Hi! If you are running implicit solvent with no cutoffs, ie using the special all-vs-all kernels, then particle decomposition will be used. This exact combination (gb, all-vs-all, dd) is quite tricky to implement, and is not supported at the moment, IIRC. This could be documented better, sorry.
You could try changing constraints from all-bonds to h-bonds, meaning you will have only local constraints, which should allow you to run with particle decomposition. Or use a cut-off and domain decomposition. /Per 4 maj 2011 kl. 16.05 skrev Ozlem Ulucan: > Dear Justin, this was only a test run and I ran the simulations on my > multi-core workstations (4 cores actually). MPI is no longer required for > such a situation. Since I did not set -nt option to 1, this can be accepted > as a parallel run. So the command I sent in my previous e-mail was for the > parallel run and for serial run I set -nt to 1. > > > Dear Justin, as I said I am using a workstation of 4 processors. I have > approximately 2200 atoms in my system. That means for one processor I have > slightly more than 550 atoms. I set all the cut-offs to 0. I really need to > run this system in parallel. Any suggestions to make it work out? > > > Here is my run input file : > > ; > ; File 'mdout.mdp' was generated > ; By user: onbekend (0) > ; On host: onbekend > ; At date: Sun May 1 16:19:29 2011 > ; > > ; VARIOUS PREPROCESSING OPTIONS > ; Preprocessor information: use cpp syntax. > ; e.g.: -I/home/joe/doe -I/home/mary/roe > include = > ; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) > define = > > ; RUN CONTROL PARAMETERS > integrator = SD > ; Start time and timestep in ps > tinit = 0 > dt = 0.002 > nsteps = 500000 > ; For exact run continuation or redoing part of a run > init_step = 0 > ; Part index is updated automatically on checkpointing (keeps files separate) > simulation_part = 1 > ; mode for center of mass motion removal > comm-mode = Angular > ; number of steps for center of mass motion removal > nstcomm = 10 > ; group(s) for center of mass motion removal > comm-grps = system > > ; LANGEVIN DYNAMICS OPTIONS > ; Friction coefficient (amu/ps) and random seed > bd-fric = 0 > ld-seed = 1993 > > ; ENERGY MINIMIZATION OPTIONS > ; Force tolerance and initial step-size > emtol = 10.0 > emstep = 0.01 > ; Max number of iterations in relax_shells > niter = 20 > ; Step size (ps^2) for minimization of flexible constraints > fcstep = 0 > ; Frequency of steepest descents steps when doing CG > nstcgsteep = 1000 > nbfgscorr = 10 > > ; TEST PARTICLE INSERTION OPTIONS > rtpi = 0.05 > > ; OUTPUT CONTROL OPTIONS > ; Output frequency for coords (x), velocities (v) and forces (f) > nstxout = 1000 > nstvout = 1000 > nstfout = 0 > ; Output frequency for energies to log file and energy file > nstlog = 1000 > nstcalcenergy = -1 > nstenergy = 1000 > ; Output frequency and precision for .xtc file > nstxtcout = 0 > xtc-precision = 500 > ; This selects the subset of atoms for the .xtc file. You can > ; select multiple groups. By default all atoms will be written. > xtc-grps = Protein > ; Selection of energy groups > energygrps = Protein > > ; NEIGHBORSEARCHING PARAMETERS > ; nblist update frequency > nstlist = 0 > ; ns algorithm (simple or grid) > ns_type = simple > ; Periodic boundary conditions: xyz, no, xy > pbc = no > periodic_molecules = no > ; nblist cut-off > rlist = 0 > ; long-range cut-off for switched potentials > rlistlong = -1 > > ; OPTIONS FOR ELECTROSTATICS AND VDW > ; Method for doing electrostatics > coulombtype = cut-off > rcoulomb-switch = 0 > rcoulomb = 0 > ; Relative dielectric constant for the medium and the reaction field > epsilon_r = 1 > epsilon_rf = 1 > ; Method for doing Van der Waals > vdw-type = Cut-off > ; cut-off lengths > rvdw-switch = 0 > rvdw = 0 > ; Apply long range dispersion corrections for Energy and Pressure > DispCorr = No > ; Extension of the potential lookup tables beyond the cut-off > table-extension = 1 > ; Seperate tables between