Improve workload data structures' docs

[gromacs.git] / src / gromacs / listed_forces / listed_forces.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 2014,2015,2016,2017,2018,2019, 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
 * of the License, or (at your option) any later version.
 *
 * GROMACS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with GROMACS; if not, see
 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
 *
 * If you want to redistribute modifications to GROMACS, please
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 * official version at http://www.gromacs.org.
 *
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 */
/*! \internal \file
 *
 * \brief This file defines high-level functions for mdrun to compute
 * energies and forces for listed interactions.
 *
 * \author Mark Abraham <mark.j.abraham@gmail.com>
 *
 * \ingroup module_listed_forces
 */
#include "gmxpre.h"

#include "listed_forces.h"

#include <cassert>

#include <algorithm>
#include <array>

#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/listed_forces/bonded.h"
#include "gromacs/listed_forces/disre.h"
#include "gromacs/listed_forces/orires.h"
#include "gromacs/listed_forces/pairs.h"
#include "gromacs/listed_forces/position_restraints.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/enerdata_utils.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/fcdata.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/simulation_workload.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"

#include "listed_internal.h"
#include "utilities.h"

namespace
{

/*! \brief Return true if ftype is an explicit pair-listed LJ or
 * COULOMB interaction type: bonded LJ (usually 1-4), or special
 * listed non-bonded for FEP. */
bool
isPairInteraction(int ftype)
{
    return ((ftype) >= F_LJ14 && (ftype) <= F_LJC_PAIRS_NB);
}

/*! \brief Zero thread-local output buffers */
void
zero_thread_output(f_thread_t *f_t)
{
    constexpr int nelem_fa = sizeof(f_t->f[0])/sizeof(real);

    for (int i = 0; i < f_t->nblock_used; i++)
    {
        int a0 = f_t->block_index[i]*reduction_block_size;
        int a1 = a0 + reduction_block_size;
        for (int a = a0; a < a1; a++)
        {
            for (int d = 0; d < nelem_fa; d++)
            {
                f_t->f[a][d] = 0;
            }
        }
    }

    for (int i = 0; i < SHIFTS; i++)
    {
        clear_rvec(f_t->fshift[i]);
    }
    for (int i = 0; i < F_NRE; i++)
    {
        f_t->ener[i] = 0;
    }
    for (int i = 0; i < egNR; i++)
    {
        for (int j = 0; j < f_t->grpp.nener; j++)
        {
            f_t->grpp.ener[i][j] = 0;
        }
    }
    for (int i = 0; i < efptNR; i++)
    {
        f_t->dvdl[i] = 0;
    }
}

/*! \brief The max thread number is arbitrary, we used a fixed number
 * to avoid memory management.  Using more than 16 threads is probably
 * never useful performance wise. */
#define MAX_BONDED_THREADS 256

/*! \brief Reduce thread-local force buffers */
void
reduce_thread_forces(int                        n,
                     gmx::ArrayRef<gmx::RVec>   force,
                     const bonded_threading_t  *bt,
                     int                        nthreads)
{
    if (nthreads > MAX_BONDED_THREADS)
    {
        gmx_fatal(FARGS, "Can not reduce bonded forces on more than %d threads",
                  MAX_BONDED_THREADS);
    }

    rvec * gmx_restrict f = as_rvec_array(force.data());

    /* This reduction can run on any number of threads,
     * independently of bt->nthreads.
     * But if nthreads matches bt->nthreads (which it currently does)
     * the uniform distribution of the touched blocks over nthreads will
     * match the distribution of bonded over threads well in most cases,
     * which means that threads mostly reduce their own data which increases
     * the number of cache hits.
     */
#pragma omp parallel for num_threads(nthreads) schedule(static)
    for (int b = 0; b < bt->nblock_used; b++)
    {
        try
        {
            int    ind = bt->block_index[b];
            rvec4 *fp[MAX_BONDED_THREADS];

