[R-sig-hpc] parallel and openblas

[beleites,claudia]

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: 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
>>> _______________________________________________
>>> R-sig-hpc mailing list
>>> R-sig-hpc at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>>
>>
>> --
>> 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
>>
>>
>>
>>
>