energy group pairs > energygrp_table = > ; Spacing for the PME/PPPM FFT grid > fourierspacing = 0.12 > ; FFT grid size, when a value is 0 fourierspacing will be used > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > ; EWALD/PME/PPPM parameters > pme_order = 4 > ewald_rtol = 1e-05 > ewald_geometry = 3d > epsilon_surface = 0 > optimize_fft = yes > > ; IMPLICIT SOLVENT ALGORITHM > implicit_solvent = GBSA > > ; GENERALIZED BORN ELECTROSTATICS > ; Algorithm for calculating Born radii > gb_algorithm = OBC > ; Frequency of calculating the Born radii inside rlist > nstgbradii = 1 > ; Cutoff for Born radii calculation; the contribution from atoms > ; between rlist and rgbradii is updated every nstlist steps > rgbradii = 0 > ; Dielectric coefficient of the implicit solvent > gb_epsilon_solvent = 80 > ; Salt concentration in M for Generalized Born models > gb_saltconc = 0 > ; Scaling factors used in the OBC GB model. Default values are OBC(II) > gb_obc_alpha = 1 > gb_obc_beta = 0.8 > gb_obc_gamma = 4.85 > gb_dielectric_offset = 0.009 > sa_algorithm = Ace-approximation > ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA > ; The value -1 will set default value for Still/HCT/OBC GB-models. > sa_surface_tension = -1 > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > ; Temperature coupling > tcoupl = v-rescale > nsttcouple = -1 > nh-chain-length = 10 > ; Groups to couple separately > tc-grps = Protein > ; Time constant (ps) and reference temperature (K) > tau-t = 0.1 > ref-t = 300 > ; Pressure coupling > Pcoupl = Parrinello-Rahman > Pcoupltype = isotropic > nstpcouple = -1 > ; Time constant (ps), compressibility (1/bar) and reference P (bar) > tau-p = 1 > compressibility = 4.5e-5 > ref-p = 1.0 > ; Scaling of reference coordinates, No, All or COM > refcoord_scaling = No > ; Random seed for Andersen thermostat > andersen_seed = 815131 > > ; OPTIONS FOR QMMM calculations > QMMM = no > ; Groups treated Quantum Mechanically > QMMM-grps = > ; QM method > QMmethod = > ; QMMM scheme > QMMMscheme = normal > ; QM basisset > QMbasis = > ; QM charge > QMcharge = > ; QM multiplicity > QMmult = > ; Surface Hopping > SH = > ; CAS space options > CASorbitals = > CASelectrons = > SAon = > SAoff = > SAsteps = > ; Scale factor for MM charges > MMChargeScaleFactor = 1 > ; Optimization of QM subsystem > bOPT = > bTS = > > ; SIMULATED ANNEALING > ; Type of annealing for each temperature group (no/single/periodic) > annealing = > ; Number of time points to use for specifying annealing in each group > annealing_npoints = > ; List of times at the annealing points for each group > annealing_time = > ; Temp. at each annealing point, for each group. > annealing_temp = > > ; GENERATE VELOCITIES FOR STARTUP RUN > gen-vel = no > gen-temp = 300 > gen-seed = 173529 > > ; OPTIONS FOR BONDS > constraints = all-bonds > ; Type of constraint algorithm > constraint-algorithm = Lincs > ; Do not constrain the start configuration > continuation = no > ; Use successive overrelaxation to reduce the number of shake iterations > Shake-SOR = no > ; Relative tolerance of shake > shake-tol = 0.0001 > ; Highest order in the expansion of the constraint coupling matrix > lincs-order = 4 > ; Number of iterations in the final step of LINCS. 1 is fine for > ; normal simulations, but use 2 to conserve energy in NVE runs. > ; For energy minimization with constraints it should be 4 to 8. > lincs-iter = 1 > ; Lincs will write a warning to the stderr if in one step a bond > ; rotates over more degrees than > lincs-warnangle = 30 > ; Convert harmonic bonds to morse potentials > morse = no > > ; ENERGY GROUP EXCLUSIONS > ; Pairs of energy groups for which all non-bonded interactions are excluded > energygrp_excl = > > ; WALLS > ; Number of walls, type, atom types, densities and box-z scale factor for > Ewald > nwall = 0 > wall_type = 9-3 > wall_r_linpot = -1 > wall_atomtype = > wall_density = > wall_ewald_zfac = 3 > > ; COM PULLING > ; Pull type: no, umbrella, constraint or