AUR (en) - r-mkl

Search Criteria

Enter search criteria

Search by

Keywords

Out of Date

Sort by

Sort order

Per page

Package Details: r-mkl 3.6.1-1

Package Actions

Git Clone URL:	https://aur.archlinux.org/r-mkl.git (read-only)
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=3.6.1
Submitter:	giniu
Maintainer:	alexanderp
Last Packager:	alexanderp
Votes:	18
Popularity:	0.065571
First Submitted:	2010-05-06 00:10
Last Updated:	2019-07-11 20:06

Dependencies (26)

bzip2 (bzip2-git, bzip2-rustify-git, bzip2-with-lbzip2-symlinks)
curl (curl-http2-git, curl-git)
gcc-fortran (gcc-fortran-multilib-x32, gcc-fortran-git, gcc-fortran-multilib-git)
gcc-libs (gcc-libs-multilib-x32, gcc-libs-git, gcc-libs-multilib-git)
icu (icu-git)
intel-common-libs
intel-mkl (intel-mkl-slim)
libjpeg (libjpeg-droppatch, mozjpeg-git, mozjpeg, libjpeg-turbo)
libpng (libpng-git)
libtiff (libtiff-git)
libxmu
libxt
ncurses (ncurses-nohex)
openmp (openmp-svn)
pango (pango-ubuntu, pango-git)
pcre (pcre-svn)
perl (perl-git)
readline (readline-athame-git)
unzip (unzip-natspec, unzip-iconv)
xz (xz-git, xz-static-git)
zip (zip-natspec)
zlib (zlib-asm, zlib-static, zlib-git)
java-environment (jdk5, jdk9-openj9-bin, jdk7, tuxjdk, jdk7-openjdk-infinality, java-8-openjdk-shenandoah, jdk8-openjdk-infinality, java-gcj-compat, jdk10-openjdk-openj9-bin, jdk9, zulu-10-bin, jdk-devel, jdk10, jdk-dcevm, jdk8-arm, jdk8-arm64, jdk8-openj9-bin, amazon-corretto-8, amazon-corretto-11, jdk8-openjdk-shenandoah, jdk8-openjdk-jetbrains, jdk8-j9-bin, jdk8, jdk11, jdk, jdk-adoptopenjdk, jdk11-adoptopenjdk, jdk6, jdk-arm, jdk12-openj9-bin, zulu-11-bin, zulu-12-bin, jdk7-j9-bin, jdk7r1-j9-bin, java-openjdk-ea-bin, jdk11-openj9-bin, zulu-embedded-jdk11, jetbrains-jre, jetbrains-jre8, graal-bin, jdk8-jetbrains, jdk-jetbrains, jdk-openjdk, jdk10-openjdk, jdk11-openjdk, jdk7-openjdk, jdk8-openjdk) (make)
tk (tk85) (make)
texlive-bin (texlive-bin-svn, texlive-installer, texlive-full) (optional) – LaTeX sty files
tk (tk85) (optional) – tcl-tk interface

Required by (247)