            /* Determine which threads contribute to this block */
            int nfb = 0;
            for (int ft = 0; ft < bt->nthreads; ft++)
            {
                if (bitmask_is_set(bt->mask[ind], ft))
                {
                    fp[nfb++] = bt->f_t[ft]->f;
                }
            }
            if (nfb > 0)
            {
                /* Reduce force buffers for threads that contribute */
                int a0 =  ind     *reduction_block_size;
                int a1 = (ind + 1)*reduction_block_size;
                /* It would be nice if we could pad f to avoid this min */
                a1     = std::min(a1, n);
                for (int a = a0; a < a1; a++)
                {
                    for (int fb = 0; fb < nfb; fb++)
                    {
                        rvec_inc(f[a], fp[fb][a]);
                    }
                }
            }
        }
        GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
    }
}

/*! \brief Reduce thread-local forces, shift forces and energies */
void
reduce_thread_output(int n, gmx::ForceWithShiftForces *forceWithShiftForces,
                     real *ener, gmx_grppairener_t *grpp, real *dvdl,
                     const bonded_threading_t *bt,
                     const gmx::StepWorkload  &stepWork)
{
    assert(bt->haveBondeds);

    if (bt->nblock_used > 0)
    {
        /* Reduce the bonded force buffer */
        reduce_thread_forces(n, forceWithShiftForces->force(), bt, bt->nthreads);
    }

    rvec * gmx_restrict fshift = as_rvec_array(forceWithShiftForces->shiftForces().data());

    /* When necessary, reduce energy and virial using one thread only */
    if ((stepWork.computeEnergy || stepWork.computeVirial || stepWork.computeDhdl) &&
        bt->nthreads > 1)
    {
        gmx::ArrayRef < const std::unique_ptr < f_thread_t>> f_t = bt->f_t;

        if (stepWork.computeVirial)
        {
            for (int i = 0; i < SHIFTS; i++)
            {
                for (int t = 1; t < bt->nthreads; t++)
                {
                    rvec_inc(fshift[i], f_t[t]->fshift[i]);
                }
            }
        }
        if (stepWork.computeEnergy)
        {
            for (int i = 0; i < F_NRE; i++)
            {
                for (int t = 1; t < bt->nthreads; t++)
                {
                    ener[i] += f_t[t]->ener[i];
                }
            }
            for (int i = 0; i < egNR; i++)
            {
                for (int j = 0; j < f_t[1]->grpp.nener; j++)
                {
                    for (int t = 1; t < bt->nthreads; t++)
                    {
                        grpp->ener[i][j] += f_t[t]->grpp.ener[i][j];
                    }
                }
            }
        }
        if (stepWork.computeDhdl)
        {
            for (int i = 0; i < efptNR; i++)
            {

                for (int t = 1; t < bt->nthreads; t++)
                {
                    dvdl[i] += f_t[t]->dvdl[i];
                }
            }
        }
    }
}

/*! \brief Returns the bonded kernel flavor
 *
 * Note that energies are always requested when the virial
 * is requested (performance gain would be small).
 * Note that currently we do not have bonded kernels that
 * do not compute forces.
 */
BondedKernelFlavor selectBondedKernelFlavor(const gmx::StepWorkload &stepWork,
                                            const bool               useSimdKernels,
                                            const bool               havePerturbedInteractions)
{
    BondedKernelFlavor flavor;
    if (stepWork.computeEnergy || stepWork.computeVirial)
    {
        if (stepWork.computeVirial)
        {
            flavor = BondedKernelFlavor::ForcesAndVirialAndEnergy;
        }
        else
        {
            flavor = BondedKernelFlavor::ForcesAndEnergy;
        }
    }
    else
    {
        if (useSimdKernels && !havePerturbedInteractions)
        {
            flavor = BondedKernelFlavor::ForcesSimdWhenAvailable;
        }
        else
        {
            flavor = BondedKernelFlavor::ForcesNoSimd;
        }
    }

