Greetings I have been trying to run a few set of simulations using high number of processors.
Using the tutorial - http://compchemmpi.wikispaces.com/file/view/Domaindecomposition_KKirchner_27Apr2012.pdf I have done calculations to evaluate the set of nodes which would be optimal for the protein. So the all the files are generated, but error occurs and the trajectory files remain empty with no error mentioned in the log file. Number of nodes to be used in multiple of 16 box in x and y dimension 8 nm In the error file, Reading file 400K_SIM2.tpr, VERSION 4.5.5 (single precision) Note: file tpx version 73, software tpx version 83 The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 1 Using 320 MPI processes NOTE: The load imbalance in PME FFT and solve is 116%. For optimal PME load balancing PME grid_x (54) and grid_y (54) should be divisible by #PME_nodes_x (140) and PME grid_y (54) and grid_z (54) should be divisible by #PME_nodes_y (1) mdp file for reference ; Bond parameters continuation = yes ; Restarting after NPT 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 = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = nose-hoover ; nose-hoover coupling tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.2 0.2 ; time constant, in ps ref_t = 400 400 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 400 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed Kindly help. I have to run simulations at 250 to 300 processors. -- 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.