3D-VA running very slow

Dear cryoSPARC community,

I am running 3D-VA for 312K particles (box size: 600pix binned 2x) with resolution cut-off ranging from 3 to 6 Å and solving for 5 models. It is taking ~3 days to run the job and it seems a bit unusual from what was described by other users am I right?

The SSD seems to be working just fine. Any suggestion on why is taking this long ?


Hi Gio,
This sounds normal considering the large box size (600pix) and high resolution range (3A). Consider running with binned particles such that nyquist is ~ 1.5x lower than your desired filter resolution (bin to 1 or 1.2 A/pix for 3A cutoff). Binning helps substantially and even using a smaller box size is helpful when you don’t need the super high resolution features, which are lost in 3DVA anyways.

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Not 600px - 300px - in my hands 300k particles in 320px box completes in ~3-4hrs with 5 components (on a 3090-Ti), just as a data point

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Sorry, you’re right, Gio. This is quite slow. On our 3080Ti, 340k particles at box 400pix runs in ~4hrs for 3 components. And 660k particles into 5 components at 400pix runs in ~10hrs.

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Also noticed that the NU-refinement took ~7h to run on that same amount of particles.

There is something up. Does anyone from the Cryosparc team want to give their opinion?

Please can you elaborate on the hardware involved.

  • GPU model
  • Amount of DRAM
  • CPU model
  • SSD model
  • some measure of SSD wear, such as wear_leveling % or Percentage Used: depending on SSD type and smartmontools or nvme-cli version

Hi @wtempel,

Here is a bit more info:

Also, the cluster script was set to run with 4 CPU’s, 1 GPU, and 48GB of memory not sure if changing anything will speed the process…

Thank you for the clarification.
Over what kind of network (protocol, speed rating) are worker nodes connected to GPFS?
Is the cache_path variable defined for cryoSPARC integration with your cluster and, if so, to what type of storage does it point?