Do not force separate PME rank to recompute reciprocal box every step

[gromacs.git] / src / gromacs / ewald / pme-only.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013,2014,2015,2016,2017, 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
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/* IMPORTANT FOR DEVELOPERS:
 *
 * Triclinic pme stuff isn't entirely trivial, and we've experienced
 * some bugs during development (many of them due to me). To avoid
 * this in the future, please check the following things if you make
 * changes in this file:
 *
 * 1. You should obtain identical (at least to the PME precision)
 *    energies, forces, and virial for
 *    a rectangular box and a triclinic one where the z (or y) axis is
 *    tilted a whole box side. For instance you could use these boxes:
 *
 *    rectangular       triclinic
 *     2  0  0           2  0  0
 *     0  2  0           0  2  0
 *     0  0  6           2  2  6
 *
 * 2. You should check the energy conservation in a triclinic box.
 *
 * It might seem an overkill, but better safe than sorry.
 * /Erik 001109
 */

#include "gmxpre.h"

#include "config.h"

#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include <cmath>

#include <memory>
#include <numeric>
#include <vector>

#include "gromacs/compat/make_unique.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/ewald/pme.h"
#include "gromacs/fft/parallel_3dfft.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/gpu_utils/hostallocator.h"
#include "gromacs/math/gmxcomplex.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/timing/cyclecounter.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/gmxomp.h"
#include "gromacs/utility/smalloc.h"

#include "pme-internal.h"
#include "pme-pp-communication.h"

//! Contains information about the PP ranks that partner this PME rank.
struct PpRanks
{
    //! The MPI rank ID of this partner PP rank.
    int rankId;
    //! The number of atoms to communicate with this partner PP rank.
    int numAtoms;
};

/*! \brief Master PP-PME communication data structure */
struct gmx_pme_pp {
    MPI_Comm             mpi_comm_mysim; /**< MPI communicator for this simulation */
    std::vector<PpRanks> ppRanks;        /**< The PP partner ranks                 */
    int                  peerRankId;     /**< The peer PP rank id                  */
    //@{
    /**< Vectors of A- and B-state parameters used to transfer vectors to PME ranks  */
    gmx::HostVector<real>      chargeA;
    std::vector<real>          chargeB;
    std::vector<real>          sqrt_c6A;
    std::vector<real>          sqrt_c6B;
    std::vector<real>          sigmaA;
    std::vector<real>          sigmaB;
    //@}
    gmx::HostVector<gmx::RVec> x; /**< Vector of atom coordinates to transfer to PME ranks */
    std::vector<gmx::RVec>     f; /**< Vector of atom forces received from PME ranks */
    //@{
    /**< Vectors of MPI objects used in non-blocking communication between multiple PP ranks per PME rank */
    std::vector<MPI_Request> req;
    std::vector<MPI_Status>  stat;
    //@}
};

/*! \brief Initialize the PME-only side of the PME <-> PP communication */
static std::unique_ptr<gmx_pme_pp> gmx_pme_pp_init(t_commrec *cr)
{
    auto pme_pp = gmx::compat::make_unique<gmx_pme_pp>();

#if GMX_MPI
    int rank;

    pme_pp->mpi_comm_mysim = cr->mpi_comm_mysim;
    MPI_Comm_rank(cr->mpi_comm_mygroup, &rank);
    auto ppRanks = get_pme_ddranks(cr, rank);
    pme_pp->ppRanks.reserve(ppRanks.size());
    for (const auto &ppRankId : ppRanks)
    {
        pme_pp->ppRanks.push_back({ppRankId, 0});
    }
    // The peer PP rank is the last one.
    pme_pp->peerRankId = pme_pp->ppRanks.back().rankId;
    pme_pp->req.resize(eCommType_NR*pme_pp->ppRanks.size());
    pme_pp->stat.resize(eCommType_NR*pme_pp->ppRanks.size());
#else
    GMX_UNUSED_VALUE(cr);
#endif

