[alexxy/gromacs.git] / src / gromacs / domdec / domdec_setup.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 2008,2009,2010,2011,2012 by the GROMACS development team.
 * Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
 * Copyright (c) 2019,2020, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
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/*! \internal \file
 *
 * \brief This file defines functions used by the domdec module
 * in its initial setup phase.
 *
 * \author Berk Hess <hess@kth.se>
 * \ingroup module_domdec
 */

#include "gmxpre.h"

#include "domdec_setup.h"

#include <cassert>
#include <cinttypes>
#include <cmath>
#include <cstdio>

#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/domdec/options.h"
#include "gromacs/ewald/pme.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/perf_est.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/stringutil.h"

#include "box.h"
#include "domdec_internal.h"
#include "utility.h"

// TODO remove this when moving domdec into gmx namespace
using gmx::DomdecOptions;

/*! \brief Margin for setting up the DD grid */
#define DD_GRID_MARGIN_PRES_SCALE 1.05

/*! \brief Factorize \p n.
 *
 * \param[in]    n     Value to factorize
 * \param[out]   fac   Vector of factors (to be allocated in this function)
 * \param[out]   mfac  Vector with the number of times each factor repeats in the factorization (to be allocated in this function)
 */
static void factorize(int n, std::vector<int>* fac, std::vector<int>* mfac)
{
    if (n <= 0)
    {
        gmx_fatal(FARGS, "Can only factorize positive integers.");
    }

    /* Decompose n in factors */
    fac->clear();
    mfac->clear();
    int d = 2;
    while (n > 1)
    {
        while (n % d == 0)
        {
            if (fac->empty() || fac->back() != d)
            {
                fac->push_back(d);
                mfac->push_back(1);
            }
            else
            {
                mfac->back()++;
            }
            n /= d;
        }
        d++;
    }
}

/*! \brief Find largest divisor of \p n smaller than \p n*/
static int largest_divisor(int n)
{
    std::vector<int> div;
    std::vector<int> mdiv;
    factorize(n, &div, &mdiv);

    return div.back();
}

/*! \brief Compute largest common divisor of \p n1 and \b n2 */
static int lcd(int n1, int n2)
{
    int d, i;

    d = 1;
    for (i = 2; (i <= n1 && i <= n2); i++)
    {
        if (n1 % i == 0 && n2 % i == 0)
        {
            d = i;
        }
    }

    return d;
}

/*! \brief Returns TRUE when there are enough PME ranks for the ratio */
static gmx_bool fits_pme_ratio(int nrank_tot, int nrank_pme, float ratio)
{
    return (static_cast<double>(nrank_pme) / static_cast<double>(nrank_tot) > 0.95 * ratio);
}

/*! \brief Returns TRUE when npme out of ntot ranks doing PME is expected to give reasonable performance */
static gmx_bool fits_pp_pme_perf(int ntot, int npme, float ratio)
{
    std::vector<int> div;
    std::vector<int> mdiv;
    factorize(ntot - npme, &div, &mdiv);

    int npp_root3  = gmx::roundToInt(std::cbrt(ntot - npme));
    int npme_root2 = gmx::roundToInt(std::sqrt(static_cast<double>(npme)));

    /* The check below gives a reasonable division:
     * factor 5 allowed at 5 or more PP ranks,
     * factor 7 allowed at 49 or more PP ranks.
     */
    if (div.back() > 3 + npp_root3)
    {
        return FALSE;
    }

    /* Check if the number of PP and PME ranks have a reasonable sized
     * denominator in common, such that we can use 2D PME decomposition
     * when required (which requires nx_pp == nx_pme).
     * The factor of 2 allows for a maximum ratio of 2^2=4
     * between nx_pme and ny_pme.
     */
    if (lcd(ntot - npme, npme) * 2 < npme_root2)
    {
        return FALSE;
    }

    /* Does this division gives a reasonable PME load? */
    return fits_pme_ratio(ntot, npme, ratio);
}

