AUR (en) - r-mkl

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)

Intel(R) Core(TM) i7-4600U CPU @ 2.10GHz Sorry for my slow replies. I don't seem to be getting notifications despite subscribing to the thread.

alexanderp commented on 2016-06-02 18:59 (UTC)

Yes, the default is GCC. On my i7-2640m the "checking examples" step doesn't take more than 1-2min. Which CPU do you have?

nacnudus commented on 2016-06-02 18:10 (UTC)

Yes, I interrupted it after about eight hours with no activity on the process. Am I compiling it with GCC? It seems to be the default since #_CC="icc" # comment to build without the Intel compiler has been commented out by default.

alexanderp commented on 2016-06-02 16:27 (UTC)

I compiled again with GCC and get no such error. This line seems strange to me: * checking examples ...^C ERROR Did you press Ctrl+C while in the middle of checking the examples?

nacnudus commented on 2016-06-02 14:00 (UTC)

Installation stalls on package mgcv with the following: checking package 'mgcv' * using log directory ‘/tmp/yaourt-tmp-nacnudus/aur-r-mkl/src/R-3.3.0/tests/mgcv.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘mgcv/DESCRIPTION’ ... OK * this is package ‘mgcv’ version ‘1.8-12’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * skipping installation test * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘gam’ * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking examples ...^C ERROR Running examples in ‘mgcv-Ex.R’ failed The error most likely occurred in: > ### Name: mgcv.parallel > ### Title: Parallel computation in mgcv. > ### Aliases: mgcv.parallel > ### Keywords: package models smooth regression > > ### ** Examples > > ## illustration of multi-threading with gam... > > require(mgcv);set.seed(9) > dat <- gamSim(1,n=2000,dist="poisson",scale=.1) Gu & Wahba 4 term additive model > k <- 12;bs <- "cr";ctrl <- list(nthreads=2) > > system.time(b1<-gam(y~s(x0,bs=bs)+s(x1,bs=bs)+s(x2,bs=bs,k=k) + ,family=poisson,data=dat,method="REML"))[3] elapsed 0.088 > > system.time(b2<-gam(y~s(x0,bs=bs)+s(x1,bs=bs)+s(x2,bs=bs,k=k), + family=poisson,data=dat,method="REML",control=ctrl))[3] Then hundreds of lines of: OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option. Finally: elapsed 5.795 > > ## Poisson example on a cluster with 'bam'. > ## Note that there is some overhead in initializing the > ## computation on the cluster, associated with loading > ## the Matrix package on each node. For this reason the > ## sample sizes here are very small to keep CRAN happy, but at > ## this low sample size you see little advantage of parallel computation. > > k <- 13 > dat <- gamSim(1,n=6000,dist="poisson",scale=.1) Gu & Wahba 4 term additive model > require(parallel) Loading required package: parallel > nc <- 2 ## cluster size, set for example portability > if (detectCores()>1) { ## no point otherwise + cl <- makeCluster(nc) + ## could also use makeForkCluster, but read warnings first! + } else cl <- NULL Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/tmp/yaourt-tmp-nacnudus/aur-r-mkl/src/R-3.3.0/tests/mgcv.Rcheck/00check.log’ for details. Makefile.common:404: recipe for target 'test-Packages-Recommended' failed make[1]: *** [test-Packages-Recommended] Interrupt Makefile:239: recipe for target 'check-recommended' failed make: *** [check-recommended] Interrupt

syne commented on 2016-05-17 13:39 (UTC)

if you're installing intel-mkl etc, edit the PKGBUILD line 299-300 from ln -s ./${_composer_xe_dir} composerxe-${_year} ln -s ./composerxe-${_year} composerxe to ln -s ./${_composer_xe_dir} composerxe don't even know why that second symlink is necessary... that fixed the mklvars problem for me.

alexanderp commented on 2016-05-16 22:04 (UTC)

Hmm I cannot seem to be able to reproduce your error. Is mklvars.sh present on your system?

<deleted-account> commented on 2016-05-16 21:17 (UTC)

I get an error when this tries to install. It complains that: /opt/intel/mkl/bin/mklvars.sh: No such file or directory

alexanderp commented on 2016-05-04 12:55 (UTC) (edited on 2016-05-04 12:55 (UTC) by alexanderp)

Warning: The newest version of the Intel Composer XE 2016 (update 3) breaks compatibility when using the Intel compilers (icc + ifort). With GCC and GFortran it compiles fine.

alexanderp commented on 2016-02-04 23:59 (UTC)

Hi tetonedge and adalardo. I've fixed the url error. I've also fixed the compilation with gcc to correctly use the MKL now and disabled the shared BLAS lib to speed up R. As a consequence, external libraries will need to be recompiled. Additionally, OpenMP is now enabled by default for both icc and gcc (using Intel's libiomp5.) On my laptop (i7-2640m), I get the following benchmark scores using http://r.research.att.com/benchmarks/R-benchmark-25.R : * R 3.2.3 + intel-mkl-2016_update1 + r-mkl (icc/ifort) Total time for all 15 tests_________________________ (sec): 6.072 Overall mean (sum of I, II and III trimmed means/3)_ (sec): 0.387 * R 3.2.3 + intel-mkl-2016_update1 + r-mkl (gcc/gfortran) Total time for all 15 tests_________________________ (sec): 6.309 Overall mean (sum of I, II and III trimmed means/3)_ (sec): 0.405

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nacnudus commented on 2016-06-03 10:06 (UTC)