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

[Spencer Graves]

	  Chapter 15 in Wickham and Bryan, R Packages, discuss "Advanced 
Testing Techniques". Their current section "15.4.1 Skip a test" includes 
the following:


test_that("some long-running thing works", {
   skip_on_cran()
   # test code that can potentially take "a while" to run
})


	  Have you tried writing directly to Jennifer Bryan 
<jenny using rstudio.com>? She and Hadley might be able to get help from the 
CRAN maintainers in getting help with this particular problem AND 
getting more documentation on this in their book ;-)


	  hope this helps.
	  spencer graves
	

On 10/24/23 6:03 AM, Greg Hunt wrote:
> 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
>>
>>          [[alternative HTML version deleted]]
>>
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> 
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