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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/ewald/pme_pp_comm_gpu.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/mdtypes/state_propagator_data_gpu.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/fixedcapacityvector.h"
110 #include "gromacs/utility/gmxassert.h"
111 #include "gromacs/utility/gmxmpi.h"
112 #include "gromacs/utility/logger.h"
113 #include "gromacs/utility/smalloc.h"
114 #include "gromacs/utility/strconvert.h"
115 #include "gromacs/utility/sysinfo.h"
117 using gmx::AtomLocality;
118 using gmx::DomainLifetimeWorkload;
119 using gmx::ForceOutputs;
120 using gmx::InteractionLocality;
121 using gmx::SimulationWorkload;
122 using gmx::StepWorkload;
124 // TODO: this environment variable allows us to verify before release
125 // that on less common architectures the total cost of polling is not larger than
126 // a blocking wait (so polling does not introduce overhead when the static
127 // PME-first ordering would suffice).
128 static const bool c_disableAlternatingWait = (getenv("GMX_DISABLE_ALTERNATING_GPU_WAIT") != nullptr);
130 static void sum_forces(rvec f[], gmx::ArrayRef<const gmx::RVec> forceToAdd)
132 const int end = forceToAdd.size();
134 int gmx_unused nt = gmx_omp_nthreads_get(emntDefault);
135 #pragma omp parallel for num_threads(nt) schedule(static)
136 for (int i = 0; i < end; i++)
138 rvec_inc(f[i], forceToAdd[i]);
142 static void calc_virial(int start,
145 const gmx::ForceWithShiftForces& forceWithShiftForces,
147 const t_graph* graph,
150 const t_forcerec* fr,
153 /* The short-range virial from surrounding boxes */
154 const rvec* fshift = as_rvec_array(forceWithShiftForces.shiftForces().data());
155 calc_vir(SHIFTS, fr->shift_vec, fshift, vir_part, ePBC == epbcSCREW, box);
156 inc_nrnb(nrnb, eNR_VIRIAL, SHIFTS);
158 /* Calculate partial virial, for local atoms only, based on short range.
159 * Total virial is computed in global_stat, called from do_md
161 const rvec* f = as_rvec_array(forceWithShiftForces.force().data());
162 f_calc_vir(start, start + homenr, x, f, vir_part, graph, box);
163 inc_nrnb(nrnb, eNR_VIRIAL, homenr);
167 pr_rvecs(debug, 0, "vir_part", vir_part, DIM);
171 static void pull_potential_wrapper(const t_commrec* cr,
172 const t_inputrec* ir,
174 gmx::ArrayRef<const gmx::RVec> x,
175 gmx::ForceWithVirial* force,
176 const t_mdatoms* mdatoms,
177 gmx_enerdata_t* enerd,
181 gmx_wallcycle_t wcycle)
186 /* Calculate the center of mass forces, this requires communication,
187 * which is why pull_potential is called close to other communication.
189 wallcycle_start(wcycle, ewcPULLPOT);
190 set_pbc(&pbc, ir->ePBC, box);
192 enerd->term[F_COM_PULL] += pull_potential(pull_work, mdatoms, &pbc, cr, t, lambda[efptRESTRAINT],
193 as_rvec_array(x.data()), force, &dvdl);
194 enerd->dvdl_lin[efptRESTRAINT] += dvdl;
195 wallcycle_stop(wcycle, ewcPULLPOT);
198 static void pme_receive_force_ener(t_forcerec* fr,
200 gmx::ForceWithVirial* forceWithVirial,
201 gmx_enerdata_t* enerd,
202 bool useGpuPmePpComms,
203 bool receivePmeForceToGpu,
204 gmx_wallcycle_t wcycle)
206 real e_q, e_lj, dvdl_q, dvdl_lj;
207 float cycles_ppdpme, cycles_seppme;
209 cycles_ppdpme = wallcycle_stop(wcycle, ewcPPDURINGPME);
210 dd_cycles_add(cr->dd, cycles_ppdpme, ddCyclPPduringPME);
212 /* In case of node-splitting, the PP nodes receive the long-range
213 * forces, virial and energy from the PME nodes here.
215 wallcycle_start(wcycle, ewcPP_PMEWAITRECVF);
218 gmx_pme_receive_f(fr->pmePpCommGpu.get(), cr, forceWithVirial, &e_q, &e_lj, &dvdl_q, &dvdl_lj,
219 useGpuPmePpComms, receivePmeForceToGpu, &cycles_seppme);
220 enerd->term[F_COUL_RECIP] += e_q;
221 enerd->term[F_LJ_RECIP] += e_lj;
222 enerd->dvdl_lin[efptCOUL] += dvdl_q;
223 enerd->dvdl_lin[efptVDW] += dvdl_lj;
227 dd_cycles_add(cr->dd, cycles_seppme, ddCyclPME);
229 wallcycle_stop(wcycle, ewcPP_PMEWAITRECVF);
232 static void print_large_forces(FILE* fp,
240 real force2Tolerance = gmx::square(forceTolerance);
241 gmx::index numNonFinite = 0;
242 for (int i = 0; i < md->homenr; i++)
244 real force2 = norm2(f[i]);
245 bool nonFinite = !std::isfinite(force2);
246 if (force2 >= force2Tolerance || nonFinite)
248 fprintf(fp, "step %" PRId64 " atom %6d x %8.3f %8.3f %8.3f force %12.5e\n", step,
249 ddglatnr(cr->dd, i), x[i][XX], x[i][YY], x[i][ZZ], std::sqrt(force2));
256 if (numNonFinite > 0)
258 /* Note that with MPI this fatal call on one rank might interrupt
259 * the printing on other ranks. But we can only avoid that with
260 * an expensive MPI barrier that we would need at each step.
262 gmx_fatal(FARGS, "At step %" PRId64 " detected non-finite forces on %td atoms", step, numNonFinite);
266 static void post_process_forces(const t_commrec* cr,
269 gmx_wallcycle_t wcycle,
270 const gmx_localtop_t* top,
273 ForceOutputs* forceOutputs,
275 const t_mdatoms* mdatoms,
276 const t_graph* graph,
277 const t_forcerec* fr,
278 const gmx_vsite_t* vsite,
279 const StepWorkload& stepWork)
281 rvec* f = as_rvec_array(forceOutputs->forceWithShiftForces().force().data());
283 if (fr->haveDirectVirialContributions)
285 auto& forceWithVirial = forceOutputs->forceWithVirial();
286 rvec* fDirectVir = as_rvec_array(forceWithVirial.force_.data());
290 /* Spread the mesh force on virtual sites to the other particles...
291 * This is parallellized. MPI communication is performed
292 * if the constructing atoms aren't local.
294 matrix virial = { { 0 } };
295 spread_vsite_f(vsite, x, fDirectVir, nullptr, stepWork.computeVirial, virial, nrnb,
296 &top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr, wcycle);
297 forceWithVirial.addVirialContribution(virial);
300 if (stepWork.computeVirial)
302 /* Now add the forces, this is local */
303 sum_forces(f, forceWithVirial.force_);
305 /* Add the direct virial contributions */
307 forceWithVirial.computeVirial_,
308 "forceWithVirial should request virial computation when we request the virial");
309 m_add(vir_force, forceWithVirial.getVirial(), vir_force);
313 pr_rvecs(debug, 0, "vir_force", vir_force, DIM);
318 if (fr->print_force >= 0)
320 print_large_forces(stderr, mdatoms, cr, step, fr->print_force, x, f);
324 static void do_nb_verlet(t_forcerec* fr,
325 const interaction_const_t* ic,
326 gmx_enerdata_t* enerd,
327 const StepWorkload& stepWork,
328 const InteractionLocality ilocality,
332 gmx_wallcycle_t wcycle)
334 if (!stepWork.computeNonbondedForces)
336 /* skip non-bonded calculation */
340 nonbonded_verlet_t* nbv = fr->nbv.get();
342 /* GPU kernel launch overhead is already timed separately */
343 if (fr->cutoff_scheme != ecutsVERLET)
345 gmx_incons("Invalid cut-off scheme passed!");
350 /* When dynamic pair-list pruning is requested, we need to prune
351 * at nstlistPrune steps.
353 if (nbv->isDynamicPruningStepCpu(step))
355 /* Prune the pair-list beyond fr->ic->rlistPrune using
356 * the current coordinates of the atoms.
