Hi all I am running some free energy tutorial calculations to learn more about how those are set up in gromacs, but have run into a problem when using different versions.
I am following the free energy tutorial on the Gromacs website (fe-tutorial-4.6), so not Justin's tutorial. With vmx 4.6.5 everything goes according to the tutorial, and I can run with four thread on my laptop. Please find what I think is the relevant section of the log file below: $/usr/local/gmx465/bin/mdrun -v -deffnm topol_465 Initializing Domain Decomposition on 4 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.239 nm, LJC-14 q, atoms 4 7 multi-body bonded interactions: 0.239 nm, Angle, atoms 2 6 Minimum cell size due to bonded interactions: 0.263 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.497 nm Estimated maximum distance required for P-LINCS: 0.497 nm This distance will limit the DD cell size, you can override this with -rcon Using 0 separate PME nodes, as there are too few total nodes for efficient splitting Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 4 cells with a minimum initial size of 0.622 nm The maximum allowed number of cells is: X 3 Y 3 Z 2 Domain decomposition grid 2 x 2 x 1, separate PME nodes 0 PME domain decomposition: 2 x 2 x 1 Domain decomposition nodeid 0, coordinates 0 0 0 Using 4 MPI threads While on the other hand, when I am using v 5.0.5 I cannot start simulations using more than one thread, otherwise the domain decomposition complains, even though the excerpt from the log file from that run is (almost) identical $/usr/local/gmx505/bin/mdrun -v -deffnm topol_505 Initializing Domain Decomposition on 4 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: 0.239 nm, LJC-14 q, atoms 4 7 multi-body bonded interactions: 0.239 nm, Angle, atoms 2 6 Minimum cell size due to bonded interactions: 0.263 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.497 nm Estimated maximum distance required for P-LINCS: 0.497 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 4 cells with a minimum initial size of 0.622 nm The maximum allowed number of cells is: X 3 Y 3 Z 2 ------------------------------------------------------- Program gmx, VERSION 5.0.5 Source code file: /Users/pk/source/gromacs-5.0.5/src/gromacs/mdlib/domdec.c, line: 6902 Fatal error: There is no domain decomposition for 4 ranks that is compatible with the given box and a minimum cell size of 0.62175 nm Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings 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 ------------------------------------------------------- Is there something that I have overlooked in v 5 that needs to be taken into consideration? I am not that familiar with the new parallelization scheme of v5, maybe there is something there? Thanks /PK -- 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.