[maker-devel] maker MPI problem

[zl c]

Here are some latest message:

[cn3360:57176] 1 more process has sent help message help-opal-runtime.txt /
opal_init:warn-fork

[cn3360:57176] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
help / error messages

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



On Tue, Aug 15, 2017 at 10:39 AM, Carson Holt <carsonhh at gmail.com> wrote:

> You may need to delete the .../maker/perl directory before doing the
> reinstall if not doing a brand new installation. Otherwise you can ignore
> the subroutine redefined warnings during compile.
>
> Have you been able to test the alternate flags on the command line for
> MPI? How about an alternate perl without threads?
>
> --Carson
>
> Sent from my iPhone
>
> On Aug 15, 2017, at 8:27 AM, zl c <chzelin at gmail.com> wrote:
>
> 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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