Dear GMX Users, I am simulating a free energy of a protein chain_A in water by parallel. Then i got domain decomposition error in mdrun. Will use 15 particle-particle and 9 PME only ranksThis is a guess, check the performance at the end of the log file -------------------------------------------------------Program mdrun_mpi, VERSION 5.1.1-dev-20150819-f10f108Source code file: /tmp/asillanp/gromacs/src/gromacs/domdec/domdec.cpp, line: 6969 Fatal error:There is no domain decomposition for 15 ranks that is compatible with the given box and a minimum cell size of 5.68559 nmChange the number of ranks or mdrun option -rddLook in the log file for details on the domain decomposition
Then i look through the .log file, there was 24 rank . So how can i change this ranks? What's wrong in here? Or something wrong in my .mdp file ? Or wrong construction on my script in parallel ? I am using just 2 nodes with 24 cpu. Then i don't think my system is too small (one protein chain, solvent is around 8000 molecules and few ions). Initializing Domain Decomposition on 24 ranksDynamic load balancing: offWill sort the charge groups at every domain (re)decompositionInitial maximum inter charge-group distances: two-body bonded interactions: 5.169 nm, LJC Pairs NB, atoms 81 558 multi-body bonded interactions: 0.404 nm, Ryckaert-Bell., atoms 521 529Minimum cell size due to bonded interactions: 5.686 nmMaximum distance for 13 constraints, at 120 deg. angles, all-trans: 0.218 nmEstimated maximum distance required for P-LINCS: 0.218 nmGuess for relative PME load: 0.38Will use 15 particle-particle and 9 PME only ranksThis is a guess, check the performance at the end of the log fileUsing 9 separate PME ranks, as guessed by mdrunOptimizing the DD grid for 15 cells with a minimum initial size of 5.686 nmThe maximum allowed number of cells is: X 1 Y 1 Z 0 Can anybody help this issue? Tnx Khatnaa -- 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.