    return flavor;
}

/*! \brief Calculate one element of the list of bonded interactions
    for this thread */
real
calc_one_bond(int thread,
              int ftype, const t_idef *idef,
              const WorkDivision &workDivision,
              const rvec x[], rvec4 f[], rvec fshift[],
              const t_forcerec *fr,
              const t_pbc *pbc, const t_graph *g,
              gmx_grppairener_t *grpp,
              t_nrnb *nrnb,
              const real *lambda, real *dvdl,
              const t_mdatoms *md, t_fcdata *fcd,
              const gmx::StepWorkload &stepWork,
              int *global_atom_index)
{
    GMX_ASSERT(idef->ilsort == ilsortNO_FE || idef->ilsort == ilsortFE_SORTED,
               "The topology should be marked either as no FE or sorted on FE");

    const bool         havePerturbedInteractions =
        (idef->ilsort == ilsortFE_SORTED &&
         idef->il[ftype].nr_nonperturbed < idef->il[ftype].nr);
    BondedKernelFlavor flavor =
        selectBondedKernelFlavor(stepWork, fr->use_simd_kernels, havePerturbedInteractions);
    int                efptFTYPE;
    if (IS_RESTRAINT_TYPE(ftype))
    {
        efptFTYPE = efptRESTRAINT;
    }
    else
    {
        efptFTYPE = efptBONDED;
    }

    const int      nat1   = interaction_function[ftype].nratoms + 1;
    const int      nbonds = idef->il[ftype].nr/nat1;
    const t_iatom *iatoms = idef->il[ftype].iatoms;

    GMX_ASSERT(fr->gpuBonded != nullptr || workDivision.end(ftype) == idef->il[ftype].nr,
               "The thread division should match the topology");

    const int nb0 = workDivision.bound(ftype, thread);
    const int nbn = workDivision.bound(ftype, thread + 1) - nb0;

    real      v = 0;
    if (!isPairInteraction(ftype))
    {
        if (ftype == F_CMAP)
        {
            /* TODO The execution time for CMAP dihedrals might be
               nice to account to its own subtimer, but first
               wallcycle needs to be extended to support calling from
               multiple threads. */
            v = cmap_dihs(nbn, iatoms+nb0,
                          idef->iparams, idef->cmap_grid,
                          x, f, fshift,
                          pbc, g, lambda[efptFTYPE], &(dvdl[efptFTYPE]),
                          md, fcd, global_atom_index);
        }
        else
        {
            v = calculateSimpleBond(ftype, nbn, iatoms + nb0,
                                    idef->iparams,
                                    x, f, fshift,
                                    pbc, g, lambda[efptFTYPE], &(dvdl[efptFTYPE]),
                                    md, fcd, global_atom_index,
                                    flavor);
        }
    }
    else
    {
        /* TODO The execution time for pairs might be nice to account
           to its own subtimer, but first wallcycle needs to be
           extended to support calling from multiple threads. */
        do_pairs(ftype, nbn, iatoms+nb0, idef->iparams, x, f, fshift,
                 pbc, g, lambda, dvdl, md, fr,
                 havePerturbedInteractions, stepWork,
                 grpp, global_atom_index);
    }

    if (thread == 0)
    {
        inc_nrnb(nrnb, nrnbIndex(ftype), nbonds);
    }

    return v;
}

} // namespace

/*! \brief Compute the bonded part of the listed forces, parallelized over threads
 */
static void
calcBondedForces(const t_idef            *idef,
                 const rvec               x[],
                 const t_forcerec        *fr,
                 const t_pbc             *pbc_null,
                 const t_graph           *g,
                 rvec                    *fshiftMasterBuffer,
                 gmx_enerdata_t          *enerd,
                 t_nrnb                  *nrnb,
                 const real              *lambda,
                 real                    *dvdl,
                 const t_mdatoms         *md,
                 t_fcdata                *fcd,
                 const gmx::StepWorkload &stepWork,
                 int                     *global_atom_index)
{
    bonded_threading_t *bt = fr->bondedThreading;

