[gmx-users] Scaling Benchmarks

[Eric Jakobsson]

How was the electrostatics treated?

At 10:35 AM 8/1/2005, you wrote:
>Hello,
>
>we want to add some new numbers to the scaling section. We used GROMACS,
>3.2.1 on the new PC2 HPCLine, with Dual INTEL Xeon 3.2 GHZ EM64T and
>InfiniBand HCA PCI-e with SCALI-MPI
>(http://wwwcs.uni-paderborn.de/pc2/). For the DPPC benchmark system,
>using -shuffle and -sort, we reached to,
>
>CPU           1      2      4       8     12     16     20     24     32
>
>ps/24h     143  322  640 1269 1834 2367 2814 3212 3945
>rel. scal.   100  113  112   111   107   103     98     94     86
>
>The performance on each node is as expected, but the fast network yields
>a superb scaling.
>
>How far is the support for Xeon 64bit in the latested CVS-Versions and
>can one expect a performance gain?
>
>
>Best wishes,
>
>Jens Krüger
>
>
>
>
>Following settings were used during compilation,
>
>FFTW
>
>#! /bin/sh
>export F77=ifort
>export CC=icc
>export MPICC="mpicc -ccl $CC"
>export CFLAGS="-O2 -no_cpprt"
>export CFLAGS="-O3 -ip"
>export FFLAGS="-O3 -ip"
>
>./configure \
>- --enable-float   \
>- --enable-type-prefix \
>- --enable-mpi \
>- --prefix=/opt/pc2/fftw
>
>
>GROMACS
>
>#! /bin/sh
>#export F77=ifort
>export CC=icc
>export CFLAGS="-O2 -no_cpprt"
>export CPPFLAGS=-I/opt/pc2/fftw/include
>export LDFLAGS=-L/opt/pc2/fftw/lib
>export MPICC="mpicc -ccl $CC"
>  ./configure \
>- --enable-mpi \
>- --prefix=/opt/pc2/gromacs
>--
>========================================================
>Jens Krüger
>mercutio at uni-paderborn.de
>dienstlich:
>Warburger Str. 100 * 33098 Paderborn * Tel.:05251-602183
>privat:
>Ellersteg 3 * 33100 Paderborn-Dahl * Tel.:0176-20042288
>========================================================
>
>
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---------------------------------
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry, and of the Center for Biophysics and Computational Biology
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909