Example #1
0
/* Read in the tpr file and save information we need later in info */
static void read_tpr_file(const char *fn_sim_tpr, t_inputinfo *info, t_state *state, gmx_mtop_t *mtop, t_inputrec *ir, real user_beta, real fracself)
{
    read_tpx_state(fn_sim_tpr, ir, state, NULL, mtop);

    /* The values of the original tpr input file are save in the first
     * place [0] of the arrays */
    info->orig_sim_steps = ir->nsteps;
    info->pme_order[0]   = ir->pme_order;
    info->rcoulomb[0]    = ir->rcoulomb;
    info->rvdw[0]        = ir->rvdw;
    info->nkx[0]         = ir->nkx;
    info->nky[0]         = ir->nky;
    info->nkz[0]         = ir->nkz;
    info->ewald_rtol[0]  = ir->ewald_rtol;
    info->fracself       = fracself;
    if (user_beta > 0)
    {
        info->ewald_beta[0] = user_beta;
    }
    else
    {
        info->ewald_beta[0]  = calc_ewaldcoeff_q(info->rcoulomb[0], info->ewald_rtol[0]);
    }

    /* Check if PME was chosen */
    if (EEL_PME(ir->coulombtype) == FALSE)
    {
        gmx_fatal(FARGS, "Can only do optimizations for simulations with PME");
    }

    /* Check if rcoulomb == rlist, which is necessary for PME */
    if (!(ir->rcoulomb == ir->rlist))
    {
        gmx_fatal(FARGS, "PME requires rcoulomb (%f) to be equal to rlist (%f).", ir->rcoulomb, ir->rlist);
    }
}
Example #2
0
void calc_verlet_buffer_size(const gmx_mtop_t *mtop, real boxvol,
                             const t_inputrec *ir,
                             real reference_temperature,
                             const verletbuf_list_setup_t *list_setup,
                             int *n_nonlin_vsite,
                             real *rlist)
{
    double                resolution;
    char                 *env;

    real                  particle_distance;
    real                  nb_clust_frac_pairs_not_in_list_at_cutoff;

    verletbuf_atomtype_t *att  = NULL;
    int                   natt = -1, i;
    double                reppow;
    real                  md1_ljd, d2_ljd, md3_ljd;
    real                  md1_ljr, d2_ljr, md3_ljr;
    real                  md1_el,  d2_el;
    real                  elfac;
    real                  kT_fac, mass_min;
    int                   ib0, ib1, ib;
    real                  rb, rl;
    real                  drift;

    if (reference_temperature < 0)
    {
        if (EI_MD(ir->eI) && ir->etc == etcNO)
        {
            /* This case should be handled outside calc_verlet_buffer_size */
            gmx_incons("calc_verlet_buffer_size called with an NVE ensemble and reference_temperature < 0");
        }

        /* We use the maximum temperature with multiple T-coupl groups.
         * We could use a per particle temperature, but since particles
         * interact, this might underestimate the buffer size.
         */
        reference_temperature = 0;
        for (i = 0; i < ir->opts.ngtc; i++)
        {
            if (ir->opts.tau_t[i] >= 0)
            {
                reference_temperature = max(reference_temperature,
                                            ir->opts.ref_t[i]);
            }
        }
    }

    /* Resolution of the buffer size */
    resolution = 0.001;

    env = getenv("GMX_VERLET_BUFFER_RES");
    if (env != NULL)
    {
        sscanf(env, "%lf", &resolution);
    }

    /* In an atom wise pair-list there would be no pairs in the list
     * beyond the pair-list cut-off.
     * However, we use a pair-list of groups vs groups of atoms.
     * For groups of 4 atoms, the parallelism of SSE instructions, only
     * 10% of the atoms pairs are not in the list just beyond the cut-off.
     * As this percentage increases slowly compared to the decrease of the
     * Gaussian displacement distribution over this range, we can simply
     * reduce the drift by this fraction.
     * For larger groups, e.g. of 8 atoms, this fraction will be lower,
     * so then buffer size will be on the conservative (large) side.
     *
     * Note that the formulas used here do not take into account
     * cancellation of errors which could occur by missing both
     * attractive and repulsive interactions.
     *
     * The only major assumption is homogeneous particle distribution.
     * For an inhomogeneous system, such as a liquid-vapor system,
     * the buffer will be underestimated. The actual energy drift
     * will be higher by the factor: local/homogeneous particle density.
     *
     * The results of this estimate have been checked againt simulations.
     * In most cases the real drift differs by less than a factor 2.
     */

