On Fri, Apr 20, 2012 at 14:49, Olivia Waring <[email protected]> wrote:
> My invocation of mdrun, using 8 processors and the following mdp file: > ... > There are: 1184 Atoms > ... > DD step 4 load imb.: force 181.0% > > Not all bonded interactions have been properly assigned to the domain > decomposition cells Hi Olivia! The translation to English would be: "you have too few atoms for a domain decomposition on 8 processors to succeed, given the parameters in your setup." :) With so few atoms, you won't get much speedup, if at all, when running on more than 1 processor. The rule of thumb posted on this very list quite often is 1000 atoms/processor for a reasonably good scaling. To convince GROMACS 4.5.x to use only one processor on a multi-core machine, run with the '-nt 1' command line option. Cheers, Bogdan -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
