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hemberg-lab / SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
http://bioconductor.org/packages/SC3
GNU General Public License v3.0
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default for `n_cores` #63

Closed stephaniehicks closed 6 years ago

stephaniehicks commented 6 years ago

Hi Vlad,

This is less of an issue and more of a suggestion, but wasn't sure where to put it. I was using SC3 and noticed the default for n_cores in sc3() function is to use n_cores <- parallel::detectCores() if n_cores is left NULL in the function (https://github.com/hemberg-lab/SC3/blob/master/R/CoreMethods.R). I checked the vignette and didn't see a mention of how the parallelization works. It would be useful to mention that in the vignette that the default is to grab all the cores available using parallel::detectCores() as a heads up.

The problem I ran into is I assumed leaving the n_cores=NULL default meant only 1 core would be used, unless I specify more. When I was running this on the cluster when just asking for 1 core, sc3() was grabbing way more than that causing troubles with my cluster admin.

Thanks Stephanie

wikiselev commented 6 years ago

Hi Stephanie,

Many thanks for your suggestion. I've added notes in both the vignette and the docs and just pushed it to GitHub (https://github.com/hemberg-lab/SC3/commit/bc2ffd0f3a1cd380e3c77f54ade4d4c55ce8e70c) and the devel branch.

Cheers, Vlad