src/gromacs/mdlib/sim_util.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
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  37 #include "gmxpre.h"
  38
  39 #include "config.h"
  40
  41 #include <cmath>
  42 #include <cstdint>
  43 #include <cstdio>
  44 #include <cstring>
  45
  46 #include <array>
  47
  48 #include "gromacs/awh/awh.h"
  49 #include "gromacs/domdec/dlbtiming.h"
  50 #include "gromacs/domdec/domdec.h"
  51 #include "gromacs/domdec/domdec_struct.h"
  52 #include "gromacs/domdec/gpuhaloexchange.h"
  53 #include "gromacs/domdec/partition.h"
  54 #include "gromacs/essentialdynamics/edsam.h"
  55 #include "gromacs/ewald/pme.h"
  56 #include "gromacs/gmxlib/chargegroup.h"
  57 #include "gromacs/gmxlib/network.h"
  58 #include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
  59 #include "gromacs/gmxlib/nonbonded/nb_kernel.h"
  60 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
  61 #include "gromacs/gpu_utils/gpu_utils.h"
  62 #include "gromacs/imd/imd.h"
  63 #include "gromacs/listed_forces/disre.h"
  64 #include "gromacs/listed_forces/gpubonded.h"
  65 #include "gromacs/listed_forces/listed_forces.h"
  66 #include "gromacs/listed_forces/manage_threading.h"
  67 #include "gromacs/listed_forces/orires.h"
  68 #include "gromacs/math/arrayrefwithpadding.h"
  69 #include "gromacs/math/functions.h"
  70 #include "gromacs/math/units.h"
  71 #include "gromacs/math/vec.h"
  72 #include "gromacs/math/vecdump.h"
  73 #include "gromacs/mdlib/calcmu.h"
  74 #include "gromacs/mdlib/calcvir.h"
  75 #include "gromacs/mdlib/constr.h"
  76 #include "gromacs/mdlib/enerdata_utils.h"
  77 #include "gromacs/mdlib/force.h"
  78 #include "gromacs/mdlib/forcerec.h"
  79 #include "gromacs/mdlib/gmx_omp_nthreads.h"
  80 #include "gromacs/mdlib/qmmm.h"
  81 #include "gromacs/mdlib/update.h"
  82 #include "gromacs/mdtypes/commrec.h"
  83 #include "gromacs/mdtypes/enerdata.h"
  84 #include "gromacs/mdtypes/forceoutput.h"
  85 #include "gromacs/mdtypes/iforceprovider.h"
  86 #include "gromacs/mdtypes/inputrec.h"
  87 #include "gromacs/mdtypes/md_enums.h"
  88 #include "gromacs/mdtypes/simulation_workload.h"
  89 #include "gromacs/mdtypes/state.h"
  90 #include "gromacs/nbnxm/atomdata.h"
  91 #include "gromacs/nbnxm/gpu_data_mgmt.h"
  92 #include "gromacs/nbnxm/nbnxm.h"
  93 #include "gromacs/pbcutil/ishift.h"
  94 #include "gromacs/pbcutil/mshift.h"
  95 #include "gromacs/pbcutil/pbc.h"
  96 #include "gromacs/pulling/pull.h"
  97 #include "gromacs/pulling/pull_rotation.h"
  98 #include "gromacs/timing/cyclecounter.h"
  99 #include "gromacs/timing/gpu_timing.h"
 100 #include "gromacs/timing/wallcycle.h"
 101 #include "gromacs/timing/wallcyclereporting.h"
 102 #include "gromacs/timing/walltime_accounting.h"
 103 #include "gromacs/topology/topology.h"
 104 #include "gromacs/utility/arrayref.h"
 105 #include "gromacs/utility/basedefinitions.h"
 106 #include "gromacs/utility/cstringutil.h"
 107 #include "gromacs/utility/exceptions.h"
 108 #include "gromacs/utility/fatalerror.h"
 109 #include "gromacs/utility/gmxassert.h"
 110 #include "gromacs/utility/gmxmpi.h"
 111 #include "gromacs/utility/logger.h"
 112 #include "gromacs/utility/smalloc.h"
 113 #include "gromacs/utility/strconvert.h"
 114 #include "gromacs/utility/sysinfo.h"
 115
 116 using gmx::ForceOutputs;
 117 using gmx::StepWorkload;
 118 using gmx::DomainLifetimeWorkload;
 119
 120 // TODO: this environment variable allows us to verify before release
 121 // that on less common architectures the total cost of polling is not larger than
 122 // a blocking wait (so polling does not introduce overhead when the static
 123 // PME-first ordering would suffice).
 124 static const bool c_disableAlternatingWait = (getenv("GMX_DISABLE_ALTERNATING_GPU_WAIT") != nullptr);
 125
 126 // environment variable to enable GPU buffer ops, to allow incremental and optional
 127 // introduction of this functionality.
 128 // TODO eventially tie this in with other existing GPU flags.
 129 static const bool c_enableGpuBufOps = (getenv("GMX_USE_GPU_BUFFER_OPS") != nullptr);
 130
 131 static void sum_forces(rvec f[], gmx::ArrayRef<const gmx::RVec> forceToAdd)
 132 {
 133     const int      end = forceToAdd.size();
 134
 135     int gmx_unused nt = gmx_omp_nthreads_get(emntDefault);
 136 #pragma omp parallel for num_threads(nt) schedule(static)
 137     for (int i = 0; i < end; i++)
 138     {
 139         rvec_inc(f[i], forceToAdd[i]);
 140     }
 141 }
 142
 143 static void calc_virial(int start, int homenr, const rvec x[],
 144                         const gmx::ForceWithShiftForces &forceWithShiftForces,
 145                         tensor vir_part, const t_graph *graph, const matrix box,
 146                         t_nrnb *nrnb, const t_forcerec *fr, int ePBC)
 147 {
 148     /* The short-range virial from surrounding boxes */
 149     const rvec *fshift = as_rvec_array(forceWithShiftForces.shiftForces().data());
 150     calc_vir(SHIFTS, fr->shift_vec, fshift, vir_part, ePBC == epbcSCREW, box);
 151     inc_nrnb(nrnb, eNR_VIRIAL, SHIFTS);
 152
 153     /* Calculate partial virial, for local atoms only, based on short range.
 154      * Total virial is computed in global_stat, called from do_md
 155      */
 156     const rvec *f = as_rvec_array(forceWithShiftForces.force().data());
 157     f_calc_vir(start, start+homenr, x, f, vir_part, graph, box);
 158     inc_nrnb(nrnb, eNR_VIRIAL, homenr);
 159
 160     if (debug)
 161     {
 162         pr_rvecs(debug, 0, "vir_part", vir_part, DIM);
 163     }
 164 }
 165
 166 static void pull_potential_wrapper(const t_commrec *cr,
 167                                    const t_inputrec *ir,
 168                                    const matrix box, gmx::ArrayRef<const gmx::RVec> x,
 169                                    gmx::ForceWithVirial *force,
 170                                    const t_mdatoms *mdatoms,
 171                                    gmx_enerdata_t *enerd,
 172                                    pull_t *pull_work,
 173                                    const real *lambda,
 174                                    double t,
 175                                    gmx_wallcycle_t wcycle)
 176 {
 177     t_pbc  pbc;
 178     real   dvdl;
 179
 180     /* Calculate the center of mass forces, this requires communication,
 181      * which is why pull_potential is called close to other communication.
 182      */
 183     wallcycle_start(wcycle, ewcPULLPOT);
 184     set_pbc(&pbc, ir->ePBC, box);
 185     dvdl                     = 0;
 186     enerd->term[F_COM_PULL] +=
 187         pull_potential(pull_work, mdatoms, &pbc,
 188                        cr, t, lambda[efptRESTRAINT], as_rvec_array(x.data()), force, &dvdl);
 189     enerd->dvdl_lin[efptRESTRAINT] += dvdl;
 190     wallcycle_stop(wcycle, ewcPULLPOT);
 191 }
 192
 193 static void pme_receive_force_ener(const t_commrec      *cr,
 194                                    gmx::ForceWithVirial *forceWithVirial,
 195                                    gmx_enerdata_t       *enerd,
 196                                    gmx_wallcycle_t       wcycle)
 197 {
 198     real   e_q, e_lj, dvdl_q, dvdl_lj;
 199     float  cycles_ppdpme, cycles_seppme;
 200
 201     cycles_ppdpme = wallcycle_stop(wcycle, ewcPPDURINGPME);
 202     dd_cycles_add(cr->dd, cycles_ppdpme, ddCyclPPduringPME);
 203
 204     /* In case of node-splitting, the PP nodes receive the long-range
 205      * forces, virial and energy from the PME nodes here.
 206      */
 207     wallcycle_start(wcycle, ewcPP_PMEWAITRECVF);
 208     dvdl_q  = 0;
 209     dvdl_lj = 0;
 210     gmx_pme_receive_f(cr, forceWithVirial, &e_q, &e_lj, &dvdl_q, &dvdl_lj,
 211                       &cycles_seppme);
 212     enerd->term[F_COUL_RECIP] += e_q;
 213     enerd->term[F_LJ_RECIP]   += e_lj;
 214     enerd->dvdl_lin[efptCOUL] += dvdl_q;
 215     enerd->dvdl_lin[efptVDW]  += dvdl_lj;
 216
 217     if (wcycle)
 218     {
 219         dd_cycles_add(cr->dd, cycles_seppme, ddCyclPME);
 220     }
 221     wallcycle_stop(wcycle, ewcPP_PMEWAITRECVF);
 222 }
 223
 224 static void print_large_forces(FILE            *fp,
 225                                const t_mdatoms *md,
 226                                const t_commrec *cr,
 227                                int64_t          step,
 228                                real             forceTolerance,
 229                                const rvec      *x,
 230                                const rvec      *f)
 231 {
 232     real           force2Tolerance = gmx::square(forceTolerance);
 233     gmx::index     numNonFinite    = 0;
 234     for (int i = 0; i < md->homenr; i++)
 235     {
 236         real force2    = norm2(f[i]);
 237         bool nonFinite = !std::isfinite(force2);
 238         if (force2 >= force2Tolerance || nonFinite)
 239         {
 240             fprintf(fp, "step %" PRId64 " atom %6d  x %8.3f %8.3f %8.3f  force %12.5e\n",
 241                     step,
 242                     ddglatnr(cr->dd, i), x[i][XX], x[i][YY], x[i][ZZ], std::sqrt(force2));
 243         }
 244         if (nonFinite)
 245         {
 246             numNonFinite++;
 247         }
 248     }
 249     if (numNonFinite > 0)
 250     {
 251         /* Note that with MPI this fatal call on one rank might interrupt
 252          * the printing on other ranks. But we can only avoid that with
 253          * an expensive MPI barrier that we would need at each step.
