Store dHdL for all neighbor lambdas

[gromacs.git] / src / gromacs / nbnxm / kerneldispatch.cpp

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#include "gmxpre.h"

#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
#include "gromacs/gmxlib/nonbonded/nonbonded.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdlib/enerdata_utils.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/forceoutput.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/simulation_workload.h"
#include "gromacs/nbnxm/gpu_data_mgmt.h"
#include "gromacs/nbnxm/nbnxm.h"
#include "gromacs/simd/simd.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"

#include "kernel_common.h"
#include "nbnxm_gpu.h"
#include "nbnxm_simd.h"
#include "pairlistset.h"
#include "pairlistsets.h"
#include "kernels_reference/kernel_gpu_ref.h"
#define INCLUDE_KERNELFUNCTION_TABLES
#include "kernels_reference/kernel_ref.h"
#ifdef GMX_NBNXN_SIMD_2XNN
#    include "kernels_simd_2xmm/kernels.h"
#endif
#ifdef GMX_NBNXN_SIMD_4XN
#    include "kernels_simd_4xm/kernels.h"
#endif
#undef INCLUDE_FUNCTION_TABLES

/*! \brief Clears the energy group output buffers
 *
 * \param[in,out] out  nbnxn kernel output struct
 */
static void clearGroupEnergies(nbnxn_atomdata_output_t* out)
{
    std::fill(out->Vvdw.begin(), out->Vvdw.end(), 0.0_real);
    std::fill(out->Vc.begin(), out->Vc.end(), 0.0_real);
    std::fill(out->VSvdw.begin(), out->VSvdw.end(), 0.0_real);
    std::fill(out->VSc.begin(), out->VSc.end(), 0.0_real);
}

/*! \brief Reduce the group-pair energy buffers produced by a SIMD kernel
 * to single terms in the output buffers.
 *
 * The SIMD kernels produce a large number of energy buffer in SIMD registers
 * to avoid scattered reads and writes.
 *
 * \tparam        unrollj         The unroll size for j-particles in the SIMD kernel
 * \param[in]     numGroups       The number of energy groups
 * \param[in]     numGroups_2log  Log2 of numGroups, rounded up
 * \param[in,out] out             Struct with energy buffers
 */
template<int unrollj>
static void reduceGroupEnergySimdBuffers(int numGroups, int numGroups_2log, nbnxn_atomdata_output_t* out)
{
    const int unrollj_half = unrollj / 2;
    /* Energies are stored in SIMD registers with size 2^numGroups_2log */
    const int numGroupsStorage = (1 << numGroups_2log);

    const real* gmx_restrict vVdwSimd     = out->VSvdw.data();
    const real* gmx_restrict vCoulombSimd = out->VSc.data();
    real* gmx_restrict vVdw               = out->Vvdw.data();
    real* gmx_restrict vCoulomb           = out->Vc.data();

    /* The size of the SIMD energy group buffer array is:
     * numGroups*numGroups*numGroupsStorage*unrollj_half*simd_width
     */
    for (int i = 0; i < numGroups; i++)
    {
        for (int j1 = 0; j1 < numGroups; j1++)
        {
            for (int j0 = 0; j0 < numGroups; j0++)
            {
                int c = ((i * numGroups + j1) * numGroupsStorage + j0) * unrollj_half * unrollj;
                for (int s = 0; s < unrollj_half; s++)
                {
                    vVdw[i * numGroups + j0] += vVdwSimd[c + 0];
                    vVdw[i * numGroups + j1] += vVdwSimd[c + 1];
                    vCoulomb[i * numGroups + j0] += vCoulombSimd[c + 0];
                    vCoulomb[i * numGroups + j1] += vCoulombSimd[c + 1];
                    c += unrollj + 2;
                }
            }
        }
    }
}

