[gmx-users] High speed performance

Asmaa El khodary asma.moh_990 at aucegypt.edu
Tue Aug 4 00:02:24 CEST 2015


Yes, I'm running the simulation on a cluster using 5 computational nodes,
each one has 8 cores, so the total number of cores is 40. The module I'm
using is GROMACS/4.6.5-goolf-1.4.10-hybrid.

On Tue, Aug 4, 2015 at 12:45 AM, Szilárd Páll <pall.szilard at gmail.com>
wrote:

> 40 cores? Are you sure it's not two 10-core CPUs with HyperThreading = 2x20
> threads supported?
>
> --
> Szilárd
>
> On Mon, Aug 3, 2015 at 3:19 PM, Asmaa El khodary <
> asma.moh_990 at aucegypt.edu>
> wrote:
>
> > Dr Carsten
> > Thank you so much for your reply. Yes, you are right, it's a 40 core CPU.
> > I'm using 2 fs time step with Particle Mesh Ewald for long-range
> > electrostatics. I've attached the parameter file I'm using for the
> > production run.
> > Best Regards
> > Asma
> >
> > On Mon, Aug 3, 2015 at 4:03 PM, Asmaa El khodary <
> > asma.moh_990 at aucegypt.edu>
> > wrote:
> >
> > > Hi,
> > > I'm currently simulating a protein consists of 2776 atoms with 173
> > > residues using CPU with 5 nodes, 40 core processors. The performance of
> > the
> > > simulation is 70 ns per day (50 ns simulation takes almost 18 hours).
> Is
> > > this realistic or not?
> > > Thanks in Advance
> > > Asma
> > >
> >
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