[maker-devel] some problem with MPI

[Michael Thon]

Hi - 

I'm installing MAKER and I can't get it to run with MPI. I'm using Ubuntu linux and the openmpi packages from the linux package manager. when I ran perl Build.pl I made sure that the paths were correct. Running Build install gave me these errors:

./Build install
Configuring MAKER with MPI support
Installing MAKER...
Configuring MAKER with MPI support
Subroutine dl_load_flags redefined at (eval 125) line 8.
Subroutine Parallel::Application::MPI::C_MPI_ANY_SOURCE redefined at (eval 125) line 9.
Subroutine Parallel::Application::MPI::C_MPI_ANY_TAG redefined at (eval 125) line 9.
Subroutine Parallel::Application::MPI::C_MPI_SUCCESS redefined at (eval 125) line 9.
Subroutine Parallel::Application::MPI::C_MPI_Init redefined at (eval 125) line 9.
Subroutine Parallel::Application::MPI::C_MPI_Finalize redefined at (eval 125) line 9.
Subroutine Parallel::Application::MPI::C_MPI_Comm_rank redefined at (eval 125) line 9.
Subroutine Parallel::Application::MPI::C_MPI_Comm_size redefined at (eval 125) line 9.
Subroutine Parallel::Application::MPI::C_MPI_Send redefined at (eval 125) line 9.
Subroutine Parallel::Application::MPI::C_MPI_Recv redefined at (eval 125) line 9.
Subroutine Parallel::Application::MPI::_comment redefined at (eval 125) line 9.
Installing /home/mike/maker/maker/src/../perl/lib/MAKER/ConfigData.pm
Installing /home/mike/maker/maker/src/../perl/lib/auto/Parallel/Application/MPI/MPI.inl
Installing /home/mike/maker/maker/src/../perl/man/MAKER::ConfigData.3pm
Skip /home/mike/maker/maker/src/../perl/config-x86_64-linux-gnu-thread-multi-5.018002 (unchanged)


Here are the errors I get when trying to run maker. Maker seems to work fine if I run it without mpi. Any suggestions are welcome.
Thanks

mpiexec -n 2  /home/mike/maker/maker/bin/maker -nodatastore >out
[odie:28576] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_paffinity_hwloc: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[odie:28576] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_carto_auto_detect: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[odie:28576] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_carto_file: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[odie:28576] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_mmap: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[odie:28576] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_posix: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[odie:28576] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_sysv: perhaps a missing symbol, or compiled for a different version of Open MPI? (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
--------------------------------------------------------------------------
[odie:28576] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file runtime/orte_init.c at line 79
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL: your MPI job will now abort
[odie:28576] 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 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)
--------------------------------------------------------------------------
[odie:28575] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_paffinity_hwloc: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[odie:28575] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_carto_auto_detect: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[odie:28575] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_carto_file: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[odie:28575] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_mmap: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[odie:28575] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_posix: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[odie:28575] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_sysv: perhaps a missing symbol, or compiled for a different version of Open MPI? (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
--------------------------------------------------------------------------
[odie:28575] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file runtime/orte_init.c at line 79
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL: your MPI job will now abort
[odie:28575] 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 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)
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------