On Mon, Oct 13, 2008 at 8:14 AM, Jeff Squyres <jsquy...@cisco.com> wrote: > We always recommend using the Open MPI "wrapper" compilers instead of > directly using gcc. There are very few scenarios where it is better to use > the native compilers directly. > > You might want to check with the RMPI authors for more details; I'm afraid > that I don't know anything about that package.
To be explicit, try: CC="mpicc" R CMD INSTALL Rmpi_0.5-6.tar.gz Sean > On Oct 13, 2008, at 5:22 AM, Simone Giannerini wrote: > >> Dear all, >> >> I have troubles installing rmpi 0.5-5 (or 0.5-6) on a quad opteron >> machine with OpenSUSE 11.0 and >> R 2.7.2 >> >> platform x86_64-unknown-linux-gnu >> arch x86_64 >> os linux-gnu >> system x86_64, linux-gnu >> status Patched >> major 2 >> minor 7.2 >> year 2008 >> month 09 >> day 18 >> svn rev 46546 >> language R >> version.string R version 2.7.2 Patched (2008-09-18 r46546) >> >> I tried the following >> >> # export MPI_ROOT=/usr/lib64/mpi/gcc/openmpi/ >> >> # R CMD INSTALL Rmpi_0.5-6.tar.gz >> >> * Installing to library '/usr/local/lib64/R/library' >> * 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 /usr/lib64/mpi/gcc/openmpi//include >> Try to find libmpi.so or libmpich.a >> checking for main in -lmpi... 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/lib64/R/include -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/mpi/gcc/openmpi//include -DMPI2 >> -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c RegQuery.c -o >> RegQuery.o >> gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/mpi/gcc/openmpi//include -DMPI2 >> -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c Rmpi.c -o Rmpi.o >> gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/mpi/gcc/openmpi//include -DMPI2 >> -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c conversion.c -o >> conversion.o >> gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/mpi/gcc/openmpi//include -DMPI2 >> -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c internal.c -o >> internal.o >> gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o >> conversion.o internal.o -L/usr/lib64/mpi/gcc/openmpi//lib -lmpi -lutil >> -lpthread -fPIC >> /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: >> cannot find -lmpi >> collect2: ld returned 1 exit status >> make: *** [Rmpi.so] Error 1 >> chmod: cannot access `/usr/local/lib64/R/library/Rmpi/libs/*': No such >> file or directory >> ERROR: compilation failed for package 'Rmpi' >> ** Removing '/usr/local/lib64/R/library/Rmpi' >> >> I also tried with >> >> R CMD INSTALL Rmpi_0.5-6.tar.gz >> --configure-args=--with-mpi=/usr/lib64/mpi/gcc/openmpi/ >> >> with the same results. >> Any help would be greatly appreciated. >> >> Regards >> >> Simone Giannerini >> >> >> >> -- >> ______________________________________________________ >> >> Simone Giannerini >> Dipartimento di Scienze Statistiche "Paolo Fortunati" >> Universita' di Bologna >> Via delle belle arti 41 - 40126 Bologna, ITALY >> Tel: +39 051 2098262 Fax: +39 051 232153 >> http://www2.stat.unibo.it/giannerini/ >> ______________________________________________________ >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > > -- > Jeff Squyres > Cisco Systems > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users >
