[maker-devel] Maker error mpiexec

[Carson Holt]

You need to make sure the same version of MPI is used to compile and run
MAKER.  When installing MAKER make sure the mpi.h and mpicc indicated during
configuration come from the same version of OpenMPI as the mpiexec command
you are using now.

Also for OpenMPI run the following command before setting up or launching
MAKER -->
export LD_PRELOAD=Š/openmpi_location/lib/libmpi.so

replace openmpi_location in the above command with the location of your
OpenMPI.

Setting LD_PRELOAD preload is required for OpenMPI to work correctly with
shared libraries.


Also you may need to add the following to your MPI command before running
MAKER.
--> -mca btl ^openib
Example --> mpiexec -mca btl ^openib -n 40 maker

Thanks,
Carson



From:  rens holmer <rens.holmer at wur.nl>
Date:  Tuesday, August 19, 2014 at 3:19 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Maker error mpiexec

Hi,

I am trying to run maker using MPI, and I get an error I do not understand.

Maker version: 2.13.6
mpiexec version: mpiexec (OpenRTE) 1.6.5

When I run ./Build status it is reported that MPI is enabled.

When I run mpiexec -n 40 maker I get the following errors:

[assembly:25562] 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)

[assembly:25563] 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)

[assembly:25562] 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)

[assembly:25563] 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)

[assembly:25563] 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)

[assembly:25562] 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)

[assembly:25563] 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)

[assembly:25563] 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)

[assembly:25562] 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)

[assembly:25562] 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)

[assembly:25563] 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)

[assembly:25562] 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

--------------------------------------------------------------------------

--------------------------------------------------------------------------





Etcetera etcetera.

However: when I search for the files reported as missing I do find them, and
I don't believe they are from a different version of MPI?

Am I using a wrong version of MPI?

Any help would be appreciated,

Sincerely,



Rens Holmer


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