[gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Oct 28 03:03:45 CET 2009
Jennifer Williams wrote:
> Hi ,
>
> I am getting the following error when I try to run in parallel (I've
> tried with 8 and 2 nodes and get the same).
>
> Not all bonded interactions have been properly assigned to the domain
> decomposition cells
>
> But my simulation works when I run in serial.
>
> I'm using gromacs 4.0.5. I am working on a mesoprous silica which I
> define as a single residue (each atom is assigned to a single charge
> group).
How many atoms in what size simulation cell? What are your v-sites?
> I've tried changing table_ext in the .mdp file (I first increased it to
> 2.5 and then 30) following advice on previous forum posts but I still
> get the same thing.
>
> Does anyone know why this is happening and how I can fix this? I could
> run in serial but it would take too long.
>
> I also get a NOTE: Periodic molecules: can not easily determine the
> required minimum bonded cut-off, using half the non-bonded cut-off
>
> Is this part of the same problem or a different thing altogether?
My random guess is that there's a single problem with the interaction
of parallel DD, PBC, vsites, periodic molecules and/or constraints. Berk did
fix a bug earlier this month whose git commit description is
"fixed v-site pbc bug with charge groups consisting ofonly multiple v-sites"
but I do not know if this is at all applicable.
Compiling the git release-4-0-patches branch and trying to run with that
may help.
See bottom of text also.
> I've pasted my md.log file below
>
> Thanks
>
>
> 010/AP_ready> more md.log
> Log file opened on Tue Oct 27 13:31:44 2009
> Host: vlxbig20.see.ed.ac.uk pid: 6930 nodeid: 0 nnodes: 8
> The Gromacs distribution was built Tue Jul 21 13:18:34 BST 2009 by
>
>
> parameters of the run:
> integrator = md
> nsteps = 5000000
> init_step = 0
> ns_type = Grid
> nstlist = 10
> ndelta = 2
> nstcomm = 0
> comm_mode = None
> nstlog = 1000
> nstxout = 1000
> nstvout = 1000
> nstfout = 1000
> nstenergy = 1000
> nstxtcout = 1000
> init_t = 0
> delta_t = 0.001
> xtcprec = 1000
> nkx = 39
> nky = 39
> nkz = 64
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 0
> epsilon_surface = 0
> optimize_fft = TRUE
> ePBC = xyz
> bPeriodicMols = TRUE
> bContinuation = FALSE
> bShakeSOR = FALSE
> etc = Nose-Hoover
> epc = No
> epctype = Isotropic
> tau_p = 1
> ref_p (3x3):
> ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> compress (3x3):
> compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> refcoord_scaling = No
> posres_com (3):
> posres_com[0]= 0.00000e+00
> posres_com[1]= 0.00000e+00
> posres_com[2]= 0.00000e+00
> posres_comB (3):
> posres_comB[0]= 0.00000e+00
> posres_comB[1]= 0.00000e+00
> posres_comB[2]= 0.00000e+00
> andersen_seed = 815131
> rlist = 1.5
> rtpi = 0.05
> coulombtype = PME
> rcoulomb_switch = 0
> rcoulomb = 1.5
> vdwtype = Shift
> rvdw_switch = 1.2
> rvdw = 1.5
> epsilon_r = 1
> epsilon_rf = 1
> tabext = 2.5
> implicit_solvent = No
> gb_algorithm = Still
> gb_epsilon_solvent = 80
> nstgbradii = 1
> rgbradii = 2
> gb_saltconc = 0
> gb_obc_alpha = 1
> gb_obc_beta = 0.8
> gb_obc_gamma = 4.85
> sa_surface_tension = 2.092
> DispCorr = EnerPres
> free_energy = no
> init_lambda = 0
> sc_alpha = 0
> sc_power = 0
> sc_sigma = 0.3
> delta_lambda = 0
> nwall = 0
> wall_type = 9-3
> wall_atomtype[0] = -1
> wall_atomtype[1] = -1
> wall_density[0] = 0
> wall_density[1] = 0
> wall_ewald_zfac = 3
> pull = no
> disre = No
> disre_weighting = Conservative
> disre_mixed = FALSE
> dr_fc = 1000
> dr_tau = 0
> nstdisreout = 100
> orires_fc = 0
> orires_tau = 0
> nstorireout = 100
> dihre-fc = 1000
> em_stepsize = 0.01
> em_tol = 10
> niter = 20
> fc_stepsize = 0
> nstcgsteep = 1000
> nbfgscorr = 10
> ConstAlg = Lincs
> shake_tol = 0.0001
> lincs_order = 4
> lincs_warnangle = 30
> lincs_iter = 1
> bd_fric = 0
> ld_seed = 1993
> cos_accel = 0
> deform (3x3):
> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> userint1 = 0
> userint2 = 0
> userint3 = 0
> userint4 = 0
> userreal1 = 0
> userreal2 = 0
> userreal3 = 0
> userreal4 = 0
> grpopts:
> nrdf: 5392
> ref_t: 300
> tau_t: 0.1
> anneal: No
> ann_npoints: 0
> acc: 0 0 0
> nfreeze: Y Y Y N
> N N