358 wallcycle_sub_start(wcycle, ewcsNONBONDED_PRUNING);
359 nbv->dispatchPruneKernelCpu(ilocality, fr->shift_vec);
360 wallcycle_sub_stop(wcycle, ewcsNONBONDED_PRUNING);
364 nbv->dispatchNonbondedKernel(ilocality, *ic, stepWork, clearF, *fr, enerd, nrnb);
367 static inline void clear_rvecs_omp(int n, rvec v[])
369 int nth = gmx_omp_nthreads_get_simple_rvec_task(emntDefault, n);
371 /* Note that we would like to avoid this conditional by putting it
372 * into the omp pragma instead, but then we still take the full
373 * omp parallel for overhead (at least with gcc5).
377 for (int i = 0; i < n; i++)
384 #pragma omp parallel for num_threads(nth) schedule(static)
385 for (int i = 0; i < n; i++)
392 /*! \brief Return an estimate of the average kinetic energy or 0 when unreliable
394 * \param groupOptions Group options, containing T-coupling options
396 static real averageKineticEnergyEstimate(const t_grpopts& groupOptions)
398 real nrdfCoupled = 0;
399 real nrdfUncoupled = 0;
400 real kineticEnergy = 0;
401 for (int g = 0; g < groupOptions.ngtc; g++)
403 if (groupOptions.tau_t[g] >= 0)
405 nrdfCoupled += groupOptions.nrdf[g];
406 kineticEnergy += groupOptions.nrdf[g] * 0.5 * groupOptions.ref_t[g] * BOLTZ;
410 nrdfUncoupled += groupOptions.nrdf[g];
414 /* This conditional with > also catches nrdf=0 */
415 if (nrdfCoupled > nrdfUncoupled)
417 return kineticEnergy * (nrdfCoupled + nrdfUncoupled) / nrdfCoupled;
425 /*! \brief This routine checks that the potential energy is finite.
427 * Always checks that the potential energy is finite. If step equals
428 * inputrec.init_step also checks that the magnitude of the potential energy
429 * is reasonable. Terminates with a fatal error when a check fails.
430 * Note that passing this check does not guarantee finite forces,
431 * since those use slightly different arithmetics. But in most cases
432 * there is just a narrow coordinate range where forces are not finite
433 * and energies are finite.
435 * \param[in] step The step number, used for checking and printing
436 * \param[in] enerd The energy data; the non-bonded group energies need to be added to
437 * enerd.term[F_EPOT] before calling this routine \param[in] inputrec The input record
439 static void checkPotentialEnergyValidity(int64_t step, const gmx_enerdata_t& enerd, const t_inputrec& inputrec)
441 /* Threshold valid for comparing absolute potential energy against
442 * the kinetic energy. Normally one should not consider absolute
443 * potential energy values, but with a factor of one million
444 * we should never get false positives.
446 constexpr real c_thresholdFactor = 1e6;
448 bool energyIsNotFinite = !std::isfinite(enerd.term[F_EPOT]);
449 real averageKineticEnergy = 0;
450 /* We only check for large potential energy at the initial step,
451 * because that is by far the most likely step for this too occur
452 * and because computing the average kinetic energy is not free.
453 * Note: nstcalcenergy >> 1 often does not allow to catch large energies
454 * before they become NaN.
456 if (step == inputrec.init_step && EI_DYNAMICS(inputrec.eI))
458 averageKineticEnergy = averageKineticEnergyEstimate(inputrec.opts);
461 if (energyIsNotFinite
462 || (averageKineticEnergy > 0 && enerd.term[F_EPOT] > c_thresholdFactor * averageKineticEnergy))
467 ": The total potential energy is %g, which is %s. The LJ and electrostatic "
468 "contributions to the energy are %g and %g, respectively. A %s potential energy "
469 "can be caused by overlapping interactions in bonded interactions or very large%s "
470 "coordinate values. Usually this is caused by a badly- or non-equilibrated initial "
471 "configuration, incorrect interactions or parameters in the topology.",
472 step, enerd.term[F_EPOT], energyIsNotFinite ? "not finite" : "extremely high",
473 enerd.term[F_LJ], enerd.term[F_COUL_SR],
474 energyIsNotFinite ? "non-finite" : "very high", energyIsNotFinite ? " or Nan" : "");
478 /*! \brief Return true if there are special forces computed this step.
480 * The conditionals exactly correspond to those in computeSpecialForces().
482 static bool haveSpecialForces(const t_inputrec& inputrec,
483 const gmx::ForceProviders& forceProviders,
484 const pull_t* pull_work,
485 const bool computeForces,
489 return ((computeForces && forceProviders.hasForceProvider()) || // forceProviders
490 (inputrec.bPull && pull_have_potential(pull_work)) || // pull
491 inputrec.bRot || // enforced rotation
492 (ed != nullptr) || // flooding
493 (inputrec.bIMD && computeForces)); // IMD
496 /*! \brief Compute forces and/or energies for special algorithms
498 * The intention is to collect all calls to algorithms that compute
499 * forces on local atoms only and that do not contribute to the local
500 * virial sum (but add their virial contribution separately).
501 * Eventually these should likely all become ForceProviders.
502 * Within this function the intention is to have algorithms that do
503 * global communication at the end, so global barriers within the MD loop
504 * are as close together as possible.
506 * \param[in] fplog The log file
507 * \param[in] cr The communication record
508 * \param[in] inputrec The input record
509 * \param[in] awh The Awh module (nullptr if none in use).
510 * \param[in] enforcedRotation Enforced rotation module.
511 * \param[in] imdSession The IMD session
512 * \param[in] pull_work The pull work structure.
513 * \param[in] step The current MD step
514 * \param[in] t The current time
515 * \param[in,out] wcycle Wallcycle accounting struct
516 * \param[in,out] forceProviders Pointer to a list of force providers
517 * \param[in] box The unit cell
518 * \param[in] x The coordinates
519 * \param[in] mdatoms Per atom properties
520 * \param[in] lambda Array of free-energy lambda values
521 * \param[in] stepWork Step schedule flags
522 * \param[in,out] forceWithVirial Force and virial buffers
523 * \param[in,out] enerd Energy buffer
524 * \param[in,out] ed Essential dynamics pointer
525 * \param[in] didNeighborSearch Tells if we did neighbor searching this step, used for ED sampling
527 * \todo Remove didNeighborSearch, which is used incorrectly.
528 * \todo Convert all other algorithms called here to ForceProviders.
530 static void computeSpecialForces(FILE* fplog,
532 const t_inputrec* inputrec,
534 gmx_enfrot* enforcedRotation,
535 gmx::ImdSession* imdSession,
539 gmx_wallcycle_t wcycle,
540 gmx::ForceProviders* forceProviders,
542 gmx::ArrayRef<const gmx::RVec> x,
543 const t_mdatoms* mdatoms,
545 const StepWorkload& stepWork,
546 gmx::ForceWithVirial* forceWithVirial,
547 gmx_enerdata_t* enerd,
549 bool didNeighborSearch)
551 /* NOTE: Currently all ForceProviders only provide forces.
552 * When they also provide energies, remove this conditional.
554 if (stepWork.computeForces)
556 gmx::ForceProviderInput forceProviderInput(x, *mdatoms, t, box, *cr);
557 gmx::ForceProviderOutput forceProviderOutput(forceWithVirial, enerd);
559 /* Collect forces from modules */
560 forceProviders->calculateForces(forceProviderInput, &forceProviderOutput);
563 if (inputrec->bPull && pull_have_potential(pull_work))
565 pull_potential_wrapper(cr, inputrec, box, x, forceWithVirial, mdatoms, enerd, pull_work,
570 enerd->term[F_COM_PULL] += awh->applyBiasForcesAndUpdateBias(
571 inputrec->ePBC, *mdatoms, box, forceWithVirial, t, step, wcycle, fplog);
575 rvec* f = as_rvec_array(forceWithVirial->force_.data());
577 /* Add the forces from enforced rotation potentials (if any) */
580 wallcycle_start(wcycle, ewcROTadd);
581 enerd->term[F_COM_PULL] += add_rot_forces(enforcedRotation, f, cr, step, t);
582 wallcycle_stop(wcycle, ewcROTadd);
587 /* Note that since init_edsam() is called after the initialization
588 * of forcerec, edsam doesn't request the noVirSum force buffer.
589 * Thus if no other algorithm (e.g. PME) requires it, the forces
590 * here will contribute to the virial.
592 do_flood(cr, inputrec, as_rvec_array(x.data()), f, ed, box, step, didNeighborSearch);
595 /* Add forces from interactive molecular dynamics (IMD), if any */
596 if (inputrec->bIMD && stepWork.computeForces)
598 imdSession->applyForces(f);
602 /*! \brief Makes PME flags from StepWorkload data.