/*! \brief Dispatches the non-bonded N versus M atom cluster CPU kernels.
 *
 * OpenMP parallelization is performed within this function.
 * Energy reduction, but not force and shift force reduction, is performed
 * within this function.
 *
 * \param[in]     pairlistSet   Pairlists with local or non-local interactions to compute
 * \param[in]     kernelSetup   The non-bonded kernel setup
 * \param[in,out] nbat          The atomdata for the interactions
 * \param[in]     ic            Non-bonded interaction constants
 * \param[in]     shiftVectors  The PBC shift vectors
 * \param[in]     stepWork      Flags that tell what to compute
 * \param[in]     clearF        Enum that tells if to clear the force output buffer
 * \param[out]    vCoulomb      Output buffer for Coulomb energies
 * \param[out]    vVdw          Output buffer for Van der Waals energies
 * \param[in]     wcycle        Pointer to cycle counting data structure.
 */
static void nbnxn_kernel_cpu(const PairlistSet&         pairlistSet,
                             const Nbnxm::KernelSetup&  kernelSetup,
                             nbnxn_atomdata_t*          nbat,
                             const interaction_const_t& ic,
                             rvec*                      shiftVectors,
                             const gmx::StepWorkload&   stepWork,
                             int                        clearF,
                             real*                      vCoulomb,
                             real*                      vVdw,
                             gmx_wallcycle*             wcycle)
{

    int coulkt;
    if (EEL_RF(ic.eeltype) || ic.eeltype == eelCUT)
    {
        coulkt = coulktRF;
    }
    else
    {
        if (kernelSetup.ewaldExclusionType == Nbnxm::EwaldExclusionType::Table)
        {
            if (ic.rcoulomb == ic.rvdw)
            {
                coulkt = coulktTAB;
            }
            else
            {
                coulkt = coulktTAB_TWIN;
            }
        }
        else
        {
            if (ic.rcoulomb == ic.rvdw)
            {
                coulkt = coulktEWALD;
            }
            else
            {
                coulkt = coulktEWALD_TWIN;
            }
        }
    }

    const nbnxn_atomdata_t::Params& nbatParams = nbat->params();

    int vdwkt = 0;
    if (ic.vdwtype == evdwCUT)
    {
        switch (ic.vdw_modifier)
        {
            case eintmodNONE:
            case eintmodPOTSHIFT:
                switch (nbatParams.comb_rule)
                {
                    case ljcrGEOM: vdwkt = vdwktLJCUT_COMBGEOM; break;
                    case ljcrLB: vdwkt = vdwktLJCUT_COMBLB; break;
                    case ljcrNONE: vdwkt = vdwktLJCUT_COMBNONE; break;
                    default: GMX_RELEASE_ASSERT(false, "Unknown combination rule");
                }
                break;
            case eintmodFORCESWITCH: vdwkt = vdwktLJFORCESWITCH; break;
            case eintmodPOTSWITCH: vdwkt = vdwktLJPOTSWITCH; break;
            default: GMX_RELEASE_ASSERT(false, "Unsupported VdW interaction modifier");
        }
    }
    else if (ic.vdwtype == evdwPME)
    {
        if (ic.ljpme_comb_rule == eljpmeGEOM)
        {
            vdwkt = vdwktLJEWALDCOMBGEOM;
        }
        else
        {
            vdwkt = vdwktLJEWALDCOMBLB;
            /* At setup we (should have) selected the C reference kernel */
            GMX_RELEASE_ASSERT(kernelSetup.kernelType == Nbnxm::KernelType::Cpu4x4_PlainC,
                               "Only the C reference nbnxn SIMD kernel supports LJ-PME with LB "
                               "combination rules");
        }
    }
    else
    {
        GMX_RELEASE_ASSERT(false, "Unsupported VdW interaction type");
    }

    gmx::ArrayRef<const NbnxnPairlistCpu> pairlists = pairlistSet.cpuLists();

    int gmx_unused nthreads = gmx_omp_nthreads_get(emntNonbonded);
    wallcycle_sub_start(wcycle, ewcsNONBONDED_CLEAR);
#pragma omp parallel for schedule(static) num_threads(nthreads)
    for (gmx::index nb = 0; nb < pairlists.ssize(); nb++)
    {
        // Presently, the kernels do not call C++ code that can throw,
        // so no need for a try/catch pair in this OpenMP region.
        nbnxn_atomdata_output_t* out = &nbat->out[nb];

        if (clearF == enbvClearFYes)
        {
            clearForceBuffer(nbat, nb);

            clear_fshift(out->fshift.data());
        }

        if (nb == 0)
        {
            wallcycle_sub_stop(wcycle, ewcsNONBONDED_CLEAR);
            wallcycle_sub_start(wcycle, ewcsNONBONDED_KERNEL);
        }

