On 31/03/2012 8:29 AM, Peter C. Lai wrote:
Yeah I usually average 21ns/day on a openmpi-over-qdr infiniband cluster
using fewer than 300 nodes and with a 100K system with 60K TIPS3P (hydrogen LJ
terms) waters (single precision gromacs, ffw3, and openmpi compiled with icc
10.0.3)
On similar hardware, I have a 20K system with optimal PME balance that
gets 102ns/day on 16 cores, and I bet I could scale that linearly out to
about 8 times more atoms and cores.
Mark
It's going to depend on your forcefield and how you've optimized your system
too (PME:PP ratio etc.)
On 2012-03-30 07:07:25PM +0200, David van der Spoel wrote:
Op 30 mar 2012 om 19:02 heeft Albert<[email protected]> het volgende
geschreven:
Hello:
I am wondering does anybody have experience with GROMACS for large scale
simulation? I've heard lot of people said that it would be difficult for
Gromacs to do so. eg: I've got a 60,000 atoms system, is it possible for
GROMACS to produce 100 ns/days or even more? suppose I can use as much CPU as
possible.... My recent experience for such system, Gromacs can only produce up
to 20ns/day.... If I would like to produce 1000 ns, I have to wait for 50
days......
We are about to publish a paper where have 1,2 million atoms and get 30 ns/day.
On 2000 cores.
thank you very much
best
A.
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