/*! \brief Make a guess for the number of PME ranks to use. */
static int guess_npme(const gmx::MDLogger& mdlog,
                      const gmx_mtop_t&    mtop,
                      const t_inputrec&    ir,
                      const matrix         box,
                      int                  nrank_tot)
{
    float ratio;
    int   npme;

    ratio = pme_load_estimate(mtop, ir, box);

    GMX_LOG(mdlog.info).appendTextFormatted("Guess for relative PME load: %.2f", ratio);

    /* We assume the optimal rank ratio is close to the load ratio.
     * The communication load is neglected,
     * but (hopefully) this will balance out between PP and PME.
     */

    if (!fits_pme_ratio(nrank_tot, nrank_tot / 2, ratio))
    {
        /* We would need more than nrank_tot/2 PME only nodes,
         * which is not possible. Since the PME load is very high,
         * we will not loose much performance when all ranks do PME.
         */

        return 0;
    }

    /* First try to find npme as a factor of nrank_tot up to nrank_tot/3.
     * We start with a minimum PME node fraction of 1/16
     * and avoid ratios which lead to large prime factors in nnodes-npme.
     */
    npme = (nrank_tot + 15) / 16;
    while (npme <= nrank_tot / 3)
    {
        if (nrank_tot % npme == 0)
        {
            /* Note that fits_perf might change the PME grid,
             * in the current implementation it does not.
             */
            if (fits_pp_pme_perf(nrank_tot, npme, ratio))
            {
                break;
            }
        }
        npme++;
    }
    if (npme > nrank_tot / 3)
    {
        /* Try any possible number for npme */
        npme = 1;
        while (npme <= nrank_tot / 2)
        {
            /* Note that fits_perf may change the PME grid */
            if (fits_pp_pme_perf(nrank_tot, npme, ratio))
            {
                break;
            }
            npme++;
        }
    }
    if (npme > nrank_tot / 2)
    {
        gmx_fatal(FARGS,
                  "Could not find an appropriate number of separate PME ranks. i.e. >= %5f*#ranks "
                  "(%d) and <= #ranks/2 (%d) and reasonable performance wise (grid_x=%d, "
                  "grid_y=%d).\n"
                  "Use the -npme option of mdrun or change the number of ranks or the PME grid "
                  "dimensions, see the manual for details.",
                  ratio, gmx::roundToInt(0.95 * ratio * nrank_tot), nrank_tot / 2, ir.nkx, ir.nky);
    }
    else
    {
        GMX_LOG(mdlog.info)
                .appendTextFormatted(
                        "Will use %d particle-particle and %d PME only ranks\n"
                        "This is a guess, check the performance at the end of the log file",
                        nrank_tot - npme, npme);
    }

    return npme;
}

/*! \brief Return \p n divided by \p f rounded up to the next integer. */
static int div_up(int n, int f)
{
    return (n + f - 1) / f;
}

real comm_box_frac(const gmx::IVec& dd_nc, real cutoff, const gmx_ddbox_t& ddbox)
{
    int  i, j, k;
    rvec nw;
    real comm_vol;

    for (i = 0; i < DIM; i++)
    {
        real bt = ddbox.box_size[i] * ddbox.skew_fac[i];
        nw[i]   = dd_nc[i] * cutoff / bt;
    }

    comm_vol = 0;
    for (i = 0; i < DIM; i++)
    {
        if (dd_nc[i] > 1)
        {
            comm_vol += nw[i];
            for (j = i + 1; j < DIM; j++)
            {
                if (dd_nc[j] > 1)
                {
                    comm_vol += nw[i] * nw[j] * M_PI / 4;
                    for (k = j + 1; k < DIM; k++)
                    {
                        if (dd_nc[k] > 1)
                        {
                            comm_vol += nw[i] * nw[j] * nw[k] * M_PI / 6;
                        }
                    }
                }
            }
        }
    }

    return comm_vol;
}

/*! \brief Return whether the DD inhomogeneous in the z direction */
static gmx_bool inhomogeneous_z(const t_inputrec& ir)
{
    return ((EEL_PME(ir.coulombtype) || ir.coulombtype == eelEWALD) && ir.ePBC == epbcXYZ
            && ir.ewald_geometry == eewg3DC);
}

