[Bioclusters] Direct connect infiniband/quadrics?

Jithesh p.jithesh at qub.ac.uk
Wed Mar 16 07:51:33 EST 2005


>From my experience on AMBER, GROMACS etc on clusters and SMPs, I would
suggest to go for SMPs rather than clusters. Since there is a lot of
communication required at short intervals, scaling on many processors in
a cluster is difficult. 


P.V.Jithesh  Bioinformatician  Belfast e-Science Centre
The Queen's University of Belfast UK

On Wed, 2005-03-16 at 12:18, Tim Cutts wrote:
> On 15 Mar 2005, at 11:19 pm, Farul M. Ghazali wrote:
> > Hi all,
> >
> > Thanks for the responses so far. The applications in use are molecular
> > dynamics applications (mostly amber, some gromacs) and Autodock. There
> > will be others as well but they won't be taking up a lot of CPU time. 
> > Just
> > going from a dual to a quad-CPU machine on Amber makes a big 
> > improvement
> > as far as I can tell.
> >
> > I'll most likely be using Rocks on this cluster or manually set it up 
> > if
> > need be. For the time being at least it's small enough to manage (2 
> > nodes
> > :-)
> >
> > In terms of expansion, I'm trying to push through quad-CPU nodes over
> > duals to minimize the cost of the interconnect if the interconnects 
> > prove
> > to be faster. I haven't looked at 8 or more CPU Opterons yet, but I'd 
> > like
> > to keep away from non-standard configurations eg. the Cray XD1.
> Did you consider an 8-way SGI Altix 350?
> It might suit your application well, and might even fit in that budget 
> (just).
> The NUMALink interconnect is very fast indeed.  Although I'd probably 
> be tempted to go for a few more nodes, and use GBit for the 
> interconnect.
> How many jobs do these people typically want to run at a time?  If it's 
> more than one at a time, then buy four quad-CPU Opteron nodes, GBit 
> connected, and run up to four 4-CPU jobs at a time.  No need for the 
> MPI to use the interconnect then, and the throughput of the cluster 
> will be very good (although individual job turnaround will be slower).  
> It's worth considering.
> Tim

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