    /* Worst case assumption: HCP packing of particles gives largest distance */
    particle_distance = pow(boxvol*sqrt(2)/mtop->natoms, 1.0/3.0);

    get_verlet_buffer_atomtypes(mtop, &att, &natt, n_nonlin_vsite);
    assert(att != NULL && natt >= 0);

    if (debug)
    {
        fprintf(debug, "particle distance assuming HCP packing: %f nm\n",
                particle_distance);
        fprintf(debug, "energy drift atom types: %d\n", natt);
    }

    reppow   = mtop->ffparams.reppow;
    md1_ljd  = 0;
    d2_ljd   = 0;
    md3_ljd  = 0;
    md1_ljr  = 0;
    d2_ljr   = 0;
    md3_ljr  = 0;
    if (ir->vdwtype == evdwCUT)
    {
        real sw_range, md3_pswf;

        switch (ir->vdw_modifier)
        {
            case eintmodNONE:
            case eintmodPOTSHIFT:
                /* -dV/dr of -r^-6 and r^-reppow */
                md1_ljd =     -6*pow(ir->rvdw, -7.0);
                md1_ljr = reppow*pow(ir->rvdw, -(reppow+1));
                /* The contribution of the higher derivatives is negligible */
                break;
            case eintmodFORCESWITCH:
                /* At the cut-off: V=V'=V''=0, so we use only V''' */
                md3_ljd  = -md3_force_switch(6.0,    ir->rvdw_switch, ir->rvdw);
                md3_ljr  =  md3_force_switch(reppow, ir->rvdw_switch, ir->rvdw);
                break;
            case eintmodPOTSWITCH:
                /* At the cut-off: V=V'=V''=0.
                 * V''' is given by the original potential times
                 * the third derivative of the switch function.
                 */
                sw_range  = ir->rvdw - ir->rvdw_switch;
                md3_pswf  = 60.0*pow(sw_range, -3.0);

                md3_ljd   = -pow(ir->rvdw, -6.0   )*md3_pswf;
                md3_ljr   =  pow(ir->rvdw, -reppow)*md3_pswf;
                break;
            default:
                gmx_incons("Unimplemented VdW modifier");
        }
    }
    else if (EVDW_PME(ir->vdwtype))
    {
        real b, r, br, br2, br4, br6;
        b        = calc_ewaldcoeff_lj(ir->rvdw, ir->ewald_rtol_lj);
        r        = ir->rvdw;
        br       = b*r;
        br2      = br*br;
        br4      = br2*br2;
        br6      = br4*br2;
        /* -dV/dr of g(br)*r^-6 [where g(x) = exp(-x^2)(1+x^2+x^4/2), see LJ-PME equations in manual] and r^-reppow */
        md1_ljd  = -exp(-br2)*(br6 + 3.0*br4 + 6.0*br2 + 6.0)*pow(r, -7.0);
        md1_ljr  = reppow*pow(r, -(reppow+1));
        /* The contribution of the higher derivatives is negligible */
    }
    else
    {
        gmx_fatal(FARGS, "Energy drift calculation is only implemented for plain cut-off Lennard-Jones interactions");
    }

    elfac = ONE_4PI_EPS0/ir->epsilon_r;

    /* Determine md=-dV/dr and dd=d^2V/dr^2 */
    md1_el = 0;
    d2_el  = 0;
    if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
    {
        real eps_rf, k_rf;

        if (ir->coulombtype == eelCUT)
        {
            eps_rf = 1;
            k_rf   = 0;
        }
        else
        {
            eps_rf = ir->epsilon_rf/ir->epsilon_r;
            if (eps_rf != 0)
            {
                k_rf = pow(ir->rcoulomb, -3.0)*(eps_rf - ir->epsilon_r)/(2*eps_rf + ir->epsilon_r);
            }
            else
            {
                /* epsilon_rf = infinity */
                k_rf = 0.5*pow(ir->rcoulomb, -3.0);
            }
        }

        if (eps_rf > 0)
        {
            md1_el = elfac*(pow(ir->rcoulomb, -2.0) - 2*k_rf*ir->rcoulomb);
        }
        d2_el      = elfac*(2*pow(ir->rcoulomb, -3.0) + 2*k_rf);
    }
    else if (EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD)
    {
        real b, rc, br;

        b      = calc_ewaldcoeff_q(ir->rcoulomb, ir->ewald_rtol);
        rc     = ir->rcoulomb;
        br     = b*rc;
        md1_el = elfac*(b*exp(-br*br)*M_2_SQRTPI/rc + gmx_erfc(br)/(rc*rc));
        d2_el  = elfac/(rc*rc)*(2*b*(1 + br*br)*exp(-br*br)*M_2_SQRTPI + 2*gmx_erfc(br)/rc);
    }
    else
    {
        gmx_fatal(FARGS, "Energy drift calculation is only implemented for Reaction-Field and Ewald electrostatics");
    }

    /* Determine the variance of the atomic displacement
     * over nstlist-1 steps: kT_fac
     * For inertial dynamics (not Brownian dynamics) the mass factor
     * is not included in kT_fac, it is added later.
     */
    if (ir->eI == eiBD)
    {
        /* Get the displacement distribution from the random component only.
         * With accurate integration the systematic (force) displacement
         * should be negligible (unless nstlist is extremely large, which
         * you wouldn't do anyhow).
         */
        kT_fac = 2*BOLTZ*reference_temperature*(ir->nstlist-1)*ir->delta_t;
        if (ir->bd_fric > 0)
        {
            /* This is directly sigma^2 of the displacement */
            kT_fac /= ir->bd_fric;