/*! \brief Estimate cost of PME FFT communication
 *
 * This only takes the communication into account and not imbalance
 * in the calculation. But the imbalance in communication and calculation
 * are similar and therefore these formulas also prefer load balance
 * in the FFT and pme_solve calculation.
 */
static float comm_pme_cost_vol(int npme, int a, int b, int c)
{
    /* We use a float here, since an integer might overflow */
    float comm_vol;

    comm_vol = npme - 1;
    comm_vol *= npme;
    comm_vol *= div_up(a, npme);
    comm_vol *= div_up(b, npme);
    comm_vol *= c;

    return comm_vol;
}

/*! \brief Estimate cost of communication for a possible domain decomposition. */
static float comm_cost_est(real               limit,
                           real               cutoff,
                           const matrix       box,
                           const gmx_ddbox_t& ddbox,
                           int                natoms,
                           const t_inputrec&  ir,
                           float              pbcdxr,
                           int                npme_tot,
                           const gmx::IVec&   nc)
{
    gmx::IVec npme = { 1, 1, 1 };
    int       i, j, nk, overlap;
    rvec      bt;
    float     comm_vol, comm_vol_xf, comm_pme, cost_pbcdx;
    /* This is the cost of a pbc_dx call relative to the cost
     * of communicating the coordinate and force of an atom.
     * This will be machine dependent.
     * These factors are for x86 with SMP or Infiniband.
     */
    float pbcdx_rect_fac = 0.1;
    float pbcdx_tric_fac = 0.2;
    float temp;

    /* Check the DD algorithm restrictions */
    if ((ir.ePBC == epbcXY && ir.nwall < 2 && nc[ZZ] > 1)
        || (ir.ePBC == epbcSCREW && (nc[XX] == 1 || nc[YY] > 1 || nc[ZZ] > 1)))
    {
        return -1;
    }

    if (inhomogeneous_z(ir) && nc[ZZ] > 1)
    {
        return -1;
    }

    assert(ddbox.npbcdim <= DIM);

    /* Check if the triclinic requirements are met */
    for (i = 0; i < DIM; i++)
    {
        for (j = i + 1; j < ddbox.npbcdim; j++)
        {
            if (box[j][i] != 0 || ir.deform[j][i] != 0 || (ir.epc != epcNO && ir.compress[j][i] != 0))
            {
                if (nc[j] > 1 && nc[i] == 1)
                {
                    return -1;
                }
            }
        }
    }

    for (i = 0; i < DIM; i++)
    {
        bt[i] = ddbox.box_size[i] * ddbox.skew_fac[i];

        /* Without PBC and with 2 cells, there are no lower limits on the cell size */
        if (!(i >= ddbox.npbcdim && nc[i] <= 2) && bt[i] < nc[i] * limit)
        {
            return -1;
        }
        /* With PBC, check if the cut-off fits in nc[i]-1 cells */
        if (i < ddbox.npbcdim && nc[i] > 1 && (nc[i] - 1) * bt[i] < nc[i] * cutoff)
        {
            return -1;
        }
    }

    if (npme_tot > 1)
    {
        /* The following choices should match those
         * in init_domain_decomposition in domdec.c.
         */
        if (nc[XX] == 1 && nc[YY] > 1)
        {
            npme[XX] = 1;
            npme[YY] = npme_tot;
        }
        else if (nc[YY] == 1)
        {
            npme[XX] = npme_tot;
            npme[YY] = 1;
        }
        else
        {
            /* Will we use 1D or 2D PME decomposition? */
            npme[XX] = (npme_tot % nc[XX] == 0) ? nc[XX] : npme_tot;
            npme[YY] = npme_tot / npme[XX];
        }
    }

    if (EEL_PME(ir.coulombtype) || EVDW_PME(ir.vdwtype))
    {
        /* Check the PME grid restrictions.
         * Currently these can only be invalid here with too few grid lines
         * along the x dimension per rank doing PME.
         */
        int npme_x = (npme_tot > 1 ? npme[XX] : nc[XX]);

