Performance benchmarks?


I am trying to troubleshoot performance issues on my GPU, and figure out whether they are hardware or software related.

Does anyone (@stephan?) have completion times for the benchmark workflow ( with or without the “all job types” option?


Hi @olibclarke, here are the results from our tests with cryoSPARC v2.15 on a 4GPU machine with the T20S subset:

The Extensive Workflow takes ~3200 seconds with the default settings and ~4300 seconds with all job types enabled (note that some jobs run in parallel when enough GPUs are available).

Here are some rough average completion times for each job type:

Job Type Average Run Time (seconds)
2D Classification 285.132
Blob Picker (GPU) 11.841
CTF Estimation 69.425
CTF Refine Global 45.465
CTF Refine Local 77.166
Curate Exposures 0.806
Extract from Micrographs (multi) 27.810
Hetero Refine 921.558
Ab initio 601.736
Homo Refine (New) 1615.277
Homo Refine 591.654
Import Movies 58.820
Inspect Simple 4.757
Local Motion Correction 222.152
Non-Uniform Refine 3068.271
Patch CTF Estimation (multi) 55.271
Patch Motion Correction (multi) 262.947
Full Frame Motion Correction (multi) 84.448
Select 2D Classes 7.412
Sharpen 53.028
Template Picker (GPU) 12.117
Validation 108.980
3D Variability 694.068
3D Variability Display 195.240

That is exceedingly helpful, thank you @nfrasser!!

It seems like my root dir is very small (18G) and cryosparc was filling up /tmp/. somehow that was causing a slowdown I think, because when I move /tmp/ and symlink it back to root, I get results comparable to what @nfrasser posted, whereas previously it completely stalled overnight. Don’t know if that makes any sense but fingers crossed I think the issue is fixed, regardless!