I have some better news. While we established that 'in theory' setting the
environment variable OMP_NUM_THREADS would help (and I maintain that it is a
great PITA that CRAN does not do so as a general fix for this issue) it does
*not help* once R is started. OpenMP only considers the variable
Hi Dirk,
Looking more closely earlier failures, vignettes have always worked fine but
the note on tests said that the CPU time was only 2.7 times over elapsed time,
so maybe I was just lucky this time and got under 2.5. ;) Or testthat does
something special...
Jouni
Hi Jouni,
On 27 October 2023 at 13:02, Helske, Jouni wrote:
| Actually, the OMP_NUM_THREADS worked for vignettes and testthat tests, but
| didn't help with the examples. However, I just wrapped the problematic example
Now I am confused.
What is your understanding of why it helps in one place
Hi Dirk,
Actually, the OMP_NUM_THREADS worked for vignettes and testthat tests, but
didn't help with the examples. However, I just wrapped the problematic example
with \donttest as for some reason this issue only happened with a single
seemingly simple example (hence the "weird" in the earlier
Jouni,
My CRANberriesFeed reports a new bssm package at CRAN, congratulations for
sorting this out. [1,2] The OMP_NUM_THREADS setting is indeed all it takes,
and it _does_ seem to be read even from a running session: i.e. you can set
this inside an R session and the OpenMP code considers it in
Thanks,
I tried with OMP_NUM_THREADS=2 but unfortunately got the same NOTE as before.
Best,
Jouni
From: Dirk Eddelbuettel
Sent: Wednesday, October 25, 2023 13:27
To: Dirk Eddelbuettel ; Helske, Jouni
Cc: Ivan Krylov ; r-package-devel@r-project.org
Subject:
On 24 October 2023 at 08:15, Dirk Eddelbuettel wrote:
|
| On 24 October 2023 at 15:55, Ivan Krylov wrote:
| | В Tue, 24 Oct 2023 10:37:48 +
| | "Helske, Jouni" пишет:
| |
| | > Examples with CPU time > 2.5 times elapsed time
| | > user system elapsed ratio
| | > exchange 1.196
You are not the only one; I did the same with some of my examples.
Would it be an option to ask for a default R-option, 'max.ncores', that
specifies the maximum number of cores a process is allowed to use? CRAN
could then require that that examples, tests and vignettes respect this
option.
On 24 October 2023 at 15:55, Ivan Krylov wrote:
| В Tue, 24 Oct 2023 10:37:48 +
| "Helske, Jouni" пишет:
|
| > Examples with CPU time > 2.5 times elapsed time
| > user system elapsed ratio
| > exchange 1.196 0.04 0.159 7.774
|
| I've downloaded the archived copy of the
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
В Tue, 24 Oct 2023 10:37:48 +
"Helske, Jouni" пишет:
> Examples with CPU time > 2.5 times elapsed time
> user system elapsed ratio
> exchange 1.196 0.04 0.159 7.774
I've downloaded the archived copy of the package from the CRAN FTP
server, installed it and tried:
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 wrote:
> Thanks for the help, I now tried resubmitting with
>
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
В Thu, 19 Oct 2023 05:57:54 +
"Helske, Jouni" 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
On 19 October 2023 at 05:57, Helske, Jouni wrote:
| I am having difficulties in getting the latest version of the bssm
(https://github.com/helske/bssm) package to CRAN, as the pretest issues a NOTE
that the package uses too many cores in some of the examples ("Examples with
CPU time > 2.5
Hi,
I am having difficulties in getting the latest version of the bssm
(https://github.com/helske/bssm) package to CRAN, as the pretest issues a NOTE
that the package uses too many cores in some of the examples ("Examples with
CPU time > 2.5 times elapsed time"). I've seen plenty of discussion
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