            /* Set the masses to 1 as kT_fac is the full sigma^2,
             * but we divide by m in ener_drift().
             */
            for (i = 0; i < natt; i++)
            {
                att[i].prop.mass = 1;
            }
        }
        else
        {
            real tau_t;

            /* Per group tau_t is not implemented yet, use the maximum */
            tau_t = ir->opts.tau_t[0];
            for (i = 1; i < ir->opts.ngtc; i++)
            {
                tau_t = max(tau_t, ir->opts.tau_t[i]);
            }

            kT_fac *= tau_t;
            /* This kT_fac needs to be divided by the mass to get sigma^2 */
        }
    }
    else
    {
        kT_fac = BOLTZ*reference_temperature*sqr((ir->nstlist-1)*ir->delta_t);
    }

    mass_min = att[0].prop.mass;
    for (i = 1; i < natt; i++)
    {
        mass_min = min(mass_min, att[i].prop.mass);
    }

    if (debug)
    {
        fprintf(debug, "md1_ljd %9.2e d2_ljd %9.2e md3_ljd %9.2e\n", md1_ljd, d2_ljd, md3_ljd);
        fprintf(debug, "md1_ljr %9.2e d2_ljr %9.2e md3_ljr %9.2e\n", md1_ljr, d2_ljr, md3_ljr);
        fprintf(debug, "md1_el  %9.2e d2_el  %9.2e\n", md1_el, d2_el);
        fprintf(debug, "sqrt(kT_fac) %f\n", sqrt(kT_fac));
        fprintf(debug, "mass_min %f\n", mass_min);
    }

    /* Search using bisection */
    ib0 = -1;
    /* The drift will be neglible at 5 times the max sigma */
    ib1 = (int)(5*2*sqrt(kT_fac/mass_min)/resolution) + 1;
    while (ib1 - ib0 > 1)
    {
        ib = (ib0 + ib1)/2;
        rb = ib*resolution;
        rl = max(ir->rvdw, ir->rcoulomb) + rb;

        /* Calculate the average energy drift at the last step
         * of the nstlist steps at which the pair-list is used.
         */
        drift = ener_drift(att, natt, &mtop->ffparams,
                           kT_fac,
                           md1_ljd, d2_ljd, md3_ljd,
                           md1_ljr, d2_ljr, md3_ljr,
                           md1_el,  d2_el,
                           rb,
                           rl, boxvol);

        /* Correct for the fact that we are using a Ni x Nj particle pair list
         * and not a 1 x 1 particle pair list. This reduces the drift.
         */
        /* We don't have a formula for 8 (yet), use 4 which is conservative */
        nb_clust_frac_pairs_not_in_list_at_cutoff =
            surface_frac(min(list_setup->cluster_size_i, 4),
                         particle_distance, rl)*
            surface_frac(min(list_setup->cluster_size_j, 4),
                         particle_distance, rl);
        drift *= nb_clust_frac_pairs_not_in_list_at_cutoff;

        /* Convert the drift to drift per unit time per atom */
        drift /= ir->nstlist*ir->delta_t*mtop->natoms;

        if (debug)
        {
            fprintf(debug, "ib %3d %3d %3d rb %.3f %dx%d fac %.3f drift %.1e\n",
                    ib0, ib, ib1, rb,
                    list_setup->cluster_size_i, list_setup->cluster_size_j,
                    nb_clust_frac_pairs_not_in_list_at_cutoff,
                    drift);
        }

        if (fabs(drift) > ir->verletbuf_tol)
        {
            ib0 = ib;
        }
        else
        {
            ib1 = ib;
        }
    }

    sfree(att);

    *rlist = max(ir->rvdw, ir->rcoulomb) + ib1*resolution;
}
Example #3
0
int mdrunner(gmx_hw_opt_t *hw_opt,
             FILE *fplog, t_commrec *cr, int nfile,
             const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
             gmx_bool bCompact, int nstglobalcomm,
             ivec ddxyz, int dd_node_order, real rdd, real rconstr,
             const char *dddlb_opt, real dlb_scale,
             const char *ddcsx, const char *ddcsy, const char *ddcsz,
             const char *nbpu_opt, int nstlist_cmdline,
             gmx_int64_t nsteps_cmdline, int nstepout, int resetstep,
             int gmx_unused nmultisim, int repl_ex_nst, int repl_ex_nex,
             int repl_ex_seed, real pforce, real cpt_period, real max_hours,
             int imdport, unsigned long Flags)
{
    gmx_bool                  bForceUseGPU, bTryUseGPU, bRerunMD;
    t_inputrec               *inputrec;
    t_state                  *state = NULL;
    matrix                    box;
    gmx_ddbox_t               ddbox = {0};
    int                       npme_major, npme_minor;
    t_nrnb                   *nrnb;
    gmx_mtop_t               *mtop          = NULL;
    t_mdatoms                *mdatoms       = NULL;
    t_forcerec               *fr            = NULL;
    t_fcdata                 *fcd           = NULL;
    real                      ewaldcoeff_q  = 0;
    real                      ewaldcoeff_lj = 0;
    struct gmx_pme_t        **pmedata       = NULL;
    gmx_vsite_t              *vsite         = NULL;
    gmx_constr_t              constr;
    int                       nChargePerturbed = -1, nTypePerturbed = 0, status;
    gmx_wallcycle_t           wcycle;
    gmx_bool                  bReadEkin;
    gmx_walltime_accounting_t walltime_accounting = NULL;
    int                       rc;
    gmx_int64_t               reset_counters;
    gmx_edsam_t               ed           = NULL;
    int                       nthreads_pme = 1;
    int                       nthreads_pp  = 1;
    gmx_membed_t              membed       = NULL;
    gmx_hw_info_t            *hwinfo       = NULL;
    /* The master rank decides early on bUseGPU and broadcasts this later */
    gmx_bool                  bUseGPU      = FALSE;

