Dear gromacs users, I currently work on a project about a polarizable model of acetone molecule. Unfortunately the simulations work using only 1 MPI thread. When we attempt to parallelize it this error appears: [compute-0-4:21947] *** Process received signal *** [compute-0-4:21947] Signal: Segmentation fault (11) [compute-0-4:21947] Signal code: Address not mapped (1) [compute-0-4:21947] Failing at address: (nil) [compute-0-4:21947] [ 0] /lib64/libpthread.so.0() [0x342720f500] [compute-0-4:21947] [ 1] /share/apps/gromacs-4.6.5/bin/../lib/libgmx_mpi.so.8(put_charge_groups_in_box+0x107) [0x2ab92aaefe87] [compute-0-4:21947] [ 2] /share/apps/gromacs-4.6.5/bin/../lib/libmd_mpi.so.8(relax_shell_flexcon+0x358f) [0x2ab92a593c9f] [compute-0-4:21947] [ 3] mdrun_mpi(do_md+0x3003) [0x42cfc3] [compute-0-4:21947] [ 4] mdrun_mpi(mdrunner+0x1442) [0x410ac2] [compute-0-4:21947] [ 5] mdrun_mpi(cmain+0x183e) [0x435dae] [compute-0-4:21947] [ 6] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3426a1ecdd] [compute-0-4:21947] [ 7] mdrun_mpi() [0x407139] [compute-0-4:21947] *** End of error message ***
Someone have ever met something like this before? How this problem can be fixed? The mdp file used is : ; ; File 'mdout.mdp' was generated ; By user: spoel (291) ; On host: chagall ; At date: Mon Dec 15 13:52:23 2003 ; ; VARIOUS PREPROCESSING OPTIONS title = Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.0001 nsteps = 1000000 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed ;ref-t = 100 bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol = 100 emstep = 0.01 ; Max number of iterations in relax_shells niter = 5 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 5 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr = 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = nstvout = nstfout = ; Checkpointing helps you continue after crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 50 nstenergy = 50 ; Output frequency and precision for xtc file nstxtcout = 1 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 20 cutoff-scheme = Verlet ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; 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 = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; 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 = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = v-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 0.1 ref_t = 300 ; Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Random seed for Andersen thermostat andersen_seed = 815131 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing = no ; 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 = yes gen_temp = 300 gen_seed = 1993 ; OPTIONS FOR BONDS constraints = h-bonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration unconstrained-start = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 1e-04 ; 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 = ; 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) to energy file nstorireout = 100 ; Dihedral angle restraints: No, Simple or Ensemble dihre = No dihre-fc = 1000 dihre-tau = 0 ; Output frequency for dihedral values to energy file nstdihreout = 100 ; Free energy control stuff free-energy = no init-lambda = 0 delta-lambda = 0 sc-alpha = 0 sc-sigma = 0.3 ; Non-equilibrium MD stuff acc-grps = accelerate = freezegrps = freezedim = cos-acceleration = 0 ; 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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