[gmx-users] optimization of gromacs 4.0.5 on AIX Power6

[Mark Abraham]

Rodrigo faccioli wrote:
> I believe that this problem is about mpi installation.
> 
> What mpi version was installed ? Lampi or openmpi.

That would be plausible on a home-built linux cluster, but not so likely 
on a cluster bought from a recognized vendor like IBM, whose MPI 
installation should be dependable.

Mark

> There is a good tutorial about that in
> http://www.gromacs.org/WIKI-import/Quick_and_Dirty_Installation
> 
> Best regards,
> 
> --
> Rodrigo Antonio Faccioli
> Ph.D Student in Electrical Engineering
> University of Sao Paulo - USP
> Engineering School of Sao Carlos - EESC
> Department of Electrical Engineering - SEL
> Intelligent System in Structure Bioinformatics
> http://laips.sel.eesc.usp.br
> Phone: 55 (16) 3373-9366 Ext 229
> Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
> 
> 
> On Thu, Aug 27, 2009 at 7:14 AM, Silvia Giuliani
> <silvia.giuliani at cineca.it>wrote:
> 
>> Dear All
>>
>> Has anybody tried version 4.0.5 on an IBM Power6 (4.7Ghz) cluster?
>> We have installed the program with the following configure options (using
>> fftw we installed separately):
>>
>> ./configure --with-fft=fftw2 --enable-mpi --enable-float CC=mpcc_r
>> F77=mpxlf_r CXX=mpCC_r CFLAGS="-O3 -qarch=pwr6 -qtune=pwr6 -qcpluscmt"
>>
>> It compiles and works but the performance is poor compared to our Opteron
>>  Cluster (2.6Ghz)
>> For example with 8 procs for a small protein in water we get 5.8ns/+day
>> compared to 9.6 ns/day on the Linux cluster, which is a bit disappointing.
>> Since there alot of compiler options to play with we would be grateful if
>> somebody who has already found a good set would share them with us.
>>
>> best wishes
>> Silvia Giuliani
>>
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> 
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