[gmx-users] How to increase nodes in mdrun option

[Carsten Kutzner]

Hi Mahendran,

your minimum domain decomposition cell size seems to be 1.095 nm, as indicated
in the error message. Probably your cutoffs are near 1 nm and your system is
small. If you need to run on more processors, try 6 and 8, since then 3x2x1,
2x3x1, ...  and 2x2x2, ... decompositions can be used. Right now the only
possibilities are 5x1x1, 1x5x1, and 1x1x5, yielding a too small DD size in any
direction. (What is your max. box length divided by 5?)

Carsten


On Dec 10, 2009, at 2:38 PM, Mahendran E wrote:

> 
> 
> hi all
> 
> 
> while running gromacs in parallel environment
> 
> mpirun -np 3 -machinefile machinefile /usr/local/gromacs/bin/mdrun_mpi -s fws_md.tpr -o fws_md.trr -c fws_pmd.pdb -g md.log -e md.edr  
> for mpirun 3 nodes i got the output,
> 
> while trying to increase the nodes to 5 or 8 i am getting the following error 
> 
> the command i used is
> 
> mpirun -np 5 -machinefile machinefile /usr/local/gromacs/bin/mdrun_mpi -s fws_md.tpr -o fws_md.trr -c fws_pmd.pdb -g md.log -e md.edr
> 
> 
> error:
> 
> 
> 
> Program mdrun_mpi, VERSION 4.0.5
> Source code file: domdec.c, line: 5873
> 
> Fatal error:
> There is no domain decomposition for 5 nodes that is compatible with the given box and a minimum cell size of 1.095 nm
> Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings
> Look in the log file for details on the domain decomposition
> -------------------------------------------------------
> 
> "Everybody Wants to Be Naked and Famous" (Tricky)
> 
> Error on node 0, will try to stop all the nodes
> Halting parallel program mdrun_mpi on CPU 0 out of 5
> 
> gcq#130: "Everybody Wants to Be Naked and Famous" (Tricky)
> 
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
> p0_16810:  p4_error: : -1
>     p4_error: latest msg from perror: No such file or directory
> 
> 
> how to increase the nodes in mdrun option
> 
> thanks in advance
> 
> 
> Regards
> 
> Mahendran.E
> 
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne




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