[maker-devel] maker MPI problem

[Carson Holt]

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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