#pragma omp parallel for num_threads(bt->nthreads) schedule(static)
    for (int thread = 0; thread < bt->nthreads; thread++)
    {
        try
        {
            f_thread_t        &threadBuffers = *bt->f_t[thread];
            int                ftype;
            real              *epot, v;
            /* thread stuff */
            rvec              *fshift;
            real              *dvdlt;
            gmx_grppairener_t *grpp;

            zero_thread_output(&threadBuffers);

            rvec4 *ft = threadBuffers.f;

            /* Thread 0 writes directly to the main output buffers.
             * We might want to reconsider this.
             */
            if (thread == 0)
            {
                fshift = fshiftMasterBuffer;
                epot   = enerd->term;
                grpp   = &enerd->grpp;
                dvdlt  = dvdl;
            }
            else
            {
                fshift = threadBuffers.fshift;
                epot   = threadBuffers.ener;
                grpp   = &threadBuffers.grpp;
                dvdlt  = threadBuffers.dvdl;
            }
            /* Loop over all bonded force types to calculate the bonded forces */
            for (ftype = 0; (ftype < F_NRE); ftype++)
            {
                if (idef->il[ftype].nr > 0 && ftype_is_bonded_potential(ftype))
                {
                    v = calc_one_bond(thread, ftype, idef,
                                      fr->bondedThreading->workDivision, x,
                                      ft, fshift, fr, pbc_null, g, grpp,
                                      nrnb, lambda, dvdlt,
                                      md, fcd, stepWork,
                                      global_atom_index);
                    epot[ftype] += v;
                }
            }
        }
        GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
    }
}

bool haveRestraints(const t_idef   &idef,
                    const t_fcdata &fcd)
{
    return
        ((idef.il[F_POSRES].nr > 0) ||
         (idef.il[F_FBPOSRES].nr > 0) ||
         fcd.orires.nr > 0 ||
         fcd.disres.nres > 0);
}

bool haveCpuBondeds(const t_forcerec &fr)
{
    return fr.bondedThreading->haveBondeds;
}

bool haveCpuListedForces(const t_forcerec &fr,
                         const t_idef     &idef,
                         const t_fcdata   &fcd)
{
    return haveCpuBondeds(fr) || haveRestraints(idef, fcd);
}

void calc_listed(const t_commrec             *cr,
                 const gmx_multisim_t *ms,
                 struct gmx_wallcycle        *wcycle,
                 const t_idef *idef,
                 const rvec x[], history_t *hist,
                 gmx::ForceOutputs *forceOutputs,
                 const t_forcerec *fr,
                 const struct t_pbc *pbc,
                 const struct t_pbc *pbc_full,
                 const struct t_graph *g,
                 gmx_enerdata_t *enerd, t_nrnb *nrnb,
                 const real *lambda,
                 const t_mdatoms *md,
                 t_fcdata *fcd, int *global_atom_index,
                 const gmx::StepWorkload &stepWork)
{
    const  t_pbc              *pbc_null;
    bonded_threading_t        *bt  = fr->bondedThreading;

    if (fr->bMolPBC)
    {
        pbc_null = pbc;
    }
    else
    {
        pbc_null = nullptr;
    }

    if (haveRestraints(*idef, *fcd))
    {
        /* TODO Use of restraints triggers further function calls
           inside the loop over calc_one_bond(), but those are too
           awkward to account to this subtimer properly in the present
           code. We don't test / care much about performance with
           restraints, anyway. */
        wallcycle_sub_start(wcycle, ewcsRESTRAINTS);

        if (idef->il[F_POSRES].nr > 0)
        {
            posres_wrapper(nrnb, idef, pbc_full, x, enerd, lambda, fr,
                           &forceOutputs->forceWithVirial());
        }

        if (idef->il[F_FBPOSRES].nr > 0)
        {
            fbposres_wrapper(nrnb, idef, pbc_full, x, enerd, fr,
                             &forceOutputs->forceWithVirial());
        }

