Failed data upload: parsers/cp2k

NOMAD and FAIRmat
1

Hello!
I am trying to upload cp2k data. But I get failed data processing related to parsers/cp2k… and I can not figure out the issue. It corresponds to a typical MD run by cp2k, with .inp, .out, .xyz and a restart file.

upload id: KZGEg2lOQFu9sup5pzxX9w

I am getting:

“errors”: string"parser failed with exception"
“event”: string"process failed"
“proc”: string"Entry"
“process”: string"process_entry"
“process_worker_id”: string"eJv7h7SpSyWYm4ZoI9RqDw"
“parser”: string"parsers/cp2k"
“error”: string"‘NoneType’ object has no attribute ‘atomic_numbers’"
“step”: string"parsers/cp2k"
“logger”: string"nomad.processing"
“exception”: string"Traceback (most recent call last): File “/usr/local/lib/python3.9/site-packages/nomad/processing/data.py”, line 1484, in parsing parser.parse( File “/usr/local/lib/python3.9/site-packages/nomad/parsing/parser.py”, line 460, in parse self.mainfile_parser.parse(mainfile, archive, logger) File “/usr/local/lib/python3.9/site-packages/electronicparsers/cp2k/parser.py”, line 1806, in parse self.parse_method_quickstep() File “/usr/local/lib/python3.9/site-packages/electronicparsers/cp2k/parser.py”, line 1597, in parse_method_quickstep basis_set=self._parse_basis_set(), File “/usr/local/lib/python3.9/site-packages/electronicparsers/cp2k/parser.py”, line 1569, in _parse_basis_set ac.atom_number = self.get_atomic_number(atom.kind_label) File “/usr/local/lib/python3.9/site-packages/electronicparsers/cp2k/parser.py”, line 847, in get_atomic_number atomic_numbers = self.out_parser.get( AttributeError: ‘NoneType’ object has no attribute ‘atomic_numbers’"

Any hint on the issue?

Thanks in advance!
Guido

2

Dear Guido, thank you for reaching out.
This sounds similar to a recent bug fix that has not yet been put into production.
Let me see if the bug fix works, else I open an issue to track this.

Best,
Nathan D

3

Hi Guido,

I guess you haven’t published your upload yet. That’s completely fine, but I won’t have access to look into it.
To do this securely, pls add [email protected] as a reviewer to your upload. (I’m linking this page as proof of accreditation: https://www.fairmat-nfdi.eu/fairmat/about-fairmat/team-fairmat)
As such, I will be able to see it. Pls also provide me with the specific entry id of the process that’s failing.
I will download these files to test them locally for debugging purposed. They are removed afterwards.

Best,
Nathan D

4

Hi Nathan,

many thanks for your prompt reply. The data is now published and accessible, this is the failed entry id ATbSPX7B-BEneL8gGX-Q0tR9H5ZI.

Thanks,
G

5

Thank you Guido!

So, locally, with the patch I get the following.

Screenshot from 2024-03-04 12-28-03
Screenshot from 2024-03-04 12-28-031917×994 161 KB

Let me know if this is satisfactory.
I’ll see to push this patch to deployment ( @mscheidgen fyi), and reach out to you when it is.

Best,
Nathan

6

That’s correct. Just, the dataset connected would be the .xyz file (now it sais no dataset…), the author name sounds wrong (no S. Cooper connected to this data), and that it would be useful in the future to be able to set “structure type” as amorphous at one point. All good for the rest.
Thanks

7

S. Cooper is just a test account. Nothing will be published under this name.
All of this was done with a local installation that already has the patch. The public one just needs it rolled out.
Metadata like the dataset will reflect whichever dataset you attached.