[gmx-users] Scaling Benchmarks

[Jens Krüger]

Hello Eric,

I just used the dppc benchmark system as it is. It uses cut-off's and contains
the following settings (grompp.mdp),

title                    = dppc
cpp                      = /lib/cpp
integrator               = md
nsteps                   = 5000
nstlist                  = 10
nstxout                  = 0
nstvout                  = 0
nstxtcout                = 0
nstlog                   = 0
dt                       = 0.002
constraints = all-bonds
nstenergy                = 0
ns_type                  = grid
coulombtype              = cut-off
rlist                    = 1.0
rvdw                     = 1.0
rcoulomb                 = 1.8
tcoupl                   = berendsen
tc_grps                  = dppc sol
tau_t                    = 0.1 0.1
ref_t                    = 323 323
Pcoupl                   = no

Greetings,

Jens


Eric Jakobsson wrote:

> 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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> >Please don't post (un)subscribe requests to the list. Use the
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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
>
> _______________________________________________
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--
========================================================
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
========================================================