    return pme_pp;
}

static void reset_pmeonly_counters(gmx_wallcycle_t wcycle,
                                   gmx_walltime_accounting_t walltime_accounting,
                                   t_nrnb *nrnb, t_inputrec *ir,
                                   gmx_int64_t step)
{
    /* Reset all the counters related to performance over the run */
    wallcycle_stop(wcycle, ewcRUN);
    wallcycle_reset_all(wcycle);
    init_nrnb(nrnb);
    if (ir->nsteps >= 0)
    {
        /* ir->nsteps is not used here, but we update it for consistency */
        ir->nsteps -= step - ir->init_step;
    }
    ir->init_step = step;
    wallcycle_start(wcycle, ewcRUN);
    walltime_accounting_start(walltime_accounting);
}

static gmx_pme_t *gmx_pmeonly_switch(std::vector<gmx_pme_t *> *pmedata,
                                     const ivec grid_size,
                                     real ewaldcoeff_q, real ewaldcoeff_lj,
                                     t_commrec *cr, const t_inputrec *ir)
{
    GMX_ASSERT(pmedata, "Bad PME tuning list pointer");
    for (auto &pme : *pmedata)
    {
        GMX_ASSERT(pme, "Bad PME tuning list element pointer");
        if (pme->nkx == grid_size[XX] &&
            pme->nky == grid_size[YY] &&
            pme->nkz == grid_size[ZZ])
        {
            /* Here we have found an existing PME data structure that suits us.
             * However, in the GPU case, we have to reinitialize it - there's only one GPU structure.
             * This should not cause actual GPU reallocations, at least (the allocated buffers are never shrunk).
             * So, just some grid size updates in the GPU kernel parameters.
             * TODO: this should be something like gmx_pme_update_split_params()
             */
            gmx_pme_reinit(&pme, cr, pme, ir, grid_size, ewaldcoeff_q, ewaldcoeff_lj);
            return pme;
        }
    }

    const auto &pme          = pmedata->back();
    gmx_pme_t  *newStructure = nullptr;
    // Copy last structure with new grid params
    gmx_pme_reinit(&newStructure, cr, pme, ir, grid_size, ewaldcoeff_q, ewaldcoeff_lj);
    pmedata->push_back(newStructure);
    return newStructure;
}

/*! \brief Called by PME-only ranks to receive coefficients and coordinates
 *
 * \param[in,out] pme_pp    PME-PP communication structure.
 * \param[out] natoms       Number of received atoms.
 * \param[out] box        System box, if received.
 * \param[out] maxshift_x        Maximum shift in X direction, if received.
 * \param[out] maxshift_y        Maximum shift in Y direction, if received.
 * \param[out] lambda_q         Free-energy lambda for electrostatics, if received.
 * \param[out] lambda_lj         Free-energy lambda for Lennard-Jones, if received.
 * \param[out] bEnerVir          Set to true if this is an energy/virial calculation step, otherwise set to false.
 * \param[out] step              MD integration step number.
 * \param[out] grid_size         PME grid size, if received.
 * \param[out] ewaldcoeff_q         Ewald cut-off parameter for electrostatics, if received.
 * \param[out] ewaldcoeff_lj         Ewald cut-off parameter for Lennard-Jones, if received.
 * \param[out] atomSetChanged    Set to true only if the local domain atom data (charges/coefficients)
 *                               has been received (after DD) and should be reinitialized. Otherwise not changed.
 *
 * \retval pmerecvqxX             All parameters were set, chargeA and chargeB can be NULL.
 * \retval pmerecvqxFINISH        No parameters were set.
 * \retval pmerecvqxSWITCHGRID    Only grid_size and *ewaldcoeff were set.
 * \retval pmerecvqxRESETCOUNTERS *step was set.
 */
static int gmx_pme_recv_coeffs_coords(gmx_pme_pp        *pme_pp,
                                      int               *natoms,
                                      matrix             box,
                                      int               *maxshift_x,
                                      int               *maxshift_y,
                                      real              *lambda_q,
                                      real              *lambda_lj,
                                      gmx_bool          *bEnerVir,
                                      gmx_int64_t       *step,
                                      ivec              *grid_size,
                                      real              *ewaldcoeff_q,
                                      real              *ewaldcoeff_lj,
                                      bool              *atomSetChanged)
{
    int status = -1;
    int nat    = 0;

