Hi Anubhav,
Here is the my_fworker.yaml file:
name: CORI
category: ‘’
query: ‘{}’
env:
db_file: /global/homes/d/deshpan5/atomate/config/db.json
vasp_cmd: srun vasp_std
scratch_dir: /global/cscratch1/sd/deshpan5/atomate
Here is the FW.json file in the job folder:
{
“spec”: {
“_tasks”: [
{
“files_to_write”: [
{
“filename”: “FW–MgO-structure_optimization”,
“contents”: “”
}
],
“_fw_name”: “FileWriteTask”
},
{
“structure”: {
“@module”: “pymatgen.core.structure”,
“@class”: “Structure”,
“charge”: null,
“lattice”: {
“matrix”: [
[
2.606553,
0.0,
1.504894
],
[
0.868851,
2.457482,
1.504894
],
[
0.0,
0.0,
3.009788
]
],
“a”: 3.0097881143105405,
“b”: 3.0097883300592754,
“c”: 3.009788,
“alpha”: 60.000003627588235,
“beta”: 60.00000125635496,
“gamma”: 60.000003208803285,
“volume”: 19.279368831332597
},
“sites”: [
{
“species”: [
{
“element”: “Mg”,
“occu”: 1
}
],
“abc”: [
0.0,
0.0,
0.0
],
“xyz”: [
0.0,
0.0,
0.0
],
“label”: “Mg”
},
{
“species”: [
{
“element”: “O”,
“occu”: 1
}
],
“abc”: [
0.5,
0.5,
0.5
],
“xyz”: [
1.737702,
1.228741,
3.009788
],
“label”: “O”
}
]
},
“vasp_input_set”: {
“@module”: “pymatgen.io.vasp.sets”,
“@class”: “MPRelaxSet”,
“structure”: {
“@module”: “pymatgen.core.structure”,
“@class”: “Structure”,
“charge”: null,
“lattice”: {
“matrix”: [
[
2.606553,
0.0,
1.504894
],
[
0.868851,
2.457482,
1.504894
],
[
0.0,
0.0,
3.009788
]
],
“a”: 3.0097881143105405,
“b”: 3.0097883300592754,
“c”: 3.009788,
“alpha”: 60.000003627588235,
“beta”: 60.00000125635496,
“gamma”: 60.000003208803285,
“volume”: 19.279368831332597
},
“sites”: [
{
“species”: [
{
“element”: “Mg”,
“occu”: 1
}
],
“abc”: [
0.0,
0.0,
0.0
],
“xyz”: [
0.0,
0.0,
0.0
],
“label”: “Mg”
},
{
“species”: [
{
“element”: “O”,
“occu”: 1
}
],
“abc”: [
0.5,
0.5,
0.5
],
“xyz”: [
1.737702,
1.228741,
3.009788
],
“label”: “O”
}
]
},
“force_gamma”: true
},
“_fw_name”: “{{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}”
},
{
“vasp_cmd”: “>>vasp_cmd<<”,
“job_type”: “double_relaxation_run”,
“max_force_threshold”: 0.25,
“ediffg”: null,
“auto_npar”: “>>auto_npar<<”,
“half_kpts_first_relax”: false,
“scratch_dir”: “>>scratch_dir<<”,
“gamma_vasp_cmd”: “>>gamma_vasp_cmd<<”,
“_fw_name”: “{{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}”
},
{
“name”: “structure optimization”,
“_fw_name”: “{{atomate.common.firetasks.glue_tasks.PassCalcLocs}}”
},
{
“db_file”: “>>db_file<<”,
“additional_fields”: {
“task_label”: “structure optimization”
},
“_fw_name”: “{{atomate.vasp.firetasks.parse_outputs.VaspToDb}}”
}
]
},
“fw_id”: 13,
“created_on”: “2018-10-06T14:42:12.069950”,
“updated_on”: “2018-10-06T14:49:13.941631”,
“launches”: [
{
“fworker”: {
“name”: “CORI”,
“category”: “”,
“query”: “{}”,
“env”: {
“db_file”: “/global/homes/d/deshpan5/atomate/config/db.json”,
“vasp_cmd”: “srun vasp_std”,
“scratch_dir”: “/global/cscratch1/sd/deshpan5/atomate”
}
},
“fw_id”: 13,
“launch_dir”: “/global/u2/d/deshpan5/atomate/test/mgo-6/launcher_2018-10-06-14-49-13-899474”,
“host”: “nid00733”,
“ip”: “10.128.2.226”,
“trackers”: [],
“action”: null,
“state”: “RUNNING”,
“state_history”: [
{
“state”: “RUNNING”,
“created_on”: “2018-10-06T14:49:13.940078”,
“updated_on”: “2018-10-06T14:49:13.940081”
}
],
“launch_id”: 10
}
],
“state”: “RUNNING”,
“name”: “MgO-structure optimization”
This file is getting created in the job folder, and my directory structure looks like this:
– test_job_run_directory (contains the .py and POSCAR)
–test_job_run_directory/launcher_…/ (this has two directories, a ‘scratch link’ and a ‘tmp…’ folder) ( see the image below)
The tmpm1… folder is where the FW.json was located then.
