[R-sig-hpc] parallel and openblas

[Martin Renner]

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: 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
> 
> 
> 
>