 254          */
 255         gmx_fatal(FARGS, "At step %" PRId64 " detected non-finite forces on %td atoms", step, numNonFinite);
 256     }
 257 }
 258
 259 static void post_process_forces(const t_commrec       *cr,
 260                                 int64_t                step,
 261                                 t_nrnb                *nrnb,
 262                                 gmx_wallcycle_t        wcycle,
 263                                 const gmx_localtop_t  *top,
 264                                 const matrix           box,
 265                                 const rvec             x[],
 266                                 ForceOutputs          *forceOutputs,
 267                                 tensor                 vir_force,
 268                                 const t_mdatoms       *mdatoms,
 269                                 const t_graph         *graph,
 270                                 const t_forcerec      *fr,
 271                                 const gmx_vsite_t     *vsite,
 272                                 const StepWorkload    &stepWork)
 273 {
 274     rvec *f = as_rvec_array(forceOutputs->forceWithShiftForces().force().data());
 275
 276     if (fr->haveDirectVirialContributions)
 277     {
 278         auto &forceWithVirial = forceOutputs->forceWithVirial();
 279         rvec *fDirectVir      = as_rvec_array(forceWithVirial.force_.data());
 280
 281         if (vsite)
 282         {
 283             /* Spread the mesh force on virtual sites to the other particles...
 284              * This is parallellized. MPI communication is performed
 285              * if the constructing atoms aren't local.
 286              */
 287             matrix virial = { { 0 } };
 288             spread_vsite_f(vsite, x, fDirectVir, nullptr,
 289                            stepWork.computeVirial, virial,
 290                            nrnb,
 291                            &top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr, wcycle);
 292             forceWithVirial.addVirialContribution(virial);
 293         }
 294
 295         if (stepWork.computeVirial)
 296         {
 297             /* Now add the forces, this is local */
 298             sum_forces(f, forceWithVirial.force_);
 299
 300             /* Add the direct virial contributions */
 301             GMX_ASSERT(forceWithVirial.computeVirial_, "forceWithVirial should request virial computation when we request the virial");
 302             m_add(vir_force, forceWithVirial.getVirial(), vir_force);
 303
 304             if (debug)
 305             {
 306                 pr_rvecs(debug, 0, "vir_force", vir_force, DIM);
 307             }
 308         }
 309     }
 310
 311     if (fr->print_force >= 0)
 312     {
 313         print_large_forces(stderr, mdatoms, cr, step, fr->print_force, x, f);
 314     }
 315 }
 316
 317 static void do_nb_verlet(t_forcerec                       *fr,
 318                          const interaction_const_t        *ic,
 319                          gmx_enerdata_t                   *enerd,
 320                          const StepWorkload               &stepWork,
 321                          const Nbnxm::InteractionLocality  ilocality,
 322                          const int                         clearF,
 323                          const int64_t                     step,
 324                          t_nrnb                           *nrnb,
 325                          gmx_wallcycle_t                   wcycle)
 326 {
 327     if (!stepWork.computeNonbondedForces)
 328     {
 329         /* skip non-bonded calculation */
 330         return;
 331     }
 332
 333     nonbonded_verlet_t *nbv  = fr->nbv.get();
 334
 335     /* GPU kernel launch overhead is already timed separately */
 336     if (fr->cutoff_scheme != ecutsVERLET)
 337     {
 338         gmx_incons("Invalid cut-off scheme passed!");
 339     }
 340
 341     if (!nbv->useGpu())
 342     {
 343         /* When dynamic pair-list  pruning is requested, we need to prune
 344          * at nstlistPrune steps.
 345          */
 346         if (nbv->isDynamicPruningStepCpu(step))
 347         {
 348             /* Prune the pair-list beyond fr->ic->rlistPrune using
 349              * the current coordinates of the atoms.
 350              */
 351             wallcycle_sub_start(wcycle, ewcsNONBONDED_PRUNING);
 352             nbv->dispatchPruneKernelCpu(ilocality, fr->shift_vec);
 353             wallcycle_sub_stop(wcycle, ewcsNONBONDED_PRUNING);
 354         }
 355     }
 356
 357     nbv->dispatchNonbondedKernel(ilocality, *ic, stepWork, clearF, *fr, enerd, nrnb);
 358 }
 359
 360 static inline void clear_rvecs_omp(int n, rvec v[])
 361 {
 362     int nth = gmx_omp_nthreads_get_simple_rvec_task(emntDefault, n);
 363
 364     /* Note that we would like to avoid this conditional by putting it
 365      * into the omp pragma instead, but then we still take the full
 366      * omp parallel for overhead (at least with gcc5).
 367      */
 368     if (nth == 1)
 369     {
 370         for (int i = 0; i < n; i++)
 371         {
 372             clear_rvec(v[i]);
 373         }
 374     }
 375     else
 376     {
 377 #pragma omp parallel for num_threads(nth) schedule(static)
 378         for (int i = 0; i < n; i++)
 379         {
 380             clear_rvec(v[i]);
 381         }
 382     }
 383 }
 384
 385 /*! \brief Return an estimate of the average kinetic energy or 0 when unreliable
 386  *
 387  * \param groupOptions  Group options, containing T-coupling options
 388  */
 389 static real averageKineticEnergyEstimate(const t_grpopts &groupOptions)
 390 {
 391     real nrdfCoupled   = 0;
 392     real nrdfUncoupled = 0;
 393     real kineticEnergy = 0;
 394     for (int g = 0; g < groupOptions.ngtc; g++)
 395     {
 396         if (groupOptions.tau_t[g] >= 0)
 397         {
 398             nrdfCoupled   += groupOptions.nrdf[g];
 399             kineticEnergy += groupOptions.nrdf[g]*0.5*groupOptions.ref_t[g]*BOLTZ;
 400         }
 401         else
 402         {
 403             nrdfUncoupled += groupOptions.nrdf[g];
 404         }
 405     }
 406
 407     /* This conditional with > also catches nrdf=0 */
 408     if (nrdfCoupled > nrdfUncoupled)
 409     {
 410         return kineticEnergy*(nrdfCoupled + nrdfUncoupled)/nrdfCoupled;
 411     }
 412     else
 413     {
 414         return 0;
 415     }
 416 }
 417
 418 /*! \brief This routine checks that the potential energy is finite.
 419  *
 420  * Always checks that the potential energy is finite. If step equals
 421  * inputrec.init_step also checks that the magnitude of the potential energy
 422  * is reasonable. Terminates with a fatal error when a check fails.
 423  * Note that passing this check does not guarantee finite forces,
 424  * since those use slightly different arithmetics. But in most cases
 425  * there is just a narrow coordinate range where forces are not finite
 426  * and energies are finite.
 427  *
 428  * \param[in] step      The step number, used for checking and printing
 429  * \param[in] enerd     The energy data; the non-bonded group energies need to be added to enerd.term[F_EPOT] before calling this routine
 430  * \param[in] inputrec  The input record
 431  */
 432 static void checkPotentialEnergyValidity(int64_t               step,
 433                                          const gmx_enerdata_t &enerd,
 434                                          const t_inputrec     &inputrec)
 435 {
 436     /* Threshold valid for comparing absolute potential energy against
 437      * the kinetic energy. Normally one should not consider absolute
 438      * potential energy values, but with a factor of one million
 439      * we should never get false positives.
 440      */
 441     constexpr real c_thresholdFactor = 1e6;
 442
 443     bool           energyIsNotFinite    = !std::isfinite(enerd.term[F_EPOT]);
 444     real           averageKineticEnergy = 0;
 445     /* We only check for large potential energy at the initial step,
 446      * because that is by far the most likely step for this too occur
 447      * and because computing the average kinetic energy is not free.
 448      * Note: nstcalcenergy >> 1 often does not allow to catch large energies
 449      * before they become NaN.
 450      */
 451     if (step == inputrec.init_step && EI_DYNAMICS(inputrec.eI))
 452     {
 453         averageKineticEnergy = averageKineticEnergyEstimate(inputrec.opts);
 454     }
 455
 456     if (energyIsNotFinite || (averageKineticEnergy > 0 &&
 457                               enerd.term[F_EPOT] > c_thresholdFactor*averageKineticEnergy))
 458     {
 459         gmx_fatal(FARGS, "Step %" PRId64 ": The total potential energy is %g, which is %s. The LJ and electrostatic contributions to the energy are %g and %g, respectively. A %s potential energy can be caused by overlapping interactions in bonded interactions or very large%s coordinate values. Usually this is caused by a badly- or non-equilibrated initial configuration, incorrect interactions or parameters in the topology.",
 460                   step,
 461                   enerd.term[F_EPOT],
 462                   energyIsNotFinite ? "not finite" : "extremely high",
 463                   enerd.term[F_LJ],
 464                   enerd.term[F_COUL_SR],
 465                   energyIsNotFinite ? "non-finite" : "very high",
 466                   energyIsNotFinite ? " or Nan" : "");
 467     }
 468 }
 469
 470 /*! \brief Return true if there are special forces computed this step.
 471  *
 472  * The conditionals exactly correspond to those in computeSpecialForces().