constant_force > pull = no > > ; NMR refinement stuff > ; Distance restraints type: No, Simple or Ensemble > disre = No > ; Force weighting of pairs in one distance restraint: Conservative or Equal > disre-weighting = Conservative > ; Use sqrt of the time averaged times the instantaneous violation > disre-mixed = no > disre-fc = 1000 > disre-tau = 0 > ; Output frequency for pair distances to energy file > nstdisreout = 100 > ; Orientation restraints: No or Yes > orire = no > ; Orientation restraints force constant and tau for time averaging > orire-fc = 0 > orire-tau = 0 > orire-fitgrp = > ; Output frequency for trace(SD) and S to energy file > nstorireout = 100 > ; Dihedral angle restraints: No or Yes > dihre = no > dihre-fc = 1000 > > ; Free energy control stuff > free-energy = no > init-lambda = 0 > delta-lambda = 0 > foreign_lambda = > sc-alpha = 0 > sc-power = 0 > sc-sigma = 0.3 > nstdhdl = 10 > separate-dhdl-file = yes > dhdl-derivatives = yes > dh_hist_size = 0 > dh_hist_spacing = 0.1 > couple-moltype = > couple-lambda0 = vdw-q > couple-lambda1 = vdw-q > couple-intramol = no > > ; Non-equilibrium MD stuff > acc-grps = > accelerate = > freezegrps = > freezedim = > cos-acceleration = 0 > deform = > > ; Electric fields > ; Format is number of terms (int) and for all terms an amplitude (real) > ; and a phase angle (real) > E-x = > E-xt = > E-y = > E-yt = > E-z = > E-zt = > > ; User defined thingies > user1-grps = > user2-grps = > userint1 = 0 > userint2 = 0 > userint3 = 0 > userint4 = 0 > userreal1 = 0 > userreal2 = 0 > userreal3 = 0 > userreal4 = 0 > > > Regards, > > Ozlem > > On Wed, May 4, 2011 at 3:44 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 4/05/2011 11:23 PM, Justin A. Lemkul wrote: > > > Ozlem Ulucan wrote: > > Dear Gromacs Users, > > I have been trying to simulate a protein in implicit solvent. When I used a > single processor by setting -nt to 1 , I did not encounter any problem. But > when I tried to run the simulations using more than 1 processor I get the > following error. > > Fatal error: > Constraint dependencies further away than next-neighbor > in particle decomposition. Constraint between atoms 2177--2179 evaluated > on node 3 and 3, but atom 2177 has connections within 4 bonds (lincs_order) > of node 1, and atom 2179 has connections within 4 bonds of node 3. > Reduce the # nodes, lincs_order, or > try domain decomposition. > > I set the lincs_order parameter in .mdp file to different values. But it > did not help. I have some questions regarding the information above. > > See comments about lincs_order in 7.3.18. Obviously, only smaller values of > lincs_order can help (but if this is not obvious, please consider how obvious > "it did not help" is :-)) > > > 1) Is it possible to run implicit solvent simulations in parallel? > > > Yes. > > 2) As far as I know gromacs uses domain decomposition as default. Why does > in my simulations gromacs use the particle decomposition which I do not ask > for. > > > Without seeing the exact commands you gave, there is no plausible > explanation. DD is used by default. > > Not quite true, unfortunately. With the cutoffs set to zero, the use of the > all-against-all GB loops is triggered, and that silently requires PD. It > should write something to the log file. > > > > -Justin > > Any suggestions are appreciated very much. > I am ussing gromacs-4.5.4 with charmm force field and the OBC implicit > solvent model. If you need further informations, probably a run input file, > let me know. > > A run input file would have helped me avoid guessing above about those > cutoffs :-) > > The real issue is that not all systems can be effectively parallelized by a > given implementation. How many processors and atoms are we talking about? If > there's not hundreds of atoms per processor, then parallelism is not going to > be worthwhile. > > Mark > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? 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