On 11/15/15 8:09 PM, Agnivo Gosai wrote:
Dear Users, I tried to do a NVT run on a cluster with -np = 64. My system size is 12405 atoms ( a protein in water ) I get the following error. ERROR. There is no domain decomposition for 56 nodes that is compatible with the given box and a minimum cell size of 0.959375 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings 8 nodes were assigned for PME cal by mdrun This is the part of my NVT.mdp ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.4 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT I would still like to use 64 processes for the mdrun. Any suggestions please.
Your system is too small to decompose over 64 cores. One cannot arbitrarily parallelize any system over any number of cores/nodes.
-Justin
I am thinking of playing with -rcon. But I am not sure if it will affect the accuracy of the simulation. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University.
-- ================================================== 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.
