On Mon, Oct 13, 2008 at 03:56:19PM +0200, Simone Giannerini wrote: > Dear Dirk, > > many thanks for your reply, please see below,
Your mail is basically unreadable / impossible to attribute what is original and what is cited. Please follow convention and indent. > 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 Ok, didn't see that. But please do understand that 0.5-5 is on CRAN and released. (And yes, that is the version for which I also had to make a fix to get it build on Debian as mentioned). > | * 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 Not it does not as lib64 != lib. You probably it installed if you create a softlink from /usr/lib64/mpi/gcc/openmpi/lib64 to /usr/lib64/mpi/gcc/openmpi/lib Dirk > ./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 > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users -- Three out of two people have difficulties with fractions.
