On Wed, 2015-09-02 at 20:49 +0200, arnaud gaboury wrote:> On Wed, Sep 2, 2015 at 7:35 PM, arnaud gaboury <arnaud.gaboury at gmail.com> wrote: > > After a few days of reading and headache, I finally gave a try at > > building R from source with Intel MKL and ICC. Documentation and posts > > on this topic are rather incomplete, sometime fantasist et do not give > > much explanations about configure options. > > As I am not sure if mine is correct, I would appreciate some advices and hints. > > > > OS: Fedora 22 > > parallel_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 -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="-O3 -ipo -openmp -parallel -xAVX" > > export MAIN_LDFLAGS='-openmp' > > ./configure --with-lapack --with-blas="$MKL" --enable-R-shlib > > --enable-memory-profiling --enable-openmp --enable-BLAS-shlib > > --enable-lto F77=${F77} FC=${F77} > > ------------------------------------------------------------ > > > > After I run ./configure, it seems from config.log everything is fine: > > > > checking for dgemm_ in > > result: yes > > > > checking whether double complex BLAS can be used > > result: yes > > > > checking whether the BLAS is complete > > result: yes > > > > The only error I can see is ld complaining about not finding -lRblas > > ---------------------------------------------------------------------------- > > > > Then run $ make with no errors. > > Now, with no $ make install, I get this: > > > > -------------------------------------------------------------------- > > $ ldd bin/exec/R > > linux-vdso.so.1 (0x00007ffe073f3000) > > libR.so => /usr/lib64/R/lib/libR.so (0x00007f43939e6000) > > libRblas.so => not found > > libm.so.6 => /lib64/libm.so.6 (0x00007f43936de000) > > libiomp5.so => /opt/intel/compilers_and_libraries_2016.0.109/linux/compiler/lib/intel64/libiomp5.so > > (0x00007f439339c000) > > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f4393185000) > > libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f4392f69000) > > libc.so.6 => /lib64/libc.so.6 (0x00007f4392ba8000) > > libdl.so.2 => /lib64/libdl.so.2 (0x00007f43929a4000) > > libblas.so.3 => /lib64/libblas.so.3 (0x00007f439274b000) > > libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007f439241f000) > > libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f43921e0000) > > libreadline.so.6 => /lib64/libreadline.so.6 (0x00007f4391f96000) > > libtre.so.5 => /lib64/libtre.so.5 (0x00007f4391d85000) > > libpcre.so.1 => /lib64/libpcre.so.1 (0x00007f4391b15000) > > liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f43918ef000) > > libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f43916de000) > > libz.so.1 => /lib64/libz.so.1 (0x00007f43914c8000) > > librt.so.1 => /lib64/librt.so.1 (0x00007f43912c0000) > > libicuuc.so.54 => /lib64/libicuuc.so.54 (0x00007f4390f2e000) > > libicui18n.so.54 => /lib64/libicui18n.so.54 (0x00007f4390ad7000) > > libgomp.so.1 => /lib64/libgomp.so.1 (0x00007f43908b5000) > > /lib64/ld-linux-x86-64.so.2 (0x00005557e2243000) > > libtinfo.so.5 => /lib64/libtinfo.so.5 (0x00007f439068a000) > > libicudata.so.54 => /lib64/libicudata.so.54 (0x00007f438ec5f000) > > libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f438e8dc000) > > ----------------------------------------------------------------------------------------------- > > > > > > Now a few questions: > > > EDIT > > 1- am I not supposed to see these libraries in the list ? > > libmkl_intel_lp64.so > > libmkl_intel_thread.so > > libmkl_core.soYou are looking in the wrong place. With the option --enable-BLAS-shlib, R is linked to MKL via the library libRblas.so which you will find in the directory "lib" after building R.> > Or do I need to run $make install before ldd? > > > > 2- when visiting Intel MKL link advisor[0], here is what I get as > > configure and make options: > > Linking: -L${MKLROOT}/lib/intel64 -lmkl_intel_ilp64 -lmkl_core > > -lmkl_intel_thread -lpthread -lm > > Compiler options: -DMKL_ILP64 -qopenmp -I${MKLROOT}/include > > > > What is the difference between -openmp and -qopenmp? Shall I use > > indeed the above compiler options?The option -qopenmp replaces -openmp, which is deprecated. This is in the man page for icc. Martyn> > Thank you for help in this difficult topic for me. > > > > -- > > > > google.com/+arnaudgabourygabx > > >----------------------------------------------------------------------- This message and its attachments are strictly confidenti...{{dropped:8}}