 473  */
 474 static bool
 475 haveSpecialForces(const t_inputrec              &inputrec,
 476                   const gmx::ForceProviders     &forceProviders,
 477                   const pull_t                  *pull_work,
 478                   const bool                     computeForces,
 479                   const gmx_edsam               *ed)
 480 {
 481
 482     return
 483         ((computeForces && forceProviders.hasForceProvider()) ||         // forceProviders
 484          (inputrec.bPull && pull_have_potential(pull_work)) ||           // pull
 485          inputrec.bRot ||                                                // enforced rotation
 486          (ed != nullptr) ||                                              // flooding
 487          (inputrec.bIMD && computeForces));                              // IMD
 488 }
 489
 490 /*! \brief Compute forces and/or energies for special algorithms
 491  *
 492  * The intention is to collect all calls to algorithms that compute
 493  * forces on local atoms only and that do not contribute to the local
 494  * virial sum (but add their virial contribution separately).
 495  * Eventually these should likely all become ForceProviders.
 496  * Within this function the intention is to have algorithms that do
 497  * global communication at the end, so global barriers within the MD loop
 498  * are as close together as possible.
 499  *
 500  * \param[in]     fplog            The log file
 501  * \param[in]     cr               The communication record
 502  * \param[in]     inputrec         The input record
 503  * \param[in]     awh              The Awh module (nullptr if none in use).
 504  * \param[in]     enforcedRotation Enforced rotation module.
 505  * \param[in]     imdSession       The IMD session
 506  * \param[in]     pull_work        The pull work structure.
 507  * \param[in]     step             The current MD step
 508  * \param[in]     t                The current time
 509  * \param[in,out] wcycle           Wallcycle accounting struct
 510  * \param[in,out] forceProviders   Pointer to a list of force providers
 511  * \param[in]     box              The unit cell
 512  * \param[in]     x                The coordinates
 513  * \param[in]     mdatoms          Per atom properties
 514  * \param[in]     lambda           Array of free-energy lambda values
 515  * \param[in]     stepWork         Step schedule flags
 516  * \param[in,out] forceWithVirial  Force and virial buffers
 517  * \param[in,out] enerd            Energy buffer
 518  * \param[in,out] ed               Essential dynamics pointer
 519  * \param[in]     didNeighborSearch Tells if we did neighbor searching this step, used for ED sampling
 520  *
 521  * \todo Remove didNeighborSearch, which is used incorrectly.
 522  * \todo Convert all other algorithms called here to ForceProviders.
 523  */
 524 static void
 525 computeSpecialForces(FILE                          *fplog,
 526                      const t_commrec               *cr,
 527                      const t_inputrec              *inputrec,
 528                      gmx::Awh                      *awh,
 529                      gmx_enfrot                    *enforcedRotation,
 530                      gmx::ImdSession               *imdSession,
 531                      pull_t                        *pull_work,
 532                      int64_t                        step,
 533                      double                         t,
 534                      gmx_wallcycle_t                wcycle,
 535                      gmx::ForceProviders           *forceProviders,
 536                      const matrix                   box,
 537                      gmx::ArrayRef<const gmx::RVec> x,
 538                      const t_mdatoms               *mdatoms,
 539                      real                          *lambda,
 540                      const StepWorkload            &stepWork,
 541                      gmx::ForceWithVirial          *forceWithVirial,
 542                      gmx_enerdata_t                *enerd,
 543                      gmx_edsam                     *ed,
 544                      bool                           didNeighborSearch)
 545 {
 546     /* NOTE: Currently all ForceProviders only provide forces.
 547      *       When they also provide energies, remove this conditional.
 548      */
 549     if (stepWork.computeForces)
 550     {
 551         gmx::ForceProviderInput  forceProviderInput(x, *mdatoms, t, box, *cr);
 552         gmx::ForceProviderOutput forceProviderOutput(forceWithVirial, enerd);
 553
 554         /* Collect forces from modules */
 555         forceProviders->calculateForces(forceProviderInput, &forceProviderOutput);
 556     }
 557
 558     if (inputrec->bPull && pull_have_potential(pull_work))
 559     {
 560         pull_potential_wrapper(cr, inputrec, box, x,
 561                                forceWithVirial,
 562                                mdatoms, enerd, pull_work, lambda, t,
 563                                wcycle);
 564
 565         if (awh)
 566         {
 567             enerd->term[F_COM_PULL] +=
 568                 awh->applyBiasForcesAndUpdateBias(inputrec->ePBC, *mdatoms, box,
 569                                                   forceWithVirial,
 570                                                   t, step, wcycle, fplog);
 571         }
 572     }
 573
 574     rvec *f = as_rvec_array(forceWithVirial->force_.data());
 575
 576     /* Add the forces from enforced rotation potentials (if any) */
 577     if (inputrec->bRot)
 578     {
 579         wallcycle_start(wcycle, ewcROTadd);
 580         enerd->term[F_COM_PULL] += add_rot_forces(enforcedRotation, f, cr, step, t);
 581         wallcycle_stop(wcycle, ewcROTadd);
 582     }
 583
 584     if (ed)
 585     {
 586         /* Note that since init_edsam() is called after the initialization
 587          * of forcerec, edsam doesn't request the noVirSum force buffer.
 588          * Thus if no other algorithm (e.g. PME) requires it, the forces
 589          * here will contribute to the virial.
 590          */
 591         do_flood(cr, inputrec, as_rvec_array(x.data()), f, ed, box, step, didNeighborSearch);
 592     }
 593
 594     /* Add forces from interactive molecular dynamics (IMD), if any */
 595     if (inputrec->bIMD && stepWork.computeForces)
 596     {
 597         imdSession->applyForces(f);
 598     }
 599 }
 600
 601 /*! \brief Launch the prepare_step and spread stages of PME GPU.
 602  *
 603  * \param[in]  pmedata              The PME structure
 604  * \param[in]  box                  The box matrix
 605  * \param[in]  x                    Coordinate array
 606  * \param[in]  stepWork             Step schedule flags
 607  * \param[in]  pmeFlags             PME flags
 608  * \param[in]  useGpuForceReduction True if GPU-based force reduction is active this step
 609  * \param[in]  wcycle               The wallcycle structure
 610  */
 611 static inline void launchPmeGpuSpread(gmx_pme_t          *pmedata,
 612                                       const matrix        box,
 613                                       const rvec          x[],
 614                                       const StepWorkload &stepWork,
 615                                       int                 pmeFlags,
 616                                       bool                useGpuForceReduction,
 617                                       gmx_wallcycle_t     wcycle)
 618 {
 619     pme_gpu_prepare_computation(pmedata, stepWork.haveDynamicBox, box, wcycle, pmeFlags, useGpuForceReduction);
 620     pme_gpu_copy_coordinates_to_gpu(pmedata, x, wcycle);
 621     pme_gpu_launch_spread(pmedata, wcycle);
 622 }
 623
 624 /*! \brief Launch the FFT and gather stages of PME GPU
 625  *
 626  * This function only implements setting the output forces (no accumulation).
 627  *
 628  * \param[in]  pmedata        The PME structure
 629  * \param[in]  wcycle         The wallcycle structure
 630  */
 631 static void launchPmeGpuFftAndGather(gmx_pme_t        *pmedata,
 632                                      gmx_wallcycle_t   wcycle)
 633 {
 634     pme_gpu_launch_complex_transforms(pmedata, wcycle);
 635     pme_gpu_launch_gather(pmedata, wcycle, PmeForceOutputHandling::Set);
 636 }
 637
 638 /*! \brief
 639  *  Polling wait for either of the PME or nonbonded GPU tasks.
 640  *
 641  * Instead of a static order in waiting for GPU tasks, this function
 642  * polls checking which of the two tasks completes first, and does the
 643  * associated force buffer reduction overlapped with the other task.
 644  * By doing that, unlike static scheduling order, it can always overlap
 645  * one of the reductions, regardless of the GPU task completion order.
 646  *
 647  * \param[in]     nbv              Nonbonded verlet structure
 648  * \param[in,out] pmedata          PME module data
 649  * \param[in,out] forceOutputs     Output buffer for the forces and virial
 650  * \param[in,out] enerd            Energy data structure results are reduced into
 651  * \param[in]     stepWork         Step schedule flags
 652  * \param[in]     pmeFlags         PME flags
 653  * \param[in]     wcycle           The wallcycle structure
 654  */
 655 static void alternatePmeNbGpuWaitReduce(nonbonded_verlet_t *nbv,
 656                                         gmx_pme_t          *pmedata,
 657                                         gmx::ForceOutputs  *forceOutputs,
 658                                         gmx_enerdata_t     *enerd,
 659                                         const StepWorkload &stepWork,
 660                                         int                 pmeFlags,
 661                                         gmx_wallcycle_t     wcycle)
 662 {
 663     bool isPmeGpuDone = false;
 664     bool isNbGpuDone  = false;
 665
 666
 667
 668     gmx::ForceWithShiftForces      &forceWithShiftForces = forceOutputs->forceWithShiftForces();
 669     gmx::ForceWithVirial           &forceWithVirial      = forceOutputs->forceWithVirial();
 670
 671     gmx::ArrayRef<const gmx::RVec>  pmeGpuForces;
 672
 673     while (!isPmeGpuDone || !isNbGpuDone)
 674     {
 675         if (!isPmeGpuDone)
 676         {
 677             GpuTaskCompletion completionType = (isNbGpuDone) ? GpuTaskCompletion::Wait : GpuTaskCompletion::Check;
 678             isPmeGpuDone = pme_gpu_try_finish_task(pmedata, pmeFlags, wcycle, &forceWithVirial, enerd, completionType);
 679         }
 680
 681         if (!isNbGpuDone)
 682         {
 683             GpuTaskCompletion completionType = (isPmeGpuDone) ? GpuTaskCompletion::Wait : GpuTaskCompletion::Check;
 684             isNbGpuDone = Nbnxm::gpu_try_finish_task(nbv->gpu_nbv,
 685                                                      stepWork,
 686                                                      Nbnxm::AtomLocality::Local,
 687                                                      enerd->grpp.ener[egLJSR].data(),
 688                                                      enerd->grpp.ener[egCOULSR].data(),
 689                                                      forceWithShiftForces.shiftForces(), completionType, wcycle);
 690
 691             if (isNbGpuDone)
 692             {
 693                 nbv->atomdata_add_nbat_f_to_f(Nbnxm::AtomLocality::Local,
 694                                               forceWithShiftForces.force());
 695             }
 696         }
 697     }
 698 }
 699
 700 /*! \brief Set up the different force buffers; also does clearing.
