

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/atomate/vasp/firetasks/parse_outputs.py”, line 113, in run_task

mmdb = VaspCalcDb.from_db_file(db_file, admin=True)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/atomate/utils/database.py”, line 114, in from_db_file

creds = loadfn(db_file)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/monty/serialization.py”, line 83, in loadfn

return json.load(fp, *args, **kwargs)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/init.py”, line 296, in load

parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/init.py”, line 361, in loads

return cls(**kw).decode(s)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/monty/json.py”, line 255, in decode

d = json.JSONDecoder.decode(self, s)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/decoder.py”, line 337, in decode

obj, end = self.raw_decode(s, idx=_w(s, 0).end())

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/decoder.py”, line 353, in raw_decode

obj, end = self.scan_once(s, idx)

json.decoder.JSONDecodeError: Expecting ‘,’ delimiter: line 9 column 3 (char 219)

######################################################

For your kind information, below are my_qadapter.yaml and job_ht.sh file:

my_qadapter.yaml::::::::::::::::::

_fw_name: CommonAdapter

_fw_q_type: SLURM

_fw_template_file: /scratch/users/skumar/atomate_opt/config/job_ht.sh

rocket_launch: rlaunch -c /scratch/users/skumar/atomate_opt/config rapidfire

nodes: 1

ntasks_per_node: 28

walltime: 05:00:00

queue: null

account: null

job_name: null

pre_rocket: null

post_rocket: null

logdir: /scratch/users/skumar/atomate_opt/logs

job_ht.sh

#!/bin/bash -l

Submission script for Iris

#SBATCH -J HTS

#SBATCH --mail-type=end,fail

#SBATCH [email protected]

#SBATCH -N 1

#SBATCH --ntasks-per-node=28

#SBATCH -c 1

#SBATCH --time=0-05:00:00

#SBATCH -p batch

#SBATCH --qos=qos-batch

####SBATCH --qos=qos-besteffort

#print

echo “== Starting run at $(date)”

echo “== Job ID: ${SLURM_JOBID}”

echo “== Node list: ${SLURM_NODELIST}”

echo “== Submit dir. : ${SLURM_SUBMIT_DIR}”

Set up the python environment

Set up the linux environment, i.e. load the modules you need to run VASP

#module load swenv/default-env/devel

module load phys/VASP/5.4.4-intel-2018a

####srun -n $SLURM_NTASKS vasp_ncl

srun -n $SLURM_NTASKS vasp_std

####srun -n $SLURM_NTASKS vasp_ncl

Run the rlaunch command

rlaunch -c /scratch/users/skumar/atomate_opt/config rapidfire

Could you please tell me where I did a mistake ? I would be very thankful to you.

Thanks and regards

Sandeep

On Saturday, August 10, 2019 at 12:54:22 AM UTC+2, Anubhav Jain wrote:

Your my_qadapter.yaml should say “_fw_name: CommonAdapter” not “fw_name: CommonAdapter”

On Tuesday, August 6, 2019 at 10:28:35 AM UTC-7, Sandeep wrote:

Dear Anubhav,

Thank you very much for your reply. Actually, VASP run through a job scheduler like SLURM . So I think I should use qlaunch instead of rlaunch and for this, I set up my_qadapter.yaml file and the contain inside are below:

my_qadapter.yaml

fw_name: CommonAdapter

_fw_q_type: SLURM

_fw_template_file: /scratch/users/skumar/atomate_opt/job_ht.sh

rocket_launch: qlaunch -c /scratch/users/skumar/atomate_opt/config rapidfire

nodes: 2

walltime: 24:00:00

queue: batch

account: null

job_name: null

pre_rocket: null

post_rocket: null

logdir: /scratch/users/skumar/atomate_opt/logs

db.json

{

"host": "mongodb+srv://[cluster0-aagd1.mongodb.net/](http://cluster0-aagd1.mongodb.net/)",

"port": 27017,

"database": "test",

"collection": "test",

"admin_user": "test",

"admin_password": "12345",

"authsource": "admin"

"aliases": {}

}

But when I used qlaunch singleshot, I got an error below:

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/bin/qlaunch”, line 10, in

sys.exit(qlaunch())

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/scripts/qlaunch_run.py”, line 222, in qlaunch

do_launch(args)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/scripts/qlaunch_run.py”, line 61, in do_launch

queueadapter = load_object_from_file(args.queueadapter_file)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/utilities/fw_serializers.py”, line 394, in load_object_from_file

return load_object(m_dict)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/utilities/fw_serializers.py”, line 323, in load_object

fw_name = FW_NAME_UPDATES.get(obj_dict['_fw_name'], obj_dict['_fw_name'])

KeyError: ‘_fw_name’

However, I got VASP input files like INCAR, POTCAR, KPOINTS and POSCAR when I used rlaunch singleshot with an error. And it was like below:

2019-08-06 19:07:47,701 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-06 19:07:47,702 INFO Launching Rocket

2019-08-06 19:07:52,654 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO

2019-08-06 19:07:53,886 INFO Task started: FileWriteTask.

