[R-SIG-Mac] Build R with Intel Compiler

Simon Zehnder szehnder at uni-bonn.de
Thu Nov 7 19:30:20 CET 2013

Your and Brian’s guesses were right: the -openmp linker flag was it. It compiles now fine, though I get errors in make check-all and make install: 

Running a make check-all gives me (with and without flag -ipo)

Running examples in 'mgcv-Ex.R’ failed
Loading required package: splines
> plot(b,pages=1)
> b<-gamm(y~s(x0,bs="tr",m=2)+s(x1,bs="ps",m=c(1,3))+
+          s(x2,bs="tr",m=3)+s(x3,bs="tr",m=2),data=dat)
> plot(b$gam,pages=1)
Warning in sqrt(rowSums((P$X %*% x$Vp[first:last, first:last, drop = FALSE]) *  :
  NaNs produced
Error in if (se && pd[[i]]$se) { : missing value where TRUE/FALSE needed
Calls: plot -> plot.gam
Execution halted

A sudo make install gives me:

/opt/intel/composer_xe_2013_sp1.1.103/bin/intel64/icc -std=gnu99 -I. -I../../src/include -I../../../R-3.0.2/src/include -I/usr/X11/include/ -D__ACCELERATE__ -DHAVE_CONFIG_H    -fPIC  -O3 -ipo -openmp -xHost  -DR_HOME='"/usr/local/R/R-intel/R.framework/Versions/3.0/Resources"' -o Rscript \
installing packages ...
  building HTML index ...
dyld: Library not loaded: libiomp5.dylib
  Referenced from: /Users/simonzehnder/Downloads/build/bin/exec/R
  Reason: image not found
/bin/sh: line 1: 87375 Done                    echo "utils:::make.packages.html(.Library, verbose=FALSE, docdir=\"/usr/local/R/R-intel/R.framework/Versions/3.0/Resources/doc\")"
     87376 Trace/BPT trap: 5       | R_DEFAULT_PACKAGES=NULL LC_ALL=C ../../bin/R --vanilla --slave > /dev/null
make[2]: *** [install] Error 133
make[1]: *** [install] Error 1
make: *** [install] Error 1

It seems that it is connected with the MKL. I have in my MKL variable “-lmkl_gf_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread. It seems that libiomp5 is not linked to correctly. 

I uploaded also my config.log to https://gist.github.com/simonsays1980/7359508 




On 07 Nov 2013, at 15:33, Simon Urbanek <simon.urbanek at r-project.org> wrote:

> On Nov 7, 2013, at 7:56 AM, Simon Zehnder <szehnder at uni-bonn.de> wrote:
>> I am trying to build R with an Intel Compiler (14.0.3). Has anyone before done it and could give me a hint for the configuration? 
>> I am sourcing the compilervars.sh for Intel and then configure R with 
>> ./R-3.0.2/configure OBJC="clang" --enable-R-framework=/usr/local/R/R-intel --x-includes=/usr/X11/include/ --x-libraries=/usr/X11/lib/ --enable-memory-profiling --with-blas="$MKL" --with-lapack
>> Further Variables are:
>> CFLAGS=“-O3 -ipo -openmp -xHost”
>> CXXFLAGS=“-O3 -ipo -openmp -xHost”
>> MKL=“-lmkl_gf_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread”!
>> I get always the same error:
>> /opt/intel/composer_xe_2013_sp1.1.103/bin/intel64/icc -std=gnu99 -I../../../R-3.0.2/src/extra/zlib -I../../../R-3.0.2/src/extra/bzip2 -I../../../R-3.0.2/src/extra/pcre -I../../../R-3.0.2/src/extra  -I../../../R-3.0.2/src/extra/xz/api -I. -I../../src/include -I../../../R-3.0.2/src/include -I/usr/local/include -DHAVE_CONFIG_H    -fPIC  -O3 -ipo -openmp -xHost  -c ../../../R-3.0.2/src/main/Rmain.c -o Rmain.o
>> /opt/intel/composer_xe_2013_sp1.1.103/bin/intel64/icc -std=gnu99  -L/usr/local/lib -o R.bin Rmain.o  -L../../lib -lR
>> Undefined symbols for architecture x86_64:
>> "___kmpc_begin", referenced from:
>>     _main in ipo_icc4xtjyH.o
>> "___kmpc_end", referenced from:
>>     _main in ipo_icc4xtjyH.o
>> ld: symbol(s) not found for architecture x86_64
>> Any clue what this could be? 
> The above certainly won't work, because you're missing linker flags - I'm pretty sure that you must use -openmp in the linker for it to work, I'm not sure about -ipo -- but doesn't R detect all those automatically? I don't think you should put them in manually. The actual error comes from missing libguide link flags, but they may be implicit if you fix the other problem.
> Cheers,
> S

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