Slow deepEMhancer when executed from inside CS

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?

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


@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


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