On Fri, Sep 4, 2015 at 5:58 PM, Martyn Plummer <plummerm at iarc.fr> wrote:> On Wed, 2015-09-02 at 20:49 +0200, arnaud gaboury wrote: >> On Wed, Sep 2, 2015 at 7:35 PM, arnaud gaboury <arnaud.gaboury at gmail.com> wrote: >> > After a few days of reading and headache, I finally gave a try at >> > building R from source with Intel MKL and ICC. Documentation and posts >> > on this topic are rather incomplete, sometime fantasist et do not give >> > much explanations about configure options. >> > As I am not sure if mine is correct, I would appreciate some advices and hints. >> > >> > OS: Fedora 22 >> > parallel_studio_xe_2016 >> > Hardware : 8 Thread(s) per core: 2 Vendor ID: GenuineIntel Model name: >> > Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz - Sandybridge >> > R-3.2.2 >> > >> > Here is my build configuration: >> > >> > ------------------------------------------------------- >> > source /opt/intel/compilers_and_libraries_2016/linux/mkl/bin/mklvars.sh intel64 >> > source /opt/intel/bin/compilervars.sh intel64 >> > _mkllibpath=$MKLROOT/lib/intel64 >> > _icclibpath=$MKLROOT/linux/compiler/lib >> > export LD_LIBRARY_PATH=${_mkllibpath}:${_icclibpath} >> > export MKL="-L${_mkllibpath} -L${_icclibpath} -lmkl_intel_lp64 >> > -lmkl_intel_thread -lmkl_core -liomp5 -lpthread" >> > export CC="icc" >> > export F77="ifort" >> > export CXX="icpc" >> > export AR="xiar" >> > export LD="xild" >> > export CFLAGS="-O3 -ipo -openmp -parallel -xAVX" >> > export CXXFLAGS="-O3 -ipo -openmp -parallel -xAVX" >> > export FFLAGS="-O3 -ipo -openmp -parallel -xAVX" >> > export MAIN_LDFLAGS='-openmp' >> > ./configure --with-lapack --with-blas="$MKL" --enable-R-shlib >> > --enable-memory-profiling --enable-openmp --enable-BLAS-shlib >> > --enable-lto F77=${F77} FC=${F77} >> > ------------------------------------------------------------ >> > >> > After I run ./configure, it seems from config.log everything is fine: >> > >> > checking for dgemm_ in >> > result: yes >> > >> > checking whether double complex BLAS can be used >> > result: yes >> > >> > checking whether the BLAS is complete >> > result: yes >> > >> > The only error I can see is ld complaining about not finding -lRblas >> > ---------------------------------------------------------------------------- >> > >> > Then run $ make with no errors. >> > Now, with no $ make install, I get this: >> > >> > -------------------------------------------------------------------- >> > $ ldd bin/exec/R >> > linux-vdso.so.1 (0x00007ffe073f3000) >> > libR.so => /usr/lib64/R/lib/libR.so (0x00007f43939e6000) >> > libRblas.so => not found >> > libm.so.6 => /lib64/libm.so.6 (0x00007f43936de000) >> > libiomp5.so => /opt/intel/compilers_and_libraries_2016.0.109/linux/compiler/lib/intel64/libiomp5.so >> > (0x00007f439339c000) >> > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f4393185000) >> > libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f4392f69000) >> > libc.so.6 => /lib64/libc.so.6 (0x00007f4392ba8000) >> > libdl.so.2 => /lib64/libdl.so.2 (0x00007f43929a4000) >> > libblas.so.3 => /lib64/libblas.so.3 (0x00007f439274b000) >> > libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007f439241f000) >> > libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f43921e0000) >> > libreadline.so.6 => /lib64/libreadline.so.6 (0x00007f4391f96000) >> > libtre.so.5 => /lib64/libtre.so.5 (0x00007f4391d85000) >> > libpcre.so.1 => /lib64/libpcre.so.1 (0x00007f4391b15000) >> > liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f43918ef000) >> > libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f43916de000) >> > libz.so.1 => /lib64/libz.so.1 (0x00007f43914c8000) >> > librt.so.1 => /lib64/librt.so.1 (0x00007f43912c0000) >> > libicuuc.so.54 => /lib64/libicuuc.so.54 (0x00007f4390f2e000) >> > libicui18n.so.54 => /lib64/libicui18n.so.54 (0x00007f4390ad7000) >> > libgomp.so.1 => /lib64/libgomp.so.1 (0x00007f43908b5000) >> > /lib64/ld-linux-x86-64.so.2 (0x00005557e2243000) >> > libtinfo.so.5 => /lib64/libtinfo.so.5 (0x00007f439068a000) >> > libicudata.so.54 => /lib64/libicudata.so.54 (0x00007f438ec5f000) >> > libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f438e8dc000) >> > ----------------------------------------------------------------------------------------------- >> > >> > >> > Now a few questions: >> > >> EDIT >> > 1- am I not supposed to see these libraries in the list ? >> > libmkl_intel_lp64.so >> > libmkl_intel_thread.so >> > libmkl_core.so > > You are looking in the wrong place. With the option --enable-BLAS-shlib, > R is linked to MKL via the library libRblas.so which you will find in > the directory "lib" after building R.Right. $ ls lib libRblas.so* libRlapack.so* libR.so* $ ldd bin/exec/R returns .... libRblas.so => not found Shall I let things like that or tell R the path to libRblas.so ?>> > Or do I need to run $make install before ldd? >> > >> > 2- when visiting Intel MKL link advisor[0], here is what I get as >> > configure and make options: >> > Linking: -L${MKLROOT}/lib/intel64 -lmkl_intel_ilp64 -lmkl_core >> > -lmkl_intel_thread -lpthread -lm >> > Compiler options: -DMKL_ILP64 -qopenmp -I${MKLROOT}/include >> > >> > What is the difference between -openmp and -qopenmp? Shall I use >> > indeed the above compiler options? > > The option -qopenmp replaces -openmp, which is deprecated. This is in > the man page for icc. > > Martyn > >> > Thank you for help in this difficult topic for me. >> > >> > -- >> > >> > google.com/+arnaudgabourygabx >> >> >> > > ----------------------------------------------------------------------- > This message and its attachments are strictly confiden...{{dropped:14}}
On Sat, 2015-09-05 at 11:53 +0200, arnaud gaboury wrote:> On Fri, Sep 4, 2015 at 5:58 PM, Martyn Plummer <plummerm at iarc.fr> wrote: > > On Wed, 2015-09-02 at 20:49 +0200, arnaud gaboury wrote: > >> On Wed, Sep 2, 2015 at 7:35 PM, arnaud gaboury <arnaud.gaboury at gmail.com> wrote: > >> > After a few days of reading and headache, I finally gave a try at > >> > building R from source with Intel MKL and ICC. Documentation and posts > >> > on this topic are rather incomplete, sometime fantasist et do not give > >> > much explanations about configure options. > >> > As I am not sure if mine is correct, I would appreciate some advices and hints. > >> > > >> > OS: Fedora 22 > >> > parallel_studio_xe_2016 > >> > Hardware : 8 Thread(s) per core: 2 Vendor ID: GenuineIntel Model name: > >> > Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz - Sandybridge > >> > R-3.2.2 > >> > > >> > Here is my build configuration: > >> > > >> > ------------------------------------------------------- > >> > source /opt/intel/compilers_and_libraries_2016/linux/mkl/bin/mklvars.sh intel64 > >> > source /opt/intel/bin/compilervars.sh intel64 > >> > _mkllibpath=$MKLROOT/lib/intel64 > >> > _icclibpath=$MKLROOT/linux/compiler/lib > >> > export LD_LIBRARY_PATH=${_mkllibpath}:${_icclibpath} > >> > export MKL="-L${_mkllibpath} -L${_icclibpath} -lmkl_intel_lp64 > >> > -lmkl_intel_thread -lmkl_core -liomp5 -lpthread" > >> > export CC="icc" > >> > export F77="ifort" > >> > export CXX="icpc" > >> > export AR="xiar" > >> > export LD="xild" > >> > export CFLAGS="-O3 -ipo -openmp -parallel -xAVX" > >> > export CXXFLAGS="-O3 -ipo -openmp -parallel -xAVX" > >> > export FFLAGS="-O3 -ipo -openmp -parallel -xAVX" > >> > export MAIN_LDFLAGS='-openmp' > >> > ./configure --with-lapack --with-blas="$MKL" --enable-R-shlib > >> > --enable-memory-profiling --enable-openmp --enable-BLAS-shlib > >> > --enable-lto F77=${F77} FC=${F77} > >> > ------------------------------------------------------------ > >> > > >> > After I run ./configure, it seems from config.log everything is fine: > >> > > >> > checking for dgemm_ in > >> > result: yes > >> > > >> > checking whether double complex BLAS can be used > >> > result: yes > >> > > >> > checking