> energygrp_flags[ 0]: 0
> efield-x:
> n = 0
> efield-xt:
> n = 0
> efield-y:
> n = 0
> efield-yt:
> n = 0
> efield-z:
> n = 0
> efield-zt:
> n = 0
> bQMMM = FALSE
> QMconstraints = 0
> QMMMscheme = 0
> scalefactor = 1
> qm_opts:
> ngQM = 0
>
> Initializing Domain Decomposition on 8 nodes
> Dynamic load balancing: auto
> Will sort the charge groups at every domain (re)decomposition
>
> NOTE: Periodic molecules: can not easily determine the required minimum
> bonded cut-off, using half the non-bonded cut-off
>
> Minimum cell size due to bonded interactions: 0.750 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.376 nm
> Estimated maximum distance required for P-LINCS: 0.376 nm
> Using 0 separate PME nodes
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 8 cells with a minimum initial size of 0.938 nm
> The maximum allowed number of cells is: X 4 Y 4 Z 8
> Domain decomposition grid 2 x 1 x 4, separate PME nodes 0
> Domain decomposition nodeid 0, coordinates 0 0 0
>
> Table routines are used for coulomb: TRUE
> Table routines are used for vdw: TRUE
> Will do PME sum in reciprocal space.
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
> A smooth particle mesh Ewald method
> J. Chem. Phys. 103 (1995) pp. 8577-8592
> -------- -------- --- Thank You --- -------- --------
>
> Using a Gaussian width (1/beta) of 0.480244 nm for Ewald
> Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm
> Cut-off's: NS: 1.5 Coulomb: 1.5 LJ: 1.2
> System total charge: 0.000
> Generated table with 2000 data points for Ewald.
> Tabscale = 500 points/nm
> Generated table with 2000 data points for LJ6Shift.
> Tabscale = 500 points/nm
> Generated table with 2000 data points for LJ12Shift.
> Tabscale = 500 points/nm
> Generated table with 2000 data points for 1-4 COUL.
> Tabscale = 500 points/nm
> Generated table with 2000 data points for 1-4 LJ6.
> Tabscale = 500 points/nm
> Generated table with 2000 data points for 1-4 LJ12.
> Tabscale = 500 points/nm
> Configuring nonbonded kernels...
> Testing x86_64 SSE support... present.
>
> Initializing Parallel LINear Constraint Solver
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> B. Hess
> P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
> J. Chem. Theory Comput. 4 (2008) pp. 116-122
> -------- -------- --- Thank You --- -------- --------
>
> The number of constraints is 800
> There are inter charge-group constraints,
> will communicate selected coordinates each lincs iteration
>
> Linking all bonded interactions to atoms
> There are 3236 inter charge-group exclusions,
> will use an extra communication step for exclusion forces for PME
>
> The initial number of communication pulses is: X 1 Z 1
> The initial domain decomposition cell size is: X 2.01 nm Z 1.90 nm
>
> The maximum allowed distance for charge groups involved in interactions is:
> non-bonded interactions 1.500 nm
> two-body bonded interactions (-rdd) 1.500 nm
> multi-body bonded interactions (-rdd) 1.500 nm
> atoms separated by up to 5 constraints (-rcon) 1.896 nm
>
> When dynamic load balancing gets turned on, these settings will change to:
> The maximum number of communication pulses is: X 1 Z 1
> The minimum size for domain decomposition cells is 1.500 nm
> The requested allowed shrink of DD cells (option -dds) is: 0.80
> The allowed shrink of domain decomposition cells is: X 0.75 Z 0.79
> The maximum allowed distance for charge groups involved in interactions is:
> non-bonded interactions 1.500 nm
> two-body bonded interactions (-rdd) 1.500 nm
> multi-body bonded interactions (-rdd) 1.500 nm
> atoms separated by up to 5 constraints (-rcon) 1.500 nm
>
> Making 2D domain decomposition grid 2 x 1 x 4, home cell index 0 0 0
>
> There are: 5244 Atoms
> There are: 476 VSites
> Charge group distribution at step 0: 583 565 583 565 666 684 666 684
> Grid: 9 x 6 x 6 cells
>
> Constraining the starting coordinates (step 0)
>
> Constraining the coordinates at t0-dt (step 0)
>
> Not all bonded interactions have been properly assigned to the domain
> decomposition cells
More output should follow here, to wit, a list of missing bonded
interactions. It might also be in the stderr from the calculation. Is there any?
Mark
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