[gmx-users] Some Scaling of 5.0 Results

[Mark Abraham]

On Fri, Sep 19, 2014 at 2:50 AM, Dallas Warren <Dallas.Warren at monash.edu>
wrote:

> Some scaling results that might be of interest to some people.
>
> Machine = Barcoo @ VLSCI
> 2.7GHz Intel Sandybridge cores
> 256GB RAM
> 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?
>

Thanks for sharing. Since the best way to write code that scales well is to
write code that runs slowly, we generally prefer to look at raw ns/day.
Choosing between perfect scaling of implementation A at 10 ns/day and
imperfect scaling of implementation B starting at 50 ns/day is a
no-brainer, but only if you know the throughput.

I'd also be very suspicious of your single-core result, based on your
super-linear scaling. When using a number of cores smaller than a node, you
need to take care to pin that thread (mdrun -pin on), and not having other
processes also running on that core/node. If that result is noisy because
it ran into different other stuff over time, then every "scaling" data
point is affected.

Also, to observe the scaling benefits of the Verlet scheme, you have to get
involved with using OpenMP as the core count gets higher, since the whole
point is that it permits more than one core to share the work of a domain,
and the (short-ranged part of the) group scheme hasn't been implemented to
do that. Since you don't mention OpenMP, you're probably not using it ;-)
Similarly, the group scheme is unbuffered by default, so it's an
apples-and-oranges comparison unless you state what buffer you used there.

Cheers,

Mark

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.
>
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