[AMBER] Amber20 pmemd.cuda installation and performance problems

From: Filip Fratev <fratev.biomed.bas.bg>
Date: Sun, 17 May 2020 11:43:26 +0300


I was able to install pmemd.cuda only if I use the old ./configuration
method. In this way the link between gcc7 and cuda 10.2, as such for
example |sudo ln -s /usr/bin/gcc-7.xx /usr/local/cuda/bin/gcc| is
possible. However, this is not possible using the new cmake procedure.

Further, I notice significant performance drop of Amber20 in comparison
to Amber18. I don't know whether this is due to the compilation process
make v.s cmake as this has been already noticed for Sander.

These are the numbers obtained by GTX 2080Ti and Factor X system:

Steps            Amber20               Amber18

10K             177.06ns/day        198.31

50K             175.33ns/ day        196.18

Any comments and sharing experience by other users could be helpful.



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Received on Sun May 17 2020 - 02:00:02 PDT
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