 701  *
 702  * \param[in] fr        force record pointer
 703  * \param[in] pull_work The pull work object.
 704  * \param[in] inputrec  input record
 705  * \param[in] force     force array
 706  * \param[in] stepWork  Step schedule flags
 707  * \param[out] wcycle   wallcycle recording structure
 708  *
 709  * \returns             Cleared force output structure
 710  */
 711 static ForceOutputs
 712 setupForceOutputs(t_forcerec                          *fr,
 713                   pull_t                              *pull_work,
 714                   const t_inputrec                    &inputrec,
 715                   gmx::ArrayRefWithPadding<gmx::RVec>  force,
 716                   const StepWorkload                  &stepWork,
 717                   gmx_wallcycle_t                      wcycle)
 718 {
 719     wallcycle_sub_start(wcycle, ewcsCLEAR_FORCE_BUFFER);
 720
 721     /* NOTE: We assume fr->shiftForces is all zeros here */
 722     gmx::ForceWithShiftForces forceWithShiftForces(force, stepWork.computeVirial, fr->shiftForces);
 723
 724     if (stepWork.computeForces)
 725     {
 726         /* Clear the short- and long-range forces */
 727         clear_rvecs_omp(fr->natoms_force_constr,
 728                         as_rvec_array(forceWithShiftForces.force().data()));
 729     }
 730
 731     /* If we need to compute the virial, we might need a separate
 732      * force buffer for algorithms for which the virial is calculated
 733      * directly, such as PME. Otherwise, forceWithVirial uses the
 734      * the same force (f in legacy calls) buffer as other algorithms.
 735      */
 736     const bool useSeparateForceWithVirialBuffer = (stepWork.computeForces &&
 737                                                    (stepWork.computeVirial && fr->haveDirectVirialContributions));
 738     /* forceWithVirial uses the local atom range only */
 739     gmx::ForceWithVirial forceWithVirial(useSeparateForceWithVirialBuffer ?
 740                                          fr->forceBufferForDirectVirialContributions : force.unpaddedArrayRef(),
 741                                          stepWork.computeVirial);
 742
 743     if (useSeparateForceWithVirialBuffer)
 744     {
 745         /* TODO: update comment
 746          * We only compute forces on local atoms. Note that vsites can
 747          * spread to non-local atoms, but that part of the buffer is
 748          * cleared separately in the vsite spreading code.
 749          */
 750         clear_rvecs_omp(forceWithVirial.force_.size(), as_rvec_array(forceWithVirial.force_.data()));
 751     }
 752
 753     if (inputrec.bPull && pull_have_constraint(pull_work))
 754     {
 755         clear_pull_forces(pull_work);
 756     }
 757
 758     wallcycle_sub_stop(wcycle, ewcsCLEAR_FORCE_BUFFER);
 759
 760     return ForceOutputs(forceWithShiftForces, forceWithVirial);
 761 }
 762
 763
 764 /*! \brief Set up flags that have the lifetime of the domain indicating what type of work is there to compute.
 765  */
 766 static void
 767 setupDomainLifetimeWorkload(DomainLifetimeWorkload *domainWork,
 768                             const t_inputrec       &inputrec,
 769                             const t_forcerec       &fr,
 770                             const pull_t           *pull_work,
 771                             const gmx_edsam        *ed,
 772                             const t_idef           &idef,
 773                             const t_fcdata         &fcd,
 774                             const t_mdatoms        &mdatoms,
 775                             const StepWorkload     &stepWork)
 776 {
 777     // Note that haveSpecialForces is constant over the whole run
 778     domainWork->haveSpecialForces      = haveSpecialForces(inputrec, *fr.forceProviders, pull_work, stepWork.computeForces, ed);
 779     domainWork->haveCpuBondedWork      = haveCpuBondeds(fr);
 780     domainWork->haveGpuBondedWork      = ((fr.gpuBonded != nullptr) && fr.gpuBonded->haveInteractions());
 781     domainWork->haveRestraintsWork     = havePositionRestraints(idef, fcd);
 782     domainWork->haveCpuListedForceWork = haveCpuListedForces(fr, idef, fcd);
 783     // Note that haveFreeEnergyWork is constant over the whole run
 784     domainWork->haveFreeEnergyWork     = (fr.efep != efepNO && mdatoms.nPerturbed != 0);
 785 }
 786
 787 /*! \brief Set up force flag stuct from the force bitmask.
 788  *
 789  * \param[out]     flags                Force schedule flags
 790  * \param[in]      legacyFlags          Force bitmask flags used to construct the new flags
 791  * \param[in]      isNonbondedOn        Global override, if false forces to turn off all nonbonded calculation.
 792  */
 793 static void
 794 setupStepWorkload(StepWorkload *flags,
 795                   const int     legacyFlags,
 796                   const bool    isNonbondedOn)
 797 {
 798     flags->stateChanged           = ((legacyFlags & GMX_FORCE_STATECHANGED) != 0);
 799     flags->haveDynamicBox         = ((legacyFlags & GMX_FORCE_DYNAMICBOX) != 0);
 800     flags->doNeighborSearch       = ((legacyFlags & GMX_FORCE_NS) != 0);
 801     flags->computeVirial          = ((legacyFlags & GMX_FORCE_VIRIAL) != 0);
 802     flags->computeEnergy          = ((legacyFlags & GMX_FORCE_ENERGY) != 0);
 803     flags->computeForces          = ((legacyFlags & GMX_FORCE_FORCES) != 0);
 804     flags->computeListedForces    = ((legacyFlags & GMX_FORCE_LISTED) != 0);
 805     flags->computeNonbondedForces = ((legacyFlags & GMX_FORCE_NONBONDED) != 0) && isNonbondedOn;
 806     flags->computeDhdl            = ((legacyFlags & GMX_FORCE_DHDL) != 0);
 807 }
 808
 809
 810 /* \brief Launch end-of-step GPU tasks: buffer clearing and rolling pruning.
 811  *
 812  * TODO: eliminate the \p useGpuNonbonded and \p useGpuNonbonded when these are
 813  * incorporated in DomainLifetimeWorkload.
 814  */
 815 static void
 816 launchGpuEndOfStepTasks(nonbonded_verlet_t               *nbv,
 817                         gmx::GpuBonded                   *gpuBonded,
 818                         gmx_pme_t                        *pmedata,
 819                         gmx_enerdata_t                   *enerd,
 820                         const gmx::MdrunScheduleWorkload &runScheduleWork,
 821                         bool                              useGpuNonbonded,
 822                         bool                              useGpuPme,
 823                         int64_t                           step,
 824                         gmx_wallcycle_t                   wcycle)
 825 {
 826     if (useGpuNonbonded)
 827     {
 828         /* Launch pruning before buffer clearing because the API overhead of the
 829          * clear kernel launches can leave the GPU idle while it could be running
 830          * the prune kernel.
 831          */
 832         if (nbv->isDynamicPruningStepGpu(step))
 833         {
 834             nbv->dispatchPruneKernelGpu(step);
 835         }
 836
 837         /* now clear the GPU outputs while we finish the step on the CPU */
 838         wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
 839         wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
 840         Nbnxm::gpu_clear_outputs(nbv->gpu_nbv, runScheduleWork.stepWork.computeVirial);
 841         wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
 842         wallcycle_stop(wcycle, ewcLAUNCH_GPU);
 843     }
 844
 845     if (useGpuPme)
 846     {
 847         pme_gpu_reinit_computation(pmedata, wcycle);
 848     }
 849
 850     if (runScheduleWork.domainWork.haveGpuBondedWork && runScheduleWork.stepWork.computeEnergy)
 851     {
 852         // in principle this should be included in the DD balancing region,
 853         // but generally it is infrequent so we'll omit it for the sake of
 854         // simpler code
 855         gpuBonded->waitAccumulateEnergyTerms(enerd);
 856
 857         gpuBonded->clearEnergies();
 858     }
 859 }
 860
 861
 862 void do_force(FILE                                     *fplog,
 863               const t_commrec                          *cr,
 864               const gmx_multisim_t                     *ms,
 865               const t_inputrec                         *inputrec,
 866               gmx::Awh                                 *awh,
 867               gmx_enfrot                               *enforcedRotation,
 868               gmx::ImdSession                          *imdSession,
 869               pull_t                                   *pull_work,
 870               int64_t                                   step,
 871               t_nrnb                                   *nrnb,
 872               gmx_wallcycle_t                           wcycle,
 873               const gmx_localtop_t                     *top,
 874               const matrix                              box,
 875               gmx::ArrayRefWithPadding<gmx::RVec>       x,
 876               history_t                                *hist,
 877               gmx::ArrayRefWithPadding<gmx::RVec>       force,
 878               tensor                                    vir_force,
 879               const t_mdatoms                          *mdatoms,
 880               gmx_enerdata_t                           *enerd,
 881               t_fcdata                                 *fcd,
 882               gmx::ArrayRef<real>                       lambda,
 883               t_graph                                  *graph,
 884               t_forcerec                               *fr,
 885               gmx::MdrunScheduleWorkload               *runScheduleWork,
 886               const gmx_vsite_t                        *vsite,
 887               rvec                                      mu_tot,
 888               double                                    t,
 889               gmx_edsam                                *ed,
 890               int                                       legacyFlags,
 891               const DDBalanceRegionHandler             &ddBalanceRegionHandler)
 892 {
 893     int                  i, j;
 894     double               mu[2*DIM];
 895     gmx_bool             bFillGrid, bCalcCGCM;
 896     gmx_bool             bUseGPU, bUseOrEmulGPU;
 897     nonbonded_verlet_t  *nbv = fr->nbv.get();
 898     interaction_const_t *ic  = fr->ic;
 899
 900     // TODO remove the code below when the legacy flags are not in use anymore
 901     /* modify force flag if not doing nonbonded */
 902     if (!fr->bNonbonded)
 903     {
 904         legacyFlags &= ~GMX_FORCE_NONBONDED;
 905     }
 906     setupStepWorkload(&runScheduleWork->stepWork, legacyFlags, fr->bNonbonded);
 907
 908     const gmx::StepWorkload &stepWork = runScheduleWork->stepWork;
 909
 910     bFillGrid     = (stepWork.doNeighborSearch && stepWork.stateChanged);
 911     bCalcCGCM     = (bFillGrid && !DOMAINDECOMP(cr));
 912     bUseGPU       = fr->nbv->useGpu();
 913     bUseOrEmulGPU = bUseGPU || fr->nbv->emulateGpu();
 914
 915     const auto pmeRunMode = fr->pmedata ? pme_run_mode(fr->pmedata) : PmeRunMode::CPU;
 916     // TODO slim this conditional down - inputrec and duty checks should mean the same in proper code!
