Hi all, I appear to have a very high load imbalance on some of my runs. Values starting from approx. 7% up to 31.8% with reported vol min/aver of around 0.6 (I haven¹t found one under half yet).
When I look through the .log file at the start of the run I see: Initializing Domain Decomposition on 8 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.514 nm, LJ-14, atoms 3116 3123 multi-body bonded interactions: 0.429 nm, Proper Dih., atoms 3116 3123 Minimum cell size due to bonded interactions: 0.472 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.862 nm Estimated maximum distance required for P-LINCS: 0.862 nm This distance will limit the DD cell size, you can override this with -rcon Using 0 separate PME ranks, as there are too few total ranks for efficient splitting Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 1.077 nm The maximum allowed number of cells is: X 12 Y 12 Z 12 Domain decomposition grid 4 x 2 x 1, separate PME ranks 0 PME domain decomposition: 4 x 2 x 1 Domain decomposition rank 0, coordinates 0 0 0 Using 8 MPI processes Using 1 OpenMP thread per MPI process Having a quick look through the documentation and I see that I should consider implementing the verlet cut-off (which I am) and adjust the number of PME nodes/cut-off and PME grid spacing. Would this simply be a case of throwing more cores at the simulation or must I play around with P-LINCS parameters? Thanks Anthony -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.