604 * \param[in] stepWork Step schedule flags
607 static int makePmeFlags(const StepWorkload& stepWork)
609 return GMX_PME_SPREAD | GMX_PME_SOLVE | (stepWork.computeVirial ? GMX_PME_CALC_ENER_VIR : 0)
610 | (stepWork.computeEnergy ? GMX_PME_CALC_ENER_VIR : 0)
611 | (stepWork.computeForces ? GMX_PME_CALC_F : 0);
614 /*! \brief Launch the prepare_step and spread stages of PME GPU.
616 * \param[in] pmedata The PME structure
617 * \param[in] box The box matrix
618 * \param[in] stepWork Step schedule flags
619 * \param[in] pmeFlags PME flags
620 * \param[in] xReadyOnDevice Event synchronizer indicating that the coordinates are ready in
621 * the device memory. \param[in] wcycle The wallcycle structure
623 static inline void launchPmeGpuSpread(gmx_pme_t* pmedata,
625 const StepWorkload& stepWork,
627 GpuEventSynchronizer* xReadyOnDevice,
628 gmx_wallcycle_t wcycle)
630 pme_gpu_prepare_computation(pmedata, stepWork.haveDynamicBox, box, wcycle, pmeFlags,
631 stepWork.useGpuPmeFReduction);
632 pme_gpu_launch_spread(pmedata, xReadyOnDevice, wcycle);
635 /*! \brief Launch the FFT and gather stages of PME GPU
637 * This function only implements setting the output forces (no accumulation).
639 * \param[in] pmedata The PME structure
640 * \param[in] wcycle The wallcycle structure
642 static void launchPmeGpuFftAndGather(gmx_pme_t* pmedata, gmx_wallcycle_t wcycle)
644 pme_gpu_launch_complex_transforms(pmedata, wcycle);
645 pme_gpu_launch_gather(pmedata, wcycle, PmeForceOutputHandling::Set);
649 * Polling wait for either of the PME or nonbonded GPU tasks.
651 * Instead of a static order in waiting for GPU tasks, this function
652 * polls checking which of the two tasks completes first, and does the
653 * associated force buffer reduction overlapped with the other task.
654 * By doing that, unlike static scheduling order, it can always overlap
655 * one of the reductions, regardless of the GPU task completion order.
657 * \param[in] nbv Nonbonded verlet structure
658 * \param[in,out] pmedata PME module data
659 * \param[in,out] forceOutputs Output buffer for the forces and virial
660 * \param[in,out] enerd Energy data structure results are reduced into
661 * \param[in] stepWork Step schedule flags
662 * \param[in] pmeFlags PME flags
663 * \param[in] wcycle The wallcycle structure
665 static void alternatePmeNbGpuWaitReduce(nonbonded_verlet_t* nbv,
667 gmx::ForceOutputs* forceOutputs,
668 gmx_enerdata_t* enerd,
669 const StepWorkload& stepWork,
671 gmx_wallcycle_t wcycle)
673 bool isPmeGpuDone = false;
674 bool isNbGpuDone = false;
677 gmx::ForceWithShiftForces& forceWithShiftForces = forceOutputs->forceWithShiftForces();
678 gmx::ForceWithVirial& forceWithVirial = forceOutputs->forceWithVirial();
680 gmx::ArrayRef<const gmx::RVec> pmeGpuForces;
682 while (!isPmeGpuDone || !isNbGpuDone)
686 GpuTaskCompletion completionType =
687 (isNbGpuDone) ? GpuTaskCompletion::Wait : GpuTaskCompletion::Check;
688 isPmeGpuDone = pme_gpu_try_finish_task(pmedata, pmeFlags, wcycle, &forceWithVirial,
689 enerd, completionType);
694 GpuTaskCompletion completionType =
695 (isPmeGpuDone) ? GpuTaskCompletion::Wait : GpuTaskCompletion::Check;
696 isNbGpuDone = Nbnxm::gpu_try_finish_task(
697 nbv->gpu_nbv, stepWork, AtomLocality::Local, enerd->grpp.ener[egLJSR].data(),
698 enerd->grpp.ener[egCOULSR].data(), forceWithShiftForces.shiftForces(),
699 completionType, wcycle);
703 nbv->atomdata_add_nbat_f_to_f(AtomLocality::Local, forceWithShiftForces.force());
709 /*! \brief Set up the different force buffers; also does clearing.
711 * \param[in] fr force record pointer
712 * \param[in] pull_work The pull work object.
713 * \param[in] inputrec input record
714 * \param[in] force force array
715 * \param[in] stepWork Step schedule flags
716 * \param[out] wcycle wallcycle recording structure
718 * \returns Cleared force output structure
720 static ForceOutputs setupForceOutputs(t_forcerec* fr,
722 const t_inputrec& inputrec,
723 gmx::ArrayRefWithPadding<gmx::RVec> force,
724 const StepWorkload& stepWork,
725 gmx_wallcycle_t wcycle)
727 wallcycle_sub_start(wcycle, ewcsCLEAR_FORCE_BUFFER);
729 /* NOTE: We assume fr->shiftForces is all zeros here */
730 gmx::ForceWithShiftForces forceWithShiftForces(force, stepWork.computeVirial, fr->shiftForces);
732 if (stepWork.computeForces)
734 /* Clear the short- and long-range forces */
735 clear_rvecs_omp(fr->natoms_force_constr, as_rvec_array(forceWithShiftForces.force().data()));
738 /* If we need to compute the virial, we might need a separate
739 * force buffer for algorithms for which the virial is calculated
740 * directly, such as PME. Otherwise, forceWithVirial uses the
741 * the same force (f in legacy calls) buffer as other algorithms.
743 const bool useSeparateForceWithVirialBuffer =
744 (stepWork.computeForces && (stepWork.computeVirial && fr->haveDirectVirialContributions));
745 /* forceWithVirial uses the local atom range only */
746 gmx::ForceWithVirial forceWithVirial(useSeparateForceWithVirialBuffer ? fr->forceBufferForDirectVirialContributions
747 : force.unpaddedArrayRef(),
748 stepWork.computeVirial);
750 if (useSeparateForceWithVirialBuffer)
752 /* TODO: update comment
753 * We only compute forces on local atoms. Note that vsites can
754 * spread to non-local atoms, but that part of the buffer is
755 * cleared separately in the vsite spreading code.
757 clear_rvecs_omp(forceWithVirial.force_.size(), as_rvec_array(forceWithVirial.force_.data()));
760 if (inputrec.bPull && pull_have_constraint(pull_work))
762 clear_pull_forces(pull_work);
765 wallcycle_sub_stop(wcycle, ewcsCLEAR_FORCE_BUFFER);
767 return ForceOutputs(forceWithShiftForces, forceWithVirial);
771 /*! \brief Set up flags that have the lifetime of the domain indicating what type of work is there to compute.
773 static DomainLifetimeWorkload setupDomainLifetimeWorkload(const t_inputrec& inputrec,
774 const t_forcerec& fr,
775 const pull_t* pull_work,
779 const t_mdatoms& mdatoms,
780 const SimulationWorkload& simulationWork,
781 const StepWorkload& stepWork)
783 DomainLifetimeWorkload domainWork;
784 // Note that haveSpecialForces is constant over the whole run
785 domainWork.haveSpecialForces =
786 haveSpecialForces(inputrec, *fr.forceProviders, pull_work, stepWork.computeForces, ed);
787 domainWork.haveCpuBondedWork = haveCpuBondeds(fr);
788 domainWork.haveGpuBondedWork = ((fr.gpuBonded != nullptr) && fr.gpuBonded->haveInteractions());
789 domainWork.haveRestraintsWork = haveRestraints(idef, fcd);
790 domainWork.haveCpuListedForceWork = haveCpuListedForces(fr, idef, fcd);
791 // Note that haveFreeEnergyWork is constant over the whole run
792 domainWork.haveFreeEnergyWork = (fr.efep != efepNO && mdatoms.nPerturbed != 0);
793 // We assume we have local force work if there are CPU
794 // force tasks including PME or nonbondeds.
795 domainWork.haveCpuLocalForceWork =
796 domainWork.haveSpecialForces || domainWork.haveCpuListedForceWork
797 || domainWork.haveFreeEnergyWork || simulationWork.useCpuNonbonded || simulationWork.useCpuPme
798 || simulationWork.haveEwaldSurfaceContribution || inputrec.nwall > 0;
803 /*! \brief Set up force flag stuct from the force bitmask.
