[R-sig-hpc] parallel and openblas (original) (raw)

beleites,claudia claudia.beleites at ipht-jena.de
Tue Apr 24 18:00:19 CEST 2012

Martin,

please let me know the permanent solution - I'm still using taskset all the time (I don't have admin rights, but our admin would do it if I could tell him what exactly I need.).

Claudia

Von: Martin Renner [greatauklet at gmail.com] Gesendet: Dienstag, 24. April 2012 17:40 An: beleites,claudia Cc: r-sig-hpc at r-project.org Betreff: Re: [R-sig-hpc] parallel and openblas

Hallo Claudia,

Thank you for that hint -- this works! A bit more permanent solution would be nice though; will need to look into that.

Best, 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

On 24 Apr 2012, at 02:29 , beleites,claudia wrote:

Martin,

I possibly have/had the same problem (on a CentOS 5 system). The R was assigned to one core only, and the solution is: system(sprintf('taskset -p 0xffffffff %d', Sys.getpid())) The whole thread is this: https://stat.ethz.ch/pipermail/r-sig-hpc/2011-November/001171.html Claudia

Von: Martin Renner [greatauklet at gmail.com] Gesendet: Dienstag, 24. April 2012 10:51 An: beleites,claudia Cc: r-sig-hpc at r-project.org Betreff: Re: [R-sig-hpc] parallel and openblas Yes, Claudia, you're probaply right that all these threads are on one core. Yes, %*% is working as expected, utilizing all available cores, when R is linked to openblas. Martin

On 23 Apr 2012, at 12:07 , Claudia Beleites wrote: Martin, do you actually know each core works with 1/8th (as opposed to all 8 threads are run on the same core)? Is implicitly parallel stuff (e.g. %*%) without package parallel working OK? Claudia Am 23.04.2012 21:53, schrieb Martin Renner: 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: x8664-unknown-linux-gnu (64-bit) locale: [1] LCCTYPE=enUS.UTF-8 LCNUMERIC=C [3] LCTIME=enUS.UTF-8 LCCOLLATE=enUS.UTF-8 [5] LCMONETARY=enUS.UTF-8 LCMESSAGES=enUS.UTF-8 [7] LCPAPER=C LCNAME=C [9] LCADDRESS=C LCTELEPHONE=C [11] LCMEASUREMENT=enUS.UTF-8 LCIDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base

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-- Claudia Beleites Spectroscopy/Imaging Institute of Photonic Technology Albert-Einstein-Str. 9 07745 Jena Germany email: claudia.beleites at ipht-jena.de phone: +49 3641 206-133 fax: +49 2641 206-399

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