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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