[gmx-users] Some Scaling of 5.0 Results

Dallas Warren Dallas.Warren at monash.edu
Fri Sep 19 02:50:42 CEST 2014

Some scaling results that might be of interest to some people.

Machine = Barcoo @ VLSCI
2.7GHz Intel Sandybridge cores
16 cores per node
Mellanox FDR14 InfiniBand switch

Systems = water and octanol only with GROMOS53a6

# Atoms = 10,000 to 1,000,000

Comparison Group versus Verlet neighbour searching

Image/graphs see https://twitter.com/dr_dbw/status/512763354566254592

Basically group neighbour searching for this setup is faster and scales better than Verlet.  Was expecting that to be the case with water, since it is mentioned somewhere that is the case.  However for the pure octanol system was expecting it to be the other way around?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail. 

More information about the gromacs.org_gmx-users mailing list