[gmx-users] Domain Decomposition Error

[Mark Abraham]

Could be a bug, but unless you can reproduce it with 4.5.7 or 4.6.x then
you won't get much help there :-)

Mark


On Fri, May 31, 2013 at 9:56 PM, Parker de Waal <Parker.deWaal09 at kzoo.edu>wrote:

> Hi Everyone,
>
> I'm trying to run energy minimization on my system and I am encountering
> the following error:
>
> Getting Loaded...
> Reading file em.tpr, VERSION 4.5.5 (single precision)
> Starting 16 threads
> Loaded with Money
>
>
> Will use 10 particle-particle and 6 PME only nodes
> This is a guess, check the performance at the end of the log file
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.5
> Source code file: domdec.c, line: 6436
>
> Fatal error:
> There is no domain decomposition for 10 nodes that is compatible with the
> given box and a minimum cell size of 9.07242 nm
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> I've tested my bash script on a local server with an i7 and I've been able
> to run error free, however when running on xsede resources I continually
> encounter this error.
>
> For information here is my bash:
> #minimization
> grompp -f minim.mdp -c protein_solv_ions.gro -p protein.top -o em.tpr
> mdrun -v -deffnm em
> if [ ! $? == 0 ]
> then
>         echo "ERROR - Energy minimization"
>         exit 5
> fi
>
> and Here is my minim.mdp
>
> integrator         = steep
> emtol              = 10
> emstep         = 0.01
> nsteps             = 200
> energygrps      = System
>
> nstlist            = 5
> ns_type            = grid
> rlist              = 1.0
> coulombtype        = PME
> rcoulomb           = 1.0
> rvdw               = 1.0
> pbc                    = xyz
>
> Any input would help!
>
> Thanks,
> Parker
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