AMBER Archive (2009)

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

From: Nicolas SAPAY (nicolas.sapay_at_cermav.cnrs.fr)
Date: Mon Nov 02 2009 - 09:00:58 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.

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_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)
> _______________________________________________
> 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

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