Parsing a file stuck for months

NOMAD and FAIRmat
1

Hi, I noticed that data I uploaded 5 months ago ( FfKnLNZUSfODl9HOcbGzww) is still not parsed. I tried removing, reparsing, but all these operations are not possible until the initial parsing is complete.

Code in use - FHI-aims with i-Pi sockets (via ASE)

The file which is stuck is this one NOMAD (nomad-lab.eu) and the simulation has run until completion

Any ideas?

2

I will have a look. I am trying to re-run the processing of FfKnLNZUSfODl9HOcbGzww. Its quite beefy. Also tpJIM5uGQ0O1PxurUdoh4w seems to run into issues and a handful of entries never finished. Which in turn makes that the upload also never finished. Here we also have the added problem that the majority of your ASAP files could not be parsed at all. I opened an issue about it and we try to look into it.

Maybe we need to process this on a separate installation with some manual care taking. But I am aware now and will keep an eye on those. I get back to you soon.

3

A small update. Please let me know, if you have time constrains and I have to look into more creative solutions.

  • YaFRdJFUQQqAico_5h8rCw: all entries are now processed successfully, the upload is therefore also fully processed
  • FfKnLNZUSfODl9HOcbGzww: I restarted this yesterday. There are still ~1000 entries that are currently processing. I let you know.
  • tpJIM5uGQ0O1PxurUdoh4w: There is still ~700 entries to process. Someone is looking at the ASAP parser at the moment. If we get a fix, I will need to process this again.
4

New update: all three uploads should have been successfully processed now.

However, tpJIM5uGQ0O1PxurUdoh4w has most ASAP entries failed. There is a first fix now, will try it tomorrow and reprocess this upload again.

5

The upload tpJIM5uGQ0O1PxurUdoh4w was reprocessed now with the fixed parser.

The new parser is not yet part of the NOMAD release that powers the official NOMAD installation. If you quickly need to upload more ASAP files, let me know. Otherwise, we will update at least the staging NOMAD installation towards the end of this week and the production version the week after.

Otherwise, all you issues should be resolved. Let me know, if you encounter further problems.

6

Hi @mscheidgen,

Many thanks for your replies and hard work, I can see that the files are now processed as expected. Please accept my apologies for lack of response.

The .traj files are in fact a byproduct of working in Atomic Simulation Environment (ASE) in an ASE/i-Pi/FHI-aims setup, and not a separate QM simulation output. NOMAD parser picks up these files as the ASAP outputs based on the .traj extension.