Package Details: r-mkl 4.4.2-1

Git Clone URL: https://aur.archlinux.org/r-mkl.git (read-only, click to copy)
Package Base: r-mkl
Description: Language and environment for statistical computing and graphics, linked to the Intel(R) MKL.
Upstream URL: http://www.r-project.org/
Keywords: hpc mathematics modelling r statistics
Licenses: GPL
Conflicts: microsoft-r-open, r
Provides: r
Submitter: giniu
Maintainer: alexanderp
Last Packager: alexanderp
Votes: 25
Popularity: 0.000082
First Submitted: 2010-05-06 00:10 (UTC)
Last Updated: 2024-11-12 19:56 (UTC)

Latest Comments

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adalardo commented on 2016-02-03 19:52 (UTC)

Thank for the package alexanderp! I found an error in PKGBUILD, to fix it just change line: url=('http://www.r-project.org/') to url="http://www.r-project.org/" This is the bug commented by tetonedge. I was not able to compile the package using icc. I comment the line: #_CC="icc" # comment to build without the Intel compiler and works! Best, Alexandre

tetonedge commented on 2016-02-01 14:20 (UTC)

I get ==> ERROR: url should not be an array with the new PKGBUILD

alexanderp commented on 2016-01-20 20:59 (UTC) (edited on 2016-01-20 21:00 (UTC) by alexanderp)

I updated the PKGBUILD for R-3.2.3. The compilation uses Intel's MKL by default now, unless if commented out in the PKGBUILD. I also added OpenMP support when compiling with gcc.

alexanderp commented on 2015-12-20 15:30 (UTC) (edited on 2015-12-20 15:32 (UTC) by alexanderp)

Hi. I had trouble compiling with the Intel compilers since some old and non-optimized options were used in your PKGBUILD. Here is a patch which fixes the PKGBUILD and compiles with Intel MKL, Intel BLAS (multi-threaded) and compiler optimizations: diff --git a/PKGBUILD b/PKGBUILD index c50e724..a7934a6 100644 --- a/PKGBUILD +++ b/PKGBUILD @@ -15,7 +15,7 @@ conflicts=('r') depends=('intel-mkl' 'bzip2' 'libpng' 'libjpeg' 'libtiff' 'ncurses' 'pcre' 'readline' 'zlib' 'perl' 'gcc-libs' 'libxt' 'libxmu' 'pango' 'xz' 'desktop-file-utils' 'zip' 'unzip') -makedepends=('jdk8-openjdk' 'gcc-fortran' 'tk') +makedepends=('jdk8-openjdk-infinality' 'gcc-fortran' 'tk') optdepends=('tk: tcl/tk interface' 'texlive-bin: latex sty files' 'icc: intel compiler' 'icpc: intel compiler' 'xiar: intel compiler' 'xild: intel compiler') @@ -39,13 +39,13 @@ sha512sums=('71ba470875262b9f00fb6970f209788df4dad30e0a28373b824b60d8bc6401afb77 if [ "$CARCH" == "x86_64" ]; then _intel_arch=intel64 - _intel_lib=mkl_gf_lp64 + _intel_lib=mkl_intel_lp64 elif [ "$CARCH" == "i686" ]; then _intel_arch=ia32 _intel_lib=mkl_gf fi -#_CC="icc" # uncomment to build with the Intel compiler +_CC="icc" # uncomment to build with the Intel compiler prepare() { cd R-${pkgver} @@ -60,10 +60,17 @@ prepare() { build() { # Set up the environment for MKL source /opt/intel/mkl/bin/mklvars.sh ${_intel_arch} + source /opt/intel/composerxe/linux/bin/ifortvars.sh ${_intel_arch} _icclibpath=$(echo $MKLROOT | sed "s%mkl%compiler%g")/lib/${_intel_arch} _mkllibpath=$MKLROOT/lib/${_intel_arch} - _mkllibs=" -fopenmp -Wl,--no-as-needed -L${_mkllibpath} -l${_intel_lib} -lmkl_core -lmkl_gnu_thread -ldl -lpthread -lm" + _openmplibpath=${PROD_DIR}/compiler/lib/intel64 + _mkllibs="-L${_mkllibpath} -L${_openmplibpath} -Wl,--no-as-needed \ + -l${_intel_lib} \ + -lmkl_intel_thread \ + -lmkl_core \ + -liomp5 -ldl -lpthread -lm" LDFLAGS="${LDFLAGS} -L${_icclibpath}" + export MAIN_LDFLAGS="-qopenmp" if [ $_CC = "icc" ]; then @@ -73,6 +80,10 @@ build() { export LD="xild" export _F77="ifort" export _FC="ifort" + export CFLAGS="-O3 -ipo -qopenmp -parallel -xHost -fp-model strict -qopt-mem-layout-trans=3 -I${MKLROOT}/include" + export CXXFLAGS="-O3 -ipo -qopenmp -parallel -xHost -fp-model strict -qopt-mem-layout-trans=3 -I${MKLROOT}/include" + export FFLAGS="-O3 -ipo -qopenmp -parallel -xHost -fp-model strict -qopt-mem-layout-trans=3 -I${MKLROOT}/include" + export FCFLAGS="-O3 -ipo -qopenmp -parallel -xHost -fp-model strict -qopt-mem-layout-trans=3 -I${MKLROOT}/include" else export _F77="gfortran" export _FC="gfortran" @@ -87,11 +98,14 @@ build() { rincludedir=/usr/include/R/ \ rdocdir=/usr/share/doc/R/ \ --with-x \ - --enable-R-shlib \ - --with-blas="${_mkllibs}" \ - --with-lapack \ - F77=${_F77} \ - FC=${_FC} \ + --with-blas="${_mkllibs}" \ + --with-lapack \ + --enable-R-shlib \ + --enable-memory-profiling \ + --enable-BLAS-shlib \ + --enable-openmp \ + F77=${_F77} \ + FC=${_FC} \ LIBnn=lib # Place Intel's basic math library prior to GLIBC libm