 917     const bool useGpuPme  = EEL_PME(fr->ic->eeltype) && thisRankHasDuty(cr, DUTY_PME) &&
 918         ((pmeRunMode == PmeRunMode::GPU) || (pmeRunMode == PmeRunMode::Mixed));
 919     const int  pmeFlags = GMX_PME_SPREAD | GMX_PME_SOLVE |
 920         (stepWork.computeVirial   ? GMX_PME_CALC_ENER_VIR : 0) |
 921         (stepWork.computeEnergy ? GMX_PME_CALC_ENER_VIR : 0) |
 922         (stepWork.computeForces   ? GMX_PME_CALC_F : 0);
 923
 924     // Switches on whether to use GPU for position and force buffer operations
 925     // TODO consider all possible combinations of triggers, and how to combine optimally in each case.
 926     const BufferOpsUseGpu useGpuXBufOps = (c_enableGpuBufOps && bUseGPU && (GMX_GPU == GMX_GPU_CUDA)) ?
 927         BufferOpsUseGpu::True : BufferOpsUseGpu::False;;
 928     // GPU Force buffer ops are disabled on virial steps, because the virial calc is not yet ported to GPU
 929     const BufferOpsUseGpu useGpuFBufOps = (c_enableGpuBufOps && bUseGPU && (GMX_GPU == GMX_GPU_CUDA))
 930         && !(stepWork.computeVirial || stepWork.computeEnergy) ?
 931         BufferOpsUseGpu::True : BufferOpsUseGpu::False;
 932     // TODO: move / add this flag to the internal PME GPU data structures
 933     const bool useGpuPmeFReduction = (useGpuFBufOps == BufferOpsUseGpu::True) &&
 934         thisRankHasDuty(cr, DUTY_PME) && useGpuPme; // only supported if this rank is perfoming PME on the GPU
 935
 936     /* At a search step we need to start the first balancing region
 937      * somewhere early inside the step after communication during domain
 938      * decomposition (and not during the previous step as usual).
 939      */
 940     if (stepWork.doNeighborSearch)
 941     {
 942         ddBalanceRegionHandler.openBeforeForceComputationCpu(DdAllowBalanceRegionReopen::yes);
 943     }
 944
 945     const int start  = 0;
 946     const int homenr = mdatoms->homenr;
 947
 948     clear_mat(vir_force);
 949
 950     if (stepWork.stateChanged)
 951     {
 952         if (inputrecNeedMutot(inputrec))
 953         {
 954             /* Calculate total (local) dipole moment in a temporary common array.
 955              * This makes it possible to sum them over nodes faster.
 956              */
 957             calc_mu(start, homenr,
 958                     x.unpaddedArrayRef(), mdatoms->chargeA, mdatoms->chargeB, mdatoms->nChargePerturbed,
 959                     mu, mu+DIM);
 960         }
 961     }
 962
 963     if (fr->ePBC != epbcNONE)
 964     {
 965         /* Compute shift vectors every step,
 966          * because of pressure coupling or box deformation!
 967          */
 968         if (stepWork.haveDynamicBox && stepWork.stateChanged)
 969         {
 970             calc_shifts(box, fr->shift_vec);
 971         }
 972
 973         if (bCalcCGCM)
 974         {
 975             put_atoms_in_box_omp(fr->ePBC, box, x.unpaddedArrayRef().subArray(0, homenr), gmx_omp_nthreads_get(emntDefault));
 976             inc_nrnb(nrnb, eNR_SHIFTX, homenr);
 977         }
 978         else if (EI_ENERGY_MINIMIZATION(inputrec->eI) && graph)
 979         {
 980             unshift_self(graph, box, as_rvec_array(x.unpaddedArrayRef().data()));
 981         }
 982     }
 983
 984     nbnxn_atomdata_copy_shiftvec(stepWork.haveDynamicBox,
 985                                  fr->shift_vec, nbv->nbat.get());
 986
 987 #if GMX_MPI
 988     if (!thisRankHasDuty(cr, DUTY_PME))
 989     {
 990         /* Send particle coordinates to the pme nodes.
 991          * Since this is only implemented for domain decomposition
 992          * and domain decomposition does not use the graph,
 993          * we do not need to worry about shifting.
 994          */
 995         gmx_pme_send_coordinates(cr, box, as_rvec_array(x.unpaddedArrayRef().data()),
 996                                  lambda[efptCOUL], lambda[efptVDW],
 997                                  (stepWork.computeVirial || stepWork.computeEnergy),
 998                                  step, wcycle);
 999     }
1000 #endif /* GMX_MPI */
1001
1002     if (useGpuPme)
1003     {
1004         launchPmeGpuSpread(fr->pmedata, box, as_rvec_array(x.unpaddedArrayRef().data()), stepWork, pmeFlags, useGpuPmeFReduction, wcycle);
1005     }
1006
1007     /* do gridding for pair search */
1008     if (stepWork.doNeighborSearch)
1009     {
1010         if (graph && stepWork.stateChanged)
1011         {
1012             /* Calculate intramolecular shift vectors to make molecules whole */
1013             mk_mshift(fplog, graph, fr->ePBC, box, as_rvec_array(x.unpaddedArrayRef().data()));
1014         }
1015
1016         // TODO
1017         // - vzero is constant, do we need to pass it?
1018         // - box_diag should be passed directly to nbnxn_put_on_grid
1019         //
1020         rvec vzero;
1021         clear_rvec(vzero);
1022
1023         rvec box_diag;
1024         box_diag[XX] = box[XX][XX];
1025         box_diag[YY] = box[YY][YY];
1026         box_diag[ZZ] = box[ZZ][ZZ];
1027
1028         wallcycle_start(wcycle, ewcNS);
1029         if (!DOMAINDECOMP(cr))
1030         {
1031             wallcycle_sub_start(wcycle, ewcsNBS_GRID_LOCAL);
1032             nbnxn_put_on_grid(nbv, box,
1033                               0, vzero, box_diag,
1034                               nullptr, 0, mdatoms->homenr, -1,
1035                               fr->cginfo, x.unpaddedArrayRef(),
1036                               0, nullptr);
1037             wallcycle_sub_stop(wcycle, ewcsNBS_GRID_LOCAL);
1038         }
1039         else
1040         {
1041             wallcycle_sub_start(wcycle, ewcsNBS_GRID_NONLOCAL);
1042             nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd),
1043                                        fr->cginfo, x.unpaddedArrayRef());
1044             wallcycle_sub_stop(wcycle, ewcsNBS_GRID_NONLOCAL);
1045         }
1046
1047         nbv->setAtomProperties(*mdatoms, fr->cginfo);
1048
1049         wallcycle_stop(wcycle, ewcNS);
1050
1051         /* initialize the GPU nbnxm atom data and bonded data structures */
1052         if (bUseGPU)
1053         {
1054             wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
1055
1056             wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1057             Nbnxm::gpu_init_atomdata(nbv->gpu_nbv, nbv->nbat.get());
1058             wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1059
1060             if (fr->gpuBonded)
1061             {
1062                 /* Now we put all atoms on the grid, we can assign bonded
1063                  * interactions to the GPU, where the grid order is
1064                  * needed. Also the xq, f and fshift device buffers have
1065                  * been reallocated if needed, so the bonded code can
1066                  * learn about them. */
1067                 // TODO the xq, f, and fshift buffers are now shared
1068                 // resources, so they should be maintained by a
1069                 // higher-level object than the nb module.
1070                 fr->gpuBonded->updateInteractionListsAndDeviceBuffers(nbv->getGridIndices(),
1071                                                                       top->idef,
1072                                                                       Nbnxm::gpu_get_xq(nbv->gpu_nbv),
1073                                                                       Nbnxm::gpu_get_f(nbv->gpu_nbv),
1074                                                                       Nbnxm::gpu_get_fshift(nbv->gpu_nbv));
1075             }
1076             wallcycle_stop(wcycle, ewcLAUNCH_GPU);
1077         }
1078     }
1079
1080     if (stepWork.doNeighborSearch)
1081     {
1082         // Need to run after the GPU-offload bonded interaction lists
1083         // are set up to be able to determine whether there is bonded work.
1084         setupDomainLifetimeWorkload(&runScheduleWork->domainWork,
1085                                     *inputrec,
1086                                     *fr,
1087                                     pull_work,
1088                                     ed,
1089                                     top->idef,
1090                                     *fcd,
1091                                     *mdatoms,
1092                                     stepWork);
1093     }
1094
1095     const gmx::DomainLifetimeWorkload &domainWork = runScheduleWork->domainWork;
1096
1097     /* do local pair search */
1098     if (stepWork.doNeighborSearch)
1099     {
1100         // TODO: fuse this branch with the above stepWork.doNeighborSearch block
1101         wallcycle_start_nocount(wcycle, ewcNS);
1102         wallcycle_sub_start(wcycle, ewcsNBS_SEARCH_LOCAL);
1103         /* Note that with a GPU the launch overhead of the list transfer is not timed separately */
1104         nbv->constructPairlist(Nbnxm::InteractionLocality::Local,
1105                                &top->excls, step, nrnb);
1106
1107         nbv->setupGpuShortRangeWork(fr->gpuBonded, Nbnxm::InteractionLocality::Local);
1108
1109         wallcycle_sub_stop(wcycle, ewcsNBS_SEARCH_LOCAL);
1110         wallcycle_stop(wcycle, ewcNS);
1111
1112         if (useGpuXBufOps == BufferOpsUseGpu::True)
1113         {
1114             nbv->atomdata_init_copy_x_to_nbat_x_gpu();
1115         }
1116         // For force buffer ops, we use the below conditon rather than
1117         // useGpuFBufOps to ensure that init is performed even if this
1118         // NS step is also a virial step (on which f buf ops are deactivated).