        /* Currently we don't have the OpenMP thread count available here.
         * But with threads we have only tighter restrictions and it's
         * probably better anyhow to avoid settings where we need to reduce
         * grid lines over multiple ranks, as the thread check will do.
         */
        bool useThreads     = true;
        bool errorsAreFatal = false;
        if (!gmx_pme_check_restrictions(ir.pme_order, ir.nkx, ir.nky, ir.nkz, npme_x, useThreads,
                                        errorsAreFatal))
        {
            return -1;
        }
    }

    /* When two dimensions are (nearly) equal, use more cells
     * for the smallest index, so the decomposition does not
     * depend sensitively on the rounding of the box elements.
     */
    for (i = 0; i < DIM; i++)
    {
        for (j = i + 1; j < DIM; j++)
        {
            /* Check if the box size is nearly identical,
             * in that case we prefer nx > ny  and ny > nz.
             */
            if (std::fabs(bt[j] - bt[i]) < 0.01 * bt[i] && nc[j] > nc[i])
            {
                /* The XX/YY check is a bit compact. If nc[YY]==npme[YY]
                 * this means the swapped nc has nc[XX]==npme[XX],
                 * and we can also swap X and Y for PME.
                 */
                /* Check if dimension i and j are equivalent for PME.
                 * For x/y: if nc[YY]!=npme[YY], we can not swap x/y
                 * For y/z: we can not have PME decomposition in z
                 */
                if (npme_tot <= 1
                    || !((i == XX && j == YY && nc[YY] != npme[YY]) || (i == YY && j == ZZ && npme[YY] > 1)))
                {
                    return -1;
                }
            }
        }
    }

    /* This function determines only half of the communication cost.
     * All PP, PME and PP-PME communication is symmetric
     * and the "back"-communication cost is identical to the forward cost.
     */

    comm_vol = comm_box_frac(nc, cutoff, ddbox);

    comm_pme = 0;
    for (i = 0; i < 2; i++)
    {
        /* Determine the largest volume for PME x/f redistribution */
        if (nc[i] % npme[i] != 0)
        {
            if (nc[i] > npme[i])
            {
                comm_vol_xf = (npme[i] == 2 ? 1.0 / 3.0 : 0.5);
            }
            else
            {
                comm_vol_xf = 1.0 - lcd(nc[i], npme[i]) / static_cast<double>(npme[i]);
            }
            comm_pme += 3 * natoms * comm_vol_xf;
        }

        /* Grid overlap communication */
        if (npme[i] > 1)
        {
            nk      = (i == 0 ? ir.nkx : ir.nky);
            overlap = (nk % npme[i] == 0 ? ir.pme_order - 1 : ir.pme_order);
            temp    = npme[i];
            temp *= overlap;
            temp *= ir.nkx;
            temp *= ir.nky;
            temp *= ir.nkz;
            temp /= nk;
            comm_pme += temp;
            /* Old line comm_pme += npme[i]*overlap*ir.nkx*ir.nky*ir.nkz/nk; */
        }
    }

    comm_pme += comm_pme_cost_vol(npme[YY], ir.nky, ir.nkz, ir.nkx);
    comm_pme += comm_pme_cost_vol(npme[XX], ir.nkx, ir.nky, ir.nkz);

