[R-sig-hpc] parallel and openblas

[Claudia Beleites]

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: 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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-- 
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