peculiar scaling on the GPU

From: Ajasja Ljubetič (
Date: Tue Jul 31 2012 - 09:06:50 CDT

Dear all,

I'm noticing peculiar scaling when using a GPU (GTX 560). The graph is
shown here <>. If I run
the calculation only on the CPUs I get excellent linear scaling, but when
using the GPU there are huge jumps at 3 and 5 cores.

*What could be the reason for these jumps? *

I'm running NAMD 2.9 Linux-x86_64-multicore, the systems is ~1.5k atoms
large. The important performance parts of the conf file are below. I'm also
using the colvars module to keep track of two dihedral angles. An example
logfile is attached.

Thanks for your help,

nonbondedFreq 1
fullElectFrequency 1
stepspercycle 20

switching on
longSplitting C2
switchdist 10
cutoff 12
pairlistdist 14

PME yes
PMEGridSpacing 1

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