search

nomad-coe / nomad

NOMAD lets you manage and share your materials science data in a way that makes it truly useful to you, your group, and the community.
https://nomad-lab.eu
Apache License 2.0
71 stars 16 forks source link

Phonopy parsing fails with ModuleNotFoundError("You need to install python-h5py.") #34

Closed ondracka closed 1 year ago

ondracka commented 2 years ago

There is an issue with the phonopy parser installation at https://nomad-lab.eu/prod/v1/gui/user/uploads. When it should read a phonopy project that actually doesn't generates its own force constants but rather reads a force constants from external calculator (here in hdf5 format) it fails with missing python-h5py.

Specifically the force constants were calculated with the Quantum ESPRESSO and the q2r.x package using the experimental workflow described here: https://phonopy.github.io/phonopy/qe.html#using-q2r-x-to-create-phonopy-force-constants-file Testcase here: phonopy-test.zip

I'm not sure if there are further problems ahead after this, but this one should be easily solvable just by installing the required package for the parser.

markus1978 commented 2 years ago

@ladinesa please have a look at this and comment

ladinesa commented 2 years ago

which upload exactly? can you please provide me the upload id? Is this related to the request for new parser for the phonon module in QE? I tested the sample calculation and it seems to be parsed properly so maybe it is only the h5py that needs to be added.

ondracka commented 2 years ago

You can't reproduce with the here attached testcase? I did not publish the data, so there is no upload id. I tried to upload it again https://nomad-lab.eu/prod/v1/gui/user/uploads/upload/id/nIfODNjsQHOtbMexdNlhlA but right now it still waits for processing.

ondracka commented 2 years ago

BTW This is unrelated to the QE parser request.

ladinesa commented 2 years ago

I was trying to follow the link provided to see the actual log but I tested it and it seems to be parsed properly with h5py installed.

ondracka commented 2 years ago

Than it seems the only problem here is that python-h5py is not installed on nomad v1 main instance?

markus1978 commented 2 years ago

But h5py (3.4.0) is already installed on the current https://nomad-lab.eu/prod/v1/gui nomad.

ondracka commented 2 years ago

Let me check again when the parsing of https://nomad-lab.eu/prod/v1/gui/user/uploads/upload/id/nIfODNjsQHOtbMexdNlhlA is finally done what is the exact error message...

ondracka commented 2 years ago

Here is the failure log https://nomad-lab.eu/prod/v1/gui/user/uploads/upload/id/nIfODNjsQHOtbMexdNlhlA/entry/id/nIfODNjsQHOtbMexdNlhlA/8CzfmGwlSRelkrW8QLKSebLTuPJO

ondracka commented 2 years ago

It looks like the packge is there but has some issues: ImportError: /usr/local/lib/python3.7/site-packages/h5py/_errors.cpython-37m-x86_64-linux-gnu.so: ELF load command address/offset not properly aligned

markus1978 commented 1 year ago

With the current staging deployment and recent processings of phonon data this issue is not apprearing anymore. Please re-open when there are still problems.