    /* Add cost of pbc_dx for bondeds */
    cost_pbcdx = 0;
    if ((nc[XX] == 1 || nc[YY] == 1) || (nc[ZZ] == 1 && ir.ePBC != epbcXY))
    {
        if ((ddbox.tric_dir[XX] && nc[XX] == 1) || (ddbox.tric_dir[YY] && nc[YY] == 1))
        {
            cost_pbcdx = pbcdxr * pbcdx_tric_fac;
        }
        else
        {
            cost_pbcdx = pbcdxr * pbcdx_rect_fac;
        }
    }

    if (debug)
    {
        fprintf(debug, "nc %2d %2d %2d %2d %2d vol pp %6.4f pbcdx %6.4f pme %9.3e tot %9.3e\n",
                nc[XX], nc[YY], nc[ZZ], npme[XX], npme[YY], comm_vol, cost_pbcdx,
                comm_pme / (3 * natoms), comm_vol + cost_pbcdx + comm_pme / (3 * natoms));
    }

    return 3 * natoms * (comm_vol + cost_pbcdx) + comm_pme;
}

/*! \brief Assign penalty factors to possible domain decompositions,
 * based on the estimated communication costs. */
static void assign_factors(const real         limit,
                           const bool         request1D,
                           const real         cutoff,
                           const matrix       box,
                           const gmx_ddbox_t& ddbox,
                           int                natoms,
                           const t_inputrec&  ir,
                           float              pbcdxr,
                           int                npme,
                           int                ndiv,
                           const int*         div,
                           const int*         mdiv,
                           gmx::IVec*         irTryPtr,
                           gmx::IVec*         opt)
{
    int        x, y, i;
    float      ce;
    gmx::IVec& ir_try = *irTryPtr;

    if (ndiv == 0)
    {
        const int  maxDimensionSize        = std::max(ir_try[XX], std::max(ir_try[YY], ir_try[ZZ]));
        const int  productOfDimensionSizes = ir_try[XX] * ir_try[YY] * ir_try[ZZ];
        const bool decompositionHasOneDimension = (maxDimensionSize == productOfDimensionSizes);
        if (request1D && !decompositionHasOneDimension)
        {
            /* We requested 1D DD, but got multiple dimensions */
            return;
        }

        ce = comm_cost_est(limit, cutoff, box, ddbox, natoms, ir, pbcdxr, npme, ir_try);
        if (ce >= 0
            && ((*opt)[XX] == 0
                || ce < comm_cost_est(limit, cutoff, box, ddbox, natoms, ir, pbcdxr, npme, *opt)))
        {
            *opt = ir_try;
        }

        return;
    }

    for (x = mdiv[0]; x >= 0; x--)
    {
        for (i = 0; i < x; i++)
        {
            ir_try[XX] *= div[0];
        }
        for (y = mdiv[0] - x; y >= 0; y--)
        {
            for (i = 0; i < y; i++)
            {
                ir_try[YY] *= div[0];
            }
            for (i = 0; i < mdiv[0] - x - y; i++)
            {
                ir_try[ZZ] *= div[0];
            }

            /* recurse */
            assign_factors(limit, request1D, cutoff, box, ddbox, natoms, ir, pbcdxr, npme, ndiv - 1,
                           div + 1, mdiv + 1, irTryPtr, opt);

            for (i = 0; i < mdiv[0] - x - y; i++)
            {
                ir_try[ZZ] /= div[0];
            }
            for (i = 0; i < y; i++)
            {
                ir_try[YY] /= div[0];
            }
        }
        for (i = 0; i < x; i++)
        {
            ir_try[XX] /= div[0];
        }
    }
}

/*! \brief Determine the optimal distribution of DD cells for the
 * simulation system and number of MPI ranks
 *
 * \returns The optimal grid cell choice. The latter will contain all
 *          zeros if no valid cell choice exists. */
static gmx::IVec optimizeDDCells(const gmx::MDLogger& mdlog,
                                 const int            numRanksRequested,
                                 const int            numPmeOnlyRanks,
                                 const real           cellSizeLimit,
                                 const bool           request1DAnd1Pulse,
                                 const gmx_mtop_t&    mtop,
                                 const matrix         box,
                                 const gmx_ddbox_t&   ddbox,
                                 const t_inputrec&    ir,
                                 const DDSystemInfo&  systemInfo)
{
    double pbcdxr;

    const int numPPRanks = numRanksRequested - numPmeOnlyRanks;

