search for: lmkl_core

...te file for R is: #! /bin/sh R_PAPERSIZE=letter CFLAGS="-g -O2 -p -pg" CPPFLAGS="-I/opt/intel/mkl/10.0.1.014/include -I/usr/include -I/usr/local/include" LIBnn=lib64 BLAS_LIBS="-L/opt/intel/mkl/10.0.1.014/lib/em64t -Wl,--start-group -lmkl_gf_lp64.so -lmkl_gnu_thread.so -lmkl_core.so -l -l -l -Wl, --end-group -lguide -lpthread -lm" I have set the CONFIG_SITE environment variable to the location of the config.site.file. I am doing everything as superuser. The command I am using for configure is ./configure --disable-R-profiling --with-blas=no following the instruct...

...an/Ubuntu packages available on CRAN mirror, the following tricks may works for without some known side-effects (likes openmp breaking issues), you may try to build your own libblas.so.3gf.0 with following command: $ gfortran -L/opt/intel/lib/intel64 -liomp5 -L/opt/intel/mkl/lib/intel64 -lmkl_rt -lmkl_core -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_gf_ilp64 -lgomp -lpthread -shared -Wl,-soname,libblas.so.3gf -o libblas.so.3gf. $ sudo mkdir /usr/local/lib/MKL $ sudo cp libblas.so.3gf.0 /usr/local/lib/MKL/. $ cd /usr/local/lib/MKL $ sudo ln -s libblas.so.3gf.0 libblas.so.3gf $ sudo -s $ echo "/usr/loca...

...ask one question. I installed R-2.8.1.patched in Ubuntu 9.04 (gcc 4.3.3) using MKL 10.1.1.019. I configured correctly (following MKL userguide) with : sudo ./configure --with-blas="-I/opt/intel/mkl/10.1.1.019/include -L/opt/intel/mkl/10.1.1.019/lib/em64t -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread" --with-lapack="-I/opt/intel/mkl/10.1.1.019/include -L/opt/intel/mkl/10.1.1.019/lib/em64t -lmkl_intel_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...

...ask one question. I installed R-2.8.1.patched in Ubuntu 9.04 (gcc 4.3.3) using MKL 10.1.1.019. I configured correctly (following MKL userguide) with : sudo ./configure --with-blas="-I/opt/intel/mkl/10.1.1.019/include -L/opt/intel/mkl/10.1.1.019/lib/em64t -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread" --with-lapack="-I/opt/intel/mkl/10.1.1.019/include -L/opt/intel/mkl/10.1.1.019/lib/em64t -lmkl_intel_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...

...el64 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_thread -lmkl_core -lpthread -lm" Many thanks, Jing Hua [[alternative HTML version deleted]]

...t/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 -lpthread" > > export CC="icc" > > export F77="ifort" > > export CXX="icpc" > > export AR="xiar" > > export LD="xild" > > export CFLAGS="-O3 -ipo -openmp -parallel -xAVX" > > export C...

...11.3.3.210/mkl export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MKLROOT/lib/intel64 ./configure --prefix=/home/jhz22 LDFLAGS=-L/home/jhz22/lib CPPFLAGS=-I/home/jhz22/include \ --enable-R-shlib --with-lapack \ --with-blas="-fopenmp -m64 -I$MKL/include -L$MKL/lib/intel64 -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -lpthread -lm" The errors are as follows, /usr/bin/ld: warning: libpcre.so.1, needed by ../../lib/libR.so, not found (try using -rpath or -rpath-link) /usr/bin/ld: warning: liblzma.so.5, needed by ../../lib/libR.so, not found (try using -rpath or -rpath-link) ../../lib/libR.so: undefined r...

...s_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 -lpthread" export CC="icc" export F77="ifort" export CXX="icpc" export AR="xiar" export LD="xild" export CFLAGS="-O3 -ipo -openmp -parallel -xAVX" export CXXFLAGS="-O3 -ipo -openmp -parallel -xAVX" export FFLAGS=&qu...

...ric -c fastLm.cpp -o fastLm.o g++ -shared -L/tools/cluster/6.2/R/3.2.2_mkl/lib64/R/lib -L/usr/local/lib64 -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -L/panfs/pfs.acf.ku.edu/cluster/6.2/intel/2015/mkl/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -Wl,--start-group -lmkl_gnu_thread -lmkl_core -Wl,--end-group -fopenmp -ldl -lpthread -lm -lgfortran -lm -L/tools/cluster/6.2/R/3.2.2_mkl/lib64/R/lib -lR installing to /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.2/site-library/RcppArmadillo/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building...