    /* CAUTION: threads may be started later on in this function, so
       cr doesn't reflect the final parallel state right now */
    snew(inputrec, 1);
    snew(mtop, 1);

    if (Flags & MD_APPENDFILES)
    {
        fplog = NULL;
    }

    bRerunMD     = (Flags & MD_RERUN);
    bForceUseGPU = (strncmp(nbpu_opt, "gpu", 3) == 0);
    bTryUseGPU   = (strncmp(nbpu_opt, "auto", 4) == 0) || bForceUseGPU;

    /* Detect hardware, gather information. This is an operation that is
     * global for this process (MPI rank). */
    hwinfo = gmx_detect_hardware(fplog, cr, bTryUseGPU);

    gmx_print_detected_hardware(fplog, cr, hwinfo);

    if (fplog != NULL)
    {
        /* Print references after all software/hardware printing */
        please_cite(fplog, "Abraham2015");
        please_cite(fplog, "Pall2015");
        please_cite(fplog, "Pronk2013");
        please_cite(fplog, "Hess2008b");
        please_cite(fplog, "Spoel2005a");
        please_cite(fplog, "Lindahl2001a");
        please_cite(fplog, "Berendsen95a");
    }

    snew(state, 1);
    if (SIMMASTER(cr))
    {
        /* Read (nearly) all data required for the simulation */
        read_tpx_state(ftp2fn(efTPR, nfile, fnm), inputrec, state, NULL, mtop);

        if (inputrec->cutoff_scheme == ecutsVERLET)
        {
            /* Here the master rank decides if all ranks will use GPUs */
            bUseGPU = (hwinfo->gpu_info.n_dev_compatible > 0 ||
                       getenv("GMX_EMULATE_GPU") != NULL);

            /* TODO add GPU kernels for this and replace this check by:
             * (bUseGPU && (ir->vdwtype == evdwPME &&
             *               ir->ljpme_combination_rule == eljpmeLB))
             * update the message text and the content of nbnxn_acceleration_supported.
             */
            if (bUseGPU &&
                !nbnxn_gpu_acceleration_supported(fplog, cr, inputrec, bRerunMD))
            {
                /* Fallback message printed by nbnxn_acceleration_supported */
                if (bForceUseGPU)
                {
                    gmx_fatal(FARGS, "GPU acceleration requested, but not supported with the given input settings");
                }
                bUseGPU = FALSE;
            }

            prepare_verlet_scheme(fplog, cr,
                                  inputrec, nstlist_cmdline, mtop, state->box,
                                  bUseGPU);
        }
        else
        {
            if (nstlist_cmdline > 0)
            {
                gmx_fatal(FARGS, "Can not set nstlist with the group cut-off scheme");
            }

            if (hwinfo->gpu_info.n_dev_compatible > 0)
            {
                md_print_warn(cr, fplog,
                              "NOTE: GPU(s) found, but the current simulation can not use GPUs\n"
                              "      To use a GPU, set the mdp option: cutoff-scheme = Verlet\n");
            }

            if (bForceUseGPU)
            {
                gmx_fatal(FARGS, "GPU requested, but can't be used without cutoff-scheme=Verlet");
            }

#ifdef GMX_TARGET_BGQ
            md_print_warn(cr, fplog,
                          "NOTE: There is no SIMD implementation of the group scheme kernels on\n"
                          "      BlueGene/Q. You will observe better performance from using the\n"
                          "      Verlet cut-off scheme.\n");
#endif
        }

        if (inputrec->eI == eiSD2)
        {
            md_print_warn(cr, fplog, "The stochastic dynamics integrator %s is deprecated, since\n"
                          "it is slower than integrator %s and is slightly less accurate\n"
                          "with constraints. Use the %s integrator.",
                          ei_names[inputrec->eI], ei_names[eiSD1], ei_names[eiSD1]);
        }
    }

    /* Check and update the hardware options for internal consistency */
    check_and_update_hw_opt_1(hw_opt, cr);

    /* Early check for externally set process affinity. */
    gmx_check_thread_affinity_set(fplog, cr,
                                  hw_opt, hwinfo->nthreads_hw_avail, FALSE);

