[gmx-users] Domain decomposition error
bdmkhtn at yahoo.com
Thu Oct 29 10:04:01 CET 2015
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?
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