805 * \param[in] legacyFlags Force bitmask flags used to construct the new flags
806 * \param[in] isNonbondedOn Global override, if false forces to turn off all nonbonded calculation.
807 * \param[in] simulationWork Simulation workload description.
808 * \param[in] rankHasPmeDuty If this rank computes PME.
810 * \returns New Stepworkload description.
812 static StepWorkload setupStepWorkload(const int legacyFlags,
813 const bool isNonbondedOn,
814 const SimulationWorkload& simulationWork,
815 const bool rankHasPmeDuty)
818 flags.stateChanged = ((legacyFlags & GMX_FORCE_STATECHANGED) != 0);
819 flags.haveDynamicBox = ((legacyFlags & GMX_FORCE_DYNAMICBOX) != 0);
820 flags.doNeighborSearch = ((legacyFlags & GMX_FORCE_NS) != 0);
821 flags.computeVirial = ((legacyFlags & GMX_FORCE_VIRIAL) != 0);
822 flags.computeEnergy = ((legacyFlags & GMX_FORCE_ENERGY) != 0);
823 flags.computeForces = ((legacyFlags & GMX_FORCE_FORCES) != 0);
824 flags.computeListedForces = ((legacyFlags & GMX_FORCE_LISTED) != 0);
825 flags.computeNonbondedForces = ((legacyFlags & GMX_FORCE_NONBONDED) != 0) && isNonbondedOn;
826 flags.computeDhdl = ((legacyFlags & GMX_FORCE_DHDL) != 0);
828 if (simulationWork.useGpuBufferOps)
830 GMX_ASSERT(simulationWork.useGpuNonbonded,
831 "Can only offload buffer ops if nonbonded computation is also offloaded");
833 flags.useGpuXBufferOps = simulationWork.useGpuBufferOps;
834 // on virial steps the CPU reduction path is taken
835 flags.useGpuFBufferOps = simulationWork.useGpuBufferOps && !flags.computeVirial;
836 flags.useGpuPmeFReduction = flags.useGpuFBufferOps
837 && (simulationWork.useGpuPme
838 && (rankHasPmeDuty || simulationWork.useGpuPmePpCommunication));
844 /* \brief Launch end-of-step GPU tasks: buffer clearing and rolling pruning.
846 * TODO: eliminate the \p useGpuNonbonded and \p useGpuNonbonded when these are
847 * incorporated in DomainLifetimeWorkload.
849 static void launchGpuEndOfStepTasks(nonbonded_verlet_t* nbv,
850 gmx::GpuBonded* gpuBonded,
852 gmx_enerdata_t* enerd,
853 const gmx::MdrunScheduleWorkload& runScheduleWork,
854 bool useGpuNonbonded,
857 gmx_wallcycle_t wcycle)
861 /* Launch pruning before buffer clearing because the API overhead of the
862 * clear kernel launches can leave the GPU idle while it could be running
865 if (nbv->isDynamicPruningStepGpu(step))
867 nbv->dispatchPruneKernelGpu(step);
870 /* now clear the GPU outputs while we finish the step on the CPU */
871 wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
872 wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
873 Nbnxm::gpu_clear_outputs(nbv->gpu_nbv, runScheduleWork.stepWork.computeVirial);
874 wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
875 wallcycle_stop(wcycle, ewcLAUNCH_GPU);
880 pme_gpu_reinit_computation(pmedata, wcycle);
883 if (runScheduleWork.domainWork.haveGpuBondedWork && runScheduleWork.stepWork.computeEnergy)
885 // in principle this should be included in the DD balancing region,
886 // but generally it is infrequent so we'll omit it for the sake of
888 gpuBonded->waitAccumulateEnergyTerms(enerd);
890 gpuBonded->clearEnergies();
895 void do_force(FILE* fplog,
897 const gmx_multisim_t* ms,
898 const t_inputrec* inputrec,
900 gmx_enfrot* enforcedRotation,
901 gmx::ImdSession* imdSession,
905 gmx_wallcycle_t wcycle,
906 const gmx_localtop_t* top,
908 gmx::ArrayRefWithPadding<gmx::RVec> x,
910 gmx::ArrayRefWithPadding<gmx::RVec> force,
912 const t_mdatoms* mdatoms,
913 gmx_enerdata_t* enerd,
915 gmx::ArrayRef<real> lambda,
918 gmx::MdrunScheduleWorkload* runScheduleWork,
919 const gmx_vsite_t* vsite,
924 const DDBalanceRegionHandler& ddBalanceRegionHandler)
928 nonbonded_verlet_t* nbv = fr->nbv.get();
929 interaction_const_t* ic = fr->ic;
930 gmx::StatePropagatorDataGpu* stateGpu = fr->stateGpu;
932 // TODO remove the code below when the legacy flags are not in use anymore
933 /* modify force flag if not doing nonbonded */
936 legacyFlags &= ~GMX_FORCE_NONBONDED;
939 const SimulationWorkload& simulationWork = runScheduleWork->simulationWork;
942 runScheduleWork->stepWork = setupStepWorkload(legacyFlags, fr->bNonbonded, simulationWork,
943 thisRankHasDuty(cr, DUTY_PME));
944 const StepWorkload& stepWork = runScheduleWork->stepWork;
947 const bool useGpuPmeOnThisRank = simulationWork.useGpuPme && thisRankHasDuty(cr, DUTY_PME);
948 const int pmeFlags = makePmeFlags(stepWork);
950 // Switches on whether to use GPU for position and force buffer operations
951 // TODO consider all possible combinations of triggers, and how to combine optimally in each case.
952 const BufferOpsUseGpu useGpuXBufOps =
953 stepWork.useGpuXBufferOps ? BufferOpsUseGpu::True : BufferOpsUseGpu::False;
954 // GPU Force buffer ops are disabled on virial steps, because the virial calc is not yet ported to GPU
955 const BufferOpsUseGpu useGpuFBufOps =
956 stepWork.useGpuFBufferOps ? BufferOpsUseGpu::True : BufferOpsUseGpu::False;
958 /* At a search step we need to start the first balancing region
959 * somewhere early inside the step after communication during domain
960 * decomposition (and not during the previous step as usual).
962 if (stepWork.doNeighborSearch)
964 ddBalanceRegionHandler.openBeforeForceComputationCpu(DdAllowBalanceRegionReopen::yes);
968 const int homenr = mdatoms->homenr;
970 clear_mat(vir_force);
972 if (stepWork.stateChanged)
974 if (inputrecNeedMutot(inputrec))
976 /* Calculate total (local) dipole moment in a temporary common array.
977 * This makes it possible to sum them over nodes faster.
979 calc_mu(start, homenr, x.unpaddedArrayRef(), mdatoms->chargeA, mdatoms->chargeB,
980 mdatoms->nChargePerturbed, mu, mu + DIM);
984 if (fr->ePBC != epbcNONE)
986 /* Compute shift vectors every step,
987 * because of pressure coupling or box deformation!
989 if (stepWork.haveDynamicBox && stepWork.stateChanged)
991 calc_shifts(box, fr->shift_vec);
994 const bool fillGrid = (stepWork.doNeighborSearch && stepWork.stateChanged);
995 const bool calcCGCM = (fillGrid && !DOMAINDECOMP(cr));
998 put_atoms_in_box_omp(fr->ePBC, box, x.unpaddedArrayRef().subArray(0, homenr),
999 gmx_omp_nthreads_get(emntDefault));
1000 inc_nrnb(nrnb, eNR_SHIFTX, homenr);
1002 else if (EI_ENERGY_MINIMIZATION(inputrec->eI) && graph)
1004 unshift_self(graph, box, as_rvec_array(x.unpaddedArrayRef().data()));
1008 nbnxn_atomdata_copy_shiftvec(stepWork.haveDynamicBox, fr->shift_vec, nbv->nbat.get());
1010 // Coordinates on the device are needed if PME or BufferOps are offloaded.
1011 // The local coordinates can be copied right away.
1012 // NOTE: Consider moving this copy to right after they are updated and constrained,
1013 // if the later is not offloaded.
