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Subject: Re: [OMPI devel] OpenMPI and R
From: Ralph Castain (rhc_at_[hidden])
Date: 2012-04-03 01:39:24


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.holland_at_[hidden]> 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!
>
>
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