CPU usage by tune.splsda

Support
#1

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.

Thanks

#2

Hi @ambinary,

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

Best,

A;

#3

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?

#4

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.

#5

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!