[R-pkg-devel] Too many cores used in examples (not caused by data.table)

[Greg Hunt]

In my case recently, after an hour or so’s messing about I disabled some
tests and example executions to get rid of the offending times. I doubt
that i am the only one to do that.

On Tue, 24 Oct 2023 at 9:38 pm, Helske, Jouni <jouni.helske using jyu.fi> wrote:

> Thanks for the help, I now tried resubmitting with
> Sys.setenv("OMP_THREAD_LIMIT" = 2) at the top of the exchange example, but
> I still get the same note:
>
> Examples with CPU time > 2.5 times elapsed time
>           user system elapsed ratio
> exchange 1.196   0.04   0.159 7.774
>
> Not sure what to try next.
>
> Best,
> Jouni
> ________________________________
> From: Ivan Krylov <krylov.r00t using gmail.com>
> Sent: Friday, October 20, 2023 16:54
> To: Helske, Jouni <jouni.helske using jyu.fi>
> Cc: r-package-devel using r-project.org <r-package-devel using r-project.org>
> Subject: Re: [R-pkg-devel] Too many cores used in examples (not caused by
> data.table)
>
> В Thu, 19 Oct 2023 05:57:54 +0000
> "Helske, Jouni" <jouni.helske using jyu.fi> пишет:
>
> > But I just realised that bssm uses Armadillo via RcppArmadillo, which
> > uses OpenMP by default for some elementwise operations. So, I wonder
> > if that could be the culprit?
>
> I wasn't able to reproduce the NOTE either, despite manually setting
> the environment variable
> _R_CHECK_EXAMPLE_TIMING_CPU_TO_ELAPSED_THRESHOLD=2 before running R CMD
> check, but I think I can see the code using OpenMP. Here's what I did:
>
> 0. Temporarily lower the system protections against capturing
> performance traces of potentially sensitive parts:
>
> echo -1 | sudo tee /proc/sys/kernel/perf_event_paranoid
>
> (Set it back to 3 after you're done.)
>
> 1. Run the following command with the development version of the
> package installed:
>
> env OPENBLAS_NUM_THREADS=1 \
>  perf record --call-graph drawf,4096 \
>  R -e 'library(bssm); system.time(replicate(100, example(exchange)))'
>
> OPENBLAS_NUM_THREADS=1 will prevent OpenBLAS from spawning worker
> threads if you have it installed. (A different BLAS may need different
> environment variables.)
>
> 2. Run `perf report` and browse collected call stack information.
>
> The call stacks are hard to navigate, but I think they are not pointing
> towards Armadillo. At least, setting ARMA_OPENMP_THREADS=1 doesn't
> help, but setting OMP_THREAD_LIMIT=1 does.
>
> --
> Best regards,
> Ivan
>
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