jdarch commented on 2015-09-08 11:54 (UTC)

gabx, Intel's basic math library contains an performance-optimized subset of libm. By linking to it before linking to libm some operations might have slightly higher performance, as the call will then be handled by Intel's library. AMD has a similar library: http://developer.amd.com/tools-and-sdks/cpu-development/libm/

gabx commented on 2015-09-06 11:42 (UTC)

For information, what reason behind: # Place Intel's basic math library prior to GLIBC libm Thank you

halfhorn commented on 2015-06-27 17:39 (UTC)

@ leonardof That looks like you have a problem with your mkl installation/configuration.

leonardof commented on 2015-06-04 00:06 (UTC)

I wasn't able to compile this package. Starting build(), I got this message: /tmp/yaourt-tmp-leonardof/aur-r-mkl/./PKGBUILD: line 62: /opt/intel/mkl/bin/mklvars.sh: Arquivo ou diretório não encontrado "Arquivo ou diretório não encontrado" means "file or directory not found". That's because the script is in /opt/intel/composer_xe_2015.3.187/mkl/bin/mklvars.sh. I guess it's not really r-mkl's fault, but I thought you might want to know. Anyway, I created a symlink between the real and the expected "mkl" directory, and at last build took a little longer to fail. This time I got this message in the start of buid: /tmp/yaourt-tmp-leonardof/aur-r-mkl/./PKGBUILD: line 69: [: =: esperado operador unário "esperado operador unário" means "expected unary operator". The compilation went on, and eventually ended with this: gcc -shared -fopenmp -Wl,-O1,--sort-common,--as-needed,-z,relro -L/opt/intel/composerxe/compiler/lib/intel64 -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a -lblas -lgfortran -limf -lm -lquadmath -lreadline -lpcre -llzma -lbz2 -lz -lrt -ldl -limf -lm -licuuc -licui18n /usr/bin/ld: cannot find -limf /usr/bin/ld: cannot find -limf collect2: error: ld returned 1 exit status Makefile:185: recipe for target 'libR.so' failed make[3]: *** [libR.so] Error 1 make[3]: Leaving directory '/tmp/yaourt-tmp-leonardof/aur-r-mkl/src/R-3.2.0/src/main' Makefile:143: recipe for target 'R' failed make[2]: *** [R] Error 2 make[2]: Leaving directory '/tmp/yaourt-tmp-leonardof/aur-r-mkl/src/R-3.2.0/src/main' Makefile:28: recipe for target 'R' failed make[1]: *** [R] Error 1 make[1]: Leaving directory '/tmp/yaourt-tmp-leonardof/aur-r-mkl/src/R-3.2.0/src' Makefile:59: recipe for target 'R' failed make: *** [R] Error 1

halfhorn commented on 2015-05-06 08:08 (UTC)

This package is being maintained at https://github.com/m-wells/r-mkl if you would like to submit pull requests and help contribute to the maintenance of this package.

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