[R-sig-Debian] R, OpenBLAS and OMP_NUM_THREADS

[Ei-ji Nakama]

Hi,
I was be half asleep in the heat ...

2016-08-04 0:04 GMT+09:00 Dirk Eddelbuettel <edd at debian.org>:
>
> On 3 August 2016 at 16:45, Gordon Ball wrote:
> | On 02/08/16 03:10, Ei-ji Nakama wrote:
> | > Hi,
> | >
> | > Create /etc/profile.d/openblas.sh.
> | > Write the following during in this file.
> | > OPENBLAS_NUM_THREADS = 1
> | > export OPENBLAS_NUM_THREADS
> | >
> | > OPENBLAS_NUM_THREADS environment variable does not affect the OMP_NUM_THREADS.
>
> Thumbs up to using /etc/profile.d/ -- very nice hook.
>
> | Unfortunately neither this nor anything else I've tried today appears to
> | set the variable for sessions started through RStudio server (which may
> | or may not be an appropriate issue here).
> |
> | It appears that the rstudio server spawns sessions with a new minimal
> | environment (rstudio::core::system::launchChildProcess) and no option to
> | inject or inherit variables. (Various methods of controlling the session
> | environment are documented in the pro/paid version manual [1], but are
> | not implemented in the public codebase - enterprise features, presumably).
> |
> | Hence approaches like setting the environment in the
> | rstudio-server.service systemd unit, or creating a /etc/pam.d/rstudio
> | service profile including pam_env.so (to load the setting from
> | /etc/environment) don't work. It would probably be possible to work
> | round this by creating a small binary wrapper for the rsession binary
> | which sets the environment, but it would make a mess of the packaging.
> |
> | So I've gone with an `/etc/R/Rprofile.site` containing
> |
> | local({
> |     if (require("RhpcBLASctl", quietly=TRUE)) blas_set_num_threads(1)
> | })
> |
> | which does mean people get this library loaded in all their sessions but
> | that doesn't seem to cause any particular trouble (yet).

In this case, hook of the / etc / R / Rprofile.site would be best

local({
  if(require("RhpcBLASctl", quietly=TRUE)){
  if(Sys.getenv("OPENBLAS_NUM_THREADS")=="" &
     Sys.getenv("OMP_NUM_THREADS")=="")
        blas_set_num_threads(1)
  }
})

$ OMP_NUM_THREADS=4 R -q -e 'library(RhpcBLASctl);blas_get_num_procs()'
> library(RhpcBLASctl);blas_get_num_procs()
[1] 4

maybe confusion would be minimal.

> I was just working on something that needed environment variables (for
> automating tests to a database backend) and populating
>
>    /etc/R/Renviron.site
>
> worked for me. Otherwise explicit code in Rprofile.site is of course good, as
> is conditioning.  I do that too for some use cases.

I often forget to have set it...orz

> Dirk
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org



-- 
Best Regards,
--
Eiji NAKAMA <nakama (a) ki.rim.or.jp>
"\u4e2d\u9593\u6804\u6cbb"  <nakama (a) ki.rim.or.jp>