2019-08-06 19:07:53,891 INFO Task completed: FileWriteTask

2019-08-06 19:07:54,137 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-06 19:07:54,211 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-06 19:07:54,456 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x7f58d1ededa0>

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 205, in run_task

c.run()

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/custodian/custodian.py”, line 328, in run

self._run_job(job_n, job)

File “/home/users/skumar/anaconda3/envs/atomate_opt/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 0x7f58d1ededa0>

2019-08-06 19:08:16,703 INFO Rocket finished

Could you please suggest me what should I do ? I need your valuable suggestion to resolve this error.

Thanks and regards

Sandeep

On Tuesday, August 6, 2019 at 6:42:36 PM UTC+2, Anubhav Jain wrote:

Hi Sandeep

If you run “rlaunch singleshot”, it will run the workflow on your local system. This means that VASP will also be executed on your local system. I’d first make sure VASP is properly installed on your system.

If you feel that is the case, can you provide more details? For example, does the VASP run start at all? If so, what are the contents of the OUTCAR? Also, what does FW_job.error and FW_job.out say?

Best,

Anubhav

On Friday, August 2, 2019 at 10:03:39 AM UTC-7, Sandeep wrote:

Hi,

I am a new user for atomate. After installation, I tried to launch calculations (example of MgO band structure) using atomate. I follow the instruction (https://atomate.org/running_workflows.html#prerequisites). But after running some time, I found the “FIZZLED” state instead of running. To Add workflow to LaunchPad and running the workflow, I used below step:

lpad reset

python mgo_bandstructure.py

rlaunch singleshot

Below are mongodb functioning of fireworks:

_id

:
5d4348845d924746e1f79dd0

spec

:
Object

fw_id

:
1

created_on

:
“2019-08-01T20:16:03.198678”

updated_on

:
“2019-08-01T20:16:03.198679”

name

:
“MgO-nscf line”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd1

spec

:
Object

fw_id

:
2

created_on

:
“2019-08-01T20:16:03.198584”

updated_on

:
“2019-08-01T20:16:03.198585”

name

:
“MgO-nscf uniform”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd2

spec

:
Object

fw_id

:
3

created_on

:
“2019-08-01T20:16:03.198475”

updated_on

:
“2019-08-01T20:16:03.198476”

name

:
“MgO-static”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

```
  _id : 5d4348845d924746e1f79dd3
```

       spec : Object

```
  fw_id : 4
```

  created_on : "2019-08-01T20:16:03.198222"

 updated_on : "2019-08-01T20:17:49.993173"

```
   name : "MgO-structure optimization"
```

          launches : Array

       archived_launches : Array

0 : 1

6.         state : "FIZZLED"

And at last I got an error below when I used “rlaunch singleshot”.

2019-08-01 22:16:21,937 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-01 22:16:21,938 INFO Launching Rocket

2019-08-01 22:16:26,720 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO

2019-08-01 22:16:27,945 INFO Task started: FileWriteTask.

2019-08-01 22:16:27,946 INFO Task completed: FileWriteTask

2019-08-01 22:16:28,191 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-01 22:16:28,212 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-01 22:16:28,455 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x7fd530602400>

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 205, in run_task

c.run()

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/custodian/custodian.py”, line 328, in run

self._run_job(job_n, job)

File “/home/users/skumar/anaconda3/envs/atomate_opt/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 0x7fd530602400>

2019-08-01 22:17:50,731 INFO Rocket finished

Please suggest me what should I do to remove this error? I would be thankful.

Many thanks and regards

Sandeep

Sandeep · September 23, 2019, 1:04pm

Hi,

Thanks for reply. Please find attached the output directory.

Thanks and waiting for your response eagerly.

best regards,

Sandeep

Mgo.tar.gz (4.1 MB)

···

On Saturday, September 21, 2019 at 12:54:46 AM UTC+2, Anubhav Jain wrote:

Hi Sandeep

The gzipped is expected - there are multiple ways to turn it off if you’d like, but that would be unrelated to your error.

