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AGBNP3: the latest serial CPU performance data

posted May 1, 2015, 9:40 AM by Emilio Gallicchio   [ updated May 1, 2015, 10:03 AM ]

Over the past couple of weeks further optimizations were applied to the AGBNP3 algorithm. These mainly focused on the pairwise-descreening calculation for Born radii. Prior to this, the descreening kernel employed an interpolation procedure which utilizes two C-spline calculations. The new algorithm utilizes only one. The benefits are substantial, especially for the larger systems, as illustrated below (see May results vs. April results):

 
 Trp-Cage
trp cage

 GCN4
GCN4
 T4-Lysozyme + Chlorophenol
1LI2
 Overall AGBNP3
speed
 


 

 


These results complete the main phase of the AGBNP3 serial performance optimization project. We nearly tripled the speed of the code relative to AGBNP2 without non-bonded cutoffs and doubled it relative to AGBNP2 with cutoffs (for system sizes illustrated above).  Future efforts will focus on parallelization on multi-core and GPU architectures.

Support from the National Science Foundation is gratefully acknowledged
 
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