From: sonia ziada (sonia.ziada_at_univ-orleans.fr)
Date: Mon Nov 14 2016 - 04:11:43 CST
Dear NAMD users,
I am running NPT brute force molecular dynamics simulation with PBC on a
system of 100 000 atoms using 1 nvidia K80 gpu card.
The best performance (16.7ns/day) is obtained for a number of cpu equal
to 8 (+p8) and the GPU-utility is around 60%.
If I run a targeted molecular dynamics simulation, with the same system
and the same condition, i get a performance of 2.8ns/day (against
1.81ns/day using only 8 cpu without GPU card) and th GPU-utility is
around 12%.
Why the improvement in performance is so bad when switching from CPU to
GPU for the targeted molecular dynamics (TMD) simulation ? Is it normal
that the GPU utility is only 12% ? Are there features badly suuported
on GPU ? (like here for the TMD)
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