#ifdef GMX_THREAD_MPI
    if (SIMMASTER(cr))
    {
        if (cr->npmenodes > 0 && hw_opt->nthreads_tmpi <= 0)
        {
            gmx_fatal(FARGS, "You need to explicitly specify the number of MPI threads (-ntmpi) when using separate PME ranks");
        }

        /* Since the master knows the cut-off scheme, update hw_opt for this.
         * This is done later for normal MPI and also once more with tMPI
         * for all tMPI ranks.
         */
        check_and_update_hw_opt_2(hw_opt, inputrec->cutoff_scheme);

        /* NOW the threads will be started: */
        hw_opt->nthreads_tmpi = get_nthreads_mpi(hwinfo,
                                                 hw_opt,
                                                 inputrec, mtop,
                                                 cr, fplog, bUseGPU);

        if (hw_opt->nthreads_tmpi > 1)
        {
            t_commrec *cr_old       = cr;
            /* now start the threads. */
            cr = mdrunner_start_threads(hw_opt, fplog, cr_old, nfile, fnm,
                                        oenv, bVerbose, bCompact, nstglobalcomm,
                                        ddxyz, dd_node_order, rdd, rconstr,
                                        dddlb_opt, dlb_scale, ddcsx, ddcsy, ddcsz,
                                        nbpu_opt, nstlist_cmdline,
                                        nsteps_cmdline, nstepout, resetstep, nmultisim,
                                        repl_ex_nst, repl_ex_nex, repl_ex_seed, pforce,
                                        cpt_period, max_hours,
                                        Flags);
            /* the main thread continues here with a new cr. We don't deallocate
               the old cr because other threads may still be reading it. */
            if (cr == NULL)
            {
                gmx_comm("Failed to spawn threads");
            }
        }
    }
#endif
    /* END OF CAUTION: cr is now reliable */

    /* g_membed initialisation *
     * Because we change the mtop, init_membed is called before the init_parallel *
     * (in case we ever want to make it run in parallel) */
    if (opt2bSet("-membed", nfile, fnm))
    {
        if (MASTER(cr))
        {
            fprintf(stderr, "Initializing membed");
        }
        membed = init_membed(fplog, nfile, fnm, mtop, inputrec, state, cr, &cpt_period);
    }

    if (PAR(cr))
    {
        /* now broadcast everything to the non-master nodes/threads: */
        init_parallel(cr, inputrec, mtop);

        /* The master rank decided on the use of GPUs,
         * broadcast this information to all ranks.
         */
        gmx_bcast_sim(sizeof(bUseGPU), &bUseGPU, cr);
    }

    if (fplog != NULL)
    {
        pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
        fprintf(fplog, "\n");
    }

    /* now make sure the state is initialized and propagated */
    set_state_entries(state, inputrec);

    /* A parallel command line option consistency check that we can
       only do after any threads have started. */
    if (!PAR(cr) &&
        (ddxyz[XX] > 1 || ddxyz[YY] > 1 || ddxyz[ZZ] > 1 || cr->npmenodes > 0))
    {
        gmx_fatal(FARGS,
                  "The -dd or -npme option request a parallel simulation, "
#ifndef GMX_MPI
                  "but %s was compiled without threads or MPI enabled"
#else
#ifdef GMX_THREAD_MPI
                  "but the number of threads (option -nt) is 1"
#else
                  "but %s was not started through mpirun/mpiexec or only one rank was requested through mpirun/mpiexec"
#endif
#endif
                  , output_env_get_program_display_name(oenv)
                  );
    }

    if (bRerunMD &&
        (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
    {
        gmx_fatal(FARGS, "The .mdp file specified an energy mininization or normal mode algorithm, and these are not compatible with mdrun -rerun");
    }

    if (can_use_allvsall(inputrec, TRUE, cr, fplog) && DOMAINDECOMP(cr))
    {
        gmx_fatal(FARGS, "All-vs-all loops do not work with domain decomposition, use a single MPI rank");
    }

    if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
    {
        if (cr->npmenodes > 0)
        {
            gmx_fatal_collective(FARGS, cr, NULL,
                                 "PME-only ranks are requested, but the system does not use PME for electrostatics or LJ");
        }

        cr->npmenodes = 0;
    }

    if (bUseGPU && cr->npmenodes < 0)
    {
        /* With GPUs we don't automatically use PME-only ranks. PME ranks can
         * improve performance with many threads per GPU, since our OpenMP
         * scaling is bad, but it's difficult to automate the setup.
         */
        cr->npmenodes = 0;
    }

#ifdef GMX_FAHCORE
    if (MASTER(cr))
    {
        fcRegisterSteps(inputrec->nsteps, inputrec->init_step);
    }
#endif

    /* NMR restraints must be initialized before load_checkpoint,
     * since with time averaging the history is added to t_state.
     * For proper consistency check we therefore need to extend
     * t_state here.
     * So the PME-only nodes (if present) will also initialize
     * the distance restraints.
     */
    snew(fcd, 1);

