Re: NAMD crashes with OpenMPI/OpenMX

From: Axel Kohlmeyer (
Date: Tue Jun 14 2011 - 13:25:23 CDT

>> Does the simulation you are running scale better with an InfiniBand
>> network?
> I'm afraid that that is something we can't afford.

hmm... i wouldn't say that. you have to be a bit more creative. ;)
for example, you can set up a small 3 node cluster
without(!) an expensive switch by simply buying 3 dual
port IB cards and 3 cables. OpenSM comes with the OS
and you are in business for less than $2000. if you use
3 4-way 8-core opteron 61xx nodes with 32GB RAM with
them, you can have a kickass 100 core machine for way
under $20k (if you buy from a vendor that doesn't screw you).
that is hard to beat, even with GPUs. ;)

 ...and the NAMD ibverbs version runs really well
on these machines. we have a bunch of those
(more expensive ones with 12-core cpus) here
and i am very happy with them.


> Thomas

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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