[gmx-users] Benchmarking Gromacs 3.2.1 on Power4

[Anu Tervo]

Dear GMX-users,

I run benchmarks on IBM Power4 (aix5.2, 1.1GHz) using mdrun of Gromacs 
versions 3.1.4 and 3.2.1 and single precision. The results seem a bit 
disappointing as mdrun in version 3.1.4 was faster:

 		3.1.4		3.2.1
 		-----		-----
d.villin	4015.44		3645.888
d.poly.ch2	2368.152	2155.152
d.lzm.cutoff	1165.992	1154.328
d.lzm.pme	760.728		747.456
d.dppc		91.08		84.408

The same phenomena was observed in parallel results of d.dppc. I suspect 
that mdrun vs. 3.2.1 shouldn't be slower, but have at least the same 
performance than mdrun 3.1.4

Installation procedure of version 3.2.1 was carried out using the helpful 
tips from Fiona Reid: 
http://www.gromacs.org/pipermail/gmx-users/2004-July/011630.html
The necessary inclusion of --disable-vectorized-sqrt option might (partly) 
cause the slower performance of 3.2.1 mdrun. Has anyone else experienced 
this phenomena of a slower mdrun in vs. 3.2.1 on Power4 and found a way to 
overcome it?

Regards,
 		-Anu