[gmx-users] Scaling on SGI Altix 3700 Bx2

[Dallas B. Warren]

I have just run some scaling of one of my systems on the new APAC SGI
Altix 3700 Bx2 (http://nf.apac.edu.au/facilities/ac/hardware.php), 32
CPUs on a single image node.

For a 330,000 atom system using PME:

CPUs		Scaling
1		100%
2		82%
4		66%
8		51%
16		31%
24		21%
32		20%

Is there anything that can be done on the software side of things to get
it to scale better?  Other than not using PME and waiting for the new
release which has rumours to have improved things here with PME.

I attempted to use the sort and shuffle options to see if that would
improve (found it did with cut-offs on another system but don't use the
options as subsequent analysis is a pain) things, but it immediately
crashes with triclinic box errors.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9073
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.