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. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
