The DYLD_LIBRARY_PATH gets set by the compilervars.sh from intel and it resolves to:
echo $DYLD_LIBRARY_PATH /opt/intel/composer_xe_2013_sp1.1.103/compiler/lib:/opt/intel/composer_xe_2013_sp1.1.103/compiler/lib/intel64:/opt/intel:/opt/intel/composer_xe_2013_sp1.1.103/ipp/../compiler/lib:/opt/intel/composer_xe_2013_sp1.1.103/ipp/lib:/opt/intel/composer_xe_2013_sp1.1.103/mkl/lib:/opt/intel/composer_xe_2013_sp1.1.103/tbb/lib The first path points directly into the directory with the libiomp5.dyiib. So theoretically when following https://developer.apple.com/library/mac/documentation/DeveloperTools/Conceptual/DynamicLibraries/100-Articles/DynamicLibraryUsageGuidelines.html it should be founded during linking. Though looking into libR.dylib with otool -L I see, that the libraries from Intel are referred to only by name not by path. I think this information gets lost as soon as the dynamic library libR.dylib is build. So, I hope I understand “fix the id in the iomp library” correctly: I change via install_name_tool change @executable_path/ … the relative path to an absolute one? Best Simon On 08 Nov 2013, at 15:19, Simon Urbanek <[email protected]> wrote: > On Nov 8, 2013, at 4:05 AM, Simon Zehnder <[email protected]> wrote: > >> 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). >> > > Well, you really don't want to set DYLD_LIBRARY_PATH since it breaks > dependencies, but that's another topic. However, the error tells you that you > don't have it on the path, otherwise you wouldn't get "image not found". > Either way, as I said, what you really want is to fix the id in the iomp > library so you don't get into the path troubles in the first place. Another > way to go about it is to put the Intel dependencies into $R_HOME/lib - I > wouldn't do that for development but that's a good option if you want to > distribute the build to other machines. > > Cheers, > Simon > > >> Best >> >> Simon >> On 07 Nov 2013, at 19:52, Simon Urbanek <[email protected]> wrote: >> >>> >>> On Nov 7, 2013, at 1:30 PM, Simon Zehnder <[email protected]> wrote: >>> >>>> Your and Brian’s guesses were right: the -openmp linker flag was it. It >>>> compiles now fine, though I get errors in make check-all and make install: >>>> >>>> Running a make check-all gives me (with and without flag -ipo) >>>> >>>> Running examples in 'mgcv-Ex.R’ failed >>>> ... >>>> Loading required package: splines >>>>> plot(b,pages=1) >>>>> b<-gamm(y~s(x0,bs="tr",m=2)+s(x1,bs="ps",m=c(1,3))+ >>>> + s(x2,bs="tr",m=3)+s(x3,bs="tr",m=2),data=dat) >>>>> plot(b$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
