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

[Justin A. Lemkul]

Mahendran E wrote:
> hi all
> 
> while running gromacs in parallel environment
> 
> i am getting the following command,
> 
> 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
> 

You are specifying 5 nodes with "mpirun -np 5 ..." so just change the number 
passed to the -np flag.

-Justin

> thanks in advance
> 
> 
> Regards
> 
> Mahendran.E
> 

-- 
========================================

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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