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 <sritchi...@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....@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 <e...@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@lists.r-forge.r-project.org >>> | >>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel >>> >>> -- >>> http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org >>> _______________________________________________ >>> Rcpp-devel mailing list >>> Rcpp-devel@lists.r-forge.r-project.org >>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel >> >> >> >> >> -- >> Yixuan Qiu <yixuan....@cos.name> >> Department of Statistics, >> Purdue University >> > >
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