[maker-devel] maker MPI problem

Carson Holt carsonhh at gmail.com
Tue Aug 15 14:50:05 MDT 2017 

What is your command line? Are you running interactively or as a submitted batch? If it's a batch job what options did you give it?

--Carson

Sent from my iPhone

> On Aug 15, 2017, at 2:47 PM, zl c <chzelin at gmail.com> wrote:
> 
> Hi Carson,  Christopher, Daniel,
> 
> Thank you for your kind help.
> 
> Now it works without any other options on one nodes and 4 CPUs. I set the number of task to 2, but there's only one contigs in running. Should it be two contigs running at the same time?
> 
> Zelin
> 
> --------------------------------------------
> Zelin Chen [chzelin at gmail.com]
> 
> 
> NIH/NHGRI
> Building 50, Room 5531
> 50 SOUTH DR, MSC 8004 
> BETHESDA, MD 20892-8004
> 
>> On Tue, Aug 15, 2017 at 11:47 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> 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]
>>> 
>>> 
>>> 
>>>> 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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