Where does R in make install get its libraries/library paths from to be installed? I set DYLD_LIBRARY_PATH and libiomp5.dylib is on that path … Is there another variable to be set (DYLD_FALLBACK_LIBRARY_PATH I want to use only, if no other possibility remains).
Best Simon On 07 Nov 2013, at 19:52, Simon Urbanek <[email protected]> wrote: > > 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 _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