        /* Do pre force calculation stuff which might require communication */
        if (fcd->orires.nr > 0)
        {
            /* This assertion is to ensure we have whole molecules.
             * Unfortunately we do not have an mdrun state variable that tells
             * us if molecules in x are not broken over PBC, so we have to make
             * do with checking graph!=nullptr, which should tell us if we made
             * molecules whole before calling the current function.
             */
            GMX_RELEASE_ASSERT(fr->ePBC == epbcNONE || g != nullptr, "With orientation restraints molecules should be whole");
            enerd->term[F_ORIRESDEV] =
                calc_orires_dev(ms, idef->il[F_ORIRES].nr,
                                idef->il[F_ORIRES].iatoms,
                                idef->iparams, md, x,
                                pbc_null, fcd, hist);
        }
        if (fcd->disres.nres > 0)
        {
            calc_disres_R_6(cr, ms,
                            idef->il[F_DISRES].nr,
                            idef->il[F_DISRES].iatoms,
                            x, pbc_null,
                            fcd, hist);
        }

        wallcycle_sub_stop(wcycle, ewcsRESTRAINTS);
    }

    if (haveCpuBondeds(*fr))
    {
        gmx::ForceWithShiftForces &forceWithShiftForces = forceOutputs->forceWithShiftForces();

        wallcycle_sub_start(wcycle, ewcsLISTED);
        /* The dummy array is to have a place to store the dhdl at other values
           of lambda, which will be thrown away in the end */
        real dvdl[efptNR] = {0};
        calcBondedForces(idef, x, fr, pbc_null, g,
                         as_rvec_array(forceWithShiftForces.shiftForces().data()),
                         enerd, nrnb, lambda, dvdl, md,
                         fcd, stepWork, global_atom_index);
        wallcycle_sub_stop(wcycle, ewcsLISTED);

        wallcycle_sub_start(wcycle, ewcsLISTED_BUF_OPS);
        reduce_thread_output(fr->natoms_force, &forceWithShiftForces,
                             enerd->term, &enerd->grpp, dvdl,
                             bt,
                             stepWork);

        if (stepWork.computeDhdl)
        {
            for (int i = 0; i < efptNR; i++)
            {
                enerd->dvdl_nonlin[i] += dvdl[i];
            }
        }
        wallcycle_sub_stop(wcycle, ewcsLISTED_BUF_OPS);
    }

    /* Copy the sum of violations for the distance restraints from fcd */
    if (fcd)
    {
        enerd->term[F_DISRESVIOL] = fcd->disres.sumviol;
    }
}

void calc_listed_lambda(const t_idef *idef,
                        const rvec x[],
                        const t_forcerec *fr,
                        const struct t_pbc *pbc, const struct t_graph *g,
                        gmx_grppairener_t *grpp, real *epot, t_nrnb *nrnb,
                        const real *lambda,
                        const t_mdatoms *md,
                        t_fcdata *fcd,
                        int *global_atom_index)
{
    real               v;
    real               dvdl_dum[efptNR] = {0};
    rvec4             *f;
    rvec              *fshift;
    const  t_pbc      *pbc_null;
    t_idef             idef_fe;
    WorkDivision      &workDivision = fr->bondedThreading->foreignLambdaWorkDivision;

    if (fr->bMolPBC)
    {
        pbc_null = pbc;
    }
    else
    {
        pbc_null = nullptr;
    }

    /* Copy the whole idef, so we can modify the contents locally */
    idef_fe                  = *idef;

    /* We already have the forces, so we use temp buffers here */
    // TODO: Get rid of these allocations by using permanent force buffers
    snew(f, fr->natoms_force);
    snew(fshift, SHIFTS);

