[maker-devel] Maker error mpiexec

[rens holmer]

Thank you!

export LD_PRELOAD=Š/openmpi_location/lib/libmpi.so
mpiexec -mca btl ^openib -n 40 maker

Those two tweaks did the trick!

Sincerely,

Rens Holmer


On Thu, Aug 21, 2014 at 10:21 PM, Carson Holt <carsonhh at gmail.com> wrote:

> 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
>
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20140822/77b8399f/attachment-0003.html>