[Rcpp-devel] RcppArmadillo BLAS/LAPACK force number of threads to 1

[Dirk Eddelbuettel]

On 12 August 2014 at 10:04, Scott Ritchie wrote:
| Thanks Dirk and Yixuan,
| 
| I think I'm misstating the question.
| 
| I'm developing a package which makes use of LAPACK routines through
| RcppArmadillo, and I'm handling the parallelism from within R.
| 
| At the moment it looks like I have to write a vignette, telling the user to
| monitor their CPU usage with a tool like `top`, and if each thread is using
| more than 100%:
| 
|  1. try setting the appropriate environment variables (OPENBLAS_NUM_THREADS=1,
|     GOTO_NUM_THREADS=1,  OMP_NUM_THREADS=1) depending on their BLAS library
|  2. Switch to a single-threaded BLAS library.

It's beyond your control.

That's what "BLAS / LAPACK being an interface" means.

But as I mentioned, people abstracted the 'thread count' setter out. One
quick Google search just lead me to this:

   http://cran.r-project.org/web/packages/OpenMPController/

   OpenMPController: Control number of OpenMP threads dynamically

   The OpenMPController package provides a function 'omp_set_num_threads()'
   to set the number of OpenMP threads to be used. This may be useful, for
   example, when linking against a vendor optimised BLAS/LAPACK library
   (e.g. the AMD Core Math Library), since the defaults used by those
   libraries may not be highly performant.
 
It may do the job for you. Or it may not, in which case I am not sure what
(if anything) you can do from a user package.

Dirk


| Ideally, I'd like to be able to abstract away these details from the user, so
| they don't need to know whether they have a multithreaded or single-threaded
| version of BLAS installed. 
| 
| My first thought was to look up the multithreaded BLAS libraries, and set the
| environment variables accordingly from my main R routine. However, it seems
| like the changes made in Sys.setenv are not reflected in the RcppArmadillo
| code.
| 
| I hope this makes things clearer,
| 
| Scott 
| 
| 
| 
| On 12 August 2014 09:23, Yixuan Qiu <yixuan.qiu at cos.name> wrote:
| 
|     Good point by Dirk.
| 
|     And why not just adding a line "export OPENBLAS_NUM_THREADS=1" to your
|     .bashrc file, or compiling OpenBlas again by setting NUM_THREADS = 1 in the
|     Makefile.rule?
| 
| 
|     Best,
|     Yixuan
| 
| 
|     2014-08-11 18:55 GMT-04:00 Dirk Eddelbuettel <edd at debian.org>:
| 
| 
| 
|         Hi Scott,
| 
| 
|         On 12 August 2014 at 08:43, Scott Ritchie wrote:
|         | Hi Everyone,
|         |
|         | I'm having trouble with restricting the Armadillo function "svd_econ"
|         to run on
|         | a single thread.
|         |
|         | I am able to restrict it if I `export OPENBLAS_NUM_THREADS=1` before
|         opening an
|         | R session, but not from within R (`Sys.setenv(OPENBLAS_NUM_THREADS=1)
|         ` has no
|         | effect).
|         |
|         | I'm wondering if theirs an option native to armadillo/RcppArmadillo
|         that I'm
|         | missing to enable me to:
|         |
|         |   • Restrict the number of threads used to 1
|         |   • In a library agnostic manner (i.e. if the user has a different
|         LAPACK or
|         |     BLAS library installed).
|         |
|         | or if I can "trick" Rcpp into thinking the machine only has 1 core?
| 
|         I fear you may be misstating / misdiagnosing the problem.
| 
|         I am fairly certain that there is not a single line in Rcpp or
|         (Rcpp)Armadillo which sets thread counts for your LAPACK / BLAS.
| 
|         Rather, and this is a point that I tried to make in the 'Benchmarking
|         GPUs
|         and CPUs on Debian-based systems' package (gcbd on CRAN etc) and its
|         vignette
|         is that __BLAS and LAPACK sit behind a standardized interface__ and can
|         be
|         installed / swapped via plug and play. (Which in turn enables the
|         benchmarking ...)
| 
|         If you're on a Debian-based system, just remove openblas and use atlas.
|         Case
|         closed.  Atlas will not multithread (unless something changed
|         recently).
| 
|         There is also a helper function or package somewhere, and a post by
|         Claudia
|         Beleites on StackOverflow, which show the explicit function call to
|         reset
|         OpenBLAS in its count.  But if everything else fails -- just use a
|         different
|         BLAS.  I sometimes do that too when I use multicore / parallel to
|         launch
|         multiple R jobs and each one of those should not spawn additional
|         linear
|         algebra threads.
| 
|         Hope this helps,  Dirk
| 
| 
| 
|         | Regards,
|         |
|         | Scott Ritchie
|         | _______________________________________________
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|         http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
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|    
| 
| 
|     --
|     Yixuan Qiu <yixuan.qiu at cos.name>
|     Department of Statistics,
|     Purdue University
| 
| 

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org