[gmx-users] Replica Exchange Error
Joe Joe
ilchorny at gmail.com
Sun Apr 12 05:36:37 CEST 2009
On Sat, Apr 11, 2009 at 8:13 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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)?
I am using pdb2gmx -vsite h so I can run 4fs time steps, so virtual
hydrogens. I will try with -pd and see what happens.
>
>
> -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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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