Ferroelectric workflow job gets fizzled after static calculation

Bishal · April 23, 2019, 10:33pm

Dear all,

I am having some trouble with polarization calculation using atomate. The workflow starts and then gets fizzled after a single static calculation for polar and non-polar structures. Both the structures are already relaxed and have non-zero band gap. I have previously computed polarization manually for this structure.

2019-04-23 17:09:15,600 INFO atomate.vasp.firetasks.glue_tasks The gap is: 2.0357999999999996. Min gap: 0.01. Max gap: None

2019-04-23 17:15:23,349 INFO atomate.vasp.firetasks.glue_tasks The gap is: 1.9252000000000002. Min gap: 0.01. Max gap: None

I get the following error:

Traceback (most recent call last):

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 93, in run_task

self.copy_files()

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 132, in copy_files

file_content = f.read()

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/codecs.py”, line 322, in decode

(result, consumed) = self._buffer_decode(data, self.errors, final)

UnicodeDecodeError: ‘utf-8’ codec can’t decode byte 0xf6 in position 6: invalid start byte

Traceback (most recent call last):

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 93, in run_task

self.copy_files()

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 132, in copy_files

file_content = f.read()

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/codecs.py”, line 322, in decode

(result, consumed) = self._buffer_decode(data, self.errors, final)

UnicodeDecodeError: ‘utf-8’ codec can’t decode byte 0xab in position 5: invalid start byte

My input is as shown below:

from atomate.vasp.workflows.base.ferroelectric import get_wf_ferroelectric

polar = Structure.from_file(‘POLAR.vasp’)

nonpolar = Structure.from_file(‘NONPOLAR.vasp’)

wf = get_wf_ferroelectric(polar_structure=polar, nonpolar_structure=nonpolar, vasp_cmd=“vasp_std”, db_file=None,vasp_input_set_polar=“MPStaticSet”, vasp_input_set_nonpolar=“MPStaticSet”,relax=False, vasp_relax_input_set_polar=None, vasp_relax_input_set_nonpolar=None, nimages=5, hse=False, add_analysis_task=False, wfid=None,tags=None)

lpad = LaunchPad.auto_load()

lpad.add_wf(wf)

Thanks,

Bishal

ddidjbroberg · April 24, 2019, 6:51pm

Hi Bishal,

To help diagnose this error, could you please let us know: are the VASP files from this workflow gzipped upon completion?

Thank you,

Danny Broberg

···

On Tuesday, April 23, 2019 at 3:33:45 PM UTC-7, [email protected] wrote:

Dear all,

I am having some trouble with polarization calculation using atomate. The workflow starts and then gets fizzled after a single static calculation for polar and non-polar structures. Both the structures are already relaxed and have non-zero band gap. I have previously computed polarization manually for this structure.

2019-04-23 17:09:15,600 INFO atomate.vasp.firetasks.glue_tasks The gap is: 2.0357999999999996. Min gap: 0.01. Max gap: None

2019-04-23 17:15:23,349 INFO atomate.vasp.firetasks.glue_tasks The gap is: 1.9252000000000002. Min gap: 0.01. Max gap: None

I get the following error:

Traceback (most recent call last):

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 93, in run_task

self.copy_files()

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 132, in copy_files

file_content = f.read()

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/codecs.py”, line 322, in decode

(result, consumed) = self._buffer_decode(data, self.errors, final)

UnicodeDecodeError: ‘utf-8’ codec can’t decode byte 0xf6 in position 6: invalid start byte

Traceback (most recent call last):

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 93, in run_task

self.copy_files()

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 132, in copy_files

file_content = f.read()

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/codecs.py”, line 322, in decode

(result, consumed) = self._buffer_decode(data, self.errors, final)

UnicodeDecodeError: ‘utf-8’ codec can’t decode byte 0xab in position 5: invalid start byte

My input is as shown below:

from atomate.vasp.workflows.base.ferroelectric import get_wf_ferroelectric

polar = Structure.from_file(‘POLAR.vasp’)

nonpolar = Structure.from_file(‘NONPOLAR.vasp’)

wf = get_wf_ferroelectric(polar_structure=polar, nonpolar_structure=nonpolar, vasp_cmd=“vasp_std”, db_file=None,vasp_input_set_polar=“MPStaticSet”, vasp_input_set_nonpolar=“MPStaticSet”,relax=False, vasp_relax_input_set_polar=None, vasp_relax_input_set_nonpolar=None, nimages=5, hse=False, add_analysis_task=False, wfid=None,tags=None)

lpad = LaunchPad.auto_load()

lpad.add_wf(wf)

Thanks,

Bishal

tsmidt · April 24, 2019, 8:38pm

Hi Bishal,

I’ve never seen this error and it looks like an encoding problem of some sort which may be system dependent.

If your output files are gzipped, can you try rerunning after setting {‘gzip_output’: False} in RunVaspCustodian here?

Best,

Tess

···

On Wednesday, April 24, 2019 at 11:51:24 AM UTC-7, [email protected] wrote:

Hi Bishal,

To help diagnose this error, could you please let us know: are the VASP files from this workflow gzipped upon completion?