1014 if (useGpuPmeOnThisRank || useGpuXBufOps == BufferOpsUseGpu::True)
1016 if (stepWork.doNeighborSearch)
1018 stateGpu->reinit(mdatoms->homenr,
1019 cr->dd != nullptr ? dd_numAtomsZones(*cr->dd) : mdatoms->homenr);
1020 if (useGpuPmeOnThisRank)
1022 // TODO: This should be moved into PME setup function ( pme_gpu_prepare_computation(...) )
1023 pme_gpu_set_device_x(fr->pmedata, stateGpu->getCoordinates());
1026 // We need to copy coordinates when:
1027 // 1. Update is not offloaded
1028 // 2. The buffers were reinitialized on search step
1029 if (!simulationWork.useGpuUpdate || stepWork.doNeighborSearch)
1031 stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::Local);
1035 // TODO Update this comment when introducing SimulationWorkload
1037 // The conditions for gpuHaloExchange e.g. using GPU buffer
1038 // operations were checked before construction, so here we can
1039 // just use it and assert upon any conditions.
1040 gmx::GpuHaloExchange* gpuHaloExchange =
1041 (havePPDomainDecomposition(cr) ? cr->dd->gpuHaloExchange.get() : nullptr);
1042 const bool ddUsesGpuDirectCommunication = (gpuHaloExchange != nullptr);
1043 GMX_ASSERT(!ddUsesGpuDirectCommunication || (useGpuXBufOps == BufferOpsUseGpu::True),
1044 "Must use coordinate buffer ops with GPU halo exchange");
1045 const bool useGpuForcesHaloExchange =
1046 ddUsesGpuDirectCommunication && (useGpuFBufOps == BufferOpsUseGpu::True);
1048 // Copy coordinate from the GPU if update is on the GPU and there
1049 // are forces to be computed on the CPU, or for the computation of
1050 // virial, or if host-side data will be transferred from this task
1051 // to a remote task for halo exchange or PME-PP communication. At
1052 // search steps the current coordinates are already on the host,
1053 // hence copy is not needed.
1054 const bool haveHostPmePpComms =
1055 !thisRankHasDuty(cr, DUTY_PME) && !simulationWork.useGpuPmePpCommunication;
1056 const bool haveHostHaloExchangeComms = havePPDomainDecomposition(cr) && !ddUsesGpuDirectCommunication;
1057 if (simulationWork.useGpuUpdate && !stepWork.doNeighborSearch
1058 && (runScheduleWork->domainWork.haveCpuLocalForceWork || stepWork.computeVirial
1059 || haveHostPmePpComms || haveHostHaloExchangeComms))
1061 stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::Local);
1062 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
1065 const auto localXReadyOnDevice = (stateGpu != nullptr)
1066 ? stateGpu->getCoordinatesReadyOnDeviceEvent(
1067 AtomLocality::Local, simulationWork, stepWork)
1071 if (!thisRankHasDuty(cr, DUTY_PME))
1073 /* Send particle coordinates to the pme nodes.
1074 * Since this is only implemented for domain decomposition
1075 * and domain decomposition does not use the graph,
1076 * we do not need to worry about shifting.
1078 bool reinitGpuPmePpComms = simulationWork.useGpuPmePpCommunication && (stepWork.doNeighborSearch);
1079 bool sendCoordinatesFromGpu =
1080 simulationWork.useGpuPmePpCommunication && !(stepWork.doNeighborSearch);
1081 gmx_pme_send_coordinates(fr, cr, box, as_rvec_array(x.unpaddedArrayRef().data()), lambda[efptCOUL],
1082 lambda[efptVDW], (stepWork.computeVirial || stepWork.computeEnergy),
1083 step, simulationWork.useGpuPmePpCommunication, reinitGpuPmePpComms,
1084 sendCoordinatesFromGpu, localXReadyOnDevice, wcycle);
1086 #endif /* GMX_MPI */
1088 if (useGpuPmeOnThisRank)
1090 launchPmeGpuSpread(fr->pmedata, box, stepWork, pmeFlags, localXReadyOnDevice, wcycle);
1093 /* do gridding for pair search */
1094 if (stepWork.doNeighborSearch)
1096 if (graph && stepWork.stateChanged)
1098 /* Calculate intramolecular shift vectors to make molecules whole */
1099 mk_mshift(fplog, graph, fr->ePBC, box, as_rvec_array(x.unpaddedArrayRef().data()));
1103 // - vzero is constant, do we need to pass it?
1104 // - box_diag should be passed directly to nbnxn_put_on_grid
1110 box_diag[XX] = box[XX][XX];
1111 box_diag[YY] = box[YY][YY];
1112 box_diag[ZZ] = box[ZZ][ZZ];
1114 wallcycle_start(wcycle, ewcNS);
1115 if (!DOMAINDECOMP(cr))
1117 wallcycle_sub_start(wcycle, ewcsNBS_GRID_LOCAL);
1118 nbnxn_put_on_grid(nbv, box, 0, vzero, box_diag, nullptr, { 0, mdatoms->homenr }, -1,
1119 fr->cginfo, x.unpaddedArrayRef(), 0, nullptr);
1120 wallcycle_sub_stop(wcycle, ewcsNBS_GRID_LOCAL);
1124 wallcycle_sub_start(wcycle, ewcsNBS_GRID_NONLOCAL);
1125 nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd), fr->cginfo, x.unpaddedArrayRef());
1126 wallcycle_sub_stop(wcycle, ewcsNBS_GRID_NONLOCAL);
1129 nbv->setAtomProperties(*mdatoms, fr->cginfo);
1131 wallcycle_stop(wcycle, ewcNS);
1133 /* initialize the GPU nbnxm atom data and bonded data structures */
1134 if (simulationWork.useGpuNonbonded)
1136 wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
1138 wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1139 Nbnxm::gpu_init_atomdata(nbv->gpu_nbv, nbv->nbat.get());
1140 wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1144 /* Now we put all atoms on the grid, we can assign bonded
1145 * interactions to the GPU, where the grid order is
1146 * needed. Also the xq, f and fshift device buffers have
1147 * been reallocated if needed, so the bonded code can
1148 * learn about them. */
1149 // TODO the xq, f, and fshift buffers are now shared
1150 // resources, so they should be maintained by a
1151 // higher-level object than the nb module.
1152 fr->gpuBonded->updateInteractionListsAndDeviceBuffers(
1153 nbv->getGridIndices(), top->idef, Nbnxm::gpu_get_xq(nbv->gpu_nbv),
1154 Nbnxm::gpu_get_f(nbv->gpu_nbv), Nbnxm::gpu_get_fshift(nbv->gpu_nbv));
1156 wallcycle_stop(wcycle, ewcLAUNCH_GPU);
1160 if (stepWork.doNeighborSearch)
1162 // Need to run after the GPU-offload bonded interaction lists
1163 // are set up to be able to determine whether there is bonded work.
1164 runScheduleWork->domainWork = setupDomainLifetimeWorkload(
1165 *inputrec, *fr, pull_work, ed, top->idef, *fcd, *mdatoms, simulationWork, stepWork);
1167 wallcycle_start_nocount(wcycle, ewcNS);
1168 wallcycle_sub_start(wcycle, ewcsNBS_SEARCH_LOCAL);
1169 /* Note that with a GPU the launch overhead of the list transfer is not timed separately */
1170 nbv->constructPairlist(InteractionLocality::Local, &top->excls, step, nrnb);
1172 nbv->setupGpuShortRangeWork(fr->gpuBonded, InteractionLocality::Local);
1174 wallcycle_sub_stop(wcycle, ewcsNBS_SEARCH_LOCAL);
1175 wallcycle_stop(wcycle, ewcNS);
1177 if (useGpuXBufOps == BufferOpsUseGpu::True)
1179 nbv->atomdata_init_copy_x_to_nbat_x_gpu();
1181 // For force buffer ops, we use the below conditon rather than
1182 // useGpuFBufOps to ensure that init is performed even if this
1183 // NS step is also a virial step (on which f buf ops are deactivated).
