[maker-devel] maker MPI problem

[Fields, Christopher J]

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<mailto: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<mailto: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<mailto: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/20170815/9680e940/attachment-0003.html>