[maker-devel] maker MPI problem

[zl c]

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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