Thank you Justin. >The better question is why you're trying to decouple an entire protein; that >is >extremely impractical and unlikely to be useful.
Did i do that? then it's my mistake of less knowledge off that. How i fix that? Khatnaa On Friday, 30 October 2015, 1:14, Justin Lemkul <jalem...@vt.edu> wrote: On 10/29/15 4:56 AM, badamkhatan togoldor wrote: > 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 Given the two-body interaction length, your .mdp file probably specifies couple-intramol = no, which generates explicit pairs and exclusions for intramolecular interactions, thus driving up the minimum size of a DD cell considerably. So your system is incompatible with more than a few DD cells. The better question is why you're trying to decouple an entire protein; that is extremely impractical and unlikely to be useful. -Justin > 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 > -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.