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

[Mahendran E]

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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