apache-spark (requires r) (optional)
apache-spark-git (requires r) (optional)
diffoscope-git (requires r) (check)
diffoscope-git (requires r) (optional)
dnaa (requires r)
emacs-ess (requires r)
emacs-ess-git (requires r)
fgbio-git (requires r) (check)
folding (requires r)
gatk-bin (requires r) (optional)
grass6 (requires r) (optional)
iramuteq-bin (requires r)
jamovi-rbundle (requires r)
jamovi-rbundle (requires r) (make)
jasp-desktop-git (requires r)
jasp-desktop-git (requires r) (make)
jasp-rbundle (requires r) (make)
jasp-rbundle (requires r)
knime-desktop (requires r) (optional)
ledger-plots-git (requires r)
libcorkipset-git (requires r)
littler (requires r)
littler (requires r) (make)
littler-git (requires r)
littler-git (requires r) (make)
mange (requires r) (optional)
mapdamage (requires r) (optional)
mathematica (requires r) (optional)
mathematica-09 (requires r) (optional)
monetdb (requires r) (make)
monetdb (requires r)
nteract-bin (requires r) (optional)
nvim-r (requires r) (optional)
phantompeakqualtools (requires r)
plink (requires r)
pp-git (requires r) (optional)
python-rchitect (requires r)
python-rpy2-hg (requires r)
python2-rchitect (requires r)
qtltools-git (requires r)
quake-bio (requires r)
qualimap (requires r)
quine-relay (requires r)
r-abind (requires r)
r-askpass (requires r)
r-assertthat (requires r)
r-backports (requires r)
r-base64enc (requires r)
r-bh (requires r)
r-bindr (requires r)
r-bindrcpp (requires r)
r-biobase (requires r)
r-biocgenerics (requires r)
r-biocparallel (requires r)
r-biostrings (requires r)
r-bitops (requires r)
r-broom (requires r)
r-bsda (requires r)
r-callr (requires r)
r-cardata (requires r)
r-caret (requires r)
r-catools (requires r)
r-chron (requires r)
r-cli (requires r)
r-coda (requires r)
r-colorspace (requires r)
r-commonmark (requires r)
r-corpus (requires r)
r-covr (requires r)
r-cran-dicekriging (requires r)
r-cran-extrafont (requires r)
r-cran-extrafontdb (requires r)
r-cran-rinside (requires r)
r-cran-rttf2pt1 (requires r)
r-crayon (requires r)
r-crosstalk (requires r)
r-curl (requires r)
r-dada2 (requires r)
r-datatable (requires r)
r-delayedarray (requires r)
r-deseq2 (requires r)
r-devtools (requires r)
r-dichromat (requires r)
r-digest (requires r)
r-dplyr (requires r)
r-dt (requires r)
r-e1071 (requires r)
r-editdata (requires r)
r-egg (requires r)
r-ellipsis (requires r)
r-evaluate (requires r)
r-expm (requires r)
r-fansi (requires r)
r-forcats (requires r)
r-formatr (requires r)
r-futilelogger (requires r)
r-futileoptions (requires r)
r-gdal (requires r)
r-gdtools (requires r)
r-genomeinfodb (requires r)
r-genomeinfodbdata (requires r)
r-genomicalignments (requires r)
r-genomicranges (requires r)
r-geos (requires r)
r-geosphere (requires r)
r-ggplot2 (requires r)
r-git2r (requires r)
r-glue (requires r)
r-gridextra (requires r)
r-gtable (requires r)
r-haven (requires r)
r-highr (requires r)
r-hms (requires r)
r-htmltools (requires r)
r-htmlwidgets (requires r)
r-httpuv (requires r)
r-httr (requires r)
r-hunspell (requires r)