whether the BLAS is complete > >> > result: yes > >> > > >> > The only error I can see is ld complaining about not finding -lRblas > >> > ---------------------------------------------------------------------------- > >> > > >> > Then run $ make with no errors. > >> > Now, with no $ make install, I get this: > >> > > >> > -------------------------------------------------------------------- > >> > $ ldd bin/exec/R > >> > linux-vdso.so.1 (0x00007ffe073f3000) > >> > libR.so => /usr/lib64/R/lib/libR.so (0x00007f43939e6000) > >> > libRblas.so => not found > >> > libm.so.6 => /lib64/libm.so.6 (0x00007f43936de000) > >> > libiomp5.so => /opt/intel/compilers_and_libraries_2016.0.109/linux/compiler/lib/intel64/libiomp5.so > >> > (0x00007f439339c000) > >> > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f4393185000) > >> > libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f4392f69000) > >> > libc.so.6 => /lib64/libc.so.6 (0x00007f4392ba8000) > >> > libdl.so.2 => /lib64/libdl.so.2 (0x00007f43929a4000) > >> > libblas.so.3 => /lib64/libblas.so.3 (0x00007f439274b000) > >> > libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007f439241f000) > >> > libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f43921e0000) > >> > libreadline.so.6 => /lib64/libreadline.so.6 (0x00007f4391f96000) > >> > libtre.so.5 => /lib64/libtre.so.5 (0x00007f4391d85000) > >> > libpcre.so.1 => /lib64/libpcre.so.1 (0x00007f4391b15000) > >> > liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f43918ef000) > >> > libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f43916de000) > >> > libz.so.1 => /lib64/libz.so.1 (0x00007f43914c8000) > >> > librt.so.1 => /lib64/librt.so.1 (0x00007f43912c0000) > >> > libicuuc.so.54 => /lib64/libicuuc.so.54 (0x00007f4390f2e000) > >> > libicui18n.so.54 => /lib64/libicui18n.so.54 (0x00007f4390ad7000) > >> > libgomp.so.1 => /lib64/libgomp.so.1 (0x00007f43908b5000) > >> > /lib64/ld-linux-x86-64.so.2 (0x00005557e2243000) > >> > libtinfo.so.5 => /lib64/libtinfo.so.5 (0x00007f439068a000) > >> > libicudata.so.54 => /lib64/libicudata.so.54 (0x00007f438ec5f000) > >> > libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f438e8dc000) > >> > ----------------------------------------------------------------------------------------------- > >> > > >> > > >> > Now a few questions: > >> > > >> EDIT > >> > 1- am I not supposed to see these libraries in the list ? > >> > libmkl_intel_lp64.so > >> > libmkl_intel_thread.so > >> > libmkl_core.so > > > > You are looking in the wrong place. With the option --enable-BLAS-shlib, > > R is linked to MKL via the library libRblas.so which you will find in > > the directory "lib" after building R. > > > Right. > $ ls lib > libRblas.so* libRlapack.so* libR.so* > > $ ldd bin/exec/R returns > .... > libRblas.so => not found > > Shall I let things like that or tell R the path to libRblas.so ?No that is not a problem. R knows where to find these libaries even if they are not on the linker path. Your only problem is to tell R where the Intel libraries are at runtime, typically by setting/modifying LD_LIBRARY_PATH before launching R, e.g. on my desktop I use export LD_LIBRARY_PATH=/opt/intel/composerxe/lib/intel64:/opt/intel/composerxe/mkl/lib/intel64/ Martyn> >> > Or do I need to run $make install before ldd? > >> > > >> > 2- when visiting Intel MKL link advisor[0], here is what I get as > >> > configure and make options: > >> > Linking: -L${MKLROOT}/lib/intel64 -lmkl_intel_ilp64 -lmkl_core > >> > -lmkl_intel_thread -lpthread -lm > >> > Compiler options: -DMKL_ILP64 -qopenmp -I${MKLROOT}/include > >> > > >> > What is the difference between -openmp and -qopenmp? Shall I use > >> > indeed the above compiler options? > > > > The option -qopenmp replaces -openmp, which is deprecated. This is in > > the man page for icc. > > > > Martyn > > > >> > Thank you for help in this difficult topic for me. > >> > > >> > -- > >> > > >> > google.com/+arnaudgabourygabx > >> > >> > >> > >----------------------------------------------------------------------- This message and its attachments are strictly confidenti...{{dropped:8}}