[gmx-users] High speed performance

[Asmaa El khodary]

Dr. Carsten
Thank you so much :)

On Tue, Aug 4, 2015 at 11:44 AM, Kutzner, Carsten <ckutzne at gwdg.de> wrote:

>
> > On 04 Aug 2015, at 00:02, Asmaa El khodary <asma.moh_990 at aucegypt.edu>
> wrote:
> >
> > Yes, I’m running the simulation on a cluster using 5 computational nodes,
> In that case I would run on a single node with 8 cores first so that you
> can compare the parallel performance to a single node and can derive how
> high the parallel efficiency is. That will depend a lot on your network.
> This is worth the effort, as sometimes using less nodes results in higher
> performance :)
>
> Carsten
>
>
> > 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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> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/grubmueller/kutzner
> http://www.mpibpc.mpg.de/grubmueller/sppexa
>
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