[gmx-users] domain decomposition problems

Albert mailmd2011 at gmail.com
Sun Jan 29 10:34:06 CET 2017


I am trying to run MD simulation for a system:

box size: 105.166 x 105.166 x 105.166
atoms: 114K
FF: Amber99SB

I submitted the job with command line:

srun -n 1 gmx_mpi grompp -f mdp/01-em.mdp -o 60.tpr -n -c ion.pdb
srun -n 12 gmx_mpi mdrun -s 60.tpr -v -g 60.log -c 60.gro -x 60.xtc

but it always failed with messages:

There is no domain decomposition for 12 ranks that is compatible with 
the given box and a minimum cell size of 4.99678 nm
Change the number of ranks 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 google it, and the answer for above problem is that the system is too 
small to use a large number of CPU. However, I don't think 12 CPU is too 
big for my system which contains 114 K atoms in all.

Does anybody have other suggestions?

Thanks a lot.


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