        // TODO: Change to reference
        const NbnxnPairlistCpu* pairlist = &pairlists[nb];

        if (!stepWork.computeEnergy)
        {
            /* Don't calculate energies */
            switch (kernelSetup.kernelType)
            {
                case Nbnxm::KernelType::Cpu4x4_PlainC:
                    nbnxn_kernel_noener_ref[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
                    break;
#ifdef GMX_NBNXN_SIMD_2XNN
                case Nbnxm::KernelType::Cpu4xN_Simd_2xNN:
                    nbnxm_kernel_noener_simd_2xmm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
                    break;
#endif
#ifdef GMX_NBNXN_SIMD_4XN
                case Nbnxm::KernelType::Cpu4xN_Simd_4xN:
                    nbnxm_kernel_noener_simd_4xm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
                    break;
#endif
                default: GMX_RELEASE_ASSERT(false, "Unsupported kernel architecture");
            }
        }
        else if (out->Vvdw.size() == 1)
        {
            /* A single energy group (pair) */
            out->Vvdw[0] = 0;
            out->Vc[0]   = 0;

            switch (kernelSetup.kernelType)
            {
                case Nbnxm::KernelType::Cpu4x4_PlainC:
                    nbnxn_kernel_ener_ref[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
                    break;
#ifdef GMX_NBNXN_SIMD_2XNN
                case Nbnxm::KernelType::Cpu4xN_Simd_2xNN:
                    nbnxm_kernel_ener_simd_2xmm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
                    break;
#endif
#ifdef GMX_NBNXN_SIMD_4XN
                case Nbnxm::KernelType::Cpu4xN_Simd_4xN:
                    nbnxm_kernel_ener_simd_4xm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
                    break;
#endif
                default: GMX_RELEASE_ASSERT(false, "Unsupported kernel architecture");
            }
        }
        else
        {
            /* Calculate energy group contributions */
            clearGroupEnergies(out);

            int unrollj = 0;

            switch (kernelSetup.kernelType)
            {
                case Nbnxm::KernelType::Cpu4x4_PlainC:
                    unrollj = c_nbnxnCpuIClusterSize;
                    nbnxn_kernel_energrp_ref[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
                    break;
#ifdef GMX_NBNXN_SIMD_2XNN
                case Nbnxm::KernelType::Cpu4xN_Simd_2xNN:
                    unrollj = GMX_SIMD_REAL_WIDTH / 2;
                    nbnxm_kernel_energrp_simd_2xmm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
                    break;
#endif
#ifdef GMX_NBNXN_SIMD_4XN
                case Nbnxm::KernelType::Cpu4xN_Simd_4xN:
                    unrollj = GMX_SIMD_REAL_WIDTH;
                    nbnxm_kernel_energrp_simd_4xm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
                    break;
#endif
                default: GMX_RELEASE_ASSERT(false, "Unsupported kernel architecture");
            }

            if (kernelSetup.kernelType != Nbnxm::KernelType::Cpu4x4_PlainC)
            {
                switch (unrollj)
                {
                    case 2:
                        reduceGroupEnergySimdBuffers<2>(nbatParams.nenergrp, nbatParams.neg_2log, out);
                        break;
                    case 4:
                        reduceGroupEnergySimdBuffers<4>(nbatParams.nenergrp, nbatParams.neg_2log, out);
                        break;
                    case 8:
                        reduceGroupEnergySimdBuffers<8>(nbatParams.nenergrp, nbatParams.neg_2log, out);
                        break;
                    default: GMX_RELEASE_ASSERT(false, "Unsupported j-unroll size");
                }
            }
        }
    }
    wallcycle_sub_stop(wcycle, ewcsNONBONDED_KERNEL);

    if (stepWork.computeEnergy)
    {
        reduce_energies_over_lists(nbat, pairlists.ssize(), vVdw, vCoulomb);
    }
}

static void accountFlops(t_nrnb*                    nrnb,
                         const PairlistSet&         pairlistSet,
                         const nonbonded_verlet_t&  nbv,
                         const interaction_const_t& ic,
                         const gmx::StepWorkload&   stepWork)
{
    const bool usingGpuKernels = nbv.useGpu();

