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!