    GMX_LOG(mdlog.info)
            .appendTextFormatted(
                    "Optimizing the DD grid for %d cells with a minimum initial size of %.3f nm",
                    numPPRanks, cellSizeLimit);
    if (inhomogeneous_z(ir))
    {
        GMX_LOG(mdlog.info)
                .appendTextFormatted(
                        "Ewald_geometry=%s: assuming inhomogeneous particle distribution in z, "
                        "will not decompose in z.",
                        eewg_names[ir.ewald_geometry]);
    }


    // For cost estimates, we need the number of ranks doing PME work,
    // which is the number of PP ranks when not using separate
    // PME-only ranks.
    const int numRanksDoingPmeWork =
            (EEL_PME(ir.coulombtype) ? ((numPmeOnlyRanks > 0) ? numPmeOnlyRanks : numPPRanks) : 0);

    if (systemInfo.haveInterDomainBondeds)
    {
        /* If we can skip PBC for distance calculations in plain-C bondeds,
         * we can save some time (e.g. 3D DD with pbc=xyz).
         * Here we ignore SIMD bondeds as they always do (fast) PBC.
         */
        count_bonded_distances(mtop, ir, &pbcdxr, nullptr);
        pbcdxr /= static_cast<double>(mtop.natoms);
    }
    else
    {
        /* Every molecule is a single charge group: no pbc required */
        pbcdxr = 0;
    }

    if (cellSizeLimit > 0)
    {
        std::string maximumCells = "The maximum allowed number of cells is:";
        for (int d = 0; d < DIM; d++)
        {
            int nmax = static_cast<int>(ddbox.box_size[d] * ddbox.skew_fac[d] / cellSizeLimit);
            if (d >= ddbox.npbcdim && nmax < 2)
            {
                nmax = 2;
            }
            if (d == ZZ && inhomogeneous_z(ir))
            {
                nmax = 1;
            }
            maximumCells += gmx::formatString(" %c %d", 'X' + d, nmax);
        }
        GMX_LOG(mdlog.info).appendText(maximumCells);
    }

    if (debug)
    {
        fprintf(debug, "Average nr of pbc_dx calls per atom %.2f\n", pbcdxr);
    }

    /* Decompose numPPRanks in factors */
    std::vector<int> div;
    std::vector<int> mdiv;
    factorize(numPPRanks, &div, &mdiv);

    gmx::IVec itry       = { 1, 1, 1 };
    gmx::IVec numDomains = { 0, 0, 0 };
    assign_factors(cellSizeLimit, request1DAnd1Pulse, systemInfo.cutoff, box, ddbox, mtop.natoms, ir,
                   pbcdxr, numRanksDoingPmeWork, div.size(), div.data(), mdiv.data(), &itry, &numDomains);

    return numDomains;
}

real getDDGridSetupCellSizeLimit(const gmx::MDLogger& mdlog,
                                 const bool           request1DAnd1Pulse,
                                 const bool           bDynLoadBal,
                                 const real           dlb_scale,
                                 const t_inputrec&    ir,
                                 const real           systemInfoCellSizeLimit)
{
    real cellSizeLimit = systemInfoCellSizeLimit;
    if (request1DAnd1Pulse)
    {
        cellSizeLimit = std::max(cellSizeLimit, ir.rlist);
    }

