[gmx-users] Scaling Problems

[Dallas Warren]

Having some problems with scaling of GROMACS onto multiple boxes.  Just 
want to see if the system I am simulating is may be too small to scale 
well, or if there are some settings with may be LAM or even default GROMACS 
that I need to be adjusting.

System:
         Intel P733 Dual Processor
         Linux Redhat 7.3
         LAM 6.5.4
         100 base Ethernet

MD Simulation:
         7.5 nm cube
         16 molecules, 16 Na, + water
         42,000 atoms
         500 steps
         0.002 ps step
         PME

grompp switches:
         -sort
         -shuffle
         -np #

Initiation of mdrun:
         mpirun C mdrun -s .....

Results (time to perform the mdrun calculation):
         1 CPU / 1 box - 480 seconds
         2 CPU / 1 box - 340 seconds
         2 CPU / 2 box - 400 seconds
         4 CPU / 2 box - 420 seconds

Some suggestions and guidance would be greatly appreciated :-)

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
dallas.warren at vcp.monash.edu.au
+61 3 9903 9076
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