Ok. So do i try with PD, particle decomposition? Il 27/Giu/2016 16:41, "Justin Lemkul" <[email protected]> ha scritto:
> > > On 6/27/16 10:35 AM, Luca Banetta wrote: > >> 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? >> >> > As I mentioned before, the shell model does not support DD and will fail > in that version. There is an explicit fatal error in newer versions. > > You can parallelize via OpenMP (mdrun -nt N -ntmpi 1) but not DD. > > -Justin > > 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 >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > [email protected] | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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 [email protected]. > -- 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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