    /* Add a margin for DLB and/or pressure scaling */
    if (bDynLoadBal)
    {
        if (dlb_scale >= 1.0)
        {
            gmx_fatal(FARGS, "The value for option -dds should be smaller than 1");
        }
        GMX_LOG(mdlog.info)
                .appendTextFormatted(
                        "Scaling the initial minimum size with 1/%g (option -dds) = %g", dlb_scale,
                        1 / dlb_scale);
        cellSizeLimit /= dlb_scale;
    }
    else if (ir.epc != epcNO)
    {
        GMX_LOG(mdlog.info)
                .appendTextFormatted(
                        "To account for pressure scaling, scaling the initial minimum size with %g",
                        DD_GRID_MARGIN_PRES_SCALE);
        cellSizeLimit *= DD_GRID_MARGIN_PRES_SCALE;
    }

    return cellSizeLimit;
}
void checkForValidRankCountRequests(const int numRanksRequested, const bool usingPme, const int numPmeRanksRequested)
{
    int numPPRanksRequested = numRanksRequested;
    if (usingPme && numPmeRanksRequested > 0)
    {
        numPPRanksRequested -= numPmeRanksRequested;
        if (numPmeRanksRequested > numPPRanksRequested)
        {
            gmx_fatal(FARGS,
                      "Cannot have %d separate PME ranks with only %d PP ranks, choose fewer or no "
                      "separate PME ranks",
                      numPmeRanksRequested, numPPRanksRequested);
        }
    }

    // Once the rank count is large enough, it becomes worth
    // suggesting improvements to the user.
    const int minPPRankCountToCheckForLargePrimeFactors = 13;
    if (numPPRanksRequested >= minPPRankCountToCheckForLargePrimeFactors)
    {
        const int largestDivisor = largest_divisor(numPPRanksRequested);
        /* Check if the largest divisor is more than numPPRanks ^ (2/3) */
        if (largestDivisor * largestDivisor * largestDivisor > numPPRanksRequested * numPPRanksRequested)
        {
            gmx_fatal(FARGS,
                      "The number of ranks selected for particle-particle work (%d) "
                      "contains a large prime factor %d. In most cases this will lead to "
                      "bad performance. Choose a number with smaller prime factors or "
                      "set the decomposition (option -dd) manually.",
                      numPPRanksRequested, largestDivisor);
        }
    }
}

/*! \brief Return the number of PME-only ranks used by the simulation
 *
 * If the user did not choose a number, then decide for them. */
static int getNumPmeOnlyRanksToUse(const gmx::MDLogger& mdlog,
                                   const DomdecOptions& options,
                                   const gmx_mtop_t&    mtop,
                                   const t_inputrec&    ir,
                                   const matrix         box,
                                   const int            numRanksRequested)
{
    int         numPmeOnlyRanks;
    const char* extraMessage = "";

    if (options.numCells[XX] > 0)
    {
        if (options.numPmeRanks >= 0)
        {
            // TODO mdrun should give a fatal error with a non-PME input file and -npme > 0
            numPmeOnlyRanks = options.numPmeRanks;
        }
        else
        {
            // When the DD grid is set explicitly and -npme is set to auto,
            // don't use PME ranks. We check later if the DD grid is
            // compatible with the total number of ranks.
            numPmeOnlyRanks = 0;
        }
    }
    else
    {
        if (!EEL_PME(ir.coulombtype))
        {
            // TODO mdrun should give a fatal error with a non-PME input file and -npme > 0
            numPmeOnlyRanks = 0;
        }
        else
        {
            if (options.numPmeRanks >= 0)
            {
                numPmeOnlyRanks = options.numPmeRanks;
            }
            else
            {
                // Controls the automated choice of when to use separate PME-only ranks.
                const int minRankCountToDefaultToSeparatePmeRanks = 19;

                if (numRanksRequested < minRankCountToDefaultToSeparatePmeRanks)
                {
                    numPmeOnlyRanks = 0;
                    extraMessage =
                            ", as there are too few total\n"
                            " ranks for efficient splitting";
                }
                else
                {
                    numPmeOnlyRanks = guess_npme(mdlog, mtop, ir, box, numRanksRequested);
                    extraMessage    = ", as guessed by mdrun";
                }
            }
        }
    }
    GMX_RELEASE_ASSERT(numPmeOnlyRanks <= numRanksRequested,
                       "Cannot have more PME ranks than total ranks");
    if (EEL_PME(ir.coulombtype))
    {
        GMX_LOG(mdlog.info).appendTextFormatted("Using %d separate PME ranks%s", numPmeOnlyRanks, extraMessage);
    }

