Helix refinement needs 500GB of system Memory

Troubleshooting
1

Hi All,

  • Running Helix Refine on a box size of 960 consumes far more memory than it says it will ( A100 , ~500GB of system memory) .
  • This also happens with few particles (2000) and without symmetry applied.
  • It does not throw any errors ( unless OOM kill with < 400GB)

How do we calculate what memory to allocate and do you have any ideas what is causing this/ any workaround?
We run on version 4.6.0.

Any help appreciated!

2

Hi @AssmannG,

Indeed, we are aware that some jobs use excessive memory for certain box sizes. As a workaround, until we are able to improve this situation, I would suggest downsampling the particles.

–Harris

3

Thanks so much for the answer- we will use downsampling until this is fixed!

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