Dear Nicolas,
Thanx a lot. I think I have installed the parallel
version. But is it done properly or not I am not sure about that. Instead of
sander.MPI, sander.LES.MPI and sander.PIMD.MPI executables I am getting
sander.LES and sander.MPI executables in my directory $AMBERHOME/exe/. Is
this is ok?
On Mon, Nov 2, 2009 at 10:00 AM, Nicolas SAPAY <nicolas.sapay.cermav.cnrs.fr
> wrote:
>
> > 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.
>
> If you want to do something else that minimization, you must run your jobs
> on several procs :)
> To do that, you need a message passing interface (MPI) as well as
> recompiling Amber. Common MPIs are MPICH2 and LAMMPI. You can install them
> with a yum command. Do not install both! Install only one of them. I also
> recommend you to have a look in the Amber manual and in the mailing list
> archives. There is plenty of information about running Amber in parallel.
>
> Nicolas
>
> >
> >
> > On Mon, Nov 2, 2009 at 7:49 PM, Nicolas SAPAY
> > <nicolas.sapay.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.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.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.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.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.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.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)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.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.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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Received on Mon Nov 02 2009 - 21:30:02 PST
