[gmx-users] benchmarks

[Lieven Buts]

Andrew Shewmaker wrote:
> 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

> 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?

The assembly loops on Intel/AMD/PowerPC should be better than Fortran 
loops. On other hardware compiling the Fortran loops with a good and
platform-specific Fortran compiler is the best option.

> 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.

The log file ("run.log" in your case) tells you whether or not 
multimedia instructions were used. Look for a line containing
"CPUID". It is followed by a number of lines specifying exactly
how the simulation was run.


-- 
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel