[Bioclusters] Suggestions requested on HPC.

George Magklaras georgios at biotek.uio.no
Mon Aug 4 05:53:15 EDT 2008

I can't give you specific suggestions unless you tell me a bit about the 
scale of your envisaged molecular modeling and docking (size of data 
set, number of cores, etc). So, in a very abstract way, my view is that 
performance is often independent of the large brands and more dependent 
on the local sysadmin resources and how good they work with the work 
developers. This is true for small to moderate scale (500 cores say) 
installation and for filesystems whose size can fit well within the 
limits of DAS (directly attached storage, as opposed to fiber channel 
and other storage solutions). You could find very good deals with 
independent smaller scale hardware manufacturers at a fraction of the 
cost of the big boys. However, if your envisaged scale exceeds the 
moderate level and/or your simulation requires some sort of bespoke 
interconnect, then the big boys might have more resources to deal with 
annoying driver issues and help your local resources get more juice out 
of your setup.


George Magklaras

Senior Computer Systems Engineer/UNIX Systems Administrator
EMBnet Technical Management Board
The Biotechnology Centre of Oslo,
University of Oslo

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?
> Expecting suggestions !
> Lijo M Antony

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