[maker-devel] maker MPI problem

[zl c]

I submit a job:

sbatch --gres=lscratch:100 --time=8:00:00 --mem-per-cpu=8g -N 1-1
--ntasks=2 --ntasks-per-core=1 --job-name run06.mpi -o log/run06.mpi.o%A
run06.maker.mpi.sh

CMD in run06.maker.mpi.sh

mpiexec -n $SLURM_NTASKS maker -c 1 -base genome -g genome.fasta

Another question:
How much temporary space and memory should I use for a ~10Mb sequences and
large database like nr and uniref90.

Thanks,
zelin

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


On Tue, Aug 15, 2017 at 4:50 PM, Carson Holt <carsonhh at gmail.com> wrote:

> 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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