#if GMX_MPI
    unsigned int flags    = 0;
    int          messages = 0;

    do
    {
        gmx_pme_comm_n_box_t cnb;
        cnb.flags = 0;

        /* Receive the send count, box and time step from the peer PP node */
        MPI_Recv(&cnb, sizeof(cnb), MPI_BYTE,
                 pme_pp->peerRankId, eCommType_CNB,
                 pme_pp->mpi_comm_mysim, MPI_STATUS_IGNORE);

        /* We accumulate all received flags */
        flags |= cnb.flags;

        *step  = cnb.step;

        if (debug)
        {
            fprintf(debug, "PME only rank receiving:%s%s%s%s%s\n",
                    (cnb.flags & PP_PME_CHARGE)        ? " charges" : "",
                    (cnb.flags & PP_PME_COORD )        ? " coordinates" : "",
                    (cnb.flags & PP_PME_FINISH)        ? " finish" : "",
                    (cnb.flags & PP_PME_SWITCHGRID)    ? " switch grid" : "",
                    (cnb.flags & PP_PME_RESETCOUNTERS) ? " reset counters" : "");
        }

        if (cnb.flags & PP_PME_FINISH)
        {
            status = pmerecvqxFINISH;
        }

        if (cnb.flags & PP_PME_SWITCHGRID)
        {
            /* Special case, receive the new parameters and return */
            copy_ivec(cnb.grid_size, *grid_size);
            *ewaldcoeff_q  = cnb.ewaldcoeff_q;
            *ewaldcoeff_lj = cnb.ewaldcoeff_lj;

            status         = pmerecvqxSWITCHGRID;
        }

        if (cnb.flags & PP_PME_RESETCOUNTERS)
        {
            /* Special case, receive the step (set above) and return */
            status = pmerecvqxRESETCOUNTERS;
        }

        if (cnb.flags & (PP_PME_CHARGE | PP_PME_SQRTC6 | PP_PME_SIGMA))
        {
            *atomSetChanged = true;

            /* Receive the send counts from the other PP nodes */
            for (auto &sender : pme_pp->ppRanks)
            {
                if (sender.rankId == pme_pp->peerRankId)
                {
                    sender.numAtoms = cnb.natoms;
                }
                else
                {
                    MPI_Irecv(&sender.numAtoms, sizeof(sender.numAtoms),
                              MPI_BYTE,
                              sender.rankId, eCommType_CNB,
                              pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]);
                }
            }
            MPI_Waitall(messages, pme_pp->req.data(), pme_pp->stat.data());
            messages = 0;

            nat = 0;
            for (const auto &sender : pme_pp->ppRanks)
            {
                nat += sender.numAtoms;
            }

            if (cnb.flags & PP_PME_CHARGE)
            {
                pme_pp->chargeA.resize(nat);
            }
            if (cnb.flags & PP_PME_CHARGEB)
            {
                pme_pp->chargeB.resize(nat);
            }
            if (cnb.flags & PP_PME_SQRTC6)
            {
                pme_pp->sqrt_c6A.resize(nat);
            }
            if (cnb.flags & PP_PME_SQRTC6B)
            {
                pme_pp->sqrt_c6B.resize(nat);
            }
            if (cnb.flags & PP_PME_SIGMA)
            {
                pme_pp->sigmaA.resize(nat);
            }
            if (cnb.flags & PP_PME_SIGMAB)
            {
                pme_pp->sigmaB.resize(nat);
            }
            pme_pp->x.resize(nat);
            pme_pp->f.resize(nat);

            /* maxshift is sent when the charges are sent */
            *maxshift_x = cnb.maxshift_x;
            *maxshift_y = cnb.maxshift_y;

