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Subject: Re: [OMPI users] Performance: MPICH2 vs OpenMPI
From: Brock Palen (brockp_at_[hidden])
Date: 2008-10-10 13:08:13


Whoops didn't include the mpich2 numbers,

20M mpich2 same node,

Brock Palen
www.umich.edu/~brockp
Center for Advanced Computing
brockp_at_[hidden]
(734)936-1985

On Oct 10, 2008, at 12:57 PM, Brock Palen wrote:

> Actually I had a much differnt results,
>
> gromacs-3.3.1 one node dual core dual socket opt2218
> openmpi-1.2.7 pgi/7.2
> mpich2 gcc
>
> 19M OpenMPI
> M Mpich2
>
> So for me OpenMPI+pgi was faster, I don't know how you got such a
> low mpich2 number.
>
> On the other hand if you do this preprocess before you run:
>
> grompp -sort -shuffle -np 4
> mdrun -v
>
> With -sort and -shuffle the OpenMPI run time went down,
>
> 12M OpenMPI + sort shuffle
>
> I think my install of mpich2 may be bad, I have never installed it
> before, only mpich1, OpenMPI and LAM. So take my mpich2 numbers
> with salt, Lots of salt.
>
> On that point though -sort -shuffle may be useful for you, be sure
> to understand what they do before you use them.
> Read:
> http://cac.engin.umich.edu/resources/software/gromacs.html
>
> Last, make sure that your using the single precision version of
> gromacs for both runs. the double is about half the speed of the
> single.
>
> Brock Palen
> www.umich.edu/~brockp
> Center for Advanced Computing
> brockp_at_[hidden]
> (734)936-1985
>
>
>
> On Oct 10, 2008, at 1:15 AM, Sangamesh B wrote:
>
>>
>>
>> On Thu, Oct 9, 2008 at 7:30 PM, Brock Palen <brockp_at_[hidden]> wrote:
>> Which benchmark did you use?
>>
>> Out of 4 benchmarks I used d.dppc benchmark.
>>
>> Brock Palen
>> www.umich.edu/~brockp
>> Center for Advanced Computing
>> brockp_at_[hidden]
>> (734)936-1985
>>
>>
>>
>> On Oct 9, 2008, at 8:06 AM, Sangamesh B wrote:
>>
>>
>>
>> On Thu, Oct 9, 2008 at 5:40 AM, Jeff Squyres <jsquyres_at_[hidden]>
>> wrote:
>> On Oct 8, 2008, at 5:25 PM, Aurélien Bouteiller wrote:
>>
>> Make sure you don't use a "debug" build of Open MPI. If you use
>> trunk, the build system detects it and turns on debug by default.
>> It really kills performance. --disable-debug will remove all those
>> nasty printfs from the critical path.
>>
>> You can easily tell if you have a debug build of OMPI with the
>> ompi_info command:
>>
>> shell$ ompi_info | grep debug
>> Internal debug support: no
>> Memory debugging support: no
>> shell$
>> Yes. It is "no"
>> $ /opt/ompi127/bin/ompi_info -all | grep debug
>> Internal debug support: no
>> Memory debugging support: no
>>
>> I've tested GROMACS for a single process (mpirun -np 1):
>> Here are the results:
>>
>> OpenMPI : 120m 6s
>>
>> MPICH2 : 67m 44s
>>
>> I'm trying to bulid the codes with PGI, but facing problem with
>> compilation of GROMACS.
>>
>> You want to see "no" for both of those.
>>
>> --
>> Jeff Squyres
>> Cisco Systems
>>
>>
>>
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