1184 if (simulationWork.useGpuBufferOps && simulationWork.useGpuNonbonded && (GMX_GPU == GMX_GPU_CUDA))
1186 GMX_ASSERT(stateGpu, "stateGpu should be valid when buffer ops are offloaded");
1187 nbv->atomdata_init_add_nbat_f_to_f_gpu(stateGpu->fReducedOnDevice());
1190 else if (!EI_TPI(inputrec->eI))
1192 if (useGpuXBufOps == BufferOpsUseGpu::True)
1194 GMX_ASSERT(stateGpu, "stateGpu should be valid when buffer ops are offloaded");
1195 nbv->convertCoordinatesGpu(AtomLocality::Local, false, stateGpu->getCoordinates(),
1196 localXReadyOnDevice);
1200 nbv->convertCoordinates(AtomLocality::Local, false, x.unpaddedArrayRef());
1204 const gmx::DomainLifetimeWorkload& domainWork = runScheduleWork->domainWork;
1206 if (simulationWork.useGpuNonbonded)
1208 ddBalanceRegionHandler.openBeforeForceComputationGpu();
1210 wallcycle_start(wcycle, ewcLAUNCH_GPU);
1212 wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1213 Nbnxm::gpu_upload_shiftvec(nbv->gpu_nbv, nbv->nbat.get());
1214 if (stepWork.doNeighborSearch || (useGpuXBufOps == BufferOpsUseGpu::False))
1216 Nbnxm::gpu_copy_xq_to_gpu(nbv->gpu_nbv, nbv->nbat.get(), AtomLocality::Local);
1218 wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1219 // with X buffer ops offloaded to the GPU on all but the search steps
1221 // bonded work not split into separate local and non-local, so with DD
1222 // we can only launch the kernel after non-local coordinates have been received.
1223 if (domainWork.haveGpuBondedWork && !havePPDomainDecomposition(cr))
1225 wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_BONDED);
1226 fr->gpuBonded->launchKernel(fr, stepWork, box);
1227 wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_BONDED);
1230 /* launch local nonbonded work on GPU */
1231 wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1232 do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::Local, enbvClearFNo, step, nrnb, wcycle);
1233 wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1234 wallcycle_stop(wcycle, ewcLAUNCH_GPU);
1237 if (useGpuPmeOnThisRank)
1239 // In PME GPU and mixed mode we launch FFT / gather after the
1240 // X copy/transform to allow overlap as well as after the GPU NB
1241 // launch to avoid FFT launch overhead hijacking the CPU and delaying
1242 // the nonbonded kernel.
1243 launchPmeGpuFftAndGather(fr->pmedata, wcycle);
1246 /* Communicate coordinates and sum dipole if necessary +
1247 do non-local pair search */
1248 if (havePPDomainDecomposition(cr))
1250 if (stepWork.doNeighborSearch)
1252 // TODO: fuse this branch with the above large stepWork.doNeighborSearch block
1253 wallcycle_start_nocount(wcycle, ewcNS);
1254 wallcycle_sub_start(wcycle, ewcsNBS_SEARCH_NONLOCAL);
1255 /* Note that with a GPU the launch overhead of the list transfer is not timed separately */
1256 nbv->constructPairlist(InteractionLocality::NonLocal, &top->excls, step, nrnb);
1258 nbv->setupGpuShortRangeWork(fr->gpuBonded, InteractionLocality::NonLocal);
1259 wallcycle_sub_stop(wcycle, ewcsNBS_SEARCH_NONLOCAL);
1260 wallcycle_stop(wcycle, ewcNS);
1261 if (ddUsesGpuDirectCommunication)
1263 gpuHaloExchange->reinitHalo(stateGpu->getCoordinates(), stateGpu->getForces());
1268 if (ddUsesGpuDirectCommunication)
1270 // The following must be called after local setCoordinates (which records an event
1271 // when the coordinate data has been copied to the device).
1272 gpuHaloExchange->communicateHaloCoordinates(box, localXReadyOnDevice);
1274 if (domainWork.haveCpuBondedWork || domainWork.haveFreeEnergyWork)
1276 // non-local part of coordinate buffer must be copied back to host for CPU work
1277 stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
1282 dd_move_x(cr->dd, box, x.unpaddedArrayRef(), wcycle);
1285 if (useGpuXBufOps == BufferOpsUseGpu::True)
1287 // The condition here was (pme != nullptr && pme_gpu_get_device_x(fr->pmedata) != nullptr)
1288 if (!useGpuPmeOnThisRank && !ddUsesGpuDirectCommunication)
1290 stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
1292 nbv->convertCoordinatesGpu(AtomLocality::NonLocal, false, stateGpu->getCoordinates(),
1293 stateGpu->getCoordinatesReadyOnDeviceEvent(
1294 AtomLocality::NonLocal, simulationWork, stepWork));
1298 nbv->convertCoordinates(AtomLocality::NonLocal, false, x.unpaddedArrayRef());
1302 if (simulationWork.useGpuNonbonded)
1304 wallcycle_start(wcycle, ewcLAUNCH_GPU);
1306 if (stepWork.doNeighborSearch || (useGpuXBufOps == BufferOpsUseGpu::False))
1308 wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1309 Nbnxm::gpu_copy_xq_to_gpu(nbv->gpu_nbv, nbv->nbat.get(), AtomLocality::NonLocal);
1310 wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1313 if (domainWork.haveGpuBondedWork)
1315 wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_BONDED);
1316 fr->gpuBonded->launchKernel(fr, stepWork, box);
1317 wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_BONDED);
1320 /* launch non-local nonbonded tasks on GPU */
1321 wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1322 do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::NonLocal, enbvClearFNo, step,
1324 wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1326 wallcycle_stop(wcycle, ewcLAUNCH_GPU);
1330 if (simulationWork.useGpuNonbonded)
1332 /* launch D2H copy-back F */
1333 wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
1334 wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1336 if (havePPDomainDecomposition(cr))
1338 Nbnxm::gpu_launch_cpyback(nbv->gpu_nbv, nbv->nbat.get(), stepWork, AtomLocality::NonLocal);
1340 Nbnxm::gpu_launch_cpyback(nbv->gpu_nbv, nbv->nbat.get(), stepWork, AtomLocality::Local);
1341 wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
1343 if (domainWork.haveGpuBondedWork && stepWork.computeEnergy)
1345 fr->gpuBonded->launchEnergyTransfer();
1347 wallcycle_stop(wcycle, ewcLAUNCH_GPU);
1350 if (stepWork.stateChanged && inputrecNeedMutot(inputrec))
1354 gmx_sumd(2 * DIM, mu, cr);
1356 ddBalanceRegionHandler.reopenRegionCpu();
1359 for (i = 0; i < 2; i++)
1361 for (j = 0; j < DIM; j++)
1363 fr->mu_tot[i][j] = mu[i * DIM + j];
1367 if (mdatoms->nChargePerturbed == 0)
1369 copy_rvec(fr->mu_tot[0], mu_tot);
1373 for (j = 0; j < DIM; j++)
1375 mu_tot[j] = (1.0 - lambda[efptCOUL]) * fr->mu_tot[0][j] + lambda[efptCOUL] * fr->mu_tot[1][j];
1379 /* Reset energies */
1380 reset_enerdata(enerd);
1381 /* Clear the shift forces */
1382 // TODO: This should be linked to the shift force buffer in use, or cleared before use instead
1383 for (gmx::RVec& elem : fr->shiftForces)
1385 elem = { 0.0_real, 0.0_real, 0.0_real };
1388 if (DOMAINDECOMP(cr) && !thisRankHasDuty(cr, DUTY_PME))
1390 wallcycle_start(wcycle, ewcPPDURINGPME);
1391 dd_force_flop_start(cr->dd, nrnb);
1396 wallcycle_start(wcycle, ewcROT);
1397 do_rotation(cr, enforcedRotation, box, as_rvec_array(x.unpaddedArrayRef().data()), t, step,
1398 stepWork.doNeighborSearch);
1399 wallcycle_stop(wcycle, ewcROT);
1402 /* Start the force cycle counter.
1403 * Note that a different counter is used for dynamic load balancing.
1405 wallcycle_start(wcycle, ewcFORCE);
1407 // Set up and clear force outputs.
1408 // We use std::move to keep the compiler happy, it has no effect.
1409 ForceOutputs forceOut =
1410 setupForceOutputs(fr, pull_work, *inputrec, std::move(force), stepWork, wcycle);
1412 /* We calculate the non-bonded forces, when done on the CPU, here.
1413 * We do this before calling do_force_lowlevel, because in that
1414 * function, the listed forces are calculated before PME, which
1415 * does communication. With this order, non-bonded and listed
1416 * force calculation imbalance can be balanced out by the domain
1417 * decomposition load balancing.
1420 const bool useOrEmulateGpuNb = simulationWork.useGpuNonbonded || fr->nbv->emulateGpu();
1422 if (!useOrEmulateGpuNb)
1424 do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::Local, enbvClearFYes, step, nrnb, wcycle);
1427 if (fr->efep != efepNO)
1429 /* Calculate the local and non-local free energy interactions here.
1430 * Happens here on the CPU both with and without GPU.
