From arnaud.gaboury at gmail.com  Sat Sep  5 11:53:49 2015
From: arnaud.gaboury at gmail.com (arnaud gaboury)
Date: Sat, 5 Sep 2015 11:53:49 +0200
Subject: [Rd] Build R with MKL and ICC
In-Reply-To: <1441382281.4083.26.camel@iarc.fr>
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	<1441382281.4083.26.camel@iarc.fr>
Message-ID: <CAK1hC9vg0SePBhEbp-Xpt8W1BDH-kY3XTLr39ZHCp2k2MHxUhA@mail.gmail.com>

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}}



[Rd] Build R with MKL and ICC
arnaud gaboury