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?
And should be no problems with it?
How do you think, possibly AMBER was installed not properly on the cluster,
if it drops down in speed?
Or should be used any special parameters in input files?
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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Received on Tue May 24 2011 - 19:00:04 PDT
