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

[Scott Ritchie]

Setting the environment variables within my Rcpp function using `putenv`
also doesn't seem to have an effect.


On 12 August 2014 10:04, Scott Ritchie <sritchie73 at gmail.com> 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.
>
> 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
>>> | _______________________________________________
>>> | Rcpp-devel mailing list
>>> | Rcpp-devel at lists.r-forge.r-project.org
>>> |
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>>>
>>> --
>>> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>>> _______________________________________________
>>> Rcpp-devel mailing list
>>> Rcpp-devel at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>>
>>
>>
>>
>> --
>> Yixuan Qiu <yixuan.qiu at cos.name>
>> Department of Statistics,
>> Purdue University
>>
>
>
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