Slow deepEMhancer when executed from inside CS

Post Processing
1

I am running CS 4.4 on a new machine equipped with RTX 4090 cards.
For some reason, running deepEMhancer (Version 0.16) from within CS is painfully slow (~ 36 sec/it). For a map with a box size of 256 pixels it takes about one hour to complete.

Running t deepEMhacer from command line outside of CS using the same execution command as in CS runs much much faster, completing the same map in about 75 seconds.

Any thoughts?

2

It’s probably running on CPU. There are some detailed instructions here:

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3

@RD_Cryo Please update this post with your findings when you have a chance.
Did you eliminate the suggestion in Slow deepEMhancer when executed from inside CS - #2 by peter.cherepanov?
Did you observe faster performance of deepemhancer outside of CryoSPARC than inside

  • with identical command lines (and deepemhancer executable paths)
  • comparable system load and hardware resources

?

4

Yes, deactivating Cryosparc’s conda environment with the provided script solved the problem.
Thanks!

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