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Subject: [OMPI devel] OpenMPI and R
From: Benedict Holland (benedict.m.holland_at_[hidden])
Date: 2012-04-02 22:26:45


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!