On Tue, 24 Apr 2007, Hendrik Fuß wrote:
Hi,I've been trying here to install Rmpi on an SGI IA-64 machine with 64 processors, running SuSE Linux Enterprise Server 9, R 2.4.0 and lam-mpi 7.1.3. While I've read of similar problems on this list, I think I've got an entirely new set of error messages to contribute (see below). I'm not sure what the actual error is and what the @gprel relocation message is about. Any help greatly appreciated.
I don't know for sure, but on many 64-bit OSes you cannot link code from static libraries into dynamic shared libraries, and that seems to be the case with ia64 Linux. Almost certainly you need to re-compile LAM with -fPIC flags.
thanks Hendrik behemoth:~/Rmpi # R CMD INSTALL /home/hfuss/build/Rmpi_0.5-3.tar.gz --configure-args=--with-mpi=/usr/local/lam-mpi * Installing *source* package 'Rmpi' ... Try to find mpi.h ... Found in /usr/local/lam-mpi/include Try to find libmpi or libmpich ... Found libmpi in /usr/local/lam-mpi/lib Try to find liblam ... Found liblam in /usr/local/lam-mpi/lib checking for openpty in -lutil... no checking for main in -lpthread... no configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -I/usr/local/lib/R/include -I/usr/local/lib/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/local/lam-mpi/include -DMPI2 -I/usr/local/include -fpic -g -O2 -std=gnu99 -c RegQuery.c -o RegQuery.o gcc -I/usr/local/lib/R/include -I/usr/local/lib/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/local/lam-mpi/include -DMPI2 -I/usr/local/include -fpic -g -O2 -std=gnu99 -c Rmpi.c -o Rmpi.o gcc -I/usr/local/lib/R/include -I/usr/local/lib/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/local/lam-mpi/include -DMPI2 -I/usr/local/include -fpic -g -O2 -std=gnu99 -c conversion.c -o conversion.o gcc -I/usr/local/lib/R/include -I/usr/local/lib/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/local/lam-mpi/include -DMPI2 -I/usr/local/include -fpic -g -O2 -std=gnu99 -c internal.c -o internal.o gcc -shared -L/usr/local/lib -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/local/lam-mpi/lib -lmpi -llam /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_comms /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_argv0 /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_mpi_ao /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_ger /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_c2c /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_appnum /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_universe_size /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_jobid /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_jobid /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_mpi_ao /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_ger /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_c2c /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_appnum /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_universe_size /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_mpi_ao /usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld: /usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against dynamic symbol lam_clockskew collect2: ld returned 1 exit status make: *** [Rmpi.so] Error 1 chmod: cannot access `/usr/local/lib/R/library/Rmpi/libs/*': No such file or directory ERROR: compilation failed for package 'Rmpi' ** Removing '/usr/local/lib/R/library/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
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