Pw.x failure in tutorial examples

New to AiiDA
1

Hi,
I am a new user of AiiDa. After installing and verifying AiiDa, I tried to run given examples in:
https://aiida-vibroscopy.readthedocs.io/en/latest/tutorials/index.html
But the workflows keep failing with the following error:
<554234> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [1873|PhononWorkChain|run_base_supercell]: launching base supercell scf PwBaseWorkChain<1881>
<554234> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [1881|PwBaseWorkChain|run_process]: launching PwCalculation<1884> iteration #1
<554234> aiida.parser.PwParser: [WARNING] key ‘symmetries’ is not present in raw output dictionary
<554234> aiida.parser.PwParser: [ERROR] ERROR_OUTPUT_STDOUT_INCOMPLETE
<554234> aiida.parser.PwParser: [ERROR] Both the stdout and XML output files could not be read or parsed.
<554234> aiida.orm.nodes.process.calculation.calcjob.CalcJobNode: [WARNING] output parser returned exit code<305>: Both the stdout and XML output files could not be read or parsed.
<554234> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [1881|PwBaseWorkChain|report_error_handled]: PwCalculation<1884> failed with exit status 305: Both the stdout and XML output files could not be read or parsed.

I checked my pw.x, with:
!verdi code show pw@localhost
I also checked the read and write permissions for the working directory. I also tried the following:
!aiida-pseudo install sssp -x PBEsol --download-only
!aiida-pseudo install sssp --from-download SSSP_1.3_PBEsol_efficiency.aiida_pseudo
These were all fine but the problem persists, here is an example of what I tried to run using Jupyterhub on remote HPC:
from aiida import load_profile
load_profile()
from aiida_quantumespresso.workflows.pw.bands import PwBandsWorkChain
from aiida.orm import *
from aiida.plugins import WorkflowFactory
from aiida.engine import run_get_node
from aiida_vibroscopy.workflows.phonons.base import PhononWorkChain, PhononProperty

Manually load the codes you need (pw.x and phonopy)

pw_code = load_code(‘pw@localhost’)
phonopy_code = load_code(‘phonopy@localhost’)

from aiida.plugins import DbImporterFactory
CodDbImporter = DbImporterFactory(‘core.cod’)

cod = CodDbImporter()
results = cod.query(id=‘1526655’) # Si 1526655
structure = results[0].get_aiida_structure() # it has 8 atoms
from aiida_vibroscopy.common.properties import PhononProperty

PhononWorkChain = WorkflowFactory(“vibroscopy.phonons.phonon”)

builder = PhononWorkChain.get_builder_from_protocol(
pw_code=pw_code,
structure=structure,
protocol=“fast”,
phonopy_code=phonopy_code,
phonon_property=PhononProperty.BANDS
)
builder.supercell_matrix = List([1,1,1])

results, calc = run_get_node(builder)

------------------------Here it failed with the above error---------------------<

I would appreciate it if you could help me solve this problem.
Thanks a lot in advance!
Vahid Jamebozorgi

2

Hi Vahid,

can you please run the following command and let us know about the output:

verdi calcjob gotocomputer 1884

This will open the working directory of your failed CalcJob with pk=1884 (so you can replace the 1884 with another pk, if you want to analyze a different one) so that you can inspect the output files manually. This will hopefully show why the CalcJob failed.

3

Thank you very much for your reply. I gave your command and received the following:
Report: going to the remote work directory…
** The directory
** /…/.aiida/scratch/presto-5/4f/44/a903-6c22-46ee-bc28-e96c15eeafd6
** seems to have been deleted, I logout…

Best,
Vahid

4

Alright, the directory was cleaned after the calculation terminated. In that case, please run
verdi calcjob outputcat 1884
It will print the output file of the pw.x in your terminal.

5

Thanks a lot. I gave this command but nothing happened (appeared).

6

Hmm, then the stdout from QE is most likely empty. Let’s have a look at the stdout and stderr produced by the scheduler:

verdi calcjob outputcat 1884 _scheduler-stdout.txt
verdi calcjob outputcat 1884 _scheduler-stderr.txt
7

I gave the commands and got:
_aiidasubmit.sh: line 6: mpirun: command not found

8

Thanks!

Apparently, your system doesn’t provide the mpirun command. If this is expected, i.e. you didn’t forget to load any modules, and your localhost doesn’t support mpi, you can run the calculation without mpi by setting the following:

builder = PhononWorkChain.get_builder_from_protocol(
pw_code=pw_code,
structure=structure,
protocol=“fast”,
phonopy_code=phonopy_code,
phonon_property=PhononProperty.BANDS,
options={'withmpi': False}
)

`

9

Thanks a lot! I could successfully run pw.x. But it failed again:
‘‘PhonopyCalculation failed with exit status 312’’
So:
!verdi calcjob outputcat 404 _scheduler-stdout.txt
!verdi calcjob outputcat 404 _scheduler-stderr.txt

_aiidasubmit.sh: line 6: /path/to/phonopy: No such file or directory

But I have phonopy installed:
$ verdi code list
Full label Pk Entry point

pw@localhost 1 core.code.installed
phonopy@localhost 2 core.code.installed

!which phonopy
~/.local/bin/phonopy

Also I made sure that it was accessable:
export PATH=/…/.conda/envs/aiida_py39/bin/phonopy:$PATH

10

Hi Valid, great that you could solve the first issue.

Regarding the new one, when setting up the code, you need to provide the correct absolute path to the executable, i.e. the one that is returned by the which command. However, as printed in the error message, you’ve set the path to /path/to/phonopy. You should simply set up a new Code and specify the correct path. Afterwards, this problem should be solved.

Hope that helps!

1 Like
11

Hi,
Thank you very much! I could successfully run the example. However, I encountered another issue in the example ‘Vibrational spectra of Si’. It runs fine until I give the command:
polarized_intensities, depolarized_intensities, frequencies, labels = vibro.run_powder_raman_intensities(frequency_laser=532, temperature=300)
print(frequencies, “\n”, labels)
Then I get the error:
‘LinAlgError: Eigenvalues did not converge’
I checked the outputs using ‘verdi calcjob outputcat’, but all calculations converged. Here is the numerical accuracy of the Raman tensors:
14.0151635626189 14.011518672421136 14.000584001828