[gmx-users] Re: Opteron 1400 MHz Benchmark

Mon Dec 6 17:26:44 CET 2004

On Mon, 2004-12-06 at 16:32 +0100, Michel Cuendet wrote:
> Hi Alan,
> 
> When you set the CFLAGS= environment variable, it prevents ./configure to add other optimization flags to the compiler. With "-O3 -ip -unroll" you would see some improvements. On my opterons, it makes the icc compilation 10% faster than the gcc one (for my own system : 85000 atoms, PME)! 
> 
> The -ipo flags could does inter-file optimizations. It could help, but it doesn't work with gromacs, because of a bug in the linking (at least it didn't work in 3.1.4). 
ipo won't help you in gromacs.


> 
> Cheers,
> 
> Michel
> 
> gmx-users-request at gromacs.org wrote:
> 
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> >Today's Topics:
> >
> >   1. Opteron 1400 MHz Benchmark (Alan Wilter Sousa da Silva)
> >   2. RMSDview (Ing. Vojtech Spiwok)
> >   3. gmx bins from a box to another (Alan Wilter Sousa da Silva)
> >   4. Re: gmx bins from a box to another (David van der Spoel)
> >   5. Re: gmx bins from a box to another (Florian Haberl)
> >   6. Dual Opteron + MPI (Alan Wilter Sousa da Silva)
> >
> >
> >----------------------------------------------------------------------
> >
> >Message: 1
> >Date: Mon, 6 Dec 2004 09:50:26 -0200 (BRST)
> >From: Alan Wilter Sousa da Silva <alan at lncc.br>
> >Subject: [gmx-users] Opteron 1400 MHz Benchmark
> >To: gmx-users at gromacs.org
> >Message-ID: <Pine.GSO.4.58.0412060922560.17820 at copacabana>
> >Content-Type: TEXT/PLAIN; charset=iso-8859-1
> >
> >
> >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
> >
> >  
> >
> 
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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