[gmx-users] Replica Exchange Error

[Justin A. Lemkul]

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

========================================