[gmx-users] Genion failing in parallel runs.

[Justin A. Lemkul]

Bhanu wrote:
> Hi,
> I'm using Gromacs 3.3.3, installed with double precision. When I run 
> genion with this command:
>  
> genion_d -s *.tpr -o *.gro -g genion.log -pot pot.pdb -p *.top -neutral
>  
> the following error message was generated:
> ------------------------------------------------------------------------
>  
> Program genion_d Version 3.3.3
> sourcecode file: init.c, line 69
>  
> Fatal error:
> run input file prakash.tpr was made for 32 nodes
> while genion_d expected it to be for 1 node
> ------------------------------------------------------------------------------
>  
> System is "protein in water", dodecahedron box. Everything is fine till 
> energy minimisation. genion is failing.
>  
> Any clue??
>  

The problem is that genion is not MPI code, i.e., not parallelized.  Usually one 
does all of the preparation steps (pdb2gmx, editconf, genion) at one time, then 
begins MPI work - minimization, equilibration, production.

-Justin

> Thanks.
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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