[gmx-users] Error: no domain decomposition, Source code file: domdec.c, line: 6436

Mark Abraham Mark.Abraham at anu.edu.au
Thu Mar 22 16:25:48 CET 2012

On 23/03/2012 2:14 AM, Ashalatha Sreshty wrote:
> Dear Gromacs users,
> I am performing MD simulation of an 14 units oligosaccharide on 
> Gromacs 4.5.4. I am able to successfully do a 10 ns simulation on a 
> DELL-precision workstation and also a 5ns simulation on tyrone cluster 
> using a PBS script (shown below). However, when I am trying to proceed 
> for further consecutive 5ns simulation, I get an error saying no 
> domain decompositions error. I have tried changing the number of nodes 
> by making it to 16 but it showed the same error. whereas, when I tried 
> it on the same workstation as before, the mdrun has successfully 
> executed. Please help me in letting me know what is the problem with 
> the system and what parameters or argument I am missing while running 
> it in tyrone cluster. I am providing the md.mdp parameter and the PBS 
> script are also provided as attachments to this mail
> *
> **the error is:*
> Program mdrun_mpi_d, VERSION 4.5.4
> Source code file: domdec.c, line: 6436
> Fatal error:
> There is no domain decomposition for 32 nodes that is compatible with 
> the given box and a minimum cell size of 1.33444 nm
> Change the number of nodes or mdrun option -rdd or -dds
> Look in the log file for details on the domain decomposition
> For more information and tips for troubleshooting, please check the 
> website at http://www.gromacs.org/Documentation/Errors

Following this link will lead you to a further link with some helpful 


> *and the PBS script is as below:*
> #!/bin/sh
> #PBS -N test
> #PBS -l nodes=1:ppn=32:debug
> #PBS -l walltime=2:00:00
> #PBS -S /bin/sh
> #PBS -j oe
> curr_dir=${PBS_O_WORKDIR}
> HOSTS='cat $PBS_NODEFILE | uniq |tr '\n' ""'
> echo Running Directory is 'pwd'
> /opt/mvapich2-1.7rc1/gcc/bin/mpirun -np 32 
> /home/proj/11/mbumasha/programs/gromacs-4.5.4/bin/mdrun_mpi_d -deffnm 
> triglc-MD4 -c triglc-MD6.pdb
> *Please suggest me how to resolve this error.
> *
> Thank you in advance.
> Dr. M. Asha Latha Sreshty,
> PDF,
> Molecular Biophysics Unit,
> Indian Institute of Science,
> Bangalore,

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