    /* Loop over all bonded force types to calculate the bonded energies */
    for (int ftype = 0; (ftype < F_NRE); ftype++)
    {
        if (ftype_is_bonded_potential(ftype))
        {
            const t_ilist &ilist     = idef->il[ftype];
            /* Create a temporary t_ilist with only perturbed interactions */
            t_ilist       &ilist_fe  = idef_fe.il[ftype];
            ilist_fe.iatoms          = ilist.iatoms + ilist.nr_nonperturbed;
            ilist_fe.nr_nonperturbed = 0;
            ilist_fe.nr              = ilist.nr - ilist.nr_nonperturbed;
            /* Set the work range of thread 0 to the perturbed bondeds */
            workDivision.setBound(ftype, 0, 0);
            workDivision.setBound(ftype, 1, ilist_fe.nr);

            if (ilist_fe.nr > 0)
            {
                gmx::StepWorkload tempFlags;
                tempFlags.computeEnergy  = true;
                v = calc_one_bond(0, ftype, &idef_fe, workDivision,
                                  x, f, fshift, fr, pbc_null, g,
                                  grpp, nrnb, lambda, dvdl_dum,
                                  md, fcd, tempFlags,
                                  global_atom_index);
                epot[ftype] += v;
            }
        }
    }

    sfree(fshift);
    sfree(f);
}

void
do_force_listed(struct gmx_wallcycle          *wcycle,
                const matrix                   box,
                const t_lambda                *fepvals,
                const t_commrec               *cr,
                const gmx_multisim_t          *ms,
                const t_idef                  *idef,
                const rvec                     x[],
                history_t                     *hist,
                gmx::ForceOutputs             *forceOutputs,
                const t_forcerec              *fr,
                const struct t_pbc            *pbc,
                const struct t_graph          *graph,
                gmx_enerdata_t                *enerd,
                t_nrnb                        *nrnb,
                const real                    *lambda,
                const t_mdatoms               *md,
                t_fcdata                      *fcd,
                int                           *global_atom_index,
                const gmx::StepWorkload       &stepWork)
{
    t_pbc pbc_full; /* Full PBC is needed for position restraints */

    if (!stepWork.computeListedForces)
    {
        return;
    }

    if ((idef->il[F_POSRES].nr > 0) ||
        (idef->il[F_FBPOSRES].nr > 0))
    {
        /* Not enough flops to bother counting */
        set_pbc(&pbc_full, fr->ePBC, box);
    }
    calc_listed(cr, ms, wcycle, idef, x, hist,
                forceOutputs,
                fr, pbc, &pbc_full,
                graph, enerd, nrnb, lambda, md, fcd,
                global_atom_index, stepWork);

    /* Check if we have to determine energy differences
     * at foreign lambda's.
     */
    if (fepvals->n_lambda > 0 && stepWork.computeDhdl)
    {
        posres_wrapper_lambda(wcycle, fepvals, idef, &pbc_full, x, enerd, lambda, fr);

        if (idef->ilsort != ilsortNO_FE)
        {
            wallcycle_sub_start(wcycle, ewcsLISTED_FEP);
            if (idef->ilsort != ilsortFE_SORTED)
            {
                gmx_incons("The bonded interactions are not sorted for free energy");
            }
            for (size_t i = 0; i < enerd->enerpart_lambda.size(); i++)
            {
                real lam_i[efptNR];

                reset_foreign_enerdata(enerd);
                for (int j = 0; j < efptNR; j++)
                {
                    lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
                }
                calc_listed_lambda(idef, x, fr, pbc, graph, &(enerd->foreign_grpp), enerd->foreign_term, nrnb, lam_i, md,
                                   fcd, global_atom_index);
                sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
                enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
            }
            wallcycle_sub_stop(wcycle, ewcsLISTED_FEP);
        }
    }
}