    /* This needs to be called before read_checkpoint to extend the state */
    init_disres(fplog, mtop, inputrec, cr, fcd, state, repl_ex_nst > 0);

    init_orires(fplog, mtop, state->x, inputrec, cr, &(fcd->orires),
                state);

    if (DEFORM(*inputrec))
    {
        /* Store the deform reference box before reading the checkpoint */
        if (SIMMASTER(cr))
        {
            copy_mat(state->box, box);
        }
        if (PAR(cr))
        {
            gmx_bcast(sizeof(box), box, cr);
        }
        /* Because we do not have the update struct available yet
         * in which the reference values should be stored,
         * we store them temporarily in static variables.
         * This should be thread safe, since they are only written once
         * and with identical values.
         */
        tMPI_Thread_mutex_lock(&deform_init_box_mutex);
        deform_init_init_step_tpx = inputrec->init_step;
        copy_mat(box, deform_init_box_tpx);
        tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
    }

    if (opt2bSet("-cpi", nfile, fnm))
    {
        /* Check if checkpoint file exists before doing continuation.
         * This way we can use identical input options for the first and subsequent runs...
         */
        if (gmx_fexist_master(opt2fn_master("-cpi", nfile, fnm, cr), cr) )
        {
            load_checkpoint(opt2fn_master("-cpi", nfile, fnm, cr), &fplog,
                            cr, ddxyz,
                            inputrec, state, &bReadEkin,
                            (Flags & MD_APPENDFILES),
                            (Flags & MD_APPENDFILESSET));

            if (bReadEkin)
            {
                Flags |= MD_READ_EKIN;
            }
        }
    }

    if (MASTER(cr) && (Flags & MD_APPENDFILES))
    {
        gmx_log_open(ftp2fn(efLOG, nfile, fnm), cr,
                     Flags, &fplog);
    }

    /* override nsteps with value from cmdline */
    override_nsteps_cmdline(fplog, nsteps_cmdline, inputrec, cr);

    if (SIMMASTER(cr))
    {
        copy_mat(state->box, box);
    }

    if (PAR(cr))
    {
        gmx_bcast(sizeof(box), box, cr);
    }

    /* Essential dynamics */
    if (opt2bSet("-ei", nfile, fnm))
    {
        /* Open input and output files, allocate space for ED data structure */
        ed = ed_open(mtop->natoms, &state->edsamstate, nfile, fnm, Flags, oenv, cr);
    }

    if (PAR(cr) && !(EI_TPI(inputrec->eI) ||
                     inputrec->eI == eiNM))
    {
        cr->dd = init_domain_decomposition(fplog, cr, Flags, ddxyz, rdd, rconstr,
                                           dddlb_opt, dlb_scale,
                                           ddcsx, ddcsy, ddcsz,
                                           mtop, inputrec,
                                           box, state->x,
                                           &ddbox, &npme_major, &npme_minor);

        make_dd_communicators(fplog, cr, dd_node_order);

        /* Set overallocation to avoid frequent reallocation of arrays */
        set_over_alloc_dd(TRUE);
    }
    else
    {
        /* PME, if used, is done on all nodes with 1D decomposition */
        cr->npmenodes = 0;
        cr->duty      = (DUTY_PP | DUTY_PME);
        npme_major    = 1;
        npme_minor    = 1;

        if (inputrec->ePBC == epbcSCREW)
        {
            gmx_fatal(FARGS,
                      "pbc=%s is only implemented with domain decomposition",
                      epbc_names[inputrec->ePBC]);
        }
    }

    if (PAR(cr))
    {
        /* After possible communicator splitting in make_dd_communicators.
         * we can set up the intra/inter node communication.
         */
        gmx_setup_nodecomm(fplog, cr);
    }

    /* Initialize per-physical-node MPI process/thread ID and counters. */
    gmx_init_intranode_counters(cr);
#ifdef GMX_MPI
    if (MULTISIM(cr))
    {
        md_print_info(cr, fplog,
                      "This is simulation %d out of %d running as a composite GROMACS\n"
                      "multi-simulation job. Setup for this simulation:\n\n",
                      cr->ms->sim, cr->ms->nsim);
    }
    md_print_info(cr, fplog, "Using %d MPI %s\n",
                  cr->nnodes,
#ifdef GMX_THREAD_MPI
                  cr->nnodes == 1 ? "thread" : "threads"
#else
                  cr->nnodes == 1 ? "process" : "processes"
#endif
                  );
    fflush(stderr);
#endif

    /* Check and update hw_opt for the cut-off scheme */
    check_and_update_hw_opt_2(hw_opt, inputrec->cutoff_scheme);

    /* Check and update hw_opt for the number of MPI ranks */
    check_and_update_hw_opt_3(hw_opt);

    gmx_omp_nthreads_init(fplog, cr,
                          hwinfo->nthreads_hw_avail,
                          hw_opt->nthreads_omp,
                          hw_opt->nthreads_omp_pme,
                          (cr->duty & DUTY_PP) == 0,
                          inputrec->cutoff_scheme == ecutsVERLET);

