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"Invalid GSD version" when using GSD file exported from Ovito in HOOMD

I am trying to perform a simulation on a GSD file with HOOMD. Before I run it, I performed some modifications in Ovito and exported it with the same format (gsd). However, when I feed it into HOOMD, it gives me this error, although the original file worked:

**ERROR**: data.gsd_snapshot: Invalid GSD file version in systems/micelle.gsd
Traceback (most recent call last):
File "run_simulation.py", line 55, in <module>
snapshot = hoomd.data.gsd_snapshot(f'my_file.gsd')
File "/home/my_username/hoomd-blue/build/hoomd/data.py", line 2307, in gsd_snapshot
reader = _hoomd.GSDReader(hoomd.context.exec_conf, filename, abs(frame), frame < 0);
RuntimeError: Error opening GSD file

I'm wondering if I am exporting it incorrectly. Since I'm not allowed to upload gsd files, I have uploaded it to this link. Thank you!

The error messages suggests that OVITO wrote the GSD file in a format version not supported by your version of HOOMD. Can you please check which program version of OVITO and HOOMD you are using?

I think OVITO 2.9 writes GSD files in format version 1.0, whereas OVITO 3.0/3.1 writes version 2.0.

By the way, I have changed the configuration of this forum to allow uploads of GSD files. Your file.io link doesn't work, unfortunately. It says error 404 -page not found.

Thank you very much for that! I just checked and it seems I'm running OVITO 3.0.0 and HOOMD 2.5.1. It might be because this is a slightly outdated version of HOOMD from 2019. I couldn't find anything about GSD version compatibility in HOOMD's changlog, but I assume I just need to update my version.

Thank you for the reply!

 

Yes, please check if upgrading your HOOMD installation solves the problem. I am not a HOOMD user, so I do not know when the transition was made, but I believe the GSD format v2 was introduced last year. At least I can say that there is no way to make OVITO 3.x write format v1 GSD files (without losing the capability to read v2 files).

Okay! That's interesting about OVITO. Thank you very much for your help.