r-hwriter (requires r)
r-iranges (requires r)
r-irlba (requires r)
r-islr (requires r)
r-jsonlite (requires r)
r-juniperkernel (requires r)
r-knitr (requires r)
r-labeling (requires r)
r-lambdar (requires r)
r-later (requires r)
r-lattice (requires r)
r-latticeextra (requires r)
r-lazyeval (requires r)
r-lintr (requires r)
r-lme4 (requires r)
r-lubridate (requires r)
r-magrittr (requires r)
r-manipulatewidget (requires r)
r-maptools (requires r)
r-markdown (requires r)
r-matrix (requires r)
r-matrixmodels (requires r)
r-matrixstats (requires r)
r-mco (requires r)
r-memoise (requires r)
r-methodss3 (requires r)
r-mime (requires r)
r-miniui (requires r)
r-minqa (requires r)
r-misc3d (requires r)
r-mnormt (requires r)
r-move (requires r)
r-munsell (requires r)
r-mvtnorm (requires r)
r-nlme (requires r)
r-nloptr (requires r)
r-oo (requires r)
r-openssl (requires r)
r-pbdzmq (requires r)
r-pbkrtest (requires r)
r-pillar (requires r)
r-pkgconfig (requires r)
r-plogr (requires r)
r-plot3d (requires r)
r-plot3drgl (requires r)
r-plyr (requires r)
r-pracma (requires r)
r-praise (requires r)
r-processx (requires r)
r-promises (requires r)
r-ps (requires r)
r-psych (requires r)
r-purrr (requires r)
r-quantreg (requires r)
r-r6 (requires r)
r-raster (requires r)
r-rcolorbrewer (requires r)
r-rcpp (requires r)
r-rcppeigen (requires r)
r-rcppparallel (requires r)
r-rcurl (requires r)
r-readr (requires r)
r-repr (requires r)
r-reshape2 (requires r)
r-rgl (requires r)
r-rlang (requires r)
r-rmarkdown (requires r)
r-rsamtools (requires r)
r-rstan (requires r)
r-rstudioapi (requires r)
r-rustinr (requires r)
r-s4vectors (requires r)
r-scales (requires r)
r-sfsmisc (requires r)
r-shiny (requires r)
r-shortread (requires r)
r-snow (requires r)
r-sourcetools (requires r)
r-sp (requires r)
r-sparsem (requires r)
r-spelling (requires r)
r-stringi (requires r)
r-stringr (requires r)
r-summarizedexperiment (requires r)
r-swirl (requires r)
r-sys (requires r)
r-testit (requires r)
r-testthat (requires r)
r-tibble (requires r)
r-tidyr (requires r)
r-tidyselect (requires r)
r-timedate (requires r)
r-tinytex (requires r)
r-tkrplot (requires r)
r-unix (requires r)
r-utf8 (requires r)
r-utils (requires r)
r-vctrs (requires r)
r-viridislite (requires r)
r-webshot (requires r)
r-whisker (requires r)
r-withr (requires r)
r-xfun (requires r)
r-xml2 (requires r)
r-xtable (requires r)
r-xvector (requires r)
r-yaml (requires r)
r-zeallot (requires r)
r-zlibbioc (requires r)
r-zoo (requires r)
radian (requires r)
rkward (requires r)
rkward-git (requires r)
rsem (requires r)
rserve-sandbox-docker (requires r)
rserve-sandbox-docker-bin (requires r)
rstudio-desktop (requires r)
rstudio-desktop-bin (requires r)
rstudio-desktop-git (requires r)
rstudio-desktop-preview-bin (requires r)
rstudio-server-bin (requires r)
rstudio-server-git (requires r)
shiny-server-git (requires r)
shiny-server-git (requires r) (make)
shogun (requires r)
simpleitk (requires r) (make)
simpleitk (requires r) (optional)
taverna (requires r) (optional)
zim-git (requires r) (optional)

