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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> >
>
>
>
> --
> 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue May 24 2011 - 19:00:05 PDT
