

The Real Cost of High Performance Computing - gpoort
http://blog.rescale.com/the-real-cost-of-high-performance-computing/

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semi-extrinsic
From a CFD perspective, I think this analysis is flawed because of two things:

1) any organization thinking about buying a 1000-core cluster will have at
least one in-house code. The reason being that none of the commercial ones
really scale well to much beyond 50 cores. And that changes the comparison a
lot, since any external support for an in-house code will be really expensive.
(If you've ever looked at an in-house CFD code, you'd generally be mortified
at the coding.)

2) they say that hardware costs are only 1/3 of total costs, but they are
assuming a slow-ass interconnect that no-one in their right mind is
considering today. Once you go up to a real HPC cluster with 1:1 non-blocking
FDR or dual-rail QDR, hardware costs are more like 3/4\. And really, you need
that kind of interconnect to be able to scale around the memory bandwidth
bottleneck, which any code that does stencil operations is bound by.

But if your organization is, say, a Gromacs shop working on chemical
engineering, it could make sense.

