From: Dow_Hurst (dhurst_at_mindspring.com)
Date: Wed Jan 21 2009 - 13:12:32 CST
I've found two excellent papers on NAMD/CUDA development:
http://portal.acm.org/ft_gateway.cfm?id=1413379&type=pdf&doid2=1413370.1413379
http://www.ncsa.uiuc.edu/Projects/GPUcluster/qc_tr.pdf
A hardware description and software description of current developments basically show that the benchmarks STMV and Apoa1 run just fine and provide good speedups. A problem exists with scheduling processes reliably on gpus but is possibly being addressed by the Phoenix application development framework. So, I think from reading these papers that it is just a matter of time before NAMD/CUDA becomes available as "stable". It is not clear how long that will take and if NAMD 2.7 would be released with a CUDA enabled "stable" set of features.
Has anyone on the list tried other protein systems using QP, the gpu enabled cluster at NCSA, than the benchmarks to see how those systems compare to traditional NAMD? Has anyone tried a protein in a bilayer?
Thanks,
Dow Hurst
No sig.
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