#ifndef NDEBUG
    if (integrator[inputrec->eI].func != do_tpi &&
        inputrec->cutoff_scheme == ecutsVERLET)
    {
        gmx_feenableexcept();
    }
#endif

    if (bUseGPU)
    {
        /* Select GPU id's to use */
        gmx_select_gpu_ids(fplog, cr, &hwinfo->gpu_info, bForceUseGPU,
                           &hw_opt->gpu_opt);
    }
    else
    {
        /* Ignore (potentially) manually selected GPUs */
        hw_opt->gpu_opt.n_dev_use = 0;
    }

    /* check consistency across ranks of things like SIMD
     * support and number of GPUs selected */
    gmx_check_hw_runconf_consistency(fplog, hwinfo, cr, hw_opt, bUseGPU);

    /* Now that we know the setup is consistent, check for efficiency */
    check_resource_division_efficiency(hwinfo, hw_opt, Flags & MD_NTOMPSET,
                                       cr, fplog);

    if (DOMAINDECOMP(cr))
    {
        /* When we share GPUs over ranks, we need to know this for the DLB */
        dd_setup_dlb_resource_sharing(cr, hwinfo, hw_opt);
    }

    /* getting number of PP/PME threads
       PME: env variable should be read only on one node to make sure it is
       identical everywhere;
     */
    /* TODO nthreads_pp is only used for pinning threads.
     * This is a temporary solution until we have a hw topology library.
     */
    nthreads_pp  = gmx_omp_nthreads_get(emntNonbonded);
    nthreads_pme = gmx_omp_nthreads_get(emntPME);

    wcycle = wallcycle_init(fplog, resetstep, cr, nthreads_pp, nthreads_pme);

    if (PAR(cr))
    {
        /* Master synchronizes its value of reset_counters with all nodes
         * including PME only nodes */
        reset_counters = wcycle_get_reset_counters(wcycle);
        gmx_bcast_sim(sizeof(reset_counters), &reset_counters, cr);
        wcycle_set_reset_counters(wcycle, reset_counters);
    }

    snew(nrnb, 1);
    if (cr->duty & DUTY_PP)
    {
        bcast_state(cr, state);

        /* Initiate forcerecord */
        fr          = mk_forcerec();
        fr->hwinfo  = hwinfo;
        fr->gpu_opt = &hw_opt->gpu_opt;
        init_forcerec(fplog, oenv, fr, fcd, inputrec, mtop, cr, box,
                      opt2fn("-table", nfile, fnm),
                      opt2fn("-tabletf", nfile, fnm),
                      opt2fn("-tablep", nfile, fnm),
                      opt2fn("-tableb", nfile, fnm),
                      nbpu_opt,
                      FALSE,
                      pforce);

        /* version for PCA_NOT_READ_NODE (see md.c) */
        /*init_forcerec(fplog,fr,fcd,inputrec,mtop,cr,box,FALSE,
           "nofile","nofile","nofile","nofile",FALSE,pforce);
         */

        /* Initialize QM-MM */
        if (fr->bQMMM)
        {
            init_QMMMrec(cr, mtop, inputrec, fr);
        }

        /* Initialize the mdatoms structure.
         * mdatoms is not filled with atom data,
         * as this can not be done now with domain decomposition.
         */
        mdatoms = init_mdatoms(fplog, mtop, inputrec->efep != efepNO);

        /* Initialize the virtual site communication */
        vsite = init_vsite(mtop, cr, FALSE);

        calc_shifts(box, fr->shift_vec);

        /* With periodic molecules the charge groups should be whole at start up
         * and the virtual sites should not be far from their proper positions.
         */
        if (!inputrec->bContinuation && MASTER(cr) &&
            !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicMols))
        {
            /* Make molecules whole at start of run */
            if (fr->ePBC != epbcNONE)
            {
                do_pbc_first_mtop(fplog, inputrec->ePBC, box, mtop, state->x);
            }
            if (vsite)
            {
                /* Correct initial vsite positions are required
                 * for the initial distribution in the domain decomposition
                 * and for the initial shell prediction.
                 */
                construct_vsites_mtop(vsite, mtop, state->x);
            }
        }

        if (EEL_PME(fr->eeltype) || EVDW_PME(fr->vdwtype))
        {
            ewaldcoeff_q  = fr->ewaldcoeff_q;
            ewaldcoeff_lj = fr->ewaldcoeff_lj;
            pmedata       = &fr->pmedata;
        }
        else
        {
            pmedata = NULL;
        }
    }
    else
    {
        /* This is a PME only node */

        /* We don't need the state */
        done_state(state);

        ewaldcoeff_q  = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
        ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
        snew(pmedata, 1);
    }

    if (hw_opt->thread_affinity != threadaffOFF)
    {
        /* Before setting affinity, check whether the affinity has changed
         * - which indicates that probably the OpenMP library has changed it
         * since we first checked).
         */
        gmx_check_thread_affinity_set(fplog, cr,
                                      hw_opt, hwinfo->nthreads_hw_avail, TRUE);

        /* Set the CPU affinity */
        gmx_set_thread_affinity(fplog, cr, hw_opt, hwinfo);
    }

