AMBER Archive (2009)

Subject: Re: [AMBER] Is it taking too much time

From: nicholus bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Mon Nov 02 2009 - 08:40:25 CST

Dear Nicolas,
                 My simulation is giving more or less similar time result.
With a system 15500 atoms in a single processor system of 2.66 GHz (0.8 nm
with PME) in a fedora 9 OS with GNU compiler it is taking 6 hours to
complete 150 ps simulation. My computer has 4 processors but the job is
running in 1 processor only. By any means can I distribute by jobs in all
the processors.

On Mon, Nov 2, 2009 at 7:49 PM, Nicolas SAPAY
<nicolas.sapay_at_cermav.cnrs.fr>wrote:

> Hello Nicholus,
>
> This is not that easy to answer to your question since the performance of
> your calculation depends on many factors, including:
> - the number of processors you are using;
> - their frequency;
> - the hardware/software used by processors to communicate;
> - the number of particles in your system;
> - whether you are using PME or not;
> - ...
>
> I made a test recently with a 30000 atoms system on a single Intel proc at
> 2.4 GHz (cutoff at 0.8 nm with PME). The OS was Fedora 10 and I used the
> GNU compiler. I was able to compute 0.41 ns per day which is not
> particularly great but sufficient to setup, minimize and equilibrate a
> system (in bulk water).
>
> Cheers,
> Nicolas
>
> > On Mon, Nov 2, 2009 at 1:01 PM, manoj singh <mks.amber_at_gmail.com> wrote:
> >
> >> You can do a quick benchmarking for your system by running few ps
> >> simulations. The simulation time is proportional to the length of the
> >> simulation.
> >>
> >> On Mon, Nov 2, 2009 at 1:08 AM, nicholus bhattacharjee <
> >> nicholusbhattacharjee_at_gmail.com> wrote:
> >>
> >> > Dear community,
> >> > I am running a protein simulation in my IBM
> >> 3400
> >> > server (specification
> >> > http://www-07.ibm.com/systems/in/x/hardware/tower/x3400/specs.html)
> >> with
> >> > AMBER 9. My protein is 50 amino acid long. I am doing an explicit
> >> solvent
> >> > simulation. Can anybody suggest what is the maximum time needed for
> >> this
> >> > simulation.
> >> >
> >> > --
> >> > Nicholus Bhattacharjee
> >> > PhD Scholar
> >> > Department of Chemistry
> >> > University of Delhi
> >> > Delhi-110007 (INDIA)
> >> > Phone: 9873098743(M)
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER_at_ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER_at_ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> > My machine is taking 1/2 hour for 10 ps simulation. Is this very long?
> > --
> > Nicholus Bhattacharjee
> > PhD Scholar
> > Department of Chemistry
> > University of Delhi
> > Delhi-110007 (INDIA)
> > Phone: 9873098743(M)
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> [ Nicolas Sapay - Post-Doctoral Fellow ]
> CERMAV - www.cermav.cnrs.fr
> BP53, 38041 Grenoble cedex 9, France
> Phone: +33 (0)4 76 03 76 44/53
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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