[maker-devel] maker MPI problem

[Carson Holt]

Did it die or did you just get a warning?

Here is a list of flags to add that suppress warnings and other issues with OpenMPI. You can add them all or one at a time depending on issues you get.

#add if MPI not using all CPU given
--oversubscribe --bind-to none

#workaround for infinaband (use instead of --mca ^openib)
--mca btl vader,tcp,self --mca btl_tcp_if_include ib0

#add to stop certain other warnings
--mca orte_base_help_aggregate 0

#stop fork warnings
--mca btl_openib_want_fork_support 1 --mca mpi_warn_on_fork 0

—Carson



> On Aug 15, 2017, at 9:34 AM, zl c <chzelin at gmail.com> wrote:
> 
> 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 <mailto:chzelin at gmail.com>]
> 
> 
> 
> On Tue, Aug 15, 2017 at 10:39 AM, Carson Holt <carsonhh at gmail.com <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto:maker-devel-bounces at yandell-lab.org>> on behalf of Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
>> Date: Monday, August 14, 2017 at 2:18 PM
>> To: zl c <chzelin at gmail.com <mailto:chzelin at gmail.com>>
>> Cc: "maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org <mailto: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>_______________________________________________
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>>  
>> 
>> 
> 

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