Re: Cost of a colvar calculation

From: Jo, Sunhwan (
Date: Tue Jul 22 2014 - 19:02:20 CDT

Great! I didn’t know about the parameter.


On Jul 22, 2014, at 5:31 PM, Giacomo Fiorin <<>> wrote:

Hello Sunhwan, you can also use the option enableFitGradients to achieve the same result.


On Tue, Jul 22, 2014 at 2:06 PM, Jo, Sunhwan <<>> wrote:
RMSD colvar is particularly problematic if you use large number of CPUs. I also had about 10x slow down in performance when I had to include RMSD colvar in BG/Q. In addition, the scaling performance saturate pretty quickly. At the time, I had ~160K atoms and the scaling saturated after 32 cores with colvar turned on. I had total of 9 clovers (4 RMSDs).

At the time, I have found a bottleneck in the colvar implementation and I’d like to share it here. Below is the modification that I made in colvaratoms.C file and it almost speed up the simulation about 9x. The scaling also improved up to 128 cores. Find the lines ends with the comment “MOD”--_000_0A62B8E1B2F1430298B4D05B6243E6ADanlgov_--

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