Check out how we did this with the embedded java bindings in Open MPI; see the
comment describing exactly this issue starting here:
https://svn.open-mpi.org/trac/ompi/browser/trunk/ompi/mpi/java/c/mpi_MPI.c#L79
Feel free to compare MPJ to the OMPI java bindings -- they're shipping in 1.7.4
and have a bunch of improvements in the soon-to-be-released 1.7.5, but you must
enable them since they aren't enabled by default:
./configure --enable-mpi-java ...
FWIW, we found a few places in the Java bindings where it was necessary for the
bindings to have some insight into the internals of the MPI implementation.
Did you find the same thing with MPJ Express?
Are your bindings similar in style/signature to ours?
On Mar 12, 2014, at 6:40 AM, Bibrak Qamar <bibr...@gmail.com> wrote:
> Hi all,
>
> I am writing a new device for MPJ Express that uses a native MPI library for
> communication. Its based on JNI wrappers like the original mpiJava. The
> device works fine with MPICH3 (and MVAPICH2.2). Here is the issue with
> loading Open MPI 1.7.4 from MPJ Express.
>
> I have generated the following error message from a simple JNI to MPI
> application for clarity purposes and also to regenerate the error easily. I
> have attached the app for your consideration.
>
>
> [bibrak@localhost JNI_to_MPI]$ mpirun -np 2 java -cp .
> -Djava.library.path=/home/bibrak/work/JNI_to_MPI/ simpleJNI_MPI
> [localhost.localdomain:29086] mca: base: component_find: unable to open
> /home/bibrak/work/installs/OpenMPI_installed/lib/openmpi/mca_shmem_mmap:
> /home/bibrak/work/installs/OpenMPI_installed/lib/openmpi/mca_shmem_mmap.so:
> undefined symbol: opal_show_help (ignored)
> [localhost.localdomain:29085] mca: base: component_find: unable to open
> /home/bibrak/work/installs/OpenMPI_installed/lib/openmpi/mca_shmem_mmap:
> /home/bibrak/work/installs/OpenMPI_installed/lib/openmpi/mca_shmem_mmap.so:
> undefined symbol: opal_show_help (ignored)
> [localhost.localdomain:29085] mca: base: component_find: unable to open
> /home/bibrak/work/installs/OpenMPI_installed/lib/openmpi/mca_shmem_posix:
> /home/bibrak/work/installs/OpenMPI_installed/lib/openmpi/mca_shmem_posix.so:
> undefined symbol: opal_shmem_base_framework (ignored)
> [localhost.localdomain:29086] mca: base: component_find: unable to open
> /home/bibrak/work/installs/OpenMPI_installed/lib/openmpi/mca_shmem_posix:
> /home/bibrak/work/installs/OpenMPI_installed/lib/openmpi/mca_shmem_posix.so:
> undefined symbol: opal_shmem_base_framework (ignored)
> [localhost.localdomain:29086] mca: base: component_find: unable to open
> /home/bibrak/work/installs/OpenMPI_installed/lib/openmpi/mca_shmem_sysv:
> /home/bibrak/work/installs/OpenMPI_installed/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
> --------------------------------------------------------------------------
> [localhost.localdomain:29085] mca: base: component_find: unable to open
> /home/bibrak/work/installs/OpenMPI_installed/lib/openmpi/mca_shmem_sysv:
> /home/bibrak/work/installs/OpenMPI_installed/lib/openmpi/mca_shmem_sysv.so:
> undefined symbol: opal_show_help (ignored)
> --------------------------------------------------------------------------
> It looks like orte_init failed for some reason; your parallel process is
> likely to abort. There are many reasons that a parallel process can
> fail during orte_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_init failed
> --> Returned value Error (-1) instead of ORTE_SUCCESS
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> 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: ompi_rte_init failed
> --> Returned "Error" (-1) instead of "Success" (0)
> --------------------------------------------------------------------------
> *** An error occurred in MPI_Init
> *** on a NULL communicator
> *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
> *** and potentially your MPI job)
> [localhost.localdomain:29086] Local abort before MPI_INIT completed
> successfully; not able to aggregate error messages, and not able to guarantee
> that all other processes were killed!
> --------------------------------------------------------------------------
> 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
> --------------------------------------------------------------------------
> -------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code.. Per user-direction, the job has been aborted.
> -------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun detected that one or more processes exited with non-zero status, thus
> causing
> the job to be terminated. The first process to do so was:
>
> Process name: [[41236,1],1]
> Exit code: 1
> --------------------------------------------------------------------------
>
>
> This is a thread that I found where the Open MPI developers were having
> issues while integrating mpiJava into their stack.
>
> http://mail-archives.apache.org/mod_mbox/hadoop-common-dev/201202.mbox/%3c5ea543bd-a12e-4729-b66a-c746bc789...@open-mpi.org%3E
>
> I don't have better understanding of the internals of Open MPI, so my
> question is how to use Open MPI using JNI wrappers? Any guidelines in this
> regard?
>
> Thanks
> Bibrak
>
> <JNI_to_MPI.tar.gz>_______________________________________________
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Jeff Squyres
jsquy...@cisco.com
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