Thank you,

Danny Broberg

On Tuesday, April 23, 2019 at 3:33:45 PM UTC-7, [email protected] wrote:

Dear all,

I am having some trouble with polarization calculation using atomate. The workflow starts and then gets fizzled after a single static calculation for polar and non-polar structures. Both the structures are already relaxed and have non-zero band gap. I have previously computed polarization manually for this structure.

2019-04-23 17:09:15,600 INFO atomate.vasp.firetasks.glue_tasks The gap is: 2.0357999999999996. Min gap: 0.01. Max gap: None

2019-04-23 17:15:23,349 INFO atomate.vasp.firetasks.glue_tasks The gap is: 1.9252000000000002. Min gap: 0.01. Max gap: None

I get the following error:

Traceback (most recent call last):

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 93, in run_task

self.copy_files()

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 132, in copy_files

file_content = f.read()

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/codecs.py”, line 322, in decode

(result, consumed) = self._buffer_decode(data, self.errors, final)

UnicodeDecodeError: ‘utf-8’ codec can’t decode byte 0xf6 in position 6: invalid start byte

Traceback (most recent call last):

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 93, in run_task

self.copy_files()

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 132, in copy_files

file_content = f.read()

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/codecs.py”, line 322, in decode

(result, consumed) = self._buffer_decode(data, self.errors, final)

UnicodeDecodeError: ‘utf-8’ codec can’t decode byte 0xab in position 5: invalid start byte

My input is as shown below:

from atomate.vasp.workflows.base.ferroelectric import get_wf_ferroelectric

polar = Structure.from_file(‘POLAR.vasp’)

nonpolar = Structure.from_file(‘NONPOLAR.vasp’)

wf = get_wf_ferroelectric(polar_structure=polar, nonpolar_structure=nonpolar, vasp_cmd=“vasp_std”, db_file=None,vasp_input_set_polar=“MPStaticSet”, vasp_input_set_nonpolar=“MPStaticSet”,relax=False, vasp_relax_input_set_polar=None, vasp_relax_input_set_nonpolar=None, nimages=5, hse=False, add_analysis_task=False, wfid=None,tags=None)

lpad = LaunchPad.auto_load()

lpad.add_wf(wf)

Thanks,

Bishal

Bishal · April 25, 2019, 2:29am

Hi Tess,

Your suggestion worked. I am not getting that error anymore.

Thanks

Bishal

···

On Wednesday, April 24, 2019 at 3:38:58 PM UTC-5, [email protected] wrote:

Hi Bishal,

I’ve never seen this error and it looks like an encoding problem of some sort which may be system dependent.

If your output files are gzipped, can you try rerunning after setting {‘gzip_output’: False} in RunVaspCustodian here?

Best,

Tess

On Wednesday, April 24, 2019 at 11:51:24 AM UTC-7, [email protected] wrote:

Hi Bishal,

To help diagnose this error, could you please let us know: are the VASP files from this workflow gzipped upon completion?

Thank you,

Danny Broberg

On Tuesday, April 23, 2019 at 3:33:45 PM UTC-7, [email protected] wrote:

Dear all,

I am having some trouble with polarization calculation using atomate. The workflow starts and then gets fizzled after a single static calculation for polar and non-polar structures. Both the structures are already relaxed and have non-zero band gap. I have previously computed polarization manually for this structure.

2019-04-23 17:09:15,600 INFO atomate.vasp.firetasks.glue_tasks The gap is: 2.0357999999999996. Min gap: 0.01. Max gap: None

2019-04-23 17:15:23,349 INFO atomate.vasp.firetasks.glue_tasks The gap is: 1.9252000000000002. Min gap: 0.01. Max gap: None

I get the following error:

Traceback (most recent call last):

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 93, in run_task

self.copy_files()

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 132, in copy_files

file_content = f.read()

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/codecs.py”, line 322, in decode

(result, consumed) = self._buffer_decode(data, self.errors, final)

UnicodeDecodeError: ‘utf-8’ codec can’t decode byte 0xf6 in position 6: invalid start byte

Traceback (most recent call last):

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run

m_action = t.run_task(my_spec)

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 93, in run_task

self.copy_files()

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 132, in copy_files

file_content = f.read()

File “/work/06113/tg854123/stampede2/miniconda3/envs/atomate_env/lib/python3.7/codecs.py”, line 322, in decode

(result, consumed) = self._buffer_decode(data, self.errors, final)

UnicodeDecodeError: ‘utf-8’ codec can’t decode byte 0xab in position 5: invalid start byte

My input is as shown below:

from atomate.vasp.workflows.base.ferroelectric import get_wf_ferroelectric

polar = Structure.from_file(‘POLAR.vasp’)

nonpolar = Structure.from_file(‘NONPOLAR.vasp’)

wf = get_wf_ferroelectric(polar_structure=polar, nonpolar_structure=nonpolar, vasp_cmd=“vasp_std”, db_file=None,vasp_input_set_polar=“MPStaticSet”, vasp_input_set_nonpolar=“MPStaticSet”,relax=False, vasp_relax_input_set_polar=None, vasp_relax_input_set_nonpolar=None, nimages=5, hse=False, add_analysis_task=False, wfid=None,tags=None)

lpad = LaunchPad.auto_load()

lpad.add_wf(wf)

Thanks,

Bishal