From arnaud.gaboury at gmail.com  Wed Sep  2 20:49:57 2015
From: arnaud.gaboury at gmail.com (arnaud gaboury)
Date: Wed, 2 Sep 2015 20:49:57 +0200
Subject: [Rd] Build R with MKL and ICC
In-Reply-To: <CAK1hC9uLYSyA-7W92TwD4J9adcxDRE1a2ig1iDDPSyN43kikyg@mail.gmail.com>
References: <CAK1hC9uLYSyA-7W92TwD4J9adcxDRE1a2ig1iDDPSyN43kikyg@mail.gmail.com>
Message-ID: <CAK1hC9u0btbbXGR3+OAcAd5n3SbFwUHoH+YsT5FzVpaeyZWdEQ@mail.gmail.com>

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
>
> 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?
>
> Thank you for help in this difficult topic for me.
>
> --
>
> google.com/+arnaudgabourygabx



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[Rd] Build R with MKL and ICC
arnaud gaboury