As for why the job failed, can you send the output directory? There are dozens of possible failures (VASP not found, VASP POTCARs not found, some setting is inconsistent, etc) and it’s not possible to guess without seeing all your logs.

On Tuesday, September 17, 2019 at 2:11:42 AM UTC-7, Sandeep wrote:

Dear Anubhav,

Thank you for your response. Now the first problem is solved but now I am getting VASP output files in gzipped format and my job is fizzled:

id

:
5d7f5d4cff9ad99e63961a80

spec

:
Object

fw_id

:
4

created_on

:
“2019-09-16T10:00:42.524125”

updated_on

:
“2019-09-17T07:54:32.558292”

launches

:
Array

state

:
“FIZZLED”

name

:
“MgO-structure optimization”

archived_launches

:
Array

Please suggest what should I do.

Thanks

Sandeep

On Thursday, August 22, 2019 at 10:03:12 PM UTC+2, Anubhav Jain wrote:

hi Sandeep

As for the warnings, it looks like you did not specify the correct queue adapter file. For some reason your queue adapter file is being specified as /scratch/users/skumar/atomate_opt/config/job_ht.sh. It should instead be your path/to/my_qadapter.yaml

i.e.

qlaunch -q path/to/my_qadapter.yaml rapidfire

Since I don’t know the exact command you are typing or your exact set up, I don’t know why /scratch/users/skumar/atomate_opt/config/job_ht.sh is being read in as the my_qadapter.yaml file.

As for the error below that, first I’d fix the above error. Then let’s see if you continue getting the second error

On Saturday, August 10, 2019 at 3:16:58 AM UTC-7, Sandeep wrote:

Dear Anubhav,

Thanks a lot! Now qlaunch is working and relaxation step is done but it stops after optimization. When I used qlaunch rapidfire , I also got these warning below:

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key rocket_launch has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key nodes has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key ntasks_per_node has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/queue/queue_adapter.py:143: UserWarning: Key walltime has been specified in qadapter but it is not present in template, please check template (/scratch/users/skumar/atomate_opt/config/job_ht.sh) for supported keys.

.format(subs_key, self.template_file))

################### slurm.out##############################

== Starting run at Sat Aug 10 11:46:06 CEST 2019

== Job ID: 682351

== Node list: iris-131

== Submit dir. : /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357

Error reading item ‘VCAIMAGES’ from file INCAR.

2019-08-10 11:46:09,017 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-10 11:46:12,788 INFO Created new dir /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:12,789 INFO Launching Rocket

2019-08-10 11:46:14,744 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:15,970 INFO Task started: FileWriteTask.

2019-08-10 11:46:15,971 INFO Task completed: FileWriteTask

2019-08-10 11:46:16,214 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-10 11:46:16,297 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-10 11:46:16,539 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

2019-08-10 11:46:48,138 INFO Task completed: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}

2019-08-10 11:46:48,386 INFO Task started: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}.

2019-08-10 11:46:48,388 INFO Task completed: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}

2019-08-10 11:46:48,633 INFO Task started: {{atomate.vasp.firetasks.parse_outputs.VaspToDb}}.

2019-08-10 11:46:48,633 INFO atomate.vasp.firetasks.parse_outputs PARSING DIRECTORY: /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:48,633 INFO atomate.vasp.drones Getting task doc for base dir :/mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:48,942 INFO atomate.vasp.drones Post-processing dir:/mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:48,943 WARNING atomate.vasp.drones Transformations file does not exist.

2019-08-10 11:46:48,984 INFO atomate.vasp.drones Post-processed /mnt/lscratch/users/skumar/atomate_opt/MgO/block_2019-08-10-09-45-44-609779/launcher_2019-08-10-09-45-48-345357/launcher_2019-08-10-09-46-12-788389

2019-08-10 11:46:51,067 INFO Rocket finished

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/atomate/vasp/firetasks/parse_outputs.py”, line 113, in run_task

mmdb = VaspCalcDb.from_db_file(db_file, admin=True)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/atomate/utils/database.py”, line 114, in from_db_file

creds = loadfn(db_file)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/monty/serialization.py”, line 83, in loadfn

return json.load(fp, *args, **kwargs)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/init.py”, line 296, in load

parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/init.py”, line 361, in loads

return cls(**kw).decode(s)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/site-packages/monty/json.py”, line 255, in decode

d = json.JSONDecoder.decode(self, s)

