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Using the 92 katom [ApoA1 benchmark|http://www.ks.uiuc.edu/Research/namd/performance.html] with NAMD 2.7, performance appears to compare very favorably with previously benchmarked clusters: its \[processor cores X time per step\] values (corresponding to the ordinate on the [figure|http://www.ks.uiuc.edu/Research/namd/apoa1_bench.png] on the linked page) vary from 1.8 sec (8 CPUs) to 2.1 sec (128 CPUs).
!apoa_bench_scan.png|thumbnail! |
Using the queue system
All programs run on Darius must use the queue system. Users can check what jobs are running using qstat; XWindows users can try xpbs, although load times are long. Users can submit their jobs using the qsub command:
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