[gmx-users] Gromacs on SGI Altix

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Tue Jan 3 16:51:52 CET 2006


On Tuesday 03 January 2006 16:08, Mingfeng Yang wrote:
> Happy new year to each gromacs user!
> I just finished installation of Gromacs 3.3 on our Itanium2 based SGI
> Altix. My configuration option is
> |./configure --prefix=/home/myang/usr/local/gromacs_intel --enable-mpi
> CC=icc F77=ifort|
> The intel C++ compiler 9.021 and intel fortran compiler 9.021 were used.
> The OS is Red Hat Enterprise WS 3.0.
> The parallel efficiency is kind of disappointing. For the benchmark case
> of villin, it took 97 seconds with one CPU, 55 seconds with two CPUs,
> and 35 seconds for 4 CPUs. From the benchmark pages of Gromacs website,
> I saw the parallel efficiency can go beyond 100% under 8 CPUs. Is there
> anything I missed? What supposed to be the best options when install
> gromacs on Itanium2 based machine?

I think that d.villin is not the right benchmark for more cpus and measering 
parallel speedup.
I would prefer here d.dppc as shown on gromacs webpage. Reason for this bad 
scalling is is small system size.

> Thank you for any input!
> Mingfeng
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 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de

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