[gmx-users] benchmarks

[Andrew Shewmaker]

Hi,

I'm a cluster administrator and I don't know much about Gromacs 
although I would like to use it as a benchmark since I have 
several scientists who are interested in it.  I wanted to make 
sure that I am running the benchmarks correctly.

I basically just ran them like this:

grompp -f grompp.mdp -p topol.top -c conf.gro -o run.tpr
mdrun -s run.tpr -o run.trr -c conf.gro -v -g run.log

Then I take the ps/(node hour) and multiply by 24h/day to 
get a number that I can compare to the table on the website.

I compiled Gromacs and FFTW with GCC 3.2, and I enabled threads 
in FFTW (should I not?).  I don't have g77 and I thought I read 
that I should use a Fortran compiler if possible for best 
performance.  Is that true?

I was looking at src/config.h to try and determine how much and 
what kind of optimization was being done and I saw:

/* Use X86 SSE2 multimedia assembly code */
/* #undef USE_X86_SSE2 */

/* Use X86 SSE/3DNow multimedia assembly code */
/* #undef USE_X86_SSE_AND_3DNOW */

Does this mean that I'm not using any of the multimedia assembly 
code?  I know my processor supports both.

Thanks for your help,

Andrew

-- 
Andrew Shewmaker
Associate Engineer
Phone:  208.526.1415
Fax:  208.526.4017

Idaho National Engineering and Environmental Laboratory
2525 Fremont Ave.
Idaho Falls, ID 83415-3605