[maker-devel] some problem with MPI

[Carson Holt]

Sorry for the slow reply. I’ve been away for the last week.

I’ve found that using Ubuntu’s apt-get doesn’t always set up OpenMPI and MPICH2 correctly for shared libraries.  You may have to do a manual install.

Also if using OpenMPI, make sure to set LD_PRELOAD environmental variable to the location of libmpi.so before even trying to install MAKER. It must also be set before running MAKER (or any program that uses OpenMPI's shared libraries), so it's best just to add it to your ~/.bash_profile. (i.e. export LD_PRELOAD=/usr/local/openmpi/lib/libmpi.so).

--Carson


> On Sep 23, 2015, at 1:45 AM, Michael Thon <mike.thon at gmail.com> wrote:
> 
> 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.
> --------------------------------------------------------------------------
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