    int enr_nbnxn_kernel_ljc;
    if (EEL_RF(ic.eeltype) || ic.eeltype == eelCUT)
    {
        enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_RF;
    }
    else if ((!usingGpuKernels && nbv.kernelSetup().ewaldExclusionType == Nbnxm::EwaldExclusionType::Analytical)
             || (usingGpuKernels && Nbnxm::gpu_is_kernel_ewald_analytical(nbv.gpu_nbv)))
    {
        enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_EWALD;
    }
    else
    {
        enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_TAB;
    }
    int enr_nbnxn_kernel_lj = eNR_NBNXN_LJ;
    if (stepWork.computeEnergy)
    {
        /* In eNR_??? the nbnxn F+E kernels are always the F kernel + 1 */
        enr_nbnxn_kernel_ljc += 1;
        enr_nbnxn_kernel_lj += 1;
    }

    inc_nrnb(nrnb, enr_nbnxn_kernel_ljc, pairlistSet.natpair_ljq_);
    inc_nrnb(nrnb, enr_nbnxn_kernel_lj, pairlistSet.natpair_lj_);
    /* The Coulomb-only kernels are offset -eNR_NBNXN_LJ_RF+eNR_NBNXN_RF */
    inc_nrnb(nrnb, enr_nbnxn_kernel_ljc - eNR_NBNXN_LJ_RF + eNR_NBNXN_RF, pairlistSet.natpair_q_);

    if (ic.vdw_modifier == eintmodFORCESWITCH)
    {
        /* We add up the switch cost separately */
        inc_nrnb(nrnb, eNR_NBNXN_ADD_LJ_FSW + (stepWork.computeEnergy ? 1 : 0),
                 pairlistSet.natpair_ljq_ + pairlistSet.natpair_lj_);
    }
    if (ic.vdw_modifier == eintmodPOTSWITCH)
    {
        /* We add up the switch cost separately */
        inc_nrnb(nrnb, eNR_NBNXN_ADD_LJ_PSW + (stepWork.computeEnergy ? 1 : 0),
                 pairlistSet.natpair_ljq_ + pairlistSet.natpair_lj_);
    }
    if (ic.vdwtype == evdwPME)
    {
        /* We add up the LJ Ewald cost separately */
        inc_nrnb(nrnb, eNR_NBNXN_ADD_LJ_EWALD + (stepWork.computeEnergy ? 1 : 0),
                 pairlistSet.natpair_ljq_ + pairlistSet.natpair_lj_);
    }
}

void nonbonded_verlet_t::dispatchNonbondedKernel(gmx::InteractionLocality   iLocality,
                                                 const interaction_const_t& ic,
                                                 const gmx::StepWorkload&   stepWork,
                                                 int                        clearF,
                                                 const t_forcerec&          fr,
                                                 gmx_enerdata_t*            enerd,
                                                 t_nrnb*                    nrnb)
{
    const PairlistSet& pairlistSet = pairlistSets().pairlistSet(iLocality);

    switch (kernelSetup().kernelType)
    {
        case Nbnxm::KernelType::Cpu4x4_PlainC:
        case Nbnxm::KernelType::Cpu4xN_Simd_4xN:
        case Nbnxm::KernelType::Cpu4xN_Simd_2xNN:
            nbnxn_kernel_cpu(pairlistSet, kernelSetup(), nbat.get(), ic, fr.shift_vec, stepWork,
                             clearF, enerd->grpp.ener[egCOULSR].data(),
                             fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data(),
                             wcycle_);
            break;

        case Nbnxm::KernelType::Gpu8x8x8:
            Nbnxm::gpu_launch_kernel(gpu_nbv, stepWork, iLocality);
            break;

        case Nbnxm::KernelType::Cpu8x8x8_PlainC:
            nbnxn_kernel_gpu_ref(
                    pairlistSet.gpuList(), nbat.get(), &ic, fr.shift_vec, stepWork, clearF,
                    nbat->out[0].f, nbat->out[0].fshift.data(), enerd->grpp.ener[egCOULSR].data(),
                    fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data());
            break;

        default: GMX_RELEASE_ASSERT(false, "Invalid nonbonded kernel type passed!");
    }

    accountFlops(nrnb, pairlistSet, *this, ic, stepWork);
}

void nonbonded_verlet_t::dispatchFreeEnergyKernel(gmx::InteractionLocality   iLocality,
                                                  const t_forcerec*          fr,
                                                  rvec                       x[],
                                                  gmx::ForceWithShiftForces* forceWithShiftForces,
                                                  const t_mdatoms&           mdatoms,
                                                  t_lambda*                  fepvals,
                                                  real*                      lambda,
                                                  gmx_enerdata_t*            enerd,
                                                  const gmx::StepWorkload&   stepWork,
                                                  t_nrnb*                    nrnb)
{
    const auto nbl_fep = pairlistSets().pairlistSet(iLocality).fepLists();