1432 nbv->dispatchFreeEnergyKernel(InteractionLocality::Local, fr,
1433 as_rvec_array(x.unpaddedArrayRef().data()),
1434 &forceOut.forceWithShiftForces(), *mdatoms, inputrec->fepvals,
1435 lambda.data(), enerd, stepWork, nrnb);
1437 if (havePPDomainDecomposition(cr))
1439 nbv->dispatchFreeEnergyKernel(InteractionLocality::NonLocal, fr,
1440 as_rvec_array(x.unpaddedArrayRef().data()),
1441 &forceOut.forceWithShiftForces(), *mdatoms,
1442 inputrec->fepvals, lambda.data(), enerd, stepWork, nrnb);
1446 if (!useOrEmulateGpuNb)
1448 if (havePPDomainDecomposition(cr))
1450 do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::NonLocal, enbvClearFNo, step,
1454 if (stepWork.computeForces)
1456 /* Add all the non-bonded force to the normal force array.
1457 * This can be split into a local and a non-local part when overlapping
1458 * communication with calculation with domain decomposition.
1460 wallcycle_stop(wcycle, ewcFORCE);
1461 nbv->atomdata_add_nbat_f_to_f(AtomLocality::All, forceOut.forceWithShiftForces().force());
1462 wallcycle_start_nocount(wcycle, ewcFORCE);
1465 /* If there are multiple fshift output buffers we need to reduce them */
1466 if (stepWork.computeVirial)
1468 /* This is not in a subcounter because it takes a
1469 negligible and constant-sized amount of time */
1470 nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat,
1471 forceOut.forceWithShiftForces().shiftForces());
1475 /* update QMMMrec, if necessary */
1478 update_QMMMrec(cr, fr, as_rvec_array(x.unpaddedArrayRef().data()), mdatoms, box);
1481 // TODO Force flags should include haveFreeEnergyWork for this domain
1482 if (ddUsesGpuDirectCommunication && (domainWork.haveCpuBondedWork || domainWork.haveFreeEnergyWork))
1484 /* Wait for non-local coordinate data to be copied from device */
1485 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::NonLocal);
1487 /* Compute the bonded and non-bonded energies and optionally forces */
1488 do_force_lowlevel(fr, inputrec, &(top->idef), cr, ms, nrnb, wcycle, mdatoms, x, hist, &forceOut, enerd,
1489 fcd, box, lambda.data(), graph, fr->mu_tot, stepWork, ddBalanceRegionHandler);
1491 wallcycle_stop(wcycle, ewcFORCE);
1493 computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation, imdSession, pull_work, step, t,
1494 wcycle, fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda.data(),
1495 stepWork, &forceOut.forceWithVirial(), enerd, ed, stepWork.doNeighborSearch);
1498 // Will store the amount of cycles spent waiting for the GPU that
1499 // will be later used in the DLB accounting.
1500 float cycles_wait_gpu = 0;
1501 if (useOrEmulateGpuNb)
1503 auto& forceWithShiftForces = forceOut.forceWithShiftForces();
1505 /* wait for non-local forces (or calculate in emulation mode) */
1506 if (havePPDomainDecomposition(cr))
1508 if (simulationWork.useGpuNonbonded)
1510 cycles_wait_gpu += Nbnxm::gpu_wait_finish_task(
1511 nbv->gpu_nbv, stepWork, AtomLocality::NonLocal, enerd->grpp.ener[egLJSR].data(),
1512 enerd->grpp.ener[egCOULSR].data(), forceWithShiftForces.shiftForces(), wcycle);
1516 wallcycle_start_nocount(wcycle, ewcFORCE);
1517 do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::NonLocal, enbvClearFYes,
1518 step, nrnb, wcycle);
1519 wallcycle_stop(wcycle, ewcFORCE);
1522 if (useGpuFBufOps == BufferOpsUseGpu::True)
1524 gmx::FixedCapacityVector<GpuEventSynchronizer*, 1> dependencyList;
1526 // TODO: move this into DomainLifetimeWorkload, including the second part of the
1527 // condition The bonded and free energy CPU tasks can have non-local force
1528 // contributions which are a dependency for the GPU force reduction.
1529 bool haveNonLocalForceContribInCpuBuffer =
1530 domainWork.haveCpuBondedWork || domainWork.haveFreeEnergyWork;
1532 if (haveNonLocalForceContribInCpuBuffer)
1534 stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(),
1535 AtomLocality::NonLocal);
1536 dependencyList.push_back(stateGpu->getForcesReadyOnDeviceEvent(
1537 AtomLocality::NonLocal, useGpuFBufOps == BufferOpsUseGpu::True));
1540 nbv->atomdata_add_nbat_f_to_f_gpu(AtomLocality::NonLocal, stateGpu->getForces(),
1541 pme_gpu_get_device_f(fr->pmedata), dependencyList,
1542 false, haveNonLocalForceContribInCpuBuffer);
1543 if (!useGpuForcesHaloExchange)
1545 // copy from GPU input for dd_move_f()
1546 stateGpu->copyForcesFromGpu(forceOut.forceWithShiftForces().force(),
1547 AtomLocality::NonLocal);
1552 nbv->atomdata_add_nbat_f_to_f(AtomLocality::NonLocal, forceWithShiftForces.force());
1556 if (fr->nbv->emulateGpu() && stepWork.computeVirial)
1558 nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat, forceWithShiftForces.shiftForces());
1563 if (havePPDomainDecomposition(cr))
1565 /* We are done with the CPU compute.
1566 * We will now communicate the non-local forces.
1567 * If we use a GPU this will overlap with GPU work, so in that case
1568 * we do not close the DD force balancing region here.
1570 ddBalanceRegionHandler.closeAfterForceComputationCpu();
1572 if (stepWork.computeForces)
1575 if (useGpuForcesHaloExchange)
1577 if (domainWork.haveCpuLocalForceWork)
1579 stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(), AtomLocality::Local);
1581 gpuHaloExchange->communicateHaloForces(domainWork.haveCpuLocalForceWork);
1585 if (useGpuFBufOps == BufferOpsUseGpu::True)
1587 stateGpu->waitForcesReadyOnHost(AtomLocality::NonLocal);
1589 dd_move_f(cr->dd, &forceOut.forceWithShiftForces(), wcycle);
1594 // With both nonbonded and PME offloaded a GPU on the same rank, we use
1595 // an alternating wait/reduction scheme.
1596 bool alternateGpuWait = (!c_disableAlternatingWait && useGpuPmeOnThisRank && simulationWork.useGpuNonbonded
1597 && !DOMAINDECOMP(cr) && (useGpuFBufOps == BufferOpsUseGpu::False));
1598 if (alternateGpuWait)
1600 alternatePmeNbGpuWaitReduce(fr->nbv.get(), fr->pmedata, &forceOut, enerd, stepWork, pmeFlags, wcycle);
1603 if (!alternateGpuWait && useGpuPmeOnThisRank)
1605 pme_gpu_wait_and_reduce(fr->pmedata, pmeFlags, wcycle, &forceOut.forceWithVirial(), enerd);
1608 /* Wait for local GPU NB outputs on the non-alternating wait path */
1609 if (!alternateGpuWait && simulationWork.useGpuNonbonded)
1611 /* Measured overhead on CUDA and OpenCL with(out) GPU sharing
1612 * is between 0.5 and 1.5 Mcycles. So 2 MCycles is an overestimate,
1613 * but even with a step of 0.1 ms the difference is less than 1%
1616 const float gpuWaitApiOverheadMargin = 2e6F; /* cycles */
1617 const float waitCycles = Nbnxm::gpu_wait_finish_task(
1618 nbv->gpu_nbv, stepWork, AtomLocality::Local, enerd->grpp.ener[egLJSR].data(),
1619 enerd->grpp.ener[egCOULSR].data(), forceOut.forceWithShiftForces().shiftForces(), wcycle);
1621 if (ddBalanceRegionHandler.useBalancingRegion())
1623 DdBalanceRegionWaitedForGpu waitedForGpu = DdBalanceRegionWaitedForGpu::yes;
1624 if (stepWork.computeForces && waitCycles <= gpuWaitApiOverheadMargin)
1626 /* We measured few cycles, it could be that the kernel
1627 * and transfer finished earlier and there was no actual
1628 * wait time, only API call overhead.
1629 * Then the actual time could be anywhere between 0 and
1630 * cycles_wait_est. We will use half of cycles_wait_est.