Thank you for your help
Siddharth
···
On Friday, October 5, 2018 at 2:13:20 PM UTC-4, Anubhav Jain wrote:
Hi Siddharth,
Can you attach:
- your my_fworker.yaml file?
Also is your scratch_dir set to a symbolic link rather than a normal directory?
Best,
Anubhav
On Friday, October 5, 2018 at 6:26:59 AM UTC-7, Siddharth Deshpande wrote:
Further Updates:
I was able to figure out the problem being in my my_qadapter.yaml file. I changed the rocket launch setting to ‘single_shot’ there by mistake, reverting it to ‘rapidfire’ mode fixed it.
I still encounter problems though when providing a scratch directory in my_fworker.yaml file. With this being the error output:
/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/site-packages/pymatgen/symmetry/bandstructure.py:63: UserWarning: The input structure does not match the expected standard primitive! The path can be incorrect. Use at your own risk.
warnings.warn("The input structure does not match the expected standard primitive! "
/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/site-packages/monty/shutil.py:40: UserWarning: Cannot copy /global/u2/d/deshpan5/atomate/test/mgo-5/launcher_2018-10-05-12-56-22-244753/tmpzudk7z1h to itself
warnings.warn("Cannot copy s to itself" fpath)
Traceback (most recent call last):
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run
m_action = t.run_task(my_spec)
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 204, in run_task
c.run()
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/site-packages/custodian/custodian.py”, line 345, in run
Custodian._delete_checkpoints(cwd)
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/site-packages/monty/tempfile.py”, line 118, in exit
shutil.rmtree(fpath)
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/shutil.py”, line 495, in rmtree
onerror(os.path.islink, path, sys.exc_info())
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/shutil.py”, line 493, in rmtree
raise OSError(“Cannot call rmtree on a symbolic link”)
OSError: Cannot call rmtree on a symbolic link
/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/site-packages/pymatgen/symmetry/bandstructure.py:63: UserWarning: The input structure does not match the expected standard primitive! The path can be incorrect. Use at your own risk.
warnings.warn("The input structure does not match the expected standard primitive! "
/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/site-packages/monty/shutil.py:40: UserWarning: Cannot copy /global/u2/d/deshpan5/atomate/test/mgo-5/launcher_2018-10-05-13-01-48-776341/tmpj8mx8918 to itself
warnings.warn("Cannot copy s to itself" fpath)
Traceback (most recent call last):
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run
m_action = t.run_task(my_spec)
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/site-packages/atomate/vasp/firetasks/run_calc.py”, line 204, in run_task
c.run()
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/site-packages/custodian/custodian.py”, line 345, in run
Custodian._delete_checkpoints(cwd)
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/site-packages/monty/tempfile.py”, line 118, in exit
shutil.rmtree(fpath)
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/shutil.py”, line 495, in rmtree
onerror(os.path.islink, path, sys.exc_info())
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/shutil.py”, line 493, in rmtree
raise OSError(“Cannot call rmtree on a symbolic link”)
OSError: Cannot call rmtree on a symbolic link
Thank you for you help
Siddharth
On Wednesday, October 3, 2018 at 3:42:52 PM UTC-4, Siddharth Deshpande wrote:
Further Updates on the problem:
I tried to run the test by removing the Scratch directory tag in the my_fworker.yaml file.
