CryoSparc 2.13.2: Patch motion correction (multi) runs very slow



Hi there, did anyone use the Patch motion correction (multi) in CryoSparc 2.12.2? Right now, I am using this function with K2 data in the superresolution model. It takes about 300s for one GPU (1080) to process one tif image. After one night with a 4-GPU cluster node, it only processed 700 images. Does anyone know how to speed up?
Thank you.


processing :


Hey @PeterXTH,

Thanks for providing screenshots - it looks like you’re actually on cryoSPARC v2.13.2.
The bulk of the time seems to be coming from the loading of the raw data (255.3s in the screenshot). The motion estimation itself only took about 21.6s. This may be an issue with the speed of the file transfer between the filesystem where the raw movies are stored and the GPU Workstation that is trying to process the data.

You can check out this post I found online to test and make any optimizations:


I just tested it the speed is about 300 MB/s. I do not know which step or parameter I entered is wrong.
(when I use Motioncorr2 in RELION, it takes only about 7 hours.) Any ideas?


Hi @PeterXTH,

This indicates your raw movies are stored on the same machine as where this job ran, is that correct?


The raw image is store at HPC storage and runs at HPC storage not local storage disk. The I/O speed of the HPC storage is roughly about 300 MB/s. The cryosparc is installed at a HPC cluster node.


Hi @PeterXTH,

Could it be possible that another process was hogging system resources on the HPC cluster? Can you try running the job again and see if you still get the same timings?


I will delete all jobs and try to run one job at a time.


I have tried with only single job for patch motion correction. It was still very slow with same log.