YH wrote: > Dear Dr. Saavedra, > > I would like to ask your help for my use of Gromacs. > Now I run the Gromacs 4.05 on 16 node computer, but always meet the problems > like the following. > Would you please tell me how to sovle it. > > Thank you very much in advanc, > > James, Wang(Dr.) > Dalian university of Technology, > China > ------------------------------------- > > Back Off! I just backed up pr1.log to ./#pr1.log.5# > Reading file pr1.tpr, VERSION 4.0.5 (single precision) > Will use 10 particle-particle and 6 PME only nodes > This is a guess, check the performance at the end of the log file > ------------------------------------------------------- > Program mdrun_mpi, VERSION 4.0.5 > Source code file: domdec.c, line: 5873 > Fatal error: > There is no domain decomposition for 10 nodes that is compatible with the > given box and a minimum cell size of 0.96025 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 > -------------------------------------------------------
You should read about the domain decomposition algorithm in the manual. Probably your system is too small to make effective use of this many processors with this algorithm. Mark _______________________________________________ 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
