Have you tried to compile and run a simple MPI program with your
installed Open MPI? If that works then you need to figure out what is
being done by the Makefile when it is "testing if installed package can
be loaded" and try and reproduce the issue manually.
BTW, I normally configure my OMPI with -enable-orterun-prefix-by-default
to get OMPI to pull in the right library paths instead of using ldconfig.
In the below ldconfig -p you may want to also grep for mca to make sure
the plugins being complained about in the R testing are found too,
though I suspect they are but it would be good to double check.
--td
On 4/5/2012 7:59 PM, Benedict Holland 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
<mailto: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
<mailto: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!
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--
Terry D. Dontje | Principal Software Engineer
Developer Tools Engineering | +1.781.442.2631
Oracle *- Performance Technologies*
95 Network Drive, Burlington, MA 01803
Email terry.don...@oracle.com <mailto:terry.don...@oracle.com>
