[gmx-users] How to increase nodes in mdrun option
ms
devicerandom at gmail.com
Thu Dec 10 14:27:45 CET 2009
Mahendran E ha scritto:
> 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
Increasing the number after mpirun -np , I'd say.
m.
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