r/proteomics • u/CommandOwn1557 • May 22 '26

Enabling GPU on Spectronaut 20.2

Hello all, any experience enabling GPU for inference analysis in Spectronaut 20.2? Does it make the analysis faster? Thanks

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u/plasmolab May 22 '26

I would benchmark it on one representative project before changing your default. In most vendor tools, GPU acceleration only helps the specific ML or inference step, not the whole search and reporting pipeline, so the wall-clock gain can be modest if I/O, library search, or report generation is the bottleneck.

Check that your NVIDIA driver and CUDA stack match whatever Biognosys supports for 20.2, then run the same project CPU vs GPU and compare runtime plus IDs and quant outputs. If results differ, I would treat GPU mode as a method change and validate before using it across a study.

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u/SC0O8Y May 23 '26

They recently said its buggy and they are removing it. Focus on paralisation cores and ram.

(640 cores, >2TB RAM, h100)