[Bioclusters] Suggestions requested on HPC.

Joe Landman landman at scalableinformatics.com
Mon Aug 4 06:16:34 EDT 2008

Lijo wrote:
> Hi,
> Our lab plans to erect a HPC for molecular modeling and docking. Now we face
> flood of executives from different high profile brands with  their
> customized efficiency.
>  Does the performance is free from the brands?

Hi Lijo:

   Depending upon the solution offering, performance is quite a bit more 
aligned with system configuration/design issues, OS issues, and 
associated.  Opteron/Xeon systems from many vendors will generally have 
similar performance if you isolate the computing performance.  It is how 
the overall system is designed that will have the most dramatic impact, 
and to a lesser degree, though nearly as important, what you have in 
terms of system software configuration.

   We run into designs that have no hope of working reasonably well, 
through massively over-engineered systems.  Many of the "designs" simply 
throw together brand name gear or various brands from various suppliers, 
and don't focus upon what it is you are doing.  The latter is the 
important aspect.  Which software for modeling and docking are you going 
to be using, how large are your models, what are the expected run times, 
how many runs do you need to accomplish per day?

   If you can answer those problems, we may collectively be able to 
render advice.  If (like many US universities) you have pre-existing 
purchase agreements with only one vendor, you will likely be quite 
constrained on what you can purchase.

   The more information you can share on what you are doing, the more we 
can help.


> Expecting suggestions !
> Lijo M Antony

Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 786 8423
fax  : +1 866 888 3112
cell : +1 734 612 4615

More information about the Bioclusters mailing list