[maker-devel] maker MPI problem

[zl c]

When I installed by './Build install', I got following some messages:

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.

I'm not sure whether it's correctly installed.

Thanks,

--------------------------------------------
Zelin Chen [chzelin at gmail.com]

NIH/NHGRI
Building 50, Room 5531
50 SOUTH DR, MSC 8004
BETHESDA, MD 20892-8004

On Mon, Aug 14, 2017 at 9:23 PM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

> Carson,
>
>
>
> It was attached to the initial message (named ‘run05.mpi.o47346077’).  It
> looks like a Perl issue with threads, though I don’t see why this would
> crash a cluster.  The fact there is a log file would suggest it just ended
> the job.
>
>
>
> chris
>
>
>
> *From: *maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of
> Carson Holt <carsonhh at gmail.com>
> *Date: *Monday, August 14, 2017 at 2:18 PM
> *To: *zl c <chzelin at gmail.com>
> *Cc: *"maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> *Subject: *Re: [maker-devel] maker MPI problem
>
>
>
> This is rather vague —> “crashed the computer cluster”
>
>
>
> Do you have a specific error?
>
>
>
> —Carson
>
>
>
>
>
>
>
> On Aug 14, 2017, at 12:59 PM, zl c <chzelin at gmail.com> wrote:
>
>
>
> Hello,
>
>
>
> I ran maker 3.0 with openmpi 2.0.2 and it crashed the computer cluster. I
> attached the log file. Could you help me to solve the problem?
>
>
>
> CMD:
>
> export LD_PRELOAD=/usr/local/OpenMPI/2.0.2/gcc-6.3.0/lib/libmpi.so
>
> export OMPI_MCA_mpi_warn_on_fork=0
>
> mpiexec -mca btl ^openib -n $SLURM_NTASKS maker -c 1 –base genome  -g
> genome.fasta
>
>
>
> Thanks,
>
> Zelin Chen
>
>
>
> --------------------------------------------
>
> Zelin Chen [chzelin at gmail.com]  Ph.D.
>
>
>
> NIH/NHGRI
>
> Building 50, Room 5531
> 50 SOUTH DR, MSC 8004
> BETHESDA, MD 20892-8004
>
> <run05.mpi.o47346077>_______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
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