            /* Receive the charges in place */
            for (int q = 0; q < eCommType_NR; q++)
            {
                real *bufferPtr;

                if (!(cnb.flags & (PP_PME_CHARGE<<q)))
                {
                    continue;
                }
                switch (q)
                {
                    case eCommType_ChargeA: bufferPtr = pme_pp->chargeA.data();  break;
                    case eCommType_ChargeB: bufferPtr = pme_pp->chargeB.data();  break;
                    case eCommType_SQRTC6A: bufferPtr = pme_pp->sqrt_c6A.data(); break;
                    case eCommType_SQRTC6B: bufferPtr = pme_pp->sqrt_c6B.data(); break;
                    case eCommType_SigmaA:  bufferPtr = pme_pp->sigmaA.data();   break;
                    case eCommType_SigmaB:  bufferPtr = pme_pp->sigmaB.data();   break;
                    default: gmx_incons("Wrong eCommType");
                }
                nat = 0;
                for (const auto &sender : pme_pp->ppRanks)
                {
                    if (sender.numAtoms > 0)
                    {
                        MPI_Irecv(bufferPtr+nat,
                                  sender.numAtoms*sizeof(real),
                                  MPI_BYTE,
                                  sender.rankId, q,
                                  pme_pp->mpi_comm_mysim,
                                  &pme_pp->req[messages++]);
                        nat += sender.numAtoms;
                        if (debug)
                        {
                            fprintf(debug, "Received from PP rank %d: %d %s\n",
                                    sender.rankId, sender.numAtoms,
                                    (q == eCommType_ChargeA ||
                                     q == eCommType_ChargeB) ? "charges" : "params");
                        }
                    }
                }
            }
        }

        if (cnb.flags & PP_PME_COORD)
        {
            /* The box, FE flag and lambda are sent along with the coordinates
             *  */
            copy_mat(cnb.box, box);
            *lambda_q       = cnb.lambda_q;
            *lambda_lj      = cnb.lambda_lj;
            *bEnerVir       = (cnb.flags & PP_PME_ENER_VIR);
            *step           = cnb.step;

            /* Receive the coordinates in place */
            nat = 0;
            for (const auto &sender : pme_pp->ppRanks)
            {
                if (sender.numAtoms > 0)
                {
                    MPI_Irecv(pme_pp->x[nat], sender.numAtoms*sizeof(rvec),
                              MPI_BYTE,
                              sender.rankId, eCommType_COORD,
                              pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]);
                    nat += sender.numAtoms;
                    if (debug)
                    {
                        fprintf(debug, "Received from PP rank %d: %d "
                                "coordinates\n",
                                sender.rankId, sender.numAtoms);
                    }
                }
            }

            status = pmerecvqxX;
        }

        /* Wait for the coordinates and/or charges to arrive */
        MPI_Waitall(messages, pme_pp->req.data(), pme_pp->stat.data());
        messages = 0;
    }
    while (status == -1);
#else
    GMX_UNUSED_VALUE(pme_pp);
    GMX_UNUSED_VALUE(box);
    GMX_UNUSED_VALUE(maxshift_x);
    GMX_UNUSED_VALUE(maxshift_y);
    GMX_UNUSED_VALUE(lambda_q);
    GMX_UNUSED_VALUE(lambda_lj);
    GMX_UNUSED_VALUE(bEnerVir);
    GMX_UNUSED_VALUE(step);
    GMX_UNUSED_VALUE(grid_size);
    GMX_UNUSED_VALUE(ewaldcoeff_q);
    GMX_UNUSED_VALUE(ewaldcoeff_lj);
    GMX_UNUSED_VALUE(atomSetChanged);

    status = pmerecvqxX;
#endif

    if (status == pmerecvqxX)
    {
        *natoms   = nat;
    }

    return status;
}

/*! \brief Send the PME mesh force, virial and energy to the PP-only ranks. */
static void gmx_pme_send_force_vir_ener(gmx_pme_pp *pme_pp,
                                        const rvec *f,
                                        matrix vir_q, real energy_q,
                                        matrix vir_lj, real energy_lj,
                                        real dvdlambda_q, real dvdlambda_lj,
                                        float cycles)
{
#if GMX_MPI
    gmx_pme_comm_vir_ene_t cve;
    int                    messages, ind_start, ind_end;
    cve.cycles = cycles;

