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gtonkinhill / fastbaps

A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
MIT License
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can fastbaps run in parallel? #24

Open zzsunday opened 1 year ago

zzsunday commented 1 year ago

hi, the software fastbaps is really fantastic.

but, I have a question. Can fastbaps run in multiple cpus. Recently, I have a fa file , the size of file was 900M, when I run optimise_prior step, it is so slow. so I ask whether the fastbaps can run in multiple cpus.

gtonkinhill commented 1 year ago

Hi,

The main function in fastbaps makes use of multiple cpu's but only if the package is compiled with openmp.

Unfortunately, the optimise_prior function is only single-threaded at the moment. You may be able to speed things up a bit by first reducing your alignment to only variable sites using snp-sites