name: CORI
category: ‘’
query: ‘{}’
env:
db_file: /global/homes/d/deshpan5/atomate/config/db.json
vasp_cmd: srun -n 64 vasp_std
scratch_dir: null
After running the workflow then, it exited upon the 1st workflow of optimization. I then had to make another folder and run subsequent workflows.
I used ‘qlaunch singleshot’ for submission as mentioned in the tutorial.
If I submit in the same folder, I get error of the form:
Traceback (most recent call last):
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run
m_action = t.run_task(my_spec)
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 93, in run_task
self.copy_files()
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 126, in copy_files
dest_path + gz_ext)
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/site-packages/atomate/utils/fileio.py”, line 112, in copy
shutil.copy2(src, dest)
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/shutil.py”, line 257, in copy2
copyfile(src, dst, follow_symlinks=follow_symlinks)
File “/global/homes/d/deshpan5/.conda/envs/datagen/lib/python3.7/shutil.py”, line 104, in copyfile
raise SameFileError("{!r} and {!r} are the same file".format(src, dst))
shutil.SameFileError: ‘/global/u2/d/deshpan5/atomate/test/Mgo-test1/POTCAR’ and ‘/global/u2/d/deshpan5/atomate/test/Mgo-test1/POTCAR’ are the same file
Awaiting your reply.
Thank you
Siddharth
On Wednesday, October 3, 2018 at 12:23:23 PM UTC-4, Siddharth Deshpande wrote:
Hello,
I recently installed atomate and was running several tutorial suggested. I was able to run the primary Si tutorial properly. The results append properly to the mongo database and I am able to recover the output as shown on the installation page.
However, when I run the MgO tutorial using option 3: i.e. creating a python file, the structure optimization workflow gets fizzled. When I go to the scratch linked directory to check the tarred output .error and .out files, I see the error file is empty and the following output in the .out file:
2018-10-03 09:01:09,456 INFO Hostname/IP lookup (this will take a few seconds)
2018-10-03 09:01:09,458 INFO Launching Rocket
2018-10-03 09:01:16,567 INFO RUNNING fw_id: 4 in directory: /global/u2/d/deshpan5/atomate/test/Mgo-test/block_2018-10-03-15-50-22-070666/launcher_2018-10-03-15-52-19-468059
2018-10-03 09:01:16,611 INFO Task started: FileWriteTask.
2018-10-03 09:01:16,626 INFO Task completed: FileWriteTask
2018-10-03 09:01:16,639 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.
2018-10-03 09:01:16,770 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}
2018-10-03 09:01:16,772 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.
Here are last few lines of the FW.json file in the same directory:
“fw_id”: 4,
“launch_dir”: “/global/u2/d/deshpan5/atomate/test/Mgo-test/block_2018-10-03-15-50-22-070666/launcher_2018-10-03-15-52-19-468059”,
“host”: “nid13033”,
“ip”: “10.128.51.80”,
“trackers”: [],
“action”: null,
“state”: “RUNNING”,
“state_history”: [
{
“state”: “RUNNING”,
“created_on”: “2018-10-03T16:01:16.504409”,
“updated_on”: “2018-10-03T16:01:16.504412”
}
],
“launch_id”: 1
}
],
“state”: “RUNNING”,
“name”: “MgO-structure optimization”
Also, the OUTCAR.relax1 and OUTCAR.relax2 both seem to have converged. The job finishes well inside the wall time also.
I notice, that there is nothing left in the test directory except the scratch link and a temporary folder. Any attempts to resubmit fizzled job gives errors.
Let me know, what might be the cause of this, or things I should do to identify the error.
Thank you for the tool
Siddharth