From: Ryan Gordon (rg563_at_drexel.edu)
Date: Thu Feb 05 2015 - 12:08:20 CST
Thank you. I was able to optimize to the best of my ability by running 7 by 15 by 7 patch grid. I never had a margin specified. I guess I was just curious if there was a way to specify the dimensions directly.
Thanks again,
Ryan
On 02/05/15, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>
> If you have "margin" set to something, remove it, since the only role of the margin parameter is to make the patches larger (and hence the number of patches smaller.
>
> You can use "twoAwayX yes" to double the patch grid in one dimension, which is done automatically at some processor count based on heuristics.
>
> Beyond that, if you are running on a cluster see if you can reduce your node count slightly without losing performance based on the suggestions at
> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdPerformanceTuning
>
> Jim
>
>
> On Thu, 5 Feb 2015, Ryan Gordon wrote:
>
> >I was wondering if there was a way to specify what you want the patch grid dimensions to be? I am running a NPT system of roughly 110,000 atoms, and I allow this to run at a temperature close to the solvent boiling point for 100 ns. I then quenched the system at three different time points from this simulation to room temperature. The way I did this was to decrease the temperature by 10K for 100 ps (enough time for the volume to equilibrate), until I reached my desired temperature (293K). When I run at 300K and up the box size is big enough to run on a patch grid of 8 by 8 by 8. When I reduce to 293K, the box size shrinks just enough to run on 7 by 7 by 7 patch grid, which causes a performance hit since there are more atoms per patch now. My first theory is to make the system slightly larger to keep the system in the 8 by 8 by 8 patch grid dimension, to optimize the computational time to complete this. This seemed tedious if there was a way to manually adjust the patch grid dimensions.
> >
> >
> >Thank you,
> >
> >Ryan GordonPh.D. Candidate
> >Chemical and Biological Engineering
> >Drexel University
> >
>
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