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

Mahendran E mahendrancse at gmail.com
Thu Dec 10 14:20:15 CET 2009

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


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
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


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