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

[Rodrigo faccioli]

I believe that this problem is about mpi installation.

What mpi version was installed ? Lampi or openmpi.

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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