Slower performance for motion correction

Motion Correction
1

After upgrading to v3, I have observed an approximately 10% increase in execution time. Did anyone else see this?
Is there an explanation or a solution?

2

Hi @jiskander,

There weren’t any changes in v3.0 that should make motion correction perform worse. I can possibly help figure out why you’re experiencing this; would you mind answering the following questions:

  • Are you comparing the processing times of the exact same data before and after the v3.0 upgrade?
  • What version are you upgrading from?
  • Could you confirm that the job you’re using is patch motion correction?
  • Are you using any non-default job parameters (in particular, are you using low memory mode)?

Thanks

  • Harris
3
  • Are you comparing the processing times of the exact same data before and after the v3.0 upgrade? Yes
  • What version are you upgrading from? 2.15
  • Could you confirm that the job you’re using is patch motion correction? yes it is
  • Are you using any non-default job parameters (in particular, are you using low memory mode)? no all default parameters except i have tried with 1,2,3 and 4 GPUs

I am benchmarking the performance on different HPC configurations so I have documented results with v2.15 and was redoing tests for v3.

4

Interesting… With those settings, patch motion correction will be using the same code path as 2.15. Some of our dependencies did change though, it’s possible there was a performance regression with one of them, as other users have reported slowdowns in other aspects of cryoSPARC. We will keep looking into this and get a solution out when we discover the cause.

Harris

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