Compiling R on Linux using Intel Composer XE

I’ve mostly followed these instructions, making a few minor changes as necessary. The entire process took the better part of a day.

1. download the R source tarball from CRAN (I used R 2.15.2) and unpack it
   

   > wget http://cran.r-project.org/src/base/R-2/R-2.15.2.tar.gz
   > tar xvzf R-2.15.2.tar.gz

2. you need a minimum version of icpc 12.1 to compile Rcpp, due to this bug (as well as icc & ifort)

   > module load intel/2011.9.293
   Lyra: Intel Studio (composer_xe_2011_sp1.9.293) module loaded.
   > icpc -V
   Intel(R) C++ Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 12.1.3.293 Build 20120212
   Copyright (C) 1985-2012 Intel Corporation.  All rights reserved.

3. in the source directory, edit the config.site file as follows:

   CC=icc
   CFLAGS="-g -O3 -wd188 -ip"
   F77=ifort
   FFLAGS="-g -O3 -fp-model source"
   SHLIB_LDFLAGS="-shared"
   LIBnn=lib64
   ICCROOT=/pkg/suse11/intel/composer_xe_2011_sp1.9.293
   ICC_LIBS=$ICCROOT/compiler/lib/intel64/
   LDFLAGS="-L$ICC_LIBS -L/usr/lib64"
   CXX=icpc
   CXXFLAGS="-g -O3 -fp-model source"
   SHLIB_CXXLD=icpc
   SHLIB_CXXLDFLAGS="-shared"
   FC=ifort
   FCFLAGS="-g -O3 -fp-model source"
   MKLPATH=$ICCROOT/mkl/lib/intel64
   MKLINCLUDE=$ICCROOT/mkl/include
   BLAS_LIBS="-L$MKLPATH -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm"

4. ./configure --prefix=$HOME --enable-R-shlib --enable-memory-profiling

   This step alone took about 2.5 hours to run.

5. make

6. make install

   By default, R will be installed under $HOME/bin with configuration files in $HOME/lib64/R

   > capabilities()
    jpeg png tiff tcltk X11 aqua http/ftp sockets 
    TRUE TRUE TRUE TRUE FALSE FALSE TRUE TRUE 
    libxml fifo cledit iconv NLS profmem cairo 
    TRUE TRUE TRUE TRUE TRUE TRUE TRUE

7. in the R home directory, edit the etc/Makeconf file as follows:

   MKLROOT = /pkg/suse11/intel/composer_xe_2011_sp1.9.293/mkl
   BLAS_LIBS = -L$(MKLROOT)/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm 
   ## LAPACK_LIBS =

8. now compile any additional packages from source – for example:

   > R CMD INSTALL --byte-compile code/fastICA_1.1-16.tar.gz 
   * installing to library â/home/n1284550/lib64/R/libraryâ
   * installing *source* package âfastICAâ ...
   ** package âfastICAâ successfully unpacked and MD5 sums checked
   checking for gcc... icc -std=gnu99
   checking whether the C compiler works... yes
   checking for C compiler default output file name... a.out
   checking for suffix of executables... 
   checking whether we are cross compiling... no
   checking for suffix of object files... o
   checking whether we are using the GNU C compiler... yes
   checking whether icc -std=gnu99 accepts -g... yes
   checking for icc -std=gnu99 option to accept ISO C89... none needed
   checking how to run the C preprocessor... icc -std=gnu99 -E
   checking for grep that handles long lines and -e... /usr/bin/grep
   checking for egrep... /usr/bin/grep -E
   checking for ANSI C header files... yes
   checking for sys/types.h... yes
   checking for sys/stat.h... yes
   checking for stdlib.h... yes
   checking for string.h... yes
   checking for memory.h... yes
   checking for strings.h... yes
   checking for inttypes.h... yes
   checking for stdint.h... yes
   checking for unistd.h... yes
   checking math.h usability... yes
   checking math.h presence... yes
   checking for math.h... yes
   checking for scopy in -L/pkg/suse11/intel/composer_xe_2011_sp1.9.293/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm... yes
   checking for sgesdd_... yes
   checking for lsame_... yes
   configure: creating ./config.status
   config.status: creating src/Makevars
   ** libs
   icc -std=gnu99 -I/home/n1284550/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O3 -wd188 -ip -c ica.c -o ica.o
   icc -std=gnu99 -shared -L/pkg/suse11/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/ -L/usr/lib64 -o fastICA.so ica.o -L/pkg/suse11/intel/composer_xe_2011_sp1.9.293/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -L/home/n1284550/lib64/R/lib -lR
   installing to /home/n1284550/lib64/R/library/fastICA/libs
   ** R
   ** inst
   ** byte-compile and prepare package for lazy loading
   ** help
   *** installing help indices
   ** building package indices
   ** testing if installed package can be loaded
   * DONE (fastICA)