[R-sig-hpc] parallel and openblas

[Whit Armstrong]

I believe you can set an env variable to determine the number of
threads to use.  Perhaps search the openblas doc.

Alternatively, execute on 8 different machines...

But for that you might need... rzmq.

-Whit


On Mon, Apr 23, 2012 at 3:53 PM, Martin Renner <greatauklet at gmail.com> wrote:
> Parallel and openblas don't seem to mix well on my machine. If I link openblas, a job executed through parallel (using either the multicore or snow (local socket cluster) setup), each of my 8 cores only operates at 1/8 of 100% (taking a little longer than serial execution). Linking to the reference blas or to single-threaded atlas does not cause this handicap when running snow or multicore.
>
> Is this a known problem (My google attempts were fruitless)? If yes, is there a fix for it? Do MKL or multi-threaded atlas have the same issues?
>
> Thank you for your time.
>
> Martin
>
>
>
> Martin Renner
> Post-doctoral Fellow                            phone: 907-226 4672
> University of Washington                           or: 907-235 0728
> School of Aquatic and Fishery Sciences          Seattle, USA
>
>
>
>
>
> debian squeeze on 8-core Xeon
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C                 LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
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