Poor scaling in NAMD simulations

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Fri Nov 08 2013 - 22:11:41 CST

Hi all,

I'm running a moderately-sized (~380k atom) simulation in NAMD 2.9 on the new national compute server here in Australia (http://nf.nci.org.au/facilities/fujitsu.php). I'm seeing some strange behaviour in terms of scaling, and was hoping to get some ideas on where it might be coming from. The raw numbers are below. The most obvious problem is the enormous slowdown past 384 cores; my contact at the national facility tells me this is likely an OpenMPI problem which they've also seen in other packages once message sizes get too small. This isn't really my concern, since I typically stick to 256 cores. What worries me more is the ~50% loss in efficiency between 16 and 128 cores, when most benchmarks I've seen on other systems show near-linear scaling in this range. Is there anything I can do from my end to improve on this?



Cores CPU-seconds/step s/step
16 3.74 0.234
32 4.16 0.13
64 4.99 0.078
128 5.63 0.044
256 5.89 0.023
384 5.76 0.015
512 16.90 0.033
768 82.94 0.108
1024 135.17 0.132

Tristan Croll
Faculty of Health
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443

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