[gmx-users] large scale simulation?

[Mark Abraham]

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<mailmd2011 at gmail.com>  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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>