    /* When the first list is empty, all are empty and there is nothing to do */
    if (!pairlistSets().params().haveFep || nbl_fep[0]->nrj == 0)
    {
        return;
    }

    int donb_flags = 0;
    /* Add short-range interactions */
    donb_flags |= GMX_NONBONDED_DO_SR;

    if (stepWork.computeForces)
    {
        donb_flags |= GMX_NONBONDED_DO_FORCE;
    }
    if (stepWork.computeVirial)
    {
        donb_flags |= GMX_NONBONDED_DO_SHIFTFORCE;
    }
    if (stepWork.computeEnergy)
    {
        donb_flags |= GMX_NONBONDED_DO_POTENTIAL;
    }

    nb_kernel_data_t kernel_data;
    real             dvdl_nb[efptNR] = { 0 };
    kernel_data.flags                = donb_flags;
    kernel_data.lambda               = lambda;
    kernel_data.dvdl                 = dvdl_nb;

    kernel_data.energygrp_elec = enerd->grpp.ener[egCOULSR].data();
    kernel_data.energygrp_vdw  = enerd->grpp.ener[egLJSR].data();

    GMX_ASSERT(gmx_omp_nthreads_get(emntNonbonded) == nbl_fep.ssize(),
               "Number of lists should be same as number of NB threads");

    wallcycle_sub_start(wcycle_, ewcsNONBONDED_FEP);
#pragma omp parallel for schedule(static) num_threads(nbl_fep.ssize())
    for (gmx::index th = 0; th < nbl_fep.ssize(); th++)
    {
        try
        {
            gmx_nb_free_energy_kernel(nbl_fep[th].get(), x, forceWithShiftForces, fr, &mdatoms,
                                      &kernel_data, nrnb);
        }
        GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
    }

    if (fepvals->sc_alpha != 0)
    {
        enerd->dvdl_nonlin[efptVDW] += dvdl_nb[efptVDW];
        enerd->dvdl_nonlin[efptCOUL] += dvdl_nb[efptCOUL];
    }
    else
    {
        enerd->dvdl_lin[efptVDW] += dvdl_nb[efptVDW];
        enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
    }

    /* If we do foreign lambda and we have soft-core interactions
     * we have to recalculate the (non-linear) energies contributions.
     */
    if (fepvals->n_lambda > 0 && stepWork.computeDhdl && fepvals->sc_alpha != 0)
    {
        real lam_i[efptNR];
        kernel_data.flags = (donb_flags & ~(GMX_NONBONDED_DO_FORCE | GMX_NONBONDED_DO_SHIFTFORCE))
                            | GMX_NONBONDED_DO_FOREIGNLAMBDA;
        kernel_data.lambda         = lam_i;
        kernel_data.dvdl           = dvdl_nb;
        kernel_data.energygrp_elec = enerd->foreign_grpp.ener[egCOULSR].data();
        kernel_data.energygrp_vdw  = enerd->foreign_grpp.ener[egLJSR].data();

        for (size_t i = 0; i < enerd->enerpart_lambda.size(); i++)
        {
            std::fill(std::begin(dvdl_nb), std::end(dvdl_nb), 0);
            for (int j = 0; j < efptNR; j++)
            {
                lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i - 1]);
            }
            reset_foreign_enerdata(enerd);
#pragma omp parallel for schedule(static) num_threads(nbl_fep.ssize())
            for (gmx::index th = 0; th < nbl_fep.ssize(); th++)
            {
                try
                {
                    gmx_nb_free_energy_kernel(nbl_fep[th].get(), x, forceWithShiftForces, fr,
                                              &mdatoms, &kernel_data, nrnb);
                }
                GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
            }

            sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
            enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
            enerd->dhdlLambda[i] += dvdl_nb[efptVDW] + dvdl_nb[efptCOUL];
        }
    }
    else
    {
        for (size_t i = 0; i < enerd->enerpart_lambda.size(); i++)
        {
            enerd->dhdlLambda[i] += dvdl_nb[efptVDW] + dvdl_nb[efptCOUL];
        }
    }
    wallcycle_sub_stop(wcycle_, ewcsNONBONDED_FEP);
}