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/decoder.py”, line 337, in decode

obj, end = self.raw_decode(s, idx=_w(s, 0).end())

File “/home/users/skumar/anaconda3/envs/my_env/lib/python3.7/json/decoder.py”, line 353, in raw_decode

obj, end = self.scan_once(s, idx)

json.decoder.JSONDecodeError: Expecting ‘,’ delimiter: line 9 column 3 (char 219)

######################################################

For your kind information, below are my_qadapter.yaml and job_ht.sh file:

my_qadapter.yaml::::::::::::::::::

_fw_name: CommonAdapter

_fw_q_type: SLURM

_fw_template_file: /scratch/users/skumar/atomate_opt/config/job_ht.sh

rocket_launch: rlaunch -c /scratch/users/skumar/atomate_opt/config rapidfire

nodes: 1

ntasks_per_node: 28

walltime: 05:00:00

queue: null

account: null

job_name: null

pre_rocket: null

post_rocket: null

logdir: /scratch/users/skumar/atomate_opt/logs

job_ht.sh

#!/bin/bash -l

Submission script for Iris

#SBATCH -J HTS

#SBATCH --mail-type=end,fail

#SBATCH [email protected]

#SBATCH -N 1

#SBATCH --ntasks-per-node=28

#SBATCH -c 1

#SBATCH --time=0-05:00:00

#SBATCH -p batch

#SBATCH --qos=qos-batch

####SBATCH --qos=qos-besteffort

#print

echo “== Starting run at $(date)”

echo “== Job ID: ${SLURM_JOBID}”

echo “== Node list: ${SLURM_NODELIST}”

echo “== Submit dir. : ${SLURM_SUBMIT_DIR}”

Set up the python environment

Set up the linux environment, i.e. load the modules you need to run VASP

#module load swenv/default-env/devel

module load phys/VASP/5.4.4-intel-2018a

####srun -n $SLURM_NTASKS vasp_ncl

srun -n $SLURM_NTASKS vasp_std

####srun -n $SLURM_NTASKS vasp_ncl

Run the rlaunch command

rlaunch -c /scratch/users/skumar/atomate_opt/config rapidfire

Could you please tell me where I did a mistake ? I would be very thankful to you.

Thanks and regards

Sandeep

On Saturday, August 10, 2019 at 12:54:22 AM UTC+2, Anubhav Jain wrote:

Your my_qadapter.yaml should say “_fw_name: CommonAdapter” not “fw_name: CommonAdapter”

On Tuesday, August 6, 2019 at 10:28:35 AM UTC-7, Sandeep wrote:

Dear Anubhav,

Thank you very much for your reply. Actually, VASP run through a job scheduler like SLURM . So I think I should use qlaunch instead of rlaunch and for this, I set up my_qadapter.yaml file and the contain inside are below:

my_qadapter.yaml

fw_name: CommonAdapter

_fw_q_type: SLURM

_fw_template_file: /scratch/users/skumar/atomate_opt/job_ht.sh

rocket_launch: qlaunch -c /scratch/users/skumar/atomate_opt/config rapidfire

nodes: 2

walltime: 24:00:00

queue: batch

account: null

job_name: null

pre_rocket: null

post_rocket: null

logdir: /scratch/users/skumar/atomate_opt/logs

db.json

{

"host": "mongodb+srv://[cluster0-aagd1.mongodb.net/](http://cluster0-aagd1.mongodb.net/)",

"port": 27017,

"database": "test",

"collection": "test",

"admin_user": "test",

"admin_password": "12345",

"authsource": "admin"

"aliases": {}

}

But when I used qlaunch singleshot, I got an error below:

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/bin/qlaunch”, line 10, in

sys.exit(qlaunch())

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/scripts/qlaunch_run.py”, line 222, in qlaunch

do_launch(args)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/scripts/qlaunch_run.py”, line 61, in do_launch

queueadapter = load_object_from_file(args.queueadapter_file)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/utilities/fw_serializers.py”, line 394, in load_object_from_file

return load_object(m_dict)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/utilities/fw_serializers.py”, line 323, in load_object

fw_name = FW_NAME_UPDATES.get(obj_dict['_fw_name'], obj_dict['_fw_name'])

KeyError: ‘_fw_name’

However, I got VASP input files like INCAR, POTCAR, KPOINTS and POSCAR when I used rlaunch singleshot with an error. And it was like below:

2019-08-06 19:07:47,701 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-06 19:07:47,702 INFO Launching Rocket

2019-08-06 19:07:52,654 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO

2019-08-06 19:07:53,886 INFO Task started: FileWriteTask.

