Dear Dirk, many thanks for your reply, please see below,
On 13 October 2008 at 11:22, 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 Where did you get 0.5-6 from? The newest, per the author's website, is 0.5-5. http://www.stats.uwo.ca/faculty/yu/Rmpi/download/dev | * 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 At this point you have mpi.h and libmpi. Looks good. | 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 It all compiles, thanks to mpi.h. | 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' This seems to indicate that your installation of Open MPI conflicts with your setting of export MPI_ROOT=/usr/lib64/mpi/gcc/openmpi/ as this directory is expected to contain include/ and lib/ I am not sure I got this, Open MPI is installed in /usr/lib64/mpi/gcc/openmpi/ and such directory contains both include and lib folders: gauss:/usr/lib64/mpi/gcc/openmpi # ls -R bin include lib64 share ./bin: mpiCC mpicc mpiexec mpif90 mpivars.csh ompi_info opalc++ ortec++ orted mpic++ mpicxx mpif77 mpirun mpivars.sh opal_wrapper opalcc ortecc orterun ./include: mpi.h mpif-common.h mpif-config.h mpif.h openmpi ./include/openmpi: ompi opal opal_config_bottom.h orte ompi_config.h opal_config.h opal_stdint.h orte_config.h [...] ./lib64: libmca_common_sm.la libmpi_cxx.la libmpi_f90.la libopen-rte.la libmca_common_sm.so libmpi_cxx.so libmpi_f90.so libopen-rte.so libmca_common_sm.so.0 libmpi_cxx.so.0 libmpi_f90.so.0 libopen-rte.so.0 libmca_common_sm.so.0.0.0 libmpi_cxx.so.0.0.0 libmpi_f90.so.0.0.0 libopen-rte.so.0.0.0 libmpi.la libmpi_f77.la libopen-pal.la mpi.mod libmpi.so libmpi_f77.so libopen-pal.so openmpi libmpi.so.0 libmpi_f77.so.0 libopen-pal.so.0 libmpi.so.0.0.0 libmpi_f77.so.0.0.0 libopen-pal.so.0.0.0 | 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. I'd recommend having a look at configure.ac, which is pretty straightforward, and 'helping' it with the locations you have. I had to do the same for Debian's Rmpi due to use also having mpich and lam. Please, could you be more explicit? Thanks, I tried to modify line 8 of the file configure.ac without success. BTW I had also LAM and mpich installed but I removed them. Thank you for your help, Kind regards Simone