1119         if (c_enableGpuBufOps && bUseGPU && (GMX_GPU == GMX_GPU_CUDA))
1120         {
1121             nbv->atomdata_init_add_nbat_f_to_f_gpu();
1122         }
1123     }
1124     else if (!EI_TPI(inputrec->eI))
1125     {
1126         if (useGpuXBufOps == BufferOpsUseGpu::True)
1127         {
1128             // The condition here was (pme != nullptr && pme_gpu_get_device_x(fr->pmedata) != nullptr)
1129             if (!useGpuPme)
1130             {
1131                 nbv->copyCoordinatesToGpu(Nbnxm::AtomLocality::Local, false,
1132                                           x.unpaddedArrayRef());
1133             }
1134             nbv->convertCoordinatesGpu(Nbnxm::AtomLocality::Local, false,
1135                                        useGpuPme ? pme_gpu_get_device_x(fr->pmedata) : nbv->getDeviceCoordinates());
1136         }
1137         else
1138         {
1139             nbv->convertCoordinates(Nbnxm::AtomLocality::Local, false,
1140                                     x.unpaddedArrayRef());
1141         }
1142     }
1143
1144     if (bUseGPU)
1145     {
1146         ddBalanceRegionHandler.openBeforeForceComputationGpu();
1147
1148         wallcycle_start(wcycle, ewcLAUNCH_GPU);
1149
1150         wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1151         Nbnxm::gpu_upload_shiftvec(nbv->gpu_nbv, nbv->nbat.get());
1152         if (stepWork.doNeighborSearch || (useGpuXBufOps == BufferOpsUseGpu::False))
1153         {
1154             Nbnxm::gpu_copy_xq_to_gpu(nbv->gpu_nbv, nbv->nbat.get(),
1155                                       Nbnxm::AtomLocality::Local);
1156         }
1157         wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1158         // with X buffer ops offloaded to the GPU on all but the search steps
1159
1160         // bonded work not split into separate local and non-local, so with DD
1161         // we can only launch the kernel after non-local coordinates have been received.
1162         if (domainWork.haveGpuBondedWork && !havePPDomainDecomposition(cr))
1163         {
1164             wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_BONDED);
1165             fr->gpuBonded->launchKernel(fr, stepWork, box);
1166             wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_BONDED);
1167         }
1168
1169         /* launch local nonbonded work on GPU */
1170         wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1171         do_nb_verlet(fr, ic, enerd, stepWork, Nbnxm::InteractionLocality::Local, enbvClearFNo,
1172                      step, nrnb, wcycle);
1173         wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1174         wallcycle_stop(wcycle, ewcLAUNCH_GPU);
1175     }
1176
1177     if (useGpuPme)
1178     {
1179         // In PME GPU and mixed mode we launch FFT / gather after the
1180         // X copy/transform to allow overlap as well as after the GPU NB
1181         // launch to avoid FFT launch overhead hijacking the CPU and delaying
1182         // the nonbonded kernel.
1183         launchPmeGpuFftAndGather(fr->pmedata, wcycle);
1184     }
1185
1186     // TODO Update this comment when introducing SimulationWorkload
1187     //
1188     // The conditions for gpuHaloExchange e.g. using GPU buffer
1189     // operations were checked before construction, so here we can
1190     // just use it and assert upon any conditions.
1191     gmx::GpuHaloExchange *gpuHaloExchange              = (havePPDomainDecomposition(cr) ? cr->dd->gpuHaloExchange.get() : nullptr);
1192     const bool            ddUsesGpuDirectCommunication = (gpuHaloExchange != nullptr);
1193     GMX_ASSERT(!ddUsesGpuDirectCommunication || (useGpuXBufOps == BufferOpsUseGpu::True),
1194                "Must use coordinate buffer ops with GPU halo exchange");
1195
1196     /* Communicate coordinates and sum dipole if necessary +
1197        do non-local pair search */
1198     if (havePPDomainDecomposition(cr))
1199     {
1200         if (stepWork.doNeighborSearch)
1201         {
1202             // TODO: fuse this branch with the above large stepWork.doNeighborSearch block
1203             wallcycle_start_nocount(wcycle, ewcNS);
1204             wallcycle_sub_start(wcycle, ewcsNBS_SEARCH_NONLOCAL);
1205             /* Note that with a GPU the launch overhead of the list transfer is not timed separately */
1206             nbv->constructPairlist(Nbnxm::InteractionLocality::NonLocal,
1207                                    &top->excls, step, nrnb);
1208
1209             nbv->setupGpuShortRangeWork(fr->gpuBonded, Nbnxm::InteractionLocality::NonLocal);
1210             wallcycle_sub_stop(wcycle, ewcsNBS_SEARCH_NONLOCAL);
1211             wallcycle_stop(wcycle, ewcNS);
1212             if (ddUsesGpuDirectCommunication)
1213             {
1214                 rvec* d_x    = static_cast<rvec *> (nbv->get_gpu_xrvec());
1215                 rvec* d_f    = static_cast<rvec *> (nbv->get_gpu_frvec());
1216                 gpuHaloExchange->reinitHalo(d_x, d_f);
1217             }
1218         }
1219         else
1220         {
1221             if (ddUsesGpuDirectCommunication)
1222             {
1223                 // The following must be called after local setCoordinates (which records an event
1224                 // when the coordinate data has been copied to the device).
1225                 gpuHaloExchange->communicateHaloCoordinates(box);
1226
1227                 if (domainWork.haveCpuBondedWork || domainWork.haveFreeEnergyWork)
1228                 {
1229                     //non-local part of coordinate buffer must be copied back to host for CPU work
1230                     nbv->launch_copy_x_from_gpu(as_rvec_array(x.unpaddedArrayRef().data()), Nbnxm::AtomLocality::NonLocal);
1231                 }
1232             }
1233             else
1234             {
1235                 dd_move_x(cr->dd, box, x.unpaddedArrayRef(), wcycle);
1236             }
1237
1238             if (useGpuXBufOps == BufferOpsUseGpu::True)
1239             {
1240                 // The condition here was (pme != nullptr && pme_gpu_get_device_x(fr->pmedata) != nullptr)
1241                 if (!useGpuPme && !ddUsesGpuDirectCommunication)
1242                 {
1243                     nbv->copyCoordinatesToGpu(Nbnxm::AtomLocality::NonLocal, false,
1244                                               x.unpaddedArrayRef());
1245                 }
1246                 nbv->convertCoordinatesGpu(Nbnxm::AtomLocality::NonLocal, false,
1247                                            useGpuPme ? pme_gpu_get_device_x(fr->pmedata) : nbv->getDeviceCoordinates());
1248             }
1249             else
1250             {
1251                 nbv->convertCoordinates(Nbnxm::AtomLocality::NonLocal, false,
1252                                         x.unpaddedArrayRef());
1253             }
1254
1255         }
1256
1257         if (bUseGPU)
1258         {
1259             wallcycle_start(wcycle, ewcLAUNCH_GPU);
1260
1261             if (stepWork.doNeighborSearch || (useGpuXBufOps == BufferOpsUseGpu::False))
1262             {
1263                 wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1264                 Nbnxm::gpu_copy_xq_to_gpu(nbv->gpu_nbv, nbv->nbat.get(),
1265                                           Nbnxm::AtomLocality::NonLocal);
1266                 wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1267             }
1268
1269             if (domainWork.haveGpuBondedWork)
1270             {
1271                 wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_BONDED);
1272                 fr->gpuBonded->launchKernel(fr, stepWork, box);
1273                 wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_BONDED);
1274             }
1275
1276             /* launch non-local nonbonded tasks on GPU */
1277             wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1278             do_nb_verlet(fr, ic, enerd, stepWork, Nbnxm::InteractionLocality::NonLocal, enbvClearFNo,
1279                          step, nrnb, wcycle);
1280             wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1281
1282             wallcycle_stop(wcycle, ewcLAUNCH_GPU);
1283         }
1284     }
1285
1286     if (bUseGPU)
1287     {
1288         /* launch D2H copy-back F */
1289         wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
1290         wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1291
1292         bool copyBackNbForce  = (useGpuFBufOps == BufferOpsUseGpu::False);
1293
1294         if (havePPDomainDecomposition(cr))
1295         {
1296             Nbnxm::gpu_launch_cpyback(nbv->gpu_nbv, nbv->nbat.get(),
1297                                       stepWork, Nbnxm::AtomLocality::NonLocal, copyBackNbForce);
1298         }
1299         Nbnxm::gpu_launch_cpyback(nbv->gpu_nbv, nbv->nbat.get(),
1300                                   stepWork, Nbnxm::AtomLocality::Local, copyBackNbForce);
1301         wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1302
1303         if (domainWork.haveGpuBondedWork && stepWork.computeEnergy)
1304         {
1305             fr->gpuBonded->launchEnergyTransfer();
1306         }
1307         wallcycle_stop(wcycle, ewcLAUNCH_GPU);
1308     }
1309
1310     if (stepWork.stateChanged && inputrecNeedMutot(inputrec))
1311     {
1312         if (PAR(cr))
1313         {
1314             gmx_sumd(2*DIM, mu, cr);
1315
1316             ddBalanceRegionHandler.reopenRegionCpu();
1317         }
1318
1319         for (i = 0; i < 2; i++)
1320         {
1321             for (j = 0; j < DIM; j++)
1322             {
1323                 fr->mu_tot[i][j] = mu[i*DIM + j];
1324             }
1325         }
1326     }
1327     if (mdatoms->nChargePerturbed == 0)
1328     {
1329         copy_rvec(fr->mu_tot[0], mu_tot);
1330     }
1331     else
1332     {
1333         for (j = 0; j < DIM; j++)
1334         {
1335             mu_tot[j] =
1336                 (1.0 - lambda[efptCOUL])*fr->mu_tot[0][j] +
1337                 lambda[efptCOUL]*fr->mu_tot[1][j];
1338         }
1339     }
1340
1341     /* Reset energies */
1342     reset_enerdata(enerd);
1343     /* Clear the shift forces */
1344     // TODO: This should be linked to the shift force buffer in use, or cleared before use instead
1345     for (gmx::RVec &elem : fr->shiftForces)
1346     {
1347         elem = { 0.0_real, 0.0_real, 0.0_real };
1348     }
1349
1350     if (DOMAINDECOMP(cr) && !thisRankHasDuty(cr, DUTY_PME))
1351     {
1352         wallcycle_start(wcycle, ewcPPDURINGPME);
1353         dd_force_flop_start(cr->dd, nrnb);
1354     }
1355
1356     if (inputrec->bRot)
1357     {
1358         wallcycle_start(wcycle, ewcROT);
1359         do_rotation(cr, enforcedRotation, box, as_rvec_array(x.unpaddedArrayRef().data()), t, step, stepWork.doNeighborSearch);
1360         wallcycle_stop(wcycle, ewcROT);
1361     }
1362
1363     /* Start the force cycle counter.
