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BUG: ValueError in npyio.py loading oxdna topology and trajectory #487
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Hi @alphataubio thanks for the bug report! I'm away hiking for another two weeks so won't be able to look into it until then, but if possible if you could share a minimum topology and trajectory for testing that would be great. From the error it should be straight forward enough I think to fix and will require some minor tweaking, but again won't be able to fix for a couple of weeks. |
no rush at all, you need to disconnect and enjoy your vacation. |
oxDNA_performance benchmarks from @ErikPoppleton is a good source of minimal oxdna test examples. the bug i reported a few weeks ago is no longer reproducible and sorry i don't know why. the only issue now is if the oxdna trajectory does not include momenta ( [trajectory_print_momenta = false] option ) then i get the following warnings but the trajectory loads fine. this option is quite useful to reduce the size of the trajectory file by almost half, and the individual particle momenta are not needed to render a video.
however, when i try to load my original ~500k dsdna top and traj (~500 mb for 10 frames), then Blender bloats up to >20gb memory and becomes unresponsive. Either a memory leak, or a new feature to stream the oxdna trajectory frames from disk instead of loading everything into memory is needed. i cant attach these big files here and i cant find your email, so if you go to my website alphataubio.com, you can see my handwritten email in a png at the bottom. i can send you a google drive link if you want to test. no rush however, i wont be using MN until at least august or september 2024 at the earliest. focus on finishing your phd first ... |
Thanks for the tag. Sound like Molecular Nodes is loading the whole trajectory into memory instead of splitting it up. One thing you can do is use oxDNA Analysis Tools' minify script with the For both oxDNA Analysis Tools and oxView we implemented random-access trajectory readers which first scan the trajectory files for all |
thanks @ErikPoppleton for the details. Currently yes every frame is read into memory. Since I implemented this we have gained an MDAnalysis backend for MD trajectories that stream from the disk on similar to how you describe. I had a quick play around with it yesterday and was able to write an MDA trajectory reader for oxDNA that then allows streaming from the disk as well - so the issue can hopefully be addressed! |
Describe the bug
topology and trajectory created with recent version of oxDNA 3.6.1 does not load in MN
To Reproduce
[http://tacoxdna.sissa.it/XYZ_oxDNA]
[https://lorenzo-rovigatti.github.io/oxDNA/relaxation.html]
Blender:
Error Codes
Desktop (please complete the following information):
OS: MacOS 13.2.1
Hardware: Mac mini M1
Blender Version: 4.1
MolecularNodes Version: v4.1.0 for Blender 4.1
Additional context
test.oxdna and test.traj too big to attach, available on demand
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