Undocumented CPU Requirements?

pachterlab / kallisto

Near-optimal RNA-Seq quantification

https://pachterlab.github.io/kallisto

BSD 2-Clause "Simplified" License

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Undocumented CPU Requirements? #445

Open aralbright opened 1 month ago

aralbright commented 1 month ago

Hello! I have used kallisto v0.50.1 installed through conda several times successfully on a remote server, until today. The compute nodes that failed are AMD EPYC cpu nodes, for which our server folks said, "quite modern but would definitely lack AVX512 instructions if those were needed, but they do have AVX2."

I re-ran the jobs with the exact same code, instead specifying for only the most recent nodes (x86-64-v=4), and it's running just fine. Just thought I'd let you know!

Yenaled commented 1 month ago

These are known architecture issues; see https://github.com/pachterlab/kallisto/issues/431

There will be easy options to disable such optimizations in future releases.