[gmx-users] Opteron 1400 MHz Benchmark

[Alan Wilter Sousa da Silva]

Hi List!

A special thanks to Prof. van der Spoel.
BTW:
> Might be dynamic libraries. What's the error?
I did it static (or tried, at least). See below, pls.

Here are my results:
# Machine Type    N Compiler  Clock Cache Villin Lys/Cut Lys/PME DPPC Poly-CH2 Average* Rate**
# Linux   Opteron 1 Intel_8.1 1400  1024  6613   1855    1190    134  2758     287      1.64
# Linux   Opteron 1 gcc       1400  1024  6178   1738    1090    125  2585     268      1.53
# *  (V/v+LC/lc+LP/lp+D/d+P/p)*100/5, small letter = reference Athlon 800
# ** Rate=Average/Clock*800/N/100
# not tested in dual: lamboot failing

Here also comes my crude script. I hope it can help someone else. I'd
appreciate any commentary. BTW, do not take it as a "truth". There's no
warranty and I shall not take any responsability for that script. :-)

-------------------------------
#!/bin/sh
#
# To install gromacs on AMD_64
# You must be root
#
# Destination Machine:
# Dual AMD Opteron(tm) Processor 240
# cpu 1.4 GHz, cache 1024 KB
# SuSE Linux 9.1 (x86-64), kernel 2.6.4-52-smp
#
# Need to compile whole thing in Pentium IV:
# Mandrake 10, kernel 2.4.24-openmosix2 (custom)
# PIV 3.0 GHz
#
# install Intel compilers
# (here /usr/local/intel)
# get them by yourself at
# http://www.intel.com/software/products/noncom/
# noncommercial_cpp_l_N116-69163270.lic
# noncommercial_for_l_N136-36503391.lic
# l_fc_pu_8.1.021.tar.gz
# l_cc_pu_8.1.024.tar.gz

# Common
# installation folder
dir=/usr/local/gromacs
dir0=$HOME/inst_gmx_temp
mkdir $dir0
cd $dir0
# All source files at $dir0
# So go on and get them:
wget -c http://www.lam-mpi.org/download/files/lam-7.1.1.tar.bz2
wget -c http://www.fftw.org/fftw-2.1.5.tar.gz
wget -c ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.2.1.tar.gz
fftw=fftw-2.1.5.tar.gz
ifftw=fftw-2.1.5
gmx=gromacs-3.2.1.tar.gz
dgmx=gromacs-3.2.1
lam=lam-7.1.1.tar.bz2
ilam=lam-7.1.1

unset CC CXX F77 CFLAGS CXXFLAGS FFLAGS CPPFLAGS LDFLAGS

export CC=icc
export CXX=icpc
export F77=ifort
export CFLAGS="-O3 -static -static-libcxa"
export CXXFLAGS="-O3 -static -static-libcxa"
export FFLAGS="-O3 -static -static-libcxa"
# here, not working with -static, don't know
# used flags below
# export CFLAGS="-O3 -static-libcxa"
# export CXXFLAGS="-O3 -static-libcxa"
# export FFLAGS="-O3 -static-libcxa"
# to make it works in to me (since my bins are not full static)
# I had to also copy Intel lib libimf.so to my remote machine
# and export them by
# LD_LIBRARY_PATH="$HOME/lib"; export LD_LIBRARY_PATH
export CPPFLAGS=-I/$dir/include
export LDFLAGS=-L/$dir/lib

# MPI
tar xvfj $lam
cd $ilam
make distclean
./configure --prefix=$dir --with-rpi=sysv
make
make install
cd ..

# FFTW
#simple precision
tar xvfz $fftw
cd $ifftw
make distclean
./configure --prefix=$dir --enable-type-prefix --enable-mpi --enable-float
make
make install

#double precision
make distclean
./configure --prefix=$dir --enable-type-prefix --enable-mpi
make
make install
cd ..

# GMX
#simple precision
cd $dir/AMD
tar xvfz $gmx
cd $dgmx
make distclean
./configure --prefix=$dir --exec-prefix=$dir --datadir=$dir/gromacs
make
make install

#double precision
make distclean
./configure --prefix=$dir --exec-prefix=$dir --datadir=$dir/gromacs --program-suffix=_d --disable-float
make
make install

#simple precision MPI
make distclean
./configure --prefix=$dir --exec-prefix=$dir --datadir=$dir/gromacs
--program-suffix=_mpi --enable-mpi --disable-nice
make mdrun
make install-mdrun

#double precision MPI
make distclean
./configure --prefix=$dir --exec-prefix=$dir --datadir=$dir/gromacs --program-suffix=_d_mpi --enable-mpi --disable-nice --disable-float
make mdrun
make install-mdrun

exit 0

-- 
--------------------------
Alan Wilter Sousa da Silva
--------------------------
D.Sc. - IBCCF/UFRJ
Projeto BioPAUA - HP/LNCC
Petrópolis (RJ), Brasil
www.lncc.br/~alan