[gmx-users] Replica Exchange Error
Justin A. Lemkul
jalemkul at vt.edu
Sun Apr 12 05:13:30 CEST 2009
Joe Joe wrote:
> Hi Justin,
>
> Thanks for helping me with this.
>
> On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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.
>
>
> I do not get it. the input to -dd is a vector. What to the elements of
> the vector represent?
The number of DD grid cells per axis. For example, 3 1 1 means 2 divisions
along the x axis to give 3 DD cells, 1 cell in each the y- and z-axis for a
total of 3 cells. -dd 3 2 1 gives 3 x-cells, 2 y-cells, and 1 z-cell for a
total of 6 DD cells.
>
>
>
> The -rcon option is explained in mdrun -h or the manual. See what
> mdrun guessed, then increase this value.
>
>
> I tried -rcon 3.0 and got the same error. The error only occurs when I
> do the exchange. If I increase the replex from 500 to 1000 then I do not
> see the error for 1000 steps. How is the replex associated with the
> domain decomposition?
I don't know the specifics here. There may be some incompatibility between DD
and virtual sites; I know there were some bugs in previous versions. What kind
of virtual sites are you using? Does the run work successfully with -dd turned
off (i.e., mdrun -pd)?
-Justin
>
>
>
> -Justin
>
> thanks,
>
> Ilya
>
>
> On Fri, Apr 10, 2009 at 8:00 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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> <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 <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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