PATCH CTF correction is too slow

I have 8000 movies in .eer format.
I am using the latest version of CryoSPARC and UBUNTU.
And I am using 4 GPU core system
150 movies got patch CTF corrected in first two hours, and it is taking hours.
Why it is slow. Is it issue with cryosparc or my GPU server?

Are the EER movies stored locally or remotely? I saw the same recently with EER data when my local network was saturated and reading from the remote storage was bottlenecked from that.

The movies are in external HDD connected to the GPU server system.

Might be USB overhead, or too many read processes causing the HDD to thrash the heads around reading (which will slow everything down).

How many preprocessing workers did you set?

Sorry. I don’t know. How to check that?

I am a beginner in the computational biology field, less idea about the Linux and Cryosparc system.

Ah, sorry, are you using CryoSPARC Live? If so, it’s in the configuration section. If you’re using Patch Motion Correction after Import (normal CryoSPARC workflow) then how many GPUs did you set?

Welcome to the field. :smiley:

Thank you so much.
I set only one GPU.

Depending on scaling (did you set EER upsampling to 2 or 1 during Import? Did you change the default number of Fractions?) and what GPU you are using, motion correcting EER data into 8K sampling with 40 frames will run slightly faster than one micrograph/minute on a single GPU, so that isn’t completely unreasonable.

It will also depend on how fast the data can be read from the USB HDD, although reading one micrograph at once, the HDD is unlikely to be unreasonably loaded.

I really like EER as a format, but it does have overhead greater than that of TIFF…

If you want it to run faster, you can kill the job and re-run it with 4 GPUs set. Although then the USB HDD might cause a bottleneck… and you’ll lose any micrographs already motion corrected when you clear the job.

EER unsampling is set as 2.
I am using GeForce GTX 1080 Ti (NVIDIA Corporation).

Okay, thank you so much for your suggestions.

But the hdd is not overloaded, it does only have these movies (4.7TB).

By “unreasonably loaded” I meant in terms of processes trying to read different files simultaneously (SSDs are good at this, HDDs are bad).

Ah, the 1080Ti. Such a great card. However, it’s old enough that with EER upsampling set to 2, it’ll be a bit slower.

I don’t think there is anything standing out as wrong, just non-optimal (for raw speed) settings.

Thank you so much for your time and suggestions!!

I will try the unsampling setting as “8”

Upsampling can only be 1 (which is 4K sampling), 2 (which is 8K sampling) or 3 (which is 16K sampling and is only useful in very, very specific situations).

Set it to 1 for most work.

thank you so much. As there are no other errors popping out other than the system being slow, I will continue with the same.