[gmx-users] Load imbalance and Y size error

nikhil damle pdnikhil at yahoo.co.in
Thu Oct 8 09:09:40 CEST 2009


I tried to run on single node now. Now the error is different saying
"One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off"

This means that my box shrinks during dynamics (this is not constant volume MD) But when Solvent is present in the same system, this does not happen. How should i deal with it then ?


From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thu, 8 October, 2009 11:57:46 AM
Subject: Re: [gmx-users] Load imbalance and Y size error

nikhil damle wrote:
> Hi all
>          I am trying to simulate a system of 3168 atoms in vacuum in PBC box (-d=0.9 nm). Since there are no solvent molecules, i am unable to neutralise the system using addition of ions (Hence system has +3 charge). As soon as i start the MD run after putting the whole system in box, there is imbalanced force of 80% due to which right in the beginning, dynamic load balancing is turned on. But even after this, there is ~22% loss of performance and after certain steps MD crashes saying :-
> "Fatal error: The Y-size of the box (4.618413) times the triclinic skew factor (0.866051) is smaller than the number of DD cells (2) times the smallest allowed cell size(2.000000)"
> Can anyone explain the origin of this error and how to deal with it ?

Try running with one processor to see if it's your system or the domain decomposition algorithm that is the problem. DD doesn't necessarily cope well with highly heterogeneous distributions of particles.

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