Hi, I'm having an issue using mdrun in parallel on 48 cores. I'm trying to figure out which options I can include in the .mdp file to increase the number of cells in my system. The full error message is:
Initializing Domain Decomposition on 48 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: 1.368 nm, LJC Pairs NB, atoms 2123 2152 multi-body bonded interactions: 0.428 nm, Proper Dih., atoms 1105 1113 *Minimum cell size due to bonded interactions: 1.505 nm* Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 0.219 nm Estimated maximum distance required for P-LINCS: 0.219 nm Guess for relative PME load: 0.65 Using 0 separate PME ranks, as guessed by mdrun Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 *Optimizing the DD grid for 48 cells with a minimum initial size of 1.881 nmThe maximum allowed number of cells is: X 3 Y 3 Z 3* ------------------------------------------------------- Program mdrun_mpi, VERSION 5.1 Source code file: /work/y07/y07/gmx/5.1-phase2/source/src/gromacs/domdec/domdec.cpp, line: 6969 Fatal error: There is no domain decomposition for 48 ranks that is compatible with the given box and a minimum cell size of 1.88133 nm I understand the problem -- the system wants to assign one core to each grid cell, but there are only 3x3x3 = 27 cells. I don't know what I can do to fix this problem. The system is a solvated protein bound to a ligand in a ~15 nm box, and it has > 40,000 atoms. I have tried changing the lincs-order and fourier-spacing to no avail. I was able to get the system to run by adding the following flags to mdrun: -rdd 1.2 -dds 0.9 But when I did this, the force imbalance went to > 140%, and 10-30% of the cpu time was lost due to load imbalance. Can someone suggest how I could edit my .mdp file to increase the number of allowed cells? -- 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.