search for: mklvar

...nd paste if they find this thread in the future? Here it is. The script is writen for Parallel studio 2016. Change path accordingly if composerxe 2015. libRlib and libRblas are build as shared librairies. It build with static libraries too. More options can be added to configure. Best is to source mklvars and compilervars in a script so it won't polluated your shell environment once the build is done. --------------------------------------------------------------- #! /bin/sh source /opt/intel/compilers_and_libraries_2016.0.109/linux/mkl/bin/mklvars.sh intel64 source /opt/intel/bin/compilervar...

...FLAGS=-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" \ ./configure --prefix=/genetics/data/software --enable-R-shlib --enable-threads=posix --with-lapack \ --with-blas="-fopenmp -m64 -I$MKLROOT/include -L$MKLROOT/lib/intel64 -lmkl_gf_lp64 -lmkl_gnu_...

...Intel Model name: > > Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz - Sandybridge > > R-3.2.2 > > > > Here is my build configuration: > > > > ------------------------------------------------------- > > source /opt/intel/compilers_and_libraries_2016/linux/mkl/bin/mklvars.sh intel64 > > source /opt/intel/bin/compilervars.sh intel64 > > _mkllibpath=$MKLROOT/lib/intel64 > > _icclibpath=$MKLROOT/linux/compiler/lib > > export LD_LIBRARY_PATH=${_mkllibpath}:${_icclibpath} > > export MKL="-L${_mkllibpath} -L${_icclibpath} -lmkl_intel_lp...

...studio_xe_2016 Hardware : 8 Thread(s) per core: 2 Vendor ID: GenuineIntel Model name: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz - Sandybridge R-3.2.2 Here is my build configuration: ------------------------------------------------------- source /opt/intel/compilers_and_libraries_2016/linux/mkl/bin/mklvars.sh intel64 source /opt/intel/bin/compilervars.sh intel64 _mkllibpath=$MKLROOT/lib/intel64 _icclibpath=$MKLROOT/linux/compiler/lib export LD_LIBRARY_PATH=${_mkllibpath}:${_icclibpath} export MKL="-L${_mkllibpath} -L${_icclibpath} -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthrea...

On Wed, Sep 9, 2015 at 11:26 PM, Nathan Kurz <nate at verse.com> wrote: > > As a short and simple approach, I just compiled the current R release > on Ubuntu with ICC and MKL using just this: > > $ tar -xzf R-3.2.2.tar.gz > $ cd R-3.2.2 > $ CC=icc CXX=icpc AR=xiar LD=xild CFLAGS="-g -O3 -xHost" CXXFLAGS="-g > -O3 -xHost" ./configure

...lude --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" \ > ./configure --prefix=/genetics/data/software --enable-R-shlib --enable-threads=posix --with-lapack \ > --with-blas="-fopenmp -m64 -I$MKLROOT/include -L$MKLROOT/lib/intel64 -lmkl_gf_...

...d(s) per core: 2 Vendor ID: GenuineIntel Model name: > Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz - Sandybridge > R-3.2.2 > > Here is my build configuration: > > ------------------------------------------------------- > source /opt/intel/compilers_and_libraries_2016/linux/mkl/bin/mklvars.sh intel64 > source /opt/intel/bin/compilervars.sh intel64 > _mkllibpath=$MKLROOT/lib/intel64 > _icclibpath=$MKLROOT/linux/compiler/lib > export LD_LIBRARY_PATH=${_mkllibpath}:${_icclibpath} > export MKL="-L${_mkllibpath} -L${_icclibpath} -lmkl_intel_lp64 > -lmkl_intel_threa...

...gt; Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz - Sandybridge >> > R-3.2.2 >> > >> > Here is my build configuration: >> > >> > ------------------------------------------------------- >> > source /opt/intel/compilers_and_libraries_2016/linux/mkl/bin/mklvars.sh intel64 >> > source /opt/intel/bin/compilervars.sh intel64 >> > _mkllibpath=$MKLROOT/lib/intel64 >> > _icclibpath=$MKLROOT/linux/compiler/lib >> > export LD_LIBRARY_PATH=${_mkllibpath}:${_icclibpath} >> > export MKL="-L${_mkllibpath} -L${_icclib...

...lude --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" \ > ./configure --prefix=/genetics/data/software --enable-R-shlib --enable-threads=posix --with-lapack \ > --with-blas="-fopenmp -m64 -I$MKLROOT/include -L$MKLROOT/lib/intel64 -lmkl_gf_...

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

...CPU @ 3.40GHz - Sandybridge > >> > R-3.2.2 > >> > > >> > Here is my build configuration: > >> > > >> > ------------------------------------------------------- > >> > source /opt/intel/compilers_and_libraries_2016/linux/mkl/bin/mklvars.sh intel64 > >> > source /opt/intel/bin/compilervars.sh intel64 > >> > _mkllibpath=$MKLROOT/lib/intel64 > >> > _icclibpath=$MKLROOT/linux/compiler/lib > >> > export LD_LIBRARY_PATH=${_mkllibpath}:${_icclibpath} > >> > export MKL="-L$...

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