...clude -I${PCRE2DIR}/include " setenv CXXFLAGS " ${CFLAGS} " setenv FFLAGS " ${CFLAGS} " setenv FCFLAGS " ${CFLAGS} " setenv LDFLAGS " -Wl,-rpath=${MKLROOT}/lib/intel64_lin -L${MKLROOT}/lib/intel64_lin -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -Wl,-rpath=/uufs/ chpc.utah.edu/sys/installdir/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin -L/uufs/ chpc.utah.edu/sys/installdir/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin...

...xHOST -fp-model strict" export CC="icc $ICC_OPT" export CXX="icpc $ICC_OPT" export FC="ifort -mkl -xHOST" export F77="ifort -mkl -xHOST" export FPICFLAGS=" -fPIC" export AR=xiar export LD=xild export MKL="-lmkl_gf_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread" ./configure --with-x=no --with-blas=-lmkl

...ollowing resources: http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor http://cran.r-project.org/doc/manuals/R-admin.html#MKL http://software.intel.com/en-us/comment/reply/328415 and getting the following: *checking for dgemm_ in -Wl,--start-group -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -Wl,--end-group -lgomp -lpthread... no* *checking for dgemm_... no* libblas.so.3 => /usr/lib/libblas.so.3 (0x00007f8daec19000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f8dae915000) libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f8dade94000) libp...

...or there is any issue with the Intel libraries. I used some of the libraries from Intel MKL like fftw, mkl_lapack etc. I am pasting below the command that I used to configure this R package. ./configure --prefix=$INSTALL_DIR --with-blas="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_lapack -lmkl_core -lpthread -lfftw3xf_intel -lfftw3xc_intel" --with-lapack I also tried installing using Intel compilers without using Intel MKL libraries. It was done using below command. ./configure --prefix=$INSTALL_DIR Exactly same errors were there. There were no mismatch ob...

...ATH},-L${CMP_LIB_PATH},-Bdirect,--hash-style=both,-Wl,-O1" export SHLIB_LDFLAGS="-lpthread" export SHLIB_CXXLDFLAGS="-lpthread" export MAIN_LDFLAGS="-lpthread" MKL="-L${MKL_LIB_PATH} -L${INC_LIB_PATH} -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread" ./configure --prefix=${INSTALL_DIR} --enable-R-shlib --with-blas="$MKL" --with-lapack

...h 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 -lpthread" > export CC="icc" > export F77="ifort" > export CXX="icpc" > export AR="xiar" > export LD="xild" > export CFLAGS="-O3 -ipo -openmp -parallel -xAVX" > export CXXFLAGS="-O3 -ipo -openmp -par...

...vars.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 -lpthread" >> > export CC="icc" >> > export F77="ifort" >> > export CXX="icpc" >> > export AR="xiar" >> > export LD="xild" >> > export CFLAGS="-O3 -ipo -openmp -parallel -xAVX&...

...epend on the platform and compiler, this requires a bit of setup to get working. For me, the correct configure line is: bash autogen.sh && CFLAGS="-O2 -g -I/opt/intel/mkl/10.0.3.020/include/" LDFLAGS="-L/opt/intel/mkl/10.0.3.020/lib/em64t -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lm" ./configure --with-intel-mkl If you use the intel compiler, you can replace all of the '-lmkl_xx' with a single '-lmkl', and if you want threaded support, replace mkl_sequential with mkl_gnu_thread. If there are anyone from Intel reading this list: Fix your build envi...

...80ae9ec8fef04c42eed808d2f42bf31d%7c72f988bf86f141af91ab2d7cd011db47%7c1&sdata=AwdY1xC74H25uBIyciugr9HeuGhYhnDGKoQkeDUhpeQ%3d RcppArmadillo.o RcppExports.o fastLm.o -L/panfs/pfs.acf.ku.edu/cluster/6.2/intel/2015/mkl/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -Wl,--start-group -lmkl_gnu_thread -lmkl_core -Wl,--end-group -fopenmp -ldl -lpthread -lm -lgfortran -lm -L/tools/cluster/6.2/R/3.2.2_mkl/lib64/R/lib -lR installing to /panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.2/site-library/RcppArmadillo/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building...

Hi! I've been playing with MKL for a few days and I noticed the instructions in the R Installation Administration manual [1] no longer apply. It seems that since version 10.0 (the one used by the manual), libmkl_lapack.so has been renamed/split (although the official explanations seem to imply this was already the case in 10.0 [2]). As a consequence, the instructions for dynamic linking no

...> > _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 -lpthread" > >> > export CC="icc" > >> > export F77="ifort" > >> > export CXX="icpc" > >> > export AR="xiar" > >> > export LD="xild" > >> > export CFLAGS="-O3...