2019-08-06 19:07:53,891 INFO Task completed: FileWriteTask

2019-08-06 19:07:54,137 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-06 19:07:54,211 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-06 19:07:54,456 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x7f58d1ededa0>

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 205, in run_task

c.run()

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/custodian/custodian.py”, line 328, in run

self._run_job(job_n, job)

File “/home/users/skumar/anaconda3/envs/atomate_opt/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 0x7f58d1ededa0>

2019-08-06 19:08:16,703 INFO Rocket finished

Could you please suggest me what should I do ? I need your valuable suggestion to resolve this error.

Thanks and regards

Sandeep

On Tuesday, August 6, 2019 at 6:42:36 PM UTC+2, Anubhav Jain wrote:

Hi Sandeep

If you run “rlaunch singleshot”, it will run the workflow on your local system. This means that VASP will also be executed on your local system. I’d first make sure VASP is properly installed on your system.

If you feel that is the case, can you provide more details? For example, does the VASP run start at all? If so, what are the contents of the OUTCAR? Also, what does FW_job.error and FW_job.out say?

Best,

Anubhav

On Friday, August 2, 2019 at 10:03:39 AM UTC-7, Sandeep wrote:

Hi,

I am a new user for atomate. After installation, I tried to launch calculations (example of MgO band structure) using atomate. I follow the instruction (https://atomate.org/running_workflows.html#prerequisites). But after running some time, I found the “FIZZLED” state instead of running. To Add workflow to LaunchPad and running the workflow, I used below step:

lpad reset

python mgo_bandstructure.py

rlaunch singleshot

Below are mongodb functioning of fireworks:

_id

:
5d4348845d924746e1f79dd0

spec

:
Object

fw_id

:
1

created_on

:
“2019-08-01T20:16:03.198678”

updated_on

:
“2019-08-01T20:16:03.198679”

name

:
“MgO-nscf line”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd1

spec

:
Object

fw_id

:
2

created_on

:
“2019-08-01T20:16:03.198584”

updated_on

:
“2019-08-01T20:16:03.198585”

name

:
“MgO-nscf uniform”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

_id

:
5d4348845d924746e1f79dd2

spec

:
Object

fw_id

:
3

created_on

:
“2019-08-01T20:16:03.198475”

updated_on

:
“2019-08-01T20:16:03.198476”

name

:
“MgO-static”

launches

:
Array

archived_launches

:
Array

state

:
“WAITING”

```
  _id : 5d4348845d924746e1f79dd3
```

       spec : Object

```
  fw_id : 4
```

  created_on : "2019-08-01T20:16:03.198222"

 updated_on : "2019-08-01T20:17:49.993173"

```
   name : "MgO-structure optimization"
```

          launches : Array

       archived_launches : Array

0 : 1

6.         state : "FIZZLED"

And at last I got an error below when I used “rlaunch singleshot”.

2019-08-01 22:16:21,937 INFO Hostname/IP lookup (this will take a few seconds)

2019-08-01 22:16:21,938 INFO Launching Rocket

2019-08-01 22:16:26,720 INFO RUNNING fw_id: 4 in directory: /mnt/lscratch/users/skumar/atomate_opt/MgO

2019-08-01 22:16:27,945 INFO Task started: FileWriteTask.

2019-08-01 22:16:27,946 INFO Task completed: FileWriteTask

2019-08-01 22:16:28,191 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.

2019-08-01 22:16:28,212 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}

2019-08-01 22:16:28,455 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.

Validation failed: <custodian.vasp.validators.VasprunXMLValidator object at 0x7fd530602400>

Traceback (most recent call last):

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 205, in run_task

c.run()

File “/home/users/skumar/anaconda3/envs/atomate_opt/lib/python3.7/site-packages/custodian/custodian.py”, line 328, in run

self._run_job(job_n, job)

File “/home/users/skumar/anaconda3/envs/atomate_opt/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 0x7fd530602400>

2019-08-01 22:17:50,731 INFO Rocket finished

Please suggest me what should I do to remove this error? I would be thankful.

Many thanks and regards

Sandeep

Jaydu1996 · June 15, 2020, 2:02pm

Sir, how do you solve your userwarning? I have met the same problem with torque