[gmx-users] 4.6 seems improved the efficiency

[Szilárd Páll]

Additionally to the new non-bonded SIMD kernels:
- Bonded force calculation got some SIMD acceleration which should
considerably improve performance;
- There have been be major improvements in PME (courtesy of Berk Hess &
Roland Schulz), you should see anywhere between up to 1.5-2x performance
improvement. OpenMP multi-threading is supported with separate PME nodes
also with the group scheme which should reduce communication cost at high
parallelization (turn it on with -npme N -ntomp_pme M). Note that
g_tune_pme does not support tuning the number of OpenMP threads (yet).


--
Szilárd


On Mon, Feb 11, 2013 at 4:39 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> Indeed - that's about the order of improvement expected for just switching
> to 4.6 and proceeding as before on CPU-only hardware. Better use of SIMD
> instructions and calling force-only kernels when energies are not required
> are likely to be the code improvements leading to the performance
> improvement you note. (However, the new automated PME load balancing in
> mdrun may mean you don't need to use g_tune_pme for 4.6... see your log
> file.)
>
> Mark
>
> On Sat, Feb 9, 2013 at 9:38 AM, Albert <mailmd2011 at gmail.com> wrote:
>
> > Hello :
> >
> >  I found the new released 4.6 probably improved very obviously for the
> > efficiency. With the same system, I used 4.5.5 it can get 26 ns/day (144
> > CPU, 55,000 atoms, Amber FF) with g_tume_pme optimization. Now I used
> 4.6,
> > even without g_tune_pme, the  pme mesh/force can get 0.8-1.0 with
> > efficiency 32 ns/day. That's really nice.
> >
> > I don't know whether other users have similar experiences for this new
> > version.
> >
> > Albert
> >
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