If you are going to use OMPI via JNI, then you have to load the OMPI library from within your code. This is a little tricky from Java as OMPI by default builds as a set of dynamic libraries, and each component is a dynamic library as well. The solution is to either build OMPI static, or to use lt_dladvise and friends to ensure the load paths are followed.
On Mar 12, 2014, at 3:40 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>_______________________________________________ > devel mailing list > de...@open-mpi.org > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/devel > Link to this post: > http://www.open-mpi.org/community/lists/devel/2014/03/14335.php
