On Nov 7, 2013, at 1:30 PM, Simon Zehnder <[email protected]> wrote:
> 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
^^ your Intel libs (or at least libiomp5) are missing paths in the id string -
probably not installed properly? You can hack around that using
DYLD_FALLBACK_LIBRARY_PATH but it's better to fix the issue in libiomp5
directly.
> 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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