1632 waitedForGpu = DdBalanceRegionWaitedForGpu::no;
1634 ddBalanceRegionHandler.closeAfterForceComputationGpu(cycles_wait_gpu, waitedForGpu);
1638 if (fr->nbv->emulateGpu())
1640 // NOTE: emulation kernel is not included in the balancing region,
1641 // but emulation mode does not target performance anyway
1642 wallcycle_start_nocount(wcycle, ewcFORCE);
1643 do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::Local,
1644 DOMAINDECOMP(cr) ? enbvClearFNo : enbvClearFYes, step, nrnb, wcycle);
1645 wallcycle_stop(wcycle, ewcFORCE);
1648 // If on GPU PME-PP comms or GPU update path, receive forces from PME before GPU buffer ops
1649 // TODO refactor this and unify with below default-path call to the same function
1650 if (PAR(cr) && !thisRankHasDuty(cr, DUTY_PME)
1651 && (simulationWork.useGpuPmePpCommunication || simulationWork.useGpuUpdate))
1653 /* In case of node-splitting, the PP nodes receive the long-range
1654 * forces, virial and energy from the PME nodes here.
1656 pme_receive_force_ener(fr, cr, &forceOut.forceWithVirial(), enerd,
1657 simulationWork.useGpuPmePpCommunication,
1658 stepWork.useGpuPmeFReduction, wcycle);
1662 /* Do the nonbonded GPU (or emulation) force buffer reduction
1663 * on the non-alternating path. */
1664 if (useOrEmulateGpuNb && !alternateGpuWait)
1666 // TODO simplify the below conditionals. Pass buffer and sync pointers at init stage rather than here. Unify getter fns for sameGPU/otherGPU cases.
1668 stepWork.useGpuPmeFReduction
1669 ? (thisRankHasDuty(cr, DUTY_PME) ? pme_gpu_get_device_f(fr->pmedata)
1670 : // PME force buffer on same GPU
1671 fr->pmePpCommGpu->getGpuForceStagingPtr()) // buffer received from other GPU
1672 : nullptr; // PME reduction not active on GPU
1674 GpuEventSynchronizer* const pmeSynchronizer =
1675 stepWork.useGpuPmeFReduction
1676 ? (thisRankHasDuty(cr, DUTY_PME) ? pme_gpu_get_f_ready_synchronizer(fr->pmedata)
1677 : // PME force buffer on same GPU
1678 static_cast<GpuEventSynchronizer*>(
1679 fr->pmePpCommGpu->getForcesReadySynchronizer())) // buffer received from other GPU
1680 : nullptr; // PME reduction not active on GPU
1682 gmx::FixedCapacityVector<GpuEventSynchronizer*, 3> dependencyList;
1684 if (stepWork.useGpuPmeFReduction)
1686 dependencyList.push_back(pmeSynchronizer);
1689 gmx::ArrayRef<gmx::RVec> forceWithShift = forceOut.forceWithShiftForces().force();
1691 if (useGpuFBufOps == BufferOpsUseGpu::True)
1693 // Flag to specify whether the CPU force buffer has contributions to
1694 // local atoms. This depends on whether there are CPU-based force tasks
1695 // or when DD is active the halo exchange has resulted in contributions
1696 // from the non-local part.
1697 const bool haveLocalForceContribInCpuBuffer =
1698 (domainWork.haveCpuLocalForceWork || havePPDomainDecomposition(cr));
1700 // TODO: move these steps as early as possible:
1701 // - CPU f H2D should be as soon as all CPU-side forces are done
1702 // - wait for force reduction does not need to block host (at least not here, it's sufficient to wait
1703 // before the next CPU task that consumes the forces: vsite spread or update)
1704 // - copy is not perfomed if GPU force halo exchange is active, because it would overwrite the result
1705 // of the halo exchange. In that case the copy is instead performed above, before the exchange.
1706 // These should be unified.
1707 if (haveLocalForceContribInCpuBuffer && !useGpuForcesHaloExchange)
1709 // Note: AtomLocality::All is used for the non-DD case because, as in this
1710 // case copyForcesToGpu() uses a separate stream, it allows overlap of
1711 // CPU force H2D with GPU force tasks on all streams including those in the
1712 // local stream which would otherwise be implicit dependencies for the
1713 // transfer and would not overlap.
1714 auto locality = havePPDomainDecomposition(cr) ? AtomLocality::Local : AtomLocality::All;
1716 stateGpu->copyForcesToGpu(forceWithShift, locality);
1717 dependencyList.push_back(stateGpu->getForcesReadyOnDeviceEvent(
1718 locality, useGpuFBufOps == BufferOpsUseGpu::True));
1720 if (useGpuForcesHaloExchange)
1722 dependencyList.push_back(gpuHaloExchange->getForcesReadyOnDeviceEvent());
1724 nbv->atomdata_add_nbat_f_to_f_gpu(AtomLocality::Local, stateGpu->getForces(), pmeForcePtr,
1725 dependencyList, stepWork.useGpuPmeFReduction,
1726 haveLocalForceContribInCpuBuffer);
1727 // Copy forces to host if they are needed for update or if virtual sites are enabled.
1728 // If there are vsites, we need to copy forces every step to spread vsite forces on host.
1729 // TODO: When the output flags will be included in step workload, this copy can be combined with the
1730 // copy call done in sim_utils(...) for the output.
1731 // NOTE: If there are virtual sites, the forces are modified on host after this D2H copy. Hence,
1732 // they should not be copied in do_md(...) for the output.
1733 if (!simulationWork.useGpuUpdate || vsite)
1735 stateGpu->copyForcesFromGpu(forceWithShift, AtomLocality::Local);
1736 stateGpu->waitForcesReadyOnHost(AtomLocality::Local);
1741 nbv->atomdata_add_nbat_f_to_f(AtomLocality::Local, forceWithShift);
1745 launchGpuEndOfStepTasks(nbv, fr->gpuBonded, fr->pmedata, enerd, *runScheduleWork,
1746 simulationWork.useGpuNonbonded, useGpuPmeOnThisRank, step, wcycle);
1748 if (DOMAINDECOMP(cr))
1750 dd_force_flop_stop(cr->dd, nrnb);
1753 if (stepWork.computeForces)
1755 rvec* f = as_rvec_array(forceOut.forceWithShiftForces().force().data());
1757 /* If we have NoVirSum forces, but we do not calculate the virial,
1758 * we sum fr->f_novirsum=forceOut.f later.
1760 if (vsite && !(fr->haveDirectVirialContributions && !stepWork.computeVirial))
1762 rvec* fshift = as_rvec_array(forceOut.forceWithShiftForces().shiftForces().data());
1763 spread_vsite_f(vsite, as_rvec_array(x.unpaddedArrayRef().data()), f, fshift, FALSE,
1764 nullptr, nrnb, &top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr, wcycle);
1767 if (stepWork.computeVirial)
1769 /* Calculation of the virial must be done after vsites! */
1770 calc_virial(0, mdatoms->homenr, as_rvec_array(x.unpaddedArrayRef().data()),
1771 forceOut.forceWithShiftForces(), vir_force, graph, box, nrnb, fr, inputrec->ePBC);
1775 // TODO refactor this and unify with above GPU PME-PP / GPU update path call to the same function
1776 if (PAR(cr) && !thisRankHasDuty(cr, DUTY_PME) && !simulationWork.useGpuPmePpCommunication
1777 && !simulationWork.useGpuUpdate)
1779 /* In case of node-splitting, the PP nodes receive the long-range
1780 * forces, virial and energy from the PME nodes here.
1782 pme_receive_force_ener(fr, cr, &forceOut.forceWithVirial(), enerd,
1783 simulationWork.useGpuPmePpCommunication, false, wcycle);
1786 if (stepWork.computeForces)
1788 post_process_forces(cr, step, nrnb, wcycle, top, box, as_rvec_array(x.unpaddedArrayRef().data()),
1789 &forceOut, vir_force, mdatoms, graph, fr, vsite, stepWork);
1792 if (stepWork.computeEnergy)
1794 /* Sum the potential energy terms from group contributions */
1795 sum_epot(&(enerd->grpp), enerd->term);
1797 if (!EI_TPI(inputrec->eI))
1799 checkPotentialEnergyValidity(step, *enerd, *inputrec);
1803 /* In case we don't have constraints and are using GPUs, the next balancing
1804 * region starts here.
1805 * Some "special" work at the end of do_force_cuts?, such as vsite spread,
1806 * virial calculation and COM pulling, is not thus not included in
1807 * the balance timing, which is ok as most tasks do communication.
1809 ddBalanceRegionHandler.openBeforeForceComputationCpu(DdAllowBalanceRegionReopen::no);