CPU usage by tune.splsda

Hi, I am having trouble restricting resources with the tune.splsda function. Even when I set cpus = 1 it seems to want to use all the available cpus. Is there another way of restricting cpu usage? I am running it with folds = 20 and nrepeat = 50 within Rstudio on a linux server. It’s version 6.10.9.


Hi @ambinary,

The current release is 6.14.0 so updating the package should fix the issue. See Bioconductor - mixOmics



Hi aljabadi,
Unfortunately this didn’t fix the issue. Running on a 40 CPU threads server with cpus = 1 still ends up using all available resources. I think the issue is I need a way to restrict threads - is that possible?

Hi @ambinary ,

Did you restart R after re-installation?

I’m almost certainly sure the problem is not the tune.splsda function if cpus has been set to 1 and you’re using the latest release, since I just double checked.
You can run mixOmics:::.check_cpus(1) and if the result is greater than 1, then the problem is in fact the function. Otherwise, I don’t think so.

It must be something to do with the server setup. It kicks off the right number of processes but then can still use 40 threads within that single process. I’ll have a chat to the server admin and see if there’s another way of limiting it.
Thanks for your help!