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? Read http://www.gromacs.org/Support/Mailing_Lists >
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