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

[Justin A. Lemkul]

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
> -------------------------------------------------------
> 

Have you followed this advice?  There is a minimum size requirement for DD cells 
based on the cutoffs used, etc.  You can alter these parameters by using the 
mdrun options that have been spelled out for you.  If this does not work, then 
your system is simply too small to be split over more than a small amount of 
processors.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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