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Subject: Re: [OMPI users] Performance question about OpenMPI and MVAPICH2 on IB
From: Craig Tierney (Craig.Tierney_at_[hidden])
Date: 2009-08-06 19:09:50


Gus Correa wrote:
> Hi Craig, list
>
> I suppose WRF uses MPI collective calls (MPI_Reduce,
> MPI_Bcast, MPI_Alltoall etc),
> just like the climate models we run here do.
> A recursive grep on the source code will tell.
>

I will check this out. I am not the WRF expert, but
I was under the impression that most weather models are
nearest neighbor communications, not collectives.

> If that is the case, you may need to tune the collectives dynamically.
> We are experimenting with tuned collectives here also.
>
> Specifically, we had a scaling problem with the MITgcm
> (also running on an IB cluster)
> that is probably due to collectives.
> Similar problems were reported on this list before,
> with computational chemistry software.
> See these threads:
> http://www.open-mpi.org/community/lists/users/2009/07/10045.php
> http://www.open-mpi.org/community/lists/users/2009/05/9419.php
>
> If WRF outputs timing information, particularly the time spent on MPI
> routines, you may also want to compare how the OpenMPI and
> MVAPICH versions fare w.r.t. MPI collectives.
>
> I hope this helps.
>

I will look into this. Thanks for the ideas.

Craig

> Gus Correa
> ---------------------------------------------------------------------
> Gustavo Correa
> Lamont-Doherty Earth Observatory - Columbia University
> Palisades, NY, 10964-8000 - USA
> ---------------------------------------------------------------------
>
>
>
> Craig Tierney wrote:
>> I am running openmpi-1.3.3 on my cluster which is using
>> OFED-1.4.1 for Infiniband support. I am comparing performance
>> between this version of OpenMPI and Mvapich2, and seeing a
>> very large difference in performance.
>>
>> The code I am testing is WRF v3.0.1. I am running the
>> 12km benchmark.
>>
>> The two builds are the exact same codes and configuration
>> files. All I did different was use modules to switch versions
>> of MPI, and recompiled the code.
>>
>> Performance:
>>
>> Cores Mvapich2 Openmpi
>> ---------------------------
>> 8 17.3 13.9
>> 16 31.7 25.9
>> 32 62.9 51.6
>> 64 110.8 92.8
>> 128 219.2 189.4
>> 256 384.5 317.8
>> 512 687.2 516.7
>>
>> The performance number is GFlops (so larger is better).
>>
>> I am calling openmpi as:
>>
>> /opt/openmpi/1.3.3-intel/bin/mpirun --mca plm_rsh_disable_qrsh 1
>> --mca btl openib,sm,self \
>> -machinefile /tmp/6026489.1.qntest.q/machines -x LD_LIBRARY_PATH -np
>> $NSLOTS /home/ctierney/bin/noaa_affinity ./wrf.exe
>>
>> So,
>>
>> Is this expected? Are some common sense optimizations to use?
>> Is there a way to verify that I am really using the IB? When
>> I try:
>>
>> -mca bta ^tcp,openib,sm,self
>>
>> I get the errors:
>> --------------------------------------------------------------------------
>>
>> No available btl components were found!
>>
>> This means that there are no components of this type installed on your
>> system or all the components reported that they could not be used.
>>
>> This is a fatal error; your MPI process is likely to abort. Check the
>> output of the "ompi_info" command and ensure that components of this
>> type are available on your system. You may also wish to check the
>> value of the "component_path" MCA parameter and ensure that it has at
>> least one directory that contains valid MCA components.
>> --------------------------------------------------------------------------
>>
>>
>> But ompi_info is telling me that I have openib support:
>>
>> MCA btl: openib (MCA v2.0, API v2.0, Component v1.3.3)
>>
>> Note, I did rebuild OFED and put it in a different directory
>> and did not rebuild OpenMPI. However, since ompi_info isn't
>> complaining and the libraries are available, I am thinking that
>> is isn't a problem. I could be wrong.
>>
>> Thanks,
>> Craig
>
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-- 
Craig Tierney (craig.tierney_at_[hidden])