Sources (4)

Latest Comments

1 2 3 4 5 6 ... Next › Last »

alexanderp commented on 2019-07-26 07:45

Great @petronny. Thanks for your effort.

petronny commented on 2019-07-26 07:40

Hi, I provide a pre-built binary of this package at arch4edu.
Also please vote at this issue if you want more pre-built R packages.

petronny commented on 2019-07-24 07:06

Every time Intel MKL gets updated, compilation of R with icc needs to be adapted.

Actually I can deal with that, I can provide a well-built binary with every icc or r-mkl update. But I'll use gcc then since there is no gain when using icc.

alexanderp commented on 2019-07-24 06:40

Hi @petronny.

Every time Intel MKL gets updated, compilation of R with icc needs to be adapted.

I measured no gain when using icc, therefore this package defaults to gcc.

See some of my benchmarks here: https://github.com/alexisph/high_performance_r

petronny commented on 2019-07-23 07:24

And is building with gcc the recommend way by the official R group to build with MKL support?
If so I can give up building with icc and using gcc now.

petronny commented on 2019-07-23 07:21

Hi, thanks for maintaining this package.
Could you help with building with icc?
I've un-comment the line _CC="icc" but I get errors:

icc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include  -D_FORTIFY_SOURCE=2 -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O3 -fPIC -m64 -march=native -fp-model precise -fp-model source -I/opt/intel/compilers_and_libraries_2019.4.243/li
nux/mkl/include  -c envir.c -o envir.o
arithmetic.c(59): warning #274: declaration is not visible outside of function
  int matherr(struct exception *exc)
                     ^

arithmetic.c(61): error: pointer to incomplete class type is not allowed
      switch (exc->type) {
              ^

arithmetic.c(62): error: identifier "DOMAIN" is undefined
      case DOMAIN:
           ^

arithmetic.c(63): error: identifier "SING" is undefined
      case SING:
           ^

arithmetic.c(66): error: identifier "OVERFLOW" is undefined
      case OVERFLOW:
           ^

arithmetic.c(69): error: identifier "UNDERFLOW" is undefined
      case UNDERFLOW:
           ^

arithmetic.c(70): error: pointer to incomplete class type is not allowed
        exc->retval = 0.0;
        ^

icc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include  -D_FORTIFY_SOURCE=2 -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O3 -fPIC -m64 -march=native -fp-model precise -fp-model source -I/opt/intel/compilers_and_libraries_2019.4.243/li
nux/mkl/include  -c errors.c -o errors.o
icc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include  -D_FORTIFY_SOURCE=2 -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O3 -fPIC -m64 -march=native -fp-model precise -fp-model source -I/opt/intel/compilers_and_libraries_2019.4.243/li
nux/mkl/include  -c eval.c -o eval.o
icc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include  -D_FORTIFY_SOURCE=2 -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O3 -fPIC -m64 -march=native -fp-model precise -fp-model source -I/opt/intel/compilers_and_libraries_2019.4.243/li
nux/mkl/include  -c format.c -o format.o
compilation aborted for arithmetic.c (code 2)
make[3]: *** [../../Makeconf:124: arithmetic.o] Error 2
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/build/r-mkl/src/R-3.6.1/src/main'
make[2]: *** [Makefile:135: R] Error 2
make[2]: Leaving directory '/build/r-mkl/src/R-3.6.1/src/main'
make[1]: *** [Makefile:28: R] Error 1
make[1]: Leaving directory '/build/r-mkl/src/R-3.6.1/src'
make: *** [Makefile:61: R] Error 1
==> ERROR: A failure occurred in build().

blazko commented on 2019-07-15 07:40

Is anyone else facing validity checks problem with parallel_studio_xe?

==> Validating source files with sha256sums...
    parallel_studio_xe_2019_update4_cluster_edition.tgz ... FAILED
    intel_compilers.sh ... Passed
    intel_vtune-amplifier.sh ... Passed
    intel_advisor.sh ... Passed
    intel_inspector.sh ... Passed
    intel-composer.install ... Passed
    intel-common-libs.conf ... Passed
    intel-fortran.conf ... Passed
    intel-openmp.conf ... Passed
    intel-mkl.conf ... Passed
    intel-mpi.conf ... Passed
    intel-ipp.conf ... Passed
    intel-tbb.conf ... Passed
    intel-mkl.sh ... Passed
    intel-mkl.install ... Passed
    intel-mkl-th.conf ... Passed
    intel-tbb.install ... Passed
    EULA.txt ... Passed
==> ERROR: One or more files did not pass the validity check!

alexanderp commented on 2019-05-17 11:46

Thanks for the report @blazko. To be honest, those numbers look strange to me... Did you consider reporting this to the Intel MKL forums? (https://software.intel.com/en-us/forums/intel-math-kernel-library)

By the way, have you done any benchmark comparisons between the versions?

blazko commented on 2019-05-17 11:40

@alexanderp I sorted this out. For a 4 cores 8 threads CPU I should set export MKL_NUM_THREADS=32 on my laptop (instead of 8) and export MKL_NUM_THREADS=128 on the xeon (instead of 32),

After this they all work at max speeds and resources.

alexanderp commented on 2019-05-07 10:59

@blazko, Not sure... It seems that the way GNU OpenMP utilizes cores/threads is different. Just for reference, I am getting the same behaviour when using the microsoft-r-open package.

Arch Linux User Repository