I am trying to upload my VASP calculations to NOMAD. Most of them were done successfully, while several files encountered parsing errors as follows:
Traceback (most recent call last):
File "/opt/venv/lib/python3.12/site-packages/nomad/processing/data.py", line 1577, in parsing
parser.parse(
File "/opt/venv/lib/python3.12/site-packages/nomad/parsing/parser.py", line 483, in parse
self.mainfile_parser.parse(mainfile, archive, logger)
File "/opt/venv/lib/python3.12/site-packages/electronicparsers/vasp/parser.py", line 2429, in parse
self.parse_configurations()
File "/opt/venv/lib/python3.12/site-packages/electronicparsers/vasp/parser.py", line 2269, in parse_configurations
time = self.parser.get_time_calc(n)[-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^
TypeError: 'float' object is not subscriptable
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/venv/lib/python3.12/site-packages/nomad/workflows/activities.py", line 66, in process_entry_activity
entry._process_entry_local()
File "/opt/venv/lib/python3.12/site-packages/nomad/processing/data.py", line 1420, in _process_entry_local
self.parsing()
File "/opt/venv/lib/python3.12/site-packages/nomad/processing/data.py", line 1585, in parsing
raise ProcessFailure(
nomad.processing.base.ProcessFailure: parser failed with exception
Some other calculations used a similar setting have been parsed correctly. In addition, these calculations were completed, and I could find the result analysis in their Entry DATA, even though the Entry failed.
Could you please help me fix this error or give me any suggestions? Let me know if you need my vasprun.xml file.
Dear Junchi, I already tracked down the broken code. Opened an issue and will try to put in a fix asap. Pls share a sample submission (or an entry ID when published) so I can verify the fix.
Thanks, Nathan. I have uploaded a VASP calculation example to your Harden Time Extraction issue page. Please let me know if you need any additional information from me.
I can add you to this upload if you think that will be more convenient for testing (Let me know which one I should click). Or I can just send those failed examples to you by email as well.
Dear @Jiongci I managed to find your upload last week Friday. When returning today, I can’t however find it back anymore. Did you perhaps delete or otherwise modify the upload?
Hi @NateD, I manually modified the timestamp in vasprun.xml to pass the parsing, and all the data are now successfully uploaded.
I have attached the most extreme example here and hope it can help you improve the parsing code. In this vasprun.xml, the value of time name in all scstep (e.g., line 1005) is missing a space, which further results in the final totalsc in the energy block (i.e., line 1138) mistakenly showing as ****************.
I don’t know why this case happened, since there are some other calculations that work well using the same machine. I also tried to re-run the special cases, but got the same problem. Anyway, hope this special case can be helpful!
Dear @Jiongci , could you try uploading to the develop server, which has the nightly build? I tried that one myself and it seems to be passing fine (see screenshot below). Publishing there gives your entries global visibility, what test doesn’t really do. My apologies for the inconvenience.
On the upside, the fix you found exactly matches the patch I implemented. It really just came down to a delay in roll-out on test. Also my thanks to @ahmedilyas for his insight on the exact deployments!
P.s.: we recommend using develop solely for reprocessing with very recent patch releases. Generally, you should default to stable (or staging). They all share the same DB, so if stable fails, you can enter your uploads via the other links and try reprocessing without ever having to upload again. test and test-oasis are the sole exceptions here.