1364      * Note that a different counter is used for dynamic load balancing.
1365      */
1366     wallcycle_start(wcycle, ewcFORCE);
1367
1368     // Set up and clear force outputs.
1369     // We use std::move to keep the compiler happy, it has no effect.
1370     ForceOutputs forceOut = setupForceOutputs(fr, pull_work, *inputrec, std::move(force), stepWork, wcycle);
1371
1372     /* We calculate the non-bonded forces, when done on the CPU, here.
1373      * We do this before calling do_force_lowlevel, because in that
1374      * function, the listed forces are calculated before PME, which
1375      * does communication.  With this order, non-bonded and listed
1376      * force calculation imbalance can be balanced out by the domain
1377      * decomposition load balancing.
1378      */
1379
1380     if (!bUseOrEmulGPU)
1381     {
1382         do_nb_verlet(fr, ic, enerd, stepWork, Nbnxm::InteractionLocality::Local, enbvClearFYes,
1383                      step, nrnb, wcycle);
1384     }
1385
1386     if (fr->efep != efepNO)
1387     {
1388         /* Calculate the local and non-local free energy interactions here.
1389          * Happens here on the CPU both with and without GPU.
1390          */
1391         nbv->dispatchFreeEnergyKernel(Nbnxm::InteractionLocality::Local,
1392                                       fr, as_rvec_array(x.unpaddedArrayRef().data()), &forceOut.forceWithShiftForces(), *mdatoms,
1393                                       inputrec->fepvals, lambda.data(),
1394                                       enerd, stepWork, nrnb);
1395
1396         if (havePPDomainDecomposition(cr))
1397         {
1398             nbv->dispatchFreeEnergyKernel(Nbnxm::InteractionLocality::NonLocal,
1399                                           fr, as_rvec_array(x.unpaddedArrayRef().data()), &forceOut.forceWithShiftForces(), *mdatoms,
1400                                           inputrec->fepvals, lambda.data(),
1401                                           enerd, stepWork, nrnb);
1402         }
1403     }
1404
1405     if (!bUseOrEmulGPU)
1406     {
1407         if (havePPDomainDecomposition(cr))
1408         {
1409             do_nb_verlet(fr, ic, enerd, stepWork, Nbnxm::InteractionLocality::NonLocal, enbvClearFNo,
1410                          step, nrnb, wcycle);
1411         }
1412
1413         if (stepWork.computeForces)
1414         {
1415             /* Add all the non-bonded force to the normal force array.
1416              * This can be split into a local and a non-local part when overlapping
1417              * communication with calculation with domain decomposition.
1418              */
1419             wallcycle_stop(wcycle, ewcFORCE);
1420             nbv->atomdata_add_nbat_f_to_f(Nbnxm::AtomLocality::All, forceOut.forceWithShiftForces().force());
1421             wallcycle_start_nocount(wcycle, ewcFORCE);
1422         }
1423
1424         /* If there are multiple fshift output buffers we need to reduce them */
1425         if (stepWork.computeVirial)
1426         {
1427             /* This is not in a subcounter because it takes a
1428                negligible and constant-sized amount of time */
1429             nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat,
1430                                                      forceOut.forceWithShiftForces().shiftForces());
1431         }
1432     }
1433
1434     /* update QMMMrec, if necessary */
1435     if (fr->bQMMM)
1436     {
1437         update_QMMMrec(cr, fr, as_rvec_array(x.unpaddedArrayRef().data()), mdatoms, box);
1438     }
1439
1440     // TODO Force flags should include haveFreeEnergyWork for this domain
1441     if (ddUsesGpuDirectCommunication &&
1442         (domainWork.haveCpuBondedWork || domainWork.haveFreeEnergyWork))
1443     {
1444         /* Wait for non-local coordinate data to be copied from device */
1445         nbv->wait_nonlocal_x_copy_D2H_done();
1446     }
1447     /* Compute the bonded and non-bonded energies and optionally forces */
1448     do_force_lowlevel(fr, inputrec, &(top->idef),
1449                       cr, ms, nrnb, wcycle, mdatoms,
1450                       x, hist, &forceOut, enerd, fcd,
1451                       box, lambda.data(), graph, fr->mu_tot,
1452                       stepWork,
1453                       ddBalanceRegionHandler);
1454
1455     wallcycle_stop(wcycle, ewcFORCE);
1456
1457     computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation,
1458                          imdSession, pull_work, step, t, wcycle,
1459                          fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda.data(),
1460                          stepWork, &forceOut.forceWithVirial(), enerd,
1461                          ed, stepWork.doNeighborSearch);
1462
1463
1464     // Will store the amount of cycles spent waiting for the GPU that
1465     // will be later used in the DLB accounting.
1466     float cycles_wait_gpu = 0;
1467     if (bUseOrEmulGPU)
1468     {
1469         auto &forceWithShiftForces = forceOut.forceWithShiftForces();
1470
1471         /* wait for non-local forces (or calculate in emulation mode) */
1472         if (havePPDomainDecomposition(cr))
1473         {
1474             if (bUseGPU)
1475             {
1476                 cycles_wait_gpu += Nbnxm::gpu_wait_finish_task(nbv->gpu_nbv,
1477                                                                stepWork, Nbnxm::AtomLocality::NonLocal,
1478                                                                enerd->grpp.ener[egLJSR].data(),
1479                                                                enerd->grpp.ener[egCOULSR].data(),
1480                                                                forceWithShiftForces.shiftForces(),
1481                                                                wcycle);
1482             }
1483             else
1484             {
1485                 wallcycle_start_nocount(wcycle, ewcFORCE);
1486                 do_nb_verlet(fr, ic, enerd, stepWork, Nbnxm::InteractionLocality::NonLocal, enbvClearFYes,
1487                              step, nrnb, wcycle);
1488                 wallcycle_stop(wcycle, ewcFORCE);
1489             }
1490
1491             if (useGpuFBufOps == BufferOpsUseGpu::True)
1492             {
1493                 // TODO: move this into DomainLifetimeWorkload, including the second part of the condition
1494                 // The bonded and free energy CPU tasks can have non-local force contributions
1495                 // which are a dependency for the GPU force reduction.
1496                 bool  haveNonLocalForceContribInCpuBuffer = domainWork.haveCpuBondedWork || domainWork.haveFreeEnergyWork;
1497
1498                 rvec *f = as_rvec_array(forceWithShiftForces.force().data());
1499                 if (haveNonLocalForceContribInCpuBuffer)
1500                 {
1501                     nbv->launch_copy_f_to_gpu(f, Nbnxm::AtomLocality::NonLocal);
1502                 }
1503                 nbv->atomdata_add_nbat_f_to_f_gpu(Nbnxm::AtomLocality::NonLocal,
1504                                                   nbv->getDeviceForces(),
1505                                                   pme_gpu_get_device_f(fr->pmedata),
1506                                                   pme_gpu_get_f_ready_synchronizer(fr->pmedata),
1507                                                   useGpuPmeFReduction, haveNonLocalForceContribInCpuBuffer);
1508                 nbv->launch_copy_f_from_gpu(f, Nbnxm::AtomLocality::NonLocal);
1509             }
1510             else
1511             {
1512                 nbv->atomdata_add_nbat_f_to_f(Nbnxm::AtomLocality::NonLocal,
1513                                               forceWithShiftForces.force());
1514             }
1515
1516
1517             if (fr->nbv->emulateGpu() && stepWork.computeVirial)
1518             {
1519                 nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat,
1520                                                          forceWithShiftForces.shiftForces());
1521             }
1522         }
1523     }
1524
1525     const bool useGpuForcesHaloExchange = ddUsesGpuDirectCommunication && (useGpuFBufOps == BufferOpsUseGpu::True);
1526     const bool useCpuPmeFReduction      = thisRankHasDuty(cr, DUTY_PME) && !useGpuPmeFReduction;
1527     // TODO: move this into DomainLifetimeWorkload, including the second part of the condition
1528     const bool haveCpuLocalForces     = (domainWork.haveSpecialForces || domainWork.haveCpuListedForceWork || useCpuPmeFReduction ||
1529                                          (fr->efep != efepNO));
1530
1531     if (havePPDomainDecomposition(cr))
1532     {
1533         /* We are done with the CPU compute.
1534          * We will now communicate the non-local forces.
1535          * If we use a GPU this will overlap with GPU work, so in that case
1536          * we do not close the DD force balancing region here.
