Looks like you didn't set your LD_LIBRARY_PATH to point to where OMPI was installed, so the individual component libs couldn't be loaded. From the below, it looks like you need to add /usr/local to your path.
On Mon, Apr 2, 2012 at 7:26 PM, Benedict Holland < benedict.m.holl...@gmail.com> wrote: > Hi All, > > I am on ubuntu 11.10 and the only package that they have for OpenMPI is > 1.4.3 and I noticed the latest was 1.5.5 and I decided to try to use it to > get the Rmpi R package compiled against it. I failed. My R version is 2.15, > the OpenMPI is 1.5.5. I compiled it and installed it but when I tried to > compile Rmpi I get the result below. I can try to run this stuff again but > I had to use the base packages because they worked and I need to get some > stuff done. I can always recompile though, install and run the Rmpi package > against the installed OpenMPI stuff. Any ideas what I need to do? Also, is > there an Ubuntu or Debian package available with the latest and greatest > and if not, how can I make one? > > Thanks, > ~Ben > > checking for gcc... gcc -std=gnu99 > 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 -std=gnu99 accepts -g... yes > checking for gcc -std=gnu99 option to accept ISO C89... none needed > I am here /usr/local and it is OpenMPI > Trying to find mpi.h ... > Found in /usr/local/include > Trying to find libmpi.so or libmpich.a ... > Found libmpi in /usr/local/lib > checking for openpty in -lutil... yes > checking for main in -lpthread... yes > configure: creating ./config.status > config.status: creating src/Makevars > ** Creating default NAMESPACE file > ** libs > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fpic > -O3 -pipe -g -c RegQuery.c -o RegQuery.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fpic > -O3 -pipe -g -c Rmpi.c -o Rmpi.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fpic > -O3 -pipe -g -c conversion.c -o conversion.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fpic > -O3 -pipe -g -c internal.c -o internal.o > gcc -std=gnu99 -shared -o Rmpi.so RegQuery.o Rmpi.o conversion.o > internal.o -L/usr/local/lib -lmpi -lutil -lpthread -L/usr/lib/R/lib -lR > installing to /usr/local/lib/R/site-library/Rmpi/libs > ** R > ** demo > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices > ** testing if installed package can be loaded > [ben-Inspiron-1764:26048] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_paffinity_hwloc: > /usr/local/lib/openmpi/mca_paffinity_hwloc.so: undefined symbol: > opal_hwloc_topology (ignored) > [ben-Inspiron-1764:26048] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_carto_auto_detect: > /usr/local/lib/openmpi/mca_carto_auto_detect.so: undefined symbol: > opal_carto_base_graph_get_host_graph_fn (ignored) > [ben-Inspiron-1764:26048] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_carto_file: > /usr/local/lib/openmpi/mca_carto_file.so: undefined symbol: > opal_carto_base_graph_get_host_graph_fn (ignored) > [ben-Inspiron-1764:26048] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_shmem_mmap: > /usr/local/lib/openmpi/mca_shmem_mmap.so: undefined symbol: opal_show_help > (ignored) > [ben-Inspiron-1764:26048] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_shmem_posix: > /usr/local/lib/openmpi/mca_shmem_posix.so: undefined symbol: > opal_shmem_base_output (ignored) > [ben-Inspiron-1764:26048] mca: base: component_find: unable to open > /usr/local/lib/openmpi/mca_shmem_sysv: > /usr/local/lib/openmpi/mca_shmem_sysv.so: undefined symbol: opal_show_help > (ignored) > -------------------------------------------------------------------------- > It looks like opal_init failed for some reason; your parallel process is > likely to abort. There are many reasons that a parallel process can > fail during opal_init; some of which are due to configuration or > environment problems. This failure appears to be an internal failure; > here's some additional information (which may only be relevant to an > Open MPI developer): > > opal_shmem_base_select failed > --> Returned value -1 instead of OPAL_SUCCESS > -------------------------------------------------------------------------- > [ben-Inspiron-1764:26048] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in > file runtime/orte_init.c at line 79 > -------------------------------------------------------------------------- > It looks like MPI_INIT failed for some reason; your parallel process is > likely to abort. There are many reasons that a parallel process can > fail during MPI_INIT; some of which are due to configuration or environment > problems. This failure appears to be an internal failure; here's some > additional information (which may only be relevant to an Open MPI > developer): > > ompi_mpi_init: orte_init failed > --> Returned "Error" (-1) instead of "Success" (0) > -------------------------------------------------------------------------- > *** An error occurred in MPI_Init > *** on a NULL communicator > *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort > [ben-Inspiron-1764:26048] Local abort before MPI_INIT completed > successfully; not able to aggregate error messages, and not able to > guarantee that all other processes were killed! > > > _______________________________________________ > devel mailing list > de...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/devel >
