Oh how interesting and I hope this helps someone. Following another link, I had to use:
./configure --prefix /usr --enable-shared --enable-static when compiling this for Rmpi. Just curious, why isn't --enable-static a default option? ~Ben On Thu, Apr 5, 2012 at 7:59 PM, Benedict Holland < benedict.m.holl...@gmail.com> wrote: > 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 >> > >