1537          */
1538         ddBalanceRegionHandler.closeAfterForceComputationCpu();
1539
1540         if (stepWork.computeForces)
1541         {
1542             gmx::ArrayRef<gmx::RVec>  force  = forceOut.forceWithShiftForces().force();
1543             rvec                     *f      = as_rvec_array(force.data());
1544
1545             if (useGpuForcesHaloExchange)
1546             {
1547                 if (haveCpuLocalForces)
1548                 {
1549                     nbv->launch_copy_f_to_gpu(f, Nbnxm::AtomLocality::Local);
1550                 }
1551                 bool accumulateHaloForces = haveCpuLocalForces;
1552                 gpuHaloExchange->communicateHaloForces(accumulateHaloForces);
1553             }
1554             else
1555             {
1556                 if (useGpuFBufOps == BufferOpsUseGpu::True)
1557                 {
1558                     nbv->wait_for_gpu_force_reduction(Nbnxm::AtomLocality::NonLocal);
1559                 }
1560                 dd_move_f(cr->dd, &forceOut.forceWithShiftForces(), wcycle);
1561             }
1562
1563         }
1564     }
1565
1566     // With both nonbonded and PME offloaded a GPU on the same rank, we use
1567     // an alternating wait/reduction scheme.
1568     bool alternateGpuWait = (!c_disableAlternatingWait && useGpuPme && bUseGPU && !DOMAINDECOMP(cr) &&
1569                              (useGpuFBufOps == BufferOpsUseGpu::False));
1570     if (alternateGpuWait)
1571     {
1572         alternatePmeNbGpuWaitReduce(fr->nbv.get(), fr->pmedata, &forceOut, enerd,
1573                                     stepWork, pmeFlags, wcycle);
1574     }
1575
1576     if (!alternateGpuWait && useGpuPme)
1577     {
1578         pme_gpu_wait_and_reduce(fr->pmedata, pmeFlags, wcycle, &forceOut.forceWithVirial(), enerd);
1579     }
1580
1581     /* Wait for local GPU NB outputs on the non-alternating wait path */
1582     if (!alternateGpuWait && bUseGPU)
1583     {
1584         /* Measured overhead on CUDA and OpenCL with(out) GPU sharing
1585          * is between 0.5 and 1.5 Mcycles. So 2 MCycles is an overestimate,
1586          * but even with a step of 0.1 ms the difference is less than 1%
1587          * of the step time.
1588          */
1589         const float gpuWaitApiOverheadMargin = 2e6F; /* cycles */
1590         const float waitCycles               =
1591             Nbnxm::gpu_wait_finish_task(nbv->gpu_nbv,
1592                                         stepWork, Nbnxm::AtomLocality::Local,
1593                                         enerd->grpp.ener[egLJSR].data(),
1594                                         enerd->grpp.ener[egCOULSR].data(),
1595                                         forceOut.forceWithShiftForces().shiftForces(),
1596                                         wcycle);
1597
1598         if (ddBalanceRegionHandler.useBalancingRegion())
1599         {
1600             DdBalanceRegionWaitedForGpu waitedForGpu = DdBalanceRegionWaitedForGpu::yes;
1601             if (stepWork.computeForces &&  waitCycles <= gpuWaitApiOverheadMargin)
1602             {
1603                 /* We measured few cycles, it could be that the kernel
1604                  * and transfer finished earlier and there was no actual
1605                  * wait time, only API call overhead.
1606                  * Then the actual time could be anywhere between 0 and
1607                  * cycles_wait_est. We will use half of cycles_wait_est.
1608                  */
1609                 waitedForGpu = DdBalanceRegionWaitedForGpu::no;
1610             }
1611             ddBalanceRegionHandler.closeAfterForceComputationGpu(cycles_wait_gpu, waitedForGpu);
1612         }
1613     }
1614
1615     if (fr->nbv->emulateGpu())
1616     {
1617         // NOTE: emulation kernel is not included in the balancing region,
1618         // but emulation mode does not target performance anyway
1619         wallcycle_start_nocount(wcycle, ewcFORCE);
1620         do_nb_verlet(fr, ic, enerd, stepWork, Nbnxm::InteractionLocality::Local,
1621                      DOMAINDECOMP(cr) ? enbvClearFNo : enbvClearFYes,
1622                      step, nrnb, wcycle);
1623         wallcycle_stop(wcycle, ewcFORCE);
1624     }
1625
1626     /* Do the nonbonded GPU (or emulation) force buffer reduction
1627      * on the non-alternating path. */
1628     if (bUseOrEmulGPU && !alternateGpuWait)
1629     {
1630         gmx::ArrayRef<gmx::RVec>  forceWithShift = forceOut.forceWithShiftForces().force();
1631
1632         if (useGpuFBufOps == BufferOpsUseGpu::True)
1633         {
1634             // Flag to specify whether the CPU force buffer has contributions to
1635             // local atoms. This depends on whether there are CPU-based force tasks
1636             // or when DD is active the halo exchange has resulted in contributions
1637             // from the non-local part.
1638             const bool haveLocalForceContribInCpuBuffer = (haveCpuLocalForces || havePPDomainDecomposition(cr));
1639
1640             // TODO: move these steps as early as possible:
1641             // - CPU f H2D should be as soon as all CPU-side forces are done
1642             // - wait for force reduction does not need to block host (at least not here, it's sufficient to wait
1643             //   before the next CPU task that consumes the forces: vsite spread or update)
1644             // - copy is not perfomed if GPU force halo exchange is active, because it would overwrite the result
1645             //   of the halo exchange. In that case the copy is instead performed above, before the exchange.
1646             //   These should be unified.
1647             rvec *f = as_rvec_array(forceWithShift.data());
1648             if (haveLocalForceContribInCpuBuffer && !useGpuForcesHaloExchange)
1649             {
1650                 nbv->launch_copy_f_to_gpu(f, Nbnxm::AtomLocality::Local);
1651             }
1652             if (useGpuForcesHaloExchange)
1653             {
1654                 // Add a stream synchronization to satisfy a dependency
1655                 // for the local buffer ops on the result of GPU halo
1656                 // exchange, which operates in the non-local stream and
1657                 // writes to to local parf og the force buffer.
1658                 // TODO improve this through use of an event - see Redmine #3093
1659                 nbv->stream_local_wait_for_nonlocal();
1660             }
1661             nbv->atomdata_add_nbat_f_to_f_gpu(Nbnxm::AtomLocality::Local,
1662                                               nbv->getDeviceForces(),
1663                                               pme_gpu_get_device_f(fr->pmedata),
1664                                               pme_gpu_get_f_ready_synchronizer(fr->pmedata),
1665                                               useGpuPmeFReduction, haveLocalForceContribInCpuBuffer);
1666             nbv->launch_copy_f_from_gpu(f, Nbnxm::AtomLocality::Local);
1667             nbv->wait_for_gpu_force_reduction(Nbnxm::AtomLocality::Local);
1668         }
1669         else
1670         {
1671             nbv->atomdata_add_nbat_f_to_f(Nbnxm::AtomLocality::Local, forceWithShift);
1672         }
1673
1674     }
1675
1676     launchGpuEndOfStepTasks(nbv, fr->gpuBonded, fr->pmedata, enerd,
1677                             *runScheduleWork,
1678                             bUseGPU, useGpuPme,
1679                             step,
1680                             wcycle);
1681
1682     if (DOMAINDECOMP(cr))
1683     {
1684         dd_force_flop_stop(cr->dd, nrnb);
1685     }
1686
1687     if (stepWork.computeForces)
1688     {
1689         rvec *f = as_rvec_array(forceOut.forceWithShiftForces().force().data());
1690
1691         /* If we have NoVirSum forces, but we do not calculate the virial,
1692          * we sum fr->f_novirsum=forceOut.f later.
1693          */
1694         if (vsite && !(fr->haveDirectVirialContributions && !stepWork.computeVirial))
1695         {
1696             rvec *fshift = as_rvec_array(forceOut.forceWithShiftForces().shiftForces().data());
1697             spread_vsite_f(vsite, as_rvec_array(x.unpaddedArrayRef().data()), f, fshift, FALSE, nullptr, nrnb,
1698                            &top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr, wcycle);
1699         }
1700
1701         if (stepWork.computeVirial)
1702         {
1703             /* Calculation of the virial must be done after vsites! */
1704             calc_virial(0, mdatoms->homenr, as_rvec_array(x.unpaddedArrayRef().data()),
1705                         forceOut.forceWithShiftForces(),
1706                         vir_force, graph, box, nrnb, fr, inputrec->ePBC);
1707         }
1708     }
1709
1710     if (PAR(cr) && !thisRankHasDuty(cr, DUTY_PME))
1711     {
1712         /* In case of node-splitting, the PP nodes receive the long-range
1713          * forces, virial and energy from the PME nodes here.
1714          */
1715         pme_receive_force_ener(cr, &forceOut.forceWithVirial(), enerd, wcycle);
1716     }
1717
1718     if (stepWork.computeForces)
1719     {
1720         post_process_forces(cr, step, nrnb, wcycle,
1721                             top, box, as_rvec_array(x.unpaddedArrayRef().data()), &forceOut,
1722                             vir_force, mdatoms, graph, fr, vsite,
1723                             stepWork);
1724     }
1725
1726     if (stepWork.computeEnergy)
1727     {
1728         /* Sum the potential energy terms from group contributions */
1729         sum_epot(&(enerd->grpp), enerd->term);
1730
1731         if (!EI_TPI(inputrec->eI))
1732         {
1733             checkPotentialEnergyValidity(step, *enerd, *inputrec);
1734         }
1735     }
1736
1737     /* In case we don't have constraints and are using GPUs, the next balancing
1738      * region starts here.
1739      * Some "special" work at the end of do_force_cuts?, such as vsite spread,
1740      * virial calculation and COM pulling, is not thus not included in
1741      * the balance timing, which is ok as most tasks do communication.
1742      */
1743     ddBalanceRegionHandler.openBeforeForceComputationCpu(DdAllowBalanceRegionReopen::no);
1744 }