On Wed, 16 Jan 2008, Brian O'Gorman wrote: > I'm having trouble with R CMD INSTALL Rmpi_0.5-5.tar.gz > --configure-args=~/lam > > lam is is installed locally.
That's the problem. You need to build a shared library version, not a static version, to allow it to be compiled into shared objects. (--enable-shared --disable-static, as I recall.) Or at least ensure that your static library is PIC (add -fPIC to the compiler flags and rebuild from scratch). When you do, you may find that linking against some library (perhaps -lutil?) is missing, and you need to modify the Makefiles to include that. (Maybe the latest lam has that corrected: check it appears as a dependency of liblam.so.0.0.0.) You will also need to ensure the location you install is known to ldconfig or in LD_LIBRARY_PATH. I built Rmpi successfully on F8 last week, *provided* you only have the .x86_64 lam[-devel] RPMs installed and not also the .i386 ones (Rmpi looks in /usr/lib on x86_64 before /usr/lib64, which is incorrect). Just in case anyone else meets that quirk. (yum install will by default add both cputypes.) > lamboot -d (or lamboot-d and also recon) works. make -k check from the > lamtest suite passes all tests. > Is this is problem with the -fPIC compiler as in the message? Should it be > modified in the Makefile? > Any help or comments are appreciated, thanks. [And please use R-devel for technical (non-R) programming questions.] > > * Installing to library > '/u1/uaf/ogorman/R/x86_64-unknown-linux-gnu-library/2.6' > * Installing *source* package 'Rmpi' ... > checking for gcc... gcc > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > Try to find mpi.h ... > Found in /import/home/u1/uaf/ogorman/lam/include > Try to find libmpi.so or libmpich.a > checking for main in -lmpi... yes > Try to find liblam.so ... > checking for main in -llam... yes > checking for openpty in -lutil... yes > checking for main in -lpthread... yes > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > gcc -std=gnu99 -I/usr/local/pkg/r/r-2.6.1/lib64/R/include > -I/usr/local/pkg/r/r-2.6.1/lib64/R/include -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -I/import/home/u1/uaf/ogorman/lam/include -DMPI2 > -DLAM -fPIC -I/usr/local/include -fpic -g -O2 -c conversion.c -o > conversion.o > gcc -std=gnu99 -I/usr/local/pkg/r/r-2.6.1/lib64/R/include > -I/usr/local/pkg/r/r-2.6.1/lib64/R/include -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -I/import/home/u1/uaf/ogorman/lam/include -DMPI2 > -DLAM -fPIC -I/usr/local/include -fpic -g -O2 -c internal.c -o internal.o > gcc -std=gnu99 -I/usr/local/pkg/r/r-2.6.1/lib64/R/include > -I/usr/local/pkg/r/r-2.6.1/lib64/R/include -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -I/import/home/u1/uaf/ogorman/lam/include -DMPI2 > -DLAM -fPIC -I/usr/local/include -fpic -g -O2 -c RegQuery.c -o RegQuery.o > gcc -std=gnu99 -I/usr/local/pkg/r/r-2.6.1/lib64/R/include > -I/usr/local/pkg/r/r-2.6.1/lib64/R/include -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -I/import/home/u1/uaf/ogorman/lam/include -DMPI2 > -DLAM -fPIC -I/usr/local/include -fpic -g -O2 -c Rmpi.c -o Rmpi.o > gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so conversion.o internal.o > RegQuery.o Rmpi.o -L/import/home/u1/uaf/ogorman/lam/lib -lmpi -llam -lutil > -lpthread -fPIC > /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin/ld: > > /import/home/u1/uaf/ogorman/lam/lib/libmpi.a(abort.o): relocation R_X86_64_32 > can not be used when making a shared object; recompile with -fPIC > /import/home/u1/uaf/ogorman/lam/lib/libmpi.a: could not read symbols: Bad > value > collect2: ld returned 1 exit status > make: *** [Rmpi.so] Error 1 > chmod: cannot access > `/import/home/u1/uaf/ogorman/R/x86_64-unknown-linux-gnu-library/2.6/Rmpi/libs/*': > > No such file or directory > ERROR: compilation failed for package 'Rmpi' > ** Removing > '/import/home/u1/uaf/ogorman/R/x86_64-unknown-linux-gnu-library/2.6/Rmpi' > > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