    return numPmeOnlyRanks;
}

/*! \brief Sets the order of the DD dimensions, returns the number of DD dimensions */
static int set_dd_dim(const gmx::IVec& numDDCells, const DDSettings& ddSettings, ivec* dims)
{
    int ndim = 0;
    if (ddSettings.useDDOrderZYX)
    {
        /* Decomposition order z,y,x */
        for (int dim = DIM - 1; dim >= 0; dim--)
        {
            if (numDDCells[dim] > 1)
            {
                (*dims)[ndim++] = dim;
            }
        }
    }
    else
    {
        /* Decomposition order x,y,z */
        for (int dim = 0; dim < DIM; dim++)
        {
            if (numDDCells[dim] > 1)
            {
                (*dims)[ndim++] = dim;
            }
        }
    }

    if (ndim == 0)
    {
        /* Set dim[0] to avoid extra checks on ndim in several places */
        (*dims)[0] = XX;
    }

    return ndim;
}

DDGridSetup getDDGridSetup(const gmx::MDLogger&           mdlog,
                           const t_commrec*               cr,
                           const int                      numRanksRequested,
                           const DomdecOptions&           options,
                           const DDSettings&              ddSettings,
                           const DDSystemInfo&            systemInfo,
                           const real                     cellSizeLimit,
                           const gmx_mtop_t&              mtop,
                           const t_inputrec&              ir,
                           const matrix                   box,
                           gmx::ArrayRef<const gmx::RVec> xGlobal,
                           gmx_ddbox_t*                   ddbox)
{
    int numPmeOnlyRanks = getNumPmeOnlyRanksToUse(mdlog, options, mtop, ir, box, numRanksRequested);

    if (ddSettings.request1DAnd1Pulse && (numRanksRequested - numPmeOnlyRanks == 1))
    {
        // With only one PP rank, there will not be a need for
        // GPU-based halo exchange that wants to request that any DD
        // has only 1 dimension and 1 pulse.
        return DDGridSetup{};
    }

    gmx::IVec numDomains;
    if (options.numCells[XX] > 0)
    {
        numDomains                      = gmx::IVec(options.numCells);
        const ivec numDomainsLegacyIvec = { numDomains[XX], numDomains[YY], numDomains[ZZ] };
        set_ddbox_cr(*cr, &numDomainsLegacyIvec, ir, box, xGlobal, ddbox);
    }
    else
    {
        set_ddbox_cr(*cr, nullptr, ir, box, xGlobal, ddbox);

        if (MASTER(cr))
        {
            numDomains = optimizeDDCells(mdlog, numRanksRequested, numPmeOnlyRanks, cellSizeLimit,
                                         ddSettings.request1DAnd1Pulse, mtop, box, *ddbox, ir, systemInfo);
        }
    }

    /* Communicate the information set by the master to all ranks */
    gmx_bcast(sizeof(numDomains), numDomains, cr);
    if (EEL_PME(ir.coulombtype))
    {
        gmx_bcast(sizeof(numPmeOnlyRanks), &numPmeOnlyRanks, cr);
    }

    DDGridSetup ddGridSetup;
    ddGridSetup.numPmeOnlyRanks = numPmeOnlyRanks;
    ddGridSetup.numDomains[XX]  = numDomains[XX];
    ddGridSetup.numDomains[YY]  = numDomains[YY];
    ddGridSetup.numDomains[ZZ]  = numDomains[ZZ];
    ddGridSetup.numDDDimensions = set_dd_dim(numDomains, ddSettings, &ddGridSetup.ddDimensions);

    return ddGridSetup;
}