[gmx-users] Performance degradation for Verlet cutoff-scheme compared to group

[Mark Abraham]

On Fri, Oct 10, 2014 at 8:16 PM, Олег Титов <titovoi at qsar.chem.msu.ru>
wrote:

> Good day.
>
> I've got sigmificant performance degradation when trying to use Verlet
> cutoff-scheme for free energy calculation. My system contains 1
> bromobenzene molecule and 543 TIP3P waters. 16 hours of calculation on
> 8-core CPU resulted in 2.5 ns trajectory. With group scheme i've got 6.5 ns
> trajectory in 7h 40 min.
>
> Interesting that with group scheme gromacs tells me that it was using 8 MPI
> threads while with Verlet - 1 MPI and with 8 OpenMP threads. Both times
> I've launched the calculation with "mdrun -deffnm test".
>

One scheme supports OpenMP, one doesn't...


> I believe that this is caused by "plain C kernels" as GROMACS warns me. Is
> there any possibility to overcome this issue?
>

Yes...


> I have access only to old gcc 4.1.2 (without SSE4.1) and buggy icc 11.1 on
> this machine.
>

Gromacs requires a real compiler to get performance, like the install guide
says. You need to get one.

Mark


> Thanks for your help.
>
> Oleg Titov
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