Hi, If you express those as [intermolecular_interactions] then perhaps DD will cope better because it understands that they are intended to be handled separately. It doesn't matter that they are actually intramolecular!
Mark On Tue., 2 Jul. 2019, 14:27 Daniel Bauer, <ba...@cbs.tu-darmstadt.de> wrote: > Hello, > > I am trying to run a protein simulation consisting of ~100.000 atoms > (box dimensions: 8.8x8.8x9.4nm) on multiple mpi threads. For the > protein, I need to define a few distance restraints. Right now, these > are defined with harmonic bonds in the [ bond ] section of the protein: > > [ bonds ] > > ... > > 53 1952 6 2.437 1000.0 > 1952 3851 6 2.437 1000.0 > 3851 5750 6 2.437 1000.0 > 5750 53 6 2.438 1000.0 > 53 3851 6 3.447 1000.0 > 1952 5750 6 3.447 1000.0 > > Unfortunately, when I try to run this system with more than 1 mpi > thread, it fails. Apparently, the high distance for the bond does not > allow proper domain decomposition (which makes sense because the bond > cannot go over multiple domains). What are my options here? Is there no > way to run this across multiple computation nodes except using something > like plumed? > > > Initializing Domain Decomposition on 32 ranks > Dynamic load balancing: locked > Minimum cell size due to atom displacement: 1.301 nm > Initial maximum distances in bonded interactions: > two-body bonded interactions: 3.444 nm, Harmonic Pot., atoms 53 3851 > multi-body bonded interactions: 0.424 nm, Proper Dih., atoms 5136 5145 > Minimum cell size due to bonded interactions: 3.789 nm > Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.855 nm > Estimated maximum distance required for P-LINCS: 0.855 nm > Using 0 separate PME ranks > Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 > Optimizing the DD grid for 32 cells with a minimum initial size of 4.736 nm > The maximum allowed number of cells is: X 1 Y 1 Z 1 > > ------------------------------------------------------- > Program: gmx mdrun, version 2019.1 > Source file: src/gromacs/domdec/domdec.cpp (line 2403) > MPI rank: 0 (out of 32) > > Fatal error: > There is no domain decomposition for 32 ranks that is compatible with the > given box and a minimum cell size of 4.73566 nm > Change the number of ranks or mdrun option -rdd or -dds > Look in the log file for details on the domain decomposition > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > > Best regards, > > Daniel > > > -- > Daniel Bauer, M.Sc. > > TU Darmstadt > Computational Biology & Simulation > Schnittspahnstr. 2 > 64287 Darmstadt > ba...@cbs.tu-darmstadt.de > > Don't trust atoms, they make up everything. > > > -- > 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. -- 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.