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arnaud gaboury

2015-Sep-02 17:35 UTC

[Rd] Build R with MKL and ICC

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:

1- am I not supposed to see something like this in the ldd command return?
libmkl_intel_lp64.so => /opt/intel....
libmkl_intel_thread.so => /opt/intel/....
libmkl_core.so => /opt/intel/...

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

arnaud gaboury

2015-Sep-02 18:49 UTC

head link

[Rd] Build R with MKL and ICC

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


-- 

google.com/+arnaudgabourygabx

Bjørn-Helge Mevik

2015-Sep-04 07:22 UTC

head link

[Rd] Build R with MKL and ICC

arnaud gaboury <arnaud.gaboury at gmail.com> writes:
> 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.
This is how we build R with the Intel compilers and MKL on CentOS 6.x,
with different versions of R (latest version: 3.2.1) and Intel compilers
(latest version: 2015.3) on Intel SandyBridge CPUs:

fast="-ip -O3 -opt-mem-layout-trans=3 -xHost -mavx"
export CC="icc"
export CFLAGS="$fast -wd188 -fp-model precise"
export F77="ifort"
export FFLAGS="$fast -fp-model precise"
export CXX="icpc"
export CXXFLAGS="$fast -fp-model precise"
export FC="ifort"
export FCFLAGS="$fast -fp-model precise"

./configure --prefix=$destdir --with-blas='-mkl=parallel' --with-lapack
--enable-BLAS-shlib


## Notes (they might not be true anymore):
## -static and -ipo break compilation
## -no-prec-div breaks make check
## -fp-model precise is needed for make check
## -wd188 removes a lot of warnings (see R Inst. & Adm. manual)

We have successfully used this setup for a couple of years now.

-- 
Regards,
Bj?rn-Helge Mevik

arnaud gaboury

2015-Sep-04 08:01 UTC

head link

[Rd] Build R with MKL and ICC

On Fri, Sep 4, 2015, 9:24 AM Bj?rn-Helge Mevik <b.h.mevik at usit.uio.no>
wrote:

arnaud gaboury <arnaud.gaboury at gmail.com> writes:
> 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 andhints.

This is how we build R with the Intel compilers and MKL on CentOS 6.x,
with different versions of R (latest version: 3.2.1) and Intel compilers
(latest version: 2015.3) on Intel SandyBridge CPUs:

fast="-ip -O3 -opt-mem-layout-trans=3 -xHost -mavx"
export CC="icc"
export CFLAGS="$fast -wd188 -fp-model precise"
export F77="ifort"
export FFLAGS="$fast -fp-model precise"
export CXX="icpc"
export CXXFLAGS="$fast -fp-model precise"
export FC="ifort"
export FCFLAGS="$fast -fp-model precise"

./configure --prefix=$destdir --with-blas='-mkl=parallel' --with-lapack
--enable-BLAS-shlib

Thank you for this configuration. Nothing about openmp?

What about my cited missing librairies.
libmkl_intel_lp64.so
libmkl_intel_thread.so
libmkl_core.so

Any idea why they are not listed by the ldd command?

## Notes (they might not be true anymore):
## -static and -ipo break compilation
## -no-prec-div breaks make check
## -fp-model precise is needed for make check
## -wd188 removes a lot of warnings (see R Inst. & Adm. manual)

We have successfully used this setup for a couple of years now.

--
Regards,
Bj?rn-Helge Mevik

______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

	[[alternative HTML version deleted]]

Martyn Plummer

2015-Sep-04 15:58 UTC

head link

[Rd] Build R with MKL and ICC

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.
> > 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
> 
> 
> 
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