search for: mkl_num_thread

...2016 at 4:01 , Martyn Plummer <plummerm at iarc.fr> wrote: > > Alternatively, you may be able to control the maximum number of > threads > by setting and exporting an appropriate environment variable depending > on what backend you are using, e.g. OPENBLAS_NUM_THREADS or > MKL_NUM_THREADS. Thanks a lot. Running export OPENBLAS_NUM_THREADS = 1 in the bash before starting R solves both problems! Cheers, Daniel

Hello, I compiled R-2.15.2 with linux intel compilers (see below). when I execute some R code on a // 4 proc x 4 cores // server (export MKL_NUM_THREADS = 16) very often I have the situations where only one processor (4 cores) is active instead of 4 (16 cores) ! do you know this fact depends on what ? thank you ! P.S. many functions of R are single-threaded, is there a simple way to make them multi-threaded ? =================================...

Dear all, I run different R versions (3.2.1, 3.2.2 and 3.2.3) on different platforms (Arch, Ubuntu, Debian) with a different number of available cores (24, 4, 24). The following line produces very different behavior on the three machines: for(i in 1:1e6) {n <- 100; M <- matrix(rnorm(n^2), n, n); M %*% M} On the Ubuntu and Arch machine one core is used, but on the Debian machine ALL

...r compiling R 3.4 with Intel MKL -- I have been successful until R 3.3.3 but now it stops complaining about pcre though it worked without Intel MKL as follows, ./configure LDFLAGS=-L/genetics/data/software/lib CFLAGS=-fPIC -I/genetics/data/software/include --enable-R-shlib I have used, export MKL_NUM_THREADS=15 export MKLROOT=/genetics/data/software/intel/composer_xe_2013.4.183/mkl export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MKLROOT/lib/intel64 /genetics/data/software/intel/composer_xe_2013.4.183/mkl/bin/mklvars.sh intel64 CPPFLAGS="-I/genetics/data/software/include -L/genetics/data/software/lib&quo...

...ave been successful until R 3.3.3 but now it stops complaining about pcre though it worked without Intel MKL as follows, > > > ./configure LDFLAGS=-L/genetics/data/software/lib CFLAGS=-fPIC -I/genetics/data/software/include --enable-R-shlib > > > I have used, > > > export MKL_NUM_THREADS=15 > export MKLROOT=/genetics/data/software/intel/composer_xe_2013.4.183/mkl > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MKLROOT/lib/intel64 > /genetics/data/software/intel/composer_xe_2013.4.183/mkl/bin/mklvars.sh intel64 > CPPFLAGS="-I/genetics/data/software/include -L/genetics/d...

...e/LinearAlgebraLibraries As far as I know reference blas and lapack are still single threaded. Alternatively, you may be able to control the maximum number of threads by setting and exporting an appropriate environment variable depending on what backend you are using, e.g. OPENBLAS_NUM_THREADS or MKL_NUM_THREADS. Martyn > A similar problem persists with the parallel package and mclapply(): > > library(parallel) > out <- mclapply(1:1e6, function(i) { n <- 100; M <- matrix(rnorm(n^2), > n, n); M %*% M }, mc.cores = 24) > > On Arch and Debian all 24 cores run and show a hig...

...ave been successful until R 3.3.3 but now it stops complaining about pcre though it worked without Intel MKL as follows, > > > ./configure LDFLAGS=-L/genetics/data/software/lib CFLAGS=-fPIC -I/genetics/data/software/include --enable-R-shlib > > > I have used, > > > export MKL_NUM_THREADS=15 > export MKLROOT=/genetics/data/software/intel/composer_xe_2013.4.183/mkl > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MKLROOT/lib/intel64 > /genetics/data/software/intel/composer_xe_2013.4.183/mkl/bin/mklvars.sh intel64 > CPPFLAGS="-I/genetics/data/software/include -L/genetics/d...

..._lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread" But in order to compile had to edit src/modules/lapack/vecLibg95c.c and comment out the include. Weird, since I am not building for Mac. Make check returned no error. I checked with ldd that R is linked against MKL. All demos run. I set MKL_NUM_THREADS={1,2} environment var and run R-benchmark-25.R from (http://r.research.att.com/benchmarks/R-benchmark-25.R). Not all tests use MKL so you get around 20% improvement for 2 cores. Also monitoring with top you can see which tests use 2 cores. Question: Am I set? What was that error relating to vecLi...

..._lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread" But in order to compile had to edit src/modules/lapack/vecLibg95c.c and comment out the include. Weird, since I am not building for Mac. Make check returned no error. I checked with ldd that R is linked against MKL. All demos run. I set MKL_NUM_THREADS={1,2} environment var and run R-benchmark-25.R from (http://r.research.att.com/benchmarks/R-benchmark-25.R). Not all tests use MKL so you get around 20% improvement for 2 cores. Also monitoring with top you can see which tests use 2 cores. Question: Am I set? What was that error relating to vecLi...

Hi r-devel, a recent install of R-3.4.0 RC (2017-04-13 r72510)? on Linux (Ubuntu 16.04.1 LTS) x86_64-linux-gnu? with?g++ (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609 (see?http://bioconductor.org/checkResults/devel/bioc-LATEST/malbec2-NodeInfo.html?for more)? results in CXXFLAGS not containing "-O2" as optimisation flag, there is only " -Wall", while?CFLAGS are happy with

Attached is the very verbose ssh output. Just to be perverse, this time two nodes lost connectivity. The only thing I see is lines saying that the two connections are lost, although being honest I have no idea what everything else means. For reference, 8 ssh cinnections were being made at the same time for a 8x8mpi task. N.B., since the OS I am using does not have rsh, I am currently using the