    /* Now the evaluated forces have to be transferred to the PP nodes */
    messages = 0;
    ind_end  = 0;
    for (const auto &receiver : pme_pp->ppRanks)
    {
        ind_start = ind_end;
        ind_end   = ind_start + receiver.numAtoms;
        if (MPI_Isend(const_cast<void *>(static_cast<const void *>(f[ind_start])),
                      (ind_end-ind_start)*sizeof(rvec), MPI_BYTE,
                      receiver.rankId, 0,
                      pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]) != 0)
        {
            gmx_comm("MPI_Isend failed in do_pmeonly");
        }
    }

    /* send virial and energy to our last PP node */
    copy_mat(vir_q, cve.vir_q);
    copy_mat(vir_lj, cve.vir_lj);
    cve.energy_q     = energy_q;
    cve.energy_lj    = energy_lj;
    cve.dvdlambda_q  = dvdlambda_q;
    cve.dvdlambda_lj = dvdlambda_lj;
    /* check for the signals to send back to a PP node */
    cve.stop_cond = gmx_get_stop_condition();

    cve.cycles = cycles;

    if (debug)
    {
        fprintf(debug, "PME rank sending to PP rank %d: virial and energy\n",
                pme_pp->peerRankId);
    }
    MPI_Isend(&cve, sizeof(cve), MPI_BYTE,
              pme_pp->peerRankId, 1,
              pme_pp->mpi_comm_mysim, &pme_pp->req[messages++]);

    /* Wait for the forces to arrive */
    MPI_Waitall(messages, pme_pp->req.data(), pme_pp->stat.data());
#else
    gmx_call("MPI not enabled");
    GMX_UNUSED_VALUE(pme_pp);
    GMX_UNUSED_VALUE(f);
    GMX_UNUSED_VALUE(vir_q);
    GMX_UNUSED_VALUE(energy_q);
    GMX_UNUSED_VALUE(vir_lj);
    GMX_UNUSED_VALUE(energy_lj);
    GMX_UNUSED_VALUE(dvdlambda_q);
    GMX_UNUSED_VALUE(dvdlambda_lj);
    GMX_UNUSED_VALUE(cycles);
#endif
}

int gmx_pmeonly(struct gmx_pme_t *pme,
                t_commrec *cr,    t_nrnb *mynrnb,
                gmx_wallcycle_t wcycle,
                gmx_walltime_accounting_t walltime_accounting,
                t_inputrec *ir, PmeRunMode runMode)
{
    int                ret;
    int                natoms = 0;
    matrix             box;
    real               lambda_q   = 0;
    real               lambda_lj  = 0;
    int                maxshift_x = 0, maxshift_y = 0;
    real               energy_q, energy_lj, dvdlambda_q, dvdlambda_lj;
    matrix             vir_q, vir_lj;
    float              cycles;
    int                count;
    gmx_bool           bEnerVir = FALSE;
    gmx_int64_t        step;

    /* This data will only use with PME tuning, i.e. switching PME grids */
    std::vector<gmx_pme_t *> pmedata;
    pmedata.push_back(pme);

    auto       pme_pp       = gmx_pme_pp_init(cr);
    //TODO the variable below should be queried from the task assignment info
    const bool useGpuForPme = (runMode == PmeRunMode::GPU) || (runMode == PmeRunMode::Mixed);
    if (useGpuForPme)
    {
        changePinningPolicy(&pme_pp->chargeA, gmx::PinningPolicy::CanBePinned);
        changePinningPolicy(&pme_pp->x, gmx::PinningPolicy::CanBePinned);
    }

    init_nrnb(mynrnb);

