OK,
Thanks a lot!
On Wed, May 25, 2011 at 9:55 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, May 24, 2011 at 9:47 PM, Azat Mukhametov <azatccb.gmail.com>
> wrote:
>
> > Dear All,
> > thank you for your comments
> >
> > So, AMBER can utilise effectively 4 nodes with 16 cores per node for one
> > job? Am I right?
> >
>
> Correct.
>
>
> > And should be no problems with it?
>
>
> Also correct. Of course, you have to make sure that the threads are being
> locked down to each processor correctly (i.e. it's possible that with a bad
> setup, all 64 threads are locked to a single node, and then your scaling
> falls through the floor).
>
> Also, there are instances in which certain systems do not have an
> interconnect topology or memory bandwidth that lends itself to amber
> (pmemd)
> simulations, and you'll get better performance if you run 64 threads across
> a larger number of nodes (i.e. 16 nodes, leaving 12 idle cores on each
> node). (i.e. if you have 16 threads all fighting for bandwidth to read
> from
> memory which causes them to all slow down).
>
>
> > How do you think, possibly AMBER was installed not properly on the
> cluster,
> > if it drops down in speed?
> >
>
> It could be that you're not using the correct program. In the past pmemd
> was only installed in parallel (or serial, I suppose), and the executable
> was simply called pmemd. However, since Amber 11, pmemd is built in serial
> (pmemd) and parallel (pmemd.MPI) as part of the default build process.
> Therefore, if you're just using pmemd with amber11, then it's only running
> in serial, regardless of how many nodes you give it.
>
>
> > Or should be used any special parameters in input files?
> >
>
> See the benchmarks and try to fit your input files accordingly to see if
> you
> get comparable performance.
>
> HTH,
> Jason
>
>
> >
> > On Wed, May 25, 2011 at 9:32 AM, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > This is complete misinformation and whoever told you this is not
> correct.
> > > Check the amber web page for many scaling benchmarks including teragrid
> > > machines.
> > >
> > > On May 24, 2011 9:15 PM, "Azat Mukhametov" <azatccb.gmail.com> wrote:
> > >
> > > Dear Friends,
> > > My question is about scaling of AMBER on multiCPU systems.
> > > I had info, that Amber can not utilise more number of CPUs than are
> > inside
> > > one node, is it right?
> > > For example, was found that AMBER could use not more than 8 CPUs
> > > effectively
> > > when there were 8 CPUs per cluster node.
> > > Is this law working for any computer systems - as workstations as
> > clusters?
> > >
> > > Also was found that AMBER works awfully on Teragride clusters, on the
> > same
> > > reasons.
> > > May you specify the best parameters and possible speed of MD run on
> next
> > > systems:
> > > multicore workstations; Teragrid cluster
> > >
> > > Additional question. There is possibility to use Amber parameter files
> > with
> > > another MD simulation software, for example NAMD, etc. May you comment,
> > how
> > > perfectly they utilise Amber parameters, and how quality results may be
> > > created by this way?
> > >
> > > Thanks!
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
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> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Best regards,
> > Azat Mukhametov, PhD
> >
> > Centre for Chemical Biology at Universiti Sains Malaysia (CCB.USM)
> > 1st Floor, Block B,
> > No.10, Persiaran Bukit Jambul,
> > 11900 Bayan Lepas,
> > Penang, Malaysia.
> > http://www.ccbusm.com
> > Tel : +604-6535500/5573
> > Fax : +604-6535514
> > email: azatccb.gmail.com
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best regards,
Azat Mukhametov, PhD
Centre for Chemical Biology at Universiti Sains Malaysia (CCB.USM)
1st Floor, Block B,
No.10, Persiaran Bukit Jambul,
11900 Bayan Lepas,
Penang, Malaysia.
http://www.ccbusm.com
Tel : +604-6535500/5573
Fax : +604-6535514
email: azatccb.gmail.com
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Received on Tue May 24 2011 - 19:30:02 PDT
