On 25/01/2011 8:25 AM, Christian Mötzing wrote:
Hi,
I compiled mdrun-gpu and tried some waterbox systems with different
atoms counts.
atoms | GPU | CPU
2.400 | 1.015s | 774s
4.800 | 1.225s | 1.202s
9.600 | 1.142s | 1.353s
19.200 | 2.984s | 2.812s
Why does the system with 9.600 atoms finish faster than the one with
4.800? I tripple checked the simualtions and even GROMACs tells me that
the atom count in the system is like above. So I think no mistaken
there. A diff of md.log only shows differences in output values for each
step.
Is there any explanation for this behaviour?
As a guess, the cost of overheads for molecular simulations tend to have
a weaker dependence on system size than the cost of computation (or none
at all). Only once the latter dominate the cost do you see scaling with
system size.
I expect you'd see similar behaviour running systems with 64, 128, 256,
512 atoms on 64 processors.
Mark
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