So I am now back on this full time as I need this to work. OpenMPI 1.4.3 is deadlocking with Rmpi and I need the latest code. I still get the exact same problem. I configured it with a --prefix=/usr to get it to install everything in default directories and added /usr/lib/openmpi to my ldconfig. I don't have a LD_LIBRARY_PATH global variable on ubuntu 11.10.
ldconfig -p |grep mpi libvt-mpi.so.0 (libc6,x86-64) => /usr/lib/libvt-mpi.so.0 libvt-mpi.so (libc6,x86-64) => /usr/lib/libvt-mpi.so libvt-mpi-unify.so.0 (libc6,x86-64) => /usr/lib/libvt-mpi-unify.so.0 libvt-mpi-unify.so (libc6,x86-64) => /usr/lib/libvt-mpi-unify.so libopenmpi_malloc.so.0 (libc6,x86-64) => /usr/lib/libopenmpi_malloc.so.0 libompitrace.so.0 (libc6,x86-64) => /usr/lib/libompitrace.so.0 libompitrace.so (libc6,x86-64) => /usr/lib/libompitrace.so libompi_dbg_msgq.so (libc6,x86-64) => /usr/lib/openmpi/libompi_dbg_msgq.so libmpi_f90.so.1 (libc6,x86-64) => /usr/lib/libmpi_f90.so.1 libmpi_f90.so.0 (libc6,x86-64) => /usr/lib/libmpi_f90.so.0 libmpi_f90.so (libc6,x86-64) => /usr/lib/libmpi_f90.so libmpi_f77.so.1 (libc6,x86-64) => /usr/lib/libmpi_f77.so.1 libmpi_f77.so.0 (libc6,x86-64) => /usr/lib/libmpi_f77.so.0 libmpi_f77.so (libc6,x86-64) => /usr/lib/libmpi_f77.so libmpi_cxx.so.1 (libc6,x86-64) => /usr/lib/libmpi_cxx.so.1 libmpi_cxx.so.0 (libc6,x86-64) => /usr/lib/libmpi_cxx.so.0 libmpi_cxx.so (libc6,x86-64) => /usr/lib/libmpi_cxx.so libmpi.so.1 (libc6,x86-64) => /usr/lib/libmpi.so.1 libmpi.so.0 (libc6,x86-64) => /usr/lib/libmpi.so.0 libmpi.so (libc6,x86-64) => /usr/lib/libmpi.so libexempi.so.3 (libc6,x86-64) => /usr/lib/libexempi.so.3 libcompizconfig.so.0 (libc6,x86-64) => /usr/lib/libcompizconfig.so.0 Compiling Rmpi from inside R gives me: * installing *source* package ‘Rmpi’ ... 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 and it is OpenMPI Trying to find mpi.h ... Found in /usr/include Trying to find libmpi.so or libmpich.a ... Found libmpi in /usr/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/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/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/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/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/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-1764:18216] mca: base: component_find: unable to open /usr/lib/openmpi/mca_paffinity_hwloc: /usr/lib/openmpi/mca_paffinity_hwloc.so: undefined symbol: opal_hwloc_topology (ignored) [ben-Inspiron-1764:18216] mca: base: component_find: unable to open /usr/lib/openmpi/mca_shmem_posix: /usr/lib/openmpi/mca_shmem_posix.so: undefined symbol: opal_shmem_base_output (ignored) [ben-Inspiron-1764:18216] mca: base: component_find: unable to open /usr/lib/openmpi/mca_ess_hnp: /usr/lib/openmpi/mca_ess_hnp.so: undefined symbol: orte_timing_output (ignored) [ben-Inspiron-1764:18216] mca: base: component_find: unable to open /usr/lib/openmpi/mca_ess_singleton: /usr/lib/openmpi/mca_ess_singleton.so: undefined symbol: orte_local_cpu_model (ignored) [ben-Inspiron-1764:18216] mca: base: component_find: unable to open /usr/lib/openmpi/mca_ess_slurm: /usr/lib/openmpi/mca_ess_slurm.so: undefined symbol: orte_orted_exit_with_barrier (ignored) [ben-Inspiron-1764:18216] mca: base: component_find: unable to open /usr/lib/openmpi/mca_ess_slurmd: /usr/lib/openmpi/mca_ess_slurmd.so: undefined symbol: orte_pmap_t_class (ignored) [ben-Inspiron-1764:18216] [[INVALID],INVALID] ORTE_ERROR_LOG: Unknown error: -1 in file ../../../orte/runtime/orte_globals.c at line 176 input in flex scanner failed ERROR: loading failed * removing ‘/usr/local/lib/R/site-library/Rmpi’ * restoring previous ‘/usr/local/lib/R/site-library/Rmpi’ Notice that the libRmpi actually does compile but can't be installed. Other than the --prefix option I added nothing new to the ./configure script. It now knows by default where everything should be and I think I have every required package installed. Anyone have any ideas? Do you need any other files attached? Thanks, ~Ben On Tue, Apr 3, 2012 at 1:39 AM, Ralph Castain <r...@open-mpi.org> wrote: > 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 >> > > > _______________________________________________ > devel mailing list > de...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/devel >
