[gmx-users] Re: Opteron 1400 MHz Benchmark

[Michel Cuendet]

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). 

Cheers,

Michel

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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
>
>  
>

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Michel Cuendet, Ph.D. student
Laboratory of Computational Biochemistry and Chemistry
Swiss Federal Institute of Technology in Lausanne (EPFL)
CH-1015 Lausanne						
Switzerland                            Phone : +41 21 693 0324
lcbcpc21.epfl.ch/~mitch	                       +41  1 633 4194
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++