    /* Initiate PME if necessary,
     * either on all nodes or on dedicated PME nodes only. */
    if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
    {
        if (mdatoms)
        {
            nChargePerturbed = mdatoms->nChargePerturbed;
            if (EVDW_PME(inputrec->vdwtype))
            {
                nTypePerturbed   = mdatoms->nTypePerturbed;
            }
        }
        if (cr->npmenodes > 0)
        {
            /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
            gmx_bcast_sim(sizeof(nChargePerturbed), &nChargePerturbed, cr);
            gmx_bcast_sim(sizeof(nTypePerturbed), &nTypePerturbed, cr);
        }

        if (cr->duty & DUTY_PME)
        {
            status = gmx_pme_init(pmedata, cr, npme_major, npme_minor, inputrec,
                                  mtop ? mtop->natoms : 0, nChargePerturbed, nTypePerturbed,
                                  (Flags & MD_REPRODUCIBLE), nthreads_pme);
            if (status != 0)
            {
                gmx_fatal(FARGS, "Error %d initializing PME", status);
            }
        }
    }


    if (integrator[inputrec->eI].func == do_md)
    {
        /* Turn on signal handling on all nodes */
        /*
         * (A user signal from the PME nodes (if any)
         * is communicated to the PP nodes.
         */
        signal_handler_install();
    }

    if (cr->duty & DUTY_PP)
    {
        /* Assumes uniform use of the number of OpenMP threads */
        walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));

        if (inputrec->bPull)
        {
            /* Initialize pull code */
            inputrec->pull_work =
                init_pull(fplog, inputrec->pull, inputrec, nfile, fnm,
                          mtop, cr, oenv, inputrec->fepvals->init_lambda,
                          EI_DYNAMICS(inputrec->eI) && MASTER(cr), Flags);
        }

        if (inputrec->bRot)
        {
            /* Initialize enforced rotation code */
            init_rot(fplog, inputrec, nfile, fnm, cr, state->x, box, mtop, oenv,
                     bVerbose, Flags);
        }

        if (inputrec->eSwapCoords != eswapNO)
        {
            /* Initialize ion swapping code */
            init_swapcoords(fplog, bVerbose, inputrec, opt2fn_master("-swap", nfile, fnm, cr),
                            mtop, state->x, state->box, &state->swapstate, cr, oenv, Flags);
        }

        constr = init_constraints(fplog, mtop, inputrec, ed, state, cr);

        if (DOMAINDECOMP(cr))
        {
            GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
            dd_init_bondeds(fplog, cr->dd, mtop, vsite, inputrec,
                            Flags & MD_DDBONDCHECK, fr->cginfo_mb);

            set_dd_parameters(fplog, cr->dd, dlb_scale, inputrec, &ddbox);

            setup_dd_grid(fplog, cr->dd);
        }

        /* Now do whatever the user wants us to do (how flexible...) */
        integrator[inputrec->eI].func(fplog, cr, nfile, fnm,
                                      oenv, bVerbose, bCompact,
                                      nstglobalcomm,
                                      vsite, constr,
                                      nstepout, inputrec, mtop,
                                      fcd, state,
                                      mdatoms, nrnb, wcycle, ed, fr,
                                      repl_ex_nst, repl_ex_nex, repl_ex_seed,
                                      membed,
                                      cpt_period, max_hours,
                                      imdport,
                                      Flags,
                                      walltime_accounting);

        if (inputrec->bPull)
        {
            finish_pull(inputrec->pull_work);
        }

        if (inputrec->bRot)
        {
            finish_rot(inputrec->rot);
        }

    }
    else
    {
        GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
        /* do PME only */
        walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
        gmx_pmeonly(*pmedata, cr, nrnb, wcycle, walltime_accounting, ewaldcoeff_q, ewaldcoeff_lj, inputrec);
    }

    wallcycle_stop(wcycle, ewcRUN);

    /* Finish up, write some stuff
     * if rerunMD, don't write last frame again
     */
    finish_run(fplog, cr,
               inputrec, nrnb, wcycle, walltime_accounting,
               fr ? fr->nbv : NULL,
               EI_DYNAMICS(inputrec->eI) && !MULTISIM(cr));


    /* Free GPU memory and context */
    free_gpu_resources(fr, cr, &hwinfo->gpu_info, fr ? fr->gpu_opt : NULL);

    if (opt2bSet("-membed", nfile, fnm))
    {
        sfree(membed);
    }

    gmx_hardware_info_free(hwinfo);

    /* Does what it says */
    print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
    walltime_accounting_destroy(walltime_accounting);

    /* PLUMED */
    if(plumedswitch){
      plumed_finalize(plumedmain);
    }
    /* END PLUMED */

    /* Close logfile already here if we were appending to it */
    if (MASTER(cr) && (Flags & MD_APPENDFILES))
    {
        gmx_log_close(fplog);
    }

    rc = (int)gmx_get_stop_condition();

    done_ed(&ed);

#ifdef GMX_THREAD_MPI
    /* we need to join all threads. The sub-threads join when they
       exit this function, but the master thread needs to be told to
       wait for that. */
    if (PAR(cr) && MASTER(cr))
    {
        tMPI_Finalize();
    }
#endif

    return rc;
}