Error when running koopmans from within a directory that is a symlink

[similt]

I am running tutorial_1 job in koopman tutorial folder and getting error:

ValueError: "pseudo_dir" and "pseudo_library" are conflicting; please do not provide "pseudo_dir"

Do you know how to solve this issue?

[elinscott]

👋 thanks for reaching out and creating an issue. These two settings are mutually exclusive -- you should only specify one of pseudo_library and pseudo_dir.

I am surprised that you encountered this error while completing the tuturials. Can you please provide a few more details about what you were doing when you encountered the error? Can you also provide the python traceback of the error, please? You can obtain this by running koopmans with the --traceback flag.

[similt]

@elinscott Thanks for the quick response.

koopmans --traceback si.json

SyntaxWarning: "is not" with a literal. Did you mean "!="?
Traceback (most recent call last):
File "/project/k1641/koopmans/bin/koopmans", line 8, in
sys.exit(main())
File "/project/k1641/koopmans/src/koopmans/cli/main.py", line 26, in main
workflow = read(args.json)
File "/project/k1641/koopmans/src/koopmans/io/_generic.py", line 36, in read
out = read_json(fd, **kwargs)
File "/project/k1641/koopmans/src/koopmans/io/_json.py", line 54, in read_json
return workflow_cls.fromjson(fd.name, override)
File "/project/k1641/koopmans/src/koopmans/workflows/_workflow.py", line 995, in fromjson
wf = cls._fromjsondct(bigdct, override)
File "/project/k1641/koopmans/src/koopmans/workflows/_workflow.py", line 1114, in _fromjsondct
wf = cls(atoms, parameters=parameters, kpoints=kpts, calculator_parameters=calculator_parameters, **kwargs,
File "/project/k1641/koopmans/src/koopmans/workflows/_wannierize.py", line 34, in init
super().init(*args, **kwargs)
File "/project/k1641/koopmans/src/koopmans/workflows/_workflow.py", line 217, in init
raise ValueError(
ValueError: "pseudo_dir" and "pseudo_library" are conflicting; please do not provide "pseudo_dir"

I don't have a pseudo_dir keyword in my si.json.

[elinscott]

OK, strange. Can you please...

• attach the input file si.json
• tell me what version of koopmans you are using (you can get this via pip show koopmans)

[similt]

si.json

Here is the output of pip show koopmans

Name: koopmans
Version: 1.0.1
Summary: Koopmans spectral functional calculations with python and Quantum ESPRESSO
Home-page:
Author:
Author-email: Edward Linscott edward.linscott@epfl.ch, Riccardo De Gennaro riccardo.degennaro@epfl.ch, Nicola Colonna nicola.colonna@psi.ch
License:
Location: /lustre2/project/k1641/koopmans/lib/python3.9/site-packages
Editable project location: /lustre2/project/k1641/koopmans
Requires: argparse, ase-koopmans, cloudpickle, deepdiff, iniconfig, matplotlib, numpy, pandas, pybtex, scikit-learn, scipy, spglib, toml, typing, upf-to-json
Required-by:

[elinscott]

I am struggling to reproduce the error. I assume you have installed koopmans by cloning the git repo rather than via PyPI. If so, what is the hash of the most recent commit to koopmans? You can get this by running git rev-parse HEAD in /lustre2/project/k1641/koopmans.

[similt]

Yes. I cloned the git repo. Hash value is

bbefdfc

These are the loaded modules while installing:

module switch intel intel-classic/2021.4.0
module load cray-python/3.9.4.1

[elinscott]

I cannot reproduce the error with the same input file and the same version of the code. Very mysterious! I would sincerely hope that the particular modules will not affect things.

Are you able to reproduce this issue on a different machine? You would not need to compile QE in order to reproduce the bug -- all you should need to do is clone the repo again, create a virtual environment, activate the virtual environment, pip install ., and then try running koopmans si.json.

Sorry for the hassle, but what is going wrong in this instance is not obvious!

[similt]

@elinscott Thank you very much for your assistance. Our computational scientist, who is in charge of installing the software, has identified and resolved the issue. The problem was traced back to line #216 of 'src/koopmans/workflows/_workflow.py

Our installation path is “/project” is a symlink to “/lustre2/project”. The value of “pseudo_dir” after “.resolve()” is “/lustre2/project”, which is different from the one before “.resolve()”: “/project”. And that is why we got the error message “"pseudo_dir" and "pseudo_library" are conflicting; please do not provide "pseudo_dir"”.

[elinscott]

OK, thanks for the information. I am reopening this issue (and giving it a more informative title) because I think it would be good for koopmans to be robust to being run in a directory is a symlink, and when I have the time I will try and fix this.