R, OpenBLAS and OMP_NUM_THREADS

Thu, Aug 4, 2016 12:41 AM

On 04/08/16 06:39, Ei-ji Nakama wrote:

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.

Yes, that looks a bit better, allowing it to be overridden by
environment variables.

The other thing that occurred to me was whether this setting would be
inherited by child R processes (otherwise you'd get a massive thread
explosion when running something intentionally parallel), but it looks
like at least the builtin `parallel` library does retain the BLAS
settings of the parent (presumably since it uses `fork()`).

It is maybe still worth setting `Sys.setenv(OPENBLAS_NUM_THREADS=1)`
along with the `blas_set_num_threads(1)` call in case there are any
multicore libraries for which this doesn't apply.


(Also, it hadn't occurred to me earlier but I realise you're the author
of RhpcBLASctl - appreciate it)


Gordon

R, OpenBLAS and OMP_NUM_THREADS

Thread (6 messages)