[R] GotoBLAS2 with multiple cores

Prof Brian Ripley ripley at stats.ox.ac.uk
Sun Nov 24 10:21:56 CET 2013

This really is the wrong list (R-devel or R-SIG-HPC?): see the posting 
guide.  But there are two issues.

- How your BLAS controls its core usage (which is in its documentation).

- How your third-party package interacts with a BLAS which uses multiple 
cores, and for that you need to ask the package maintainers.

On 24/11/2013 09:03, Safiye Celik wrote:
> Hi,
> I am trying to use GotoBLAS2 on R 3.0 on Unix. I downloaded GotoBLAS2
> source code from TACC web site, compiled it, and replaced libRblas.so with
> libgoto2.so, following the instructions at the link
> http://www.rochester.edu/college/gradstudents/jolmsted/files/computing/BLAS.pdf.

Much better to use the definitive R documentation at 
http://cran.r-project.org/doc/manuals/r-release/R-admin.html#Shared-BLAS .

> The simple matrix operations in R like "determinant" are 20 times faster
> than before (I am using huge matrices), which is good. However, I cannot
> use many cores in parallel now.
> For example, below code runs forever. But if I use commented out "for"
> instead of "foreach", it takes just a second. When I was using R's default
> BLAS library, I could run below code (using many cores) (but it took more
> time since BLAS was not optimized, of course)..
> library("foreach")
> library("doParallel")
> registerDoParallel(cores=2)set.seed(100)
> foreach (i = 1:2) %dopar% {# for (i in 1:2) {
> a = replicate(1000, rnorm(1000))
> d = determinant(a)
> So, is it possible to use many cores at the same time with GotoBLAS2, do
> you have any ideas?
> Thanks a lot in advance.

Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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