    count = 0;
    do /****** this is a quasi-loop over time steps! */
    {
        /* The reason for having a loop here is PME grid tuning/switching */
        do
        {
            /* Domain decomposition */
            ivec newGridSize;
            bool atomSetChanged = false;
            real ewaldcoeff_q   = 0, ewaldcoeff_lj = 0;
            ret = gmx_pme_recv_coeffs_coords(pme_pp.get(),
                                             &natoms,
                                             box,
                                             &maxshift_x, &maxshift_y,
                                             &lambda_q, &lambda_lj,
                                             &bEnerVir,
                                             &step,
                                             &newGridSize,
                                             &ewaldcoeff_q,
                                             &ewaldcoeff_lj,
                                             &atomSetChanged);

            if (ret == pmerecvqxSWITCHGRID)
            {
                /* Switch the PME grid to newGridSize */
                pme = gmx_pmeonly_switch(&pmedata, newGridSize, ewaldcoeff_q, ewaldcoeff_lj, cr, ir);
            }

            if (atomSetChanged)
            {
                gmx_pme_reinit_atoms(pme, natoms, pme_pp->chargeA.data());
            }

            if (ret == pmerecvqxRESETCOUNTERS)
            {
                /* Reset the cycle and flop counters */
                reset_pmeonly_counters(wcycle, walltime_accounting, mynrnb, ir, step);
            }
        }
        while (ret == pmerecvqxSWITCHGRID || ret == pmerecvqxRESETCOUNTERS);

        if (ret == pmerecvqxFINISH)
        {
            /* We should stop: break out of the loop */
            break;
        }

        if (count == 0)
        {
            wallcycle_start(wcycle, ewcRUN);
            walltime_accounting_start(walltime_accounting);
        }

        wallcycle_start(wcycle, ewcPMEMESH);

        dvdlambda_q  = 0;
        dvdlambda_lj = 0;
        clear_mat(vir_q);
        clear_mat(vir_lj);
        energy_q  = 0;
        energy_lj = 0;

        // TODO Make a struct of array refs onto these per-atom fields
        // of pme_pp (maybe box, energy and virial, too; and likewise
        // from mdatoms for the other call to gmx_pme_do), so we have
        // fewer lines of code and less parameter passing.
        const int pmeFlags = GMX_PME_DO_ALL_F | (bEnerVir ? GMX_PME_CALC_ENER_VIR : 0);
        gmx::ArrayRef<const gmx::RVec> forces;
        if (useGpuForPme)
        {
            const bool boxChanged = false;
            //TODO this should be set properly by gmx_pme_recv_coeffs_coords,
            // or maybe use inputrecDynamicBox(ir), at the very least - change this when this codepath is tested!
            pme_gpu_prepare_computation(pme, boxChanged, box, wcycle, pmeFlags);
            pme_gpu_launch_spread(pme, as_rvec_array(pme_pp->x.data()), wcycle);
            pme_gpu_launch_complex_transforms(pme, wcycle);
            pme_gpu_launch_gather(pme, wcycle, PmeForceOutputHandling::Set);
            pme_gpu_wait_for_gpu(pme, wcycle, &forces, vir_q, &energy_q);
        }
        else
        {
            gmx_pme_do(pme, 0, natoms, as_rvec_array(pme_pp->x.data()), as_rvec_array(pme_pp->f.data()),
                       pme_pp->chargeA.data(), pme_pp->chargeB.data(),
                       pme_pp->sqrt_c6A.data(), pme_pp->sqrt_c6B.data(),
                       pme_pp->sigmaA.data(), pme_pp->sigmaB.data(), box,
                       cr, maxshift_x, maxshift_y, mynrnb, wcycle,
                       vir_q, vir_lj,
                       &energy_q, &energy_lj, lambda_q, lambda_lj, &dvdlambda_q, &dvdlambda_lj,
                       pmeFlags);
            forces = pme_pp->f;
        }

        cycles = wallcycle_stop(wcycle, ewcPMEMESH);

        gmx_pme_send_force_vir_ener(pme_pp.get(), as_rvec_array(forces.data()),
                                    vir_q, energy_q, vir_lj, energy_lj,
                                    dvdlambda_q, dvdlambda_lj, cycles);

        count++;
    } /***** end of quasi-loop, we stop with the break above */
    while (TRUE);

    walltime_accounting_end(walltime_accounting);

    return 0;
}