Joe Joe wrote:
How do I determine what those values should be? How does it affect the
simulation?
The header of your log file should have printed what the initial guesses were.
The -dd option sets how many PP nodes there are in the domain decomposition;
using 4 cores, there are probably 3 PP: 1 PME, so you probably can't tweak this
option, really.
The -rcon option is explained in mdrun -h or the manual. See what mdrun
guessed, then increase this value.
-Justin
thanks,
Ilya
On Fri, Apr 10, 2009 at 8:00 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Joe Joe wrote:
Hi All,
I get the following error when running replica exchange. I have
32 replica's with each replica running on 4 processors (128
total). How do I decrease the domain decomposition cell size,
-dss? What should I set it to?
<snip>
You're getting some hints from mdrun, I'd start there:
-------------------------------------------------------
Program mdrun_mpi, VERSION 4.0.4
Source code file: domdec_con.c, line: 679
Fatal error:
DD cell 5 0 0 could only obtain 96 of the 108 atoms that are
connected via vsites from the neighboring cells. This probably
means your vsite lengths are too long compared to the domain
decomposition cell size. Decrease the number of domain
decomposition grid cells or use the -rcon option of mdrun.
-------------------------------------------------------
...So manually set -dd and/or -rcon.
-Justin
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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