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
\
../../../R-3.0.2/src/unix/Rscript.c
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
Best
Simon
On 07 Nov 2013, at 15:33, Simon Urbanek <[email protected]> wrote:
>
> On Nov 7, 2013, at 7:56 AM, Simon Zehnder <[email protected]> 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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