[gmx-users] How to let Gromacs run 60% faster..

Vaclav Horacek vaclav.horacek at yahoo.com
Sun Oct 18 12:12:36 CEST 2009


I just bumped into the site www.yasara.org, who claims that their just released new MD algorithms are 60% faster then Gromacs.
Actually they dont say 'Gromacs', but 'closest competitor', which I assume is Gromacs looking at the benchmark numbers.

>From the numbers, I also saw that they seem to do particulary well on newer CPUs like Core 2 Duo and Xeon L5420, using code for SSSE3 and SSE 4.1.

I am not expert for this kind of low level stuff, but typing SSE4 into Wikipedia shows lots of commands that look useful for MD. For example the 'dpps' instruction does an entire dot product at once.

I looked at the gmxlib/nonbonded directory and saw that SSE2 seems to be the most supported by Gromacs. So maybe adding support for SSE3 and SSE4 can still help a lot! Are there any plans for that?



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