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39 #include "gromacs/gmxlib/nrnb.h"
40 #include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
41 #include "gromacs/gmxlib/nonbonded/nb_kernel.h"
42 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
43 #include "gromacs/math/vectypes.h"
44 #include "gromacs/mdlib/enerdata_utils.h"
45 #include "gromacs/mdlib/force.h"
46 #include "gromacs/mdlib/gmx_omp_nthreads.h"
47 #include "gromacs/mdtypes/enerdata.h"
48 #include "gromacs/mdtypes/forceoutput.h"
49 #include "gromacs/mdtypes/inputrec.h"
50 #include "gromacs/mdtypes/interaction_const.h"
51 #include "gromacs/mdtypes/md_enums.h"
52 #include "gromacs/mdtypes/mdatom.h"
53 #include "gromacs/mdtypes/simulation_workload.h"
54 #include "gromacs/nbnxm/gpu_data_mgmt.h"
55 #include "gromacs/nbnxm/nbnxm.h"
56 #include "gromacs/simd/simd.h"
57 #include "gromacs/timing/wallcycle.h"
58 #include "gromacs/utility/gmxassert.h"
59 #include "gromacs/utility/real.h"
61 #include "kernel_common.h"
62 #include "nbnxm_simd.h"
63 #include "pairlistset.h"
64 #include "pairlistsets.h"
65 #include "kernels_reference/kernel_gpu_ref.h"
66 #define INCLUDE_KERNELFUNCTION_TABLES
67 #include "kernels_reference/kernel_ref.h"
68 #ifdef GMX_NBNXN_SIMD_2XNN
69 # include "kernels_simd_2xmm/kernels.h"
71 #ifdef GMX_NBNXN_SIMD_4XN
72 # include "kernels_simd_4xm/kernels.h"
74 #undef INCLUDE_FUNCTION_TABLES
76 /*! \brief Clears the energy group output buffers
78 * \param[in,out] out nbnxn kernel output struct
80 static void clearGroupEnergies(nbnxn_atomdata_output_t* out)
82 std::fill(out->Vvdw.begin(), out->Vvdw.end(), 0.0_real);
83 std::fill(out->Vc.begin(), out->Vc.end(), 0.0_real);
84 std::fill(out->VSvdw.begin(), out->VSvdw.end(), 0.0_real);
85 std::fill(out->VSc.begin(), out->VSc.end(), 0.0_real);
88 /*! \brief Reduce the group-pair energy buffers produced by a SIMD kernel
89 * to single terms in the output buffers.
91 * The SIMD kernels produce a large number of energy buffer in SIMD registers
92 * to avoid scattered reads and writes.
94 * \tparam unrollj The unroll size for j-particles in the SIMD kernel
95 * \param[in] numGroups The number of energy groups
96 * \param[in] numGroups_2log Log2 of numGroups, rounded up
97 * \param[in,out] out Struct with energy buffers
100 static void reduceGroupEnergySimdBuffers(int numGroups, int numGroups_2log, nbnxn_atomdata_output_t* out)
102 const int unrollj_half = unrollj / 2;
103 /* Energies are stored in SIMD registers with size 2^numGroups_2log */
104 const int numGroupsStorage = (1 << numGroups_2log);
106 const real* gmx_restrict vVdwSimd = out->VSvdw.data();
107 const real* gmx_restrict vCoulombSimd = out->VSc.data();
108 real* gmx_restrict vVdw = out->Vvdw.data();
109 real* gmx_restrict vCoulomb = out->Vc.data();
111 /* The size of the SIMD energy group buffer array is:
112 * numGroups*numGroups*numGroupsStorage*unrollj_half*simd_width
114 for (int i = 0; i < numGroups; i++)
116 for (int j1 = 0; j1 < numGroups; j1++)
118 for (int j0 = 0; j0 < numGroups; j0++)
120 int c = ((i * numGroups + j1) * numGroupsStorage + j0) * unrollj_half * unrollj;
121 for (int s = 0; s < unrollj_half; s++)
123 vVdw[i * numGroups + j0] += vVdwSimd[c + 0];
124 vVdw[i * numGroups + j1] += vVdwSimd[c + 1];
125 vCoulomb[i * numGroups + j0] += vCoulombSimd[c + 0];
126 vCoulomb[i * numGroups + j1] += vCoulombSimd[c + 1];
134 /*! \brief Dispatches the non-bonded N versus M atom cluster CPU kernels.
136 * OpenMP parallelization is performed within this function.
137 * Energy reduction, but not force and shift force reduction, is performed
138 * within this function.
140 * \param[in] pairlistSet Pairlists with local or non-local interactions to compute
141 * \param[in] kernelSetup The non-bonded kernel setup
142 * \param[in,out] nbat The atomdata for the interactions
143 * \param[in] ic Non-bonded interaction constants
144 * \param[in] shiftVectors The PBC shift vectors
145 * \param[in] stepWork Flags that tell what to compute
146 * \param[in] clearF Enum that tells if to clear the force output buffer
147 * \param[out] vCoulomb Output buffer for Coulomb energies
148 * \param[out] vVdw Output buffer for Van der Waals energies
149 * \param[in] wcycle Pointer to cycle counting data structure.
151 static void nbnxn_kernel_cpu(const PairlistSet& pairlistSet,
152 const Nbnxm::KernelSetup& kernelSetup,
153 nbnxn_atomdata_t* nbat,
154 const interaction_const_t& ic,
156 const gmx::StepWorkload& stepWork,
160 gmx_wallcycle* wcycle)
164 if (EEL_RF(ic.eeltype) || ic.eeltype == eelCUT)
170 if (kernelSetup.ewaldExclusionType == Nbnxm::EwaldExclusionType::Table)
172 if (ic.rcoulomb == ic.rvdw)
178 coulkt = coulktTAB_TWIN;
183 if (ic.rcoulomb == ic.rvdw)
185 coulkt = coulktEWALD;
189 coulkt = coulktEWALD_TWIN;
194 const nbnxn_atomdata_t::Params& nbatParams = nbat->params();
197 if (ic.vdwtype == evdwCUT)
199 switch (ic.vdw_modifier)
202 case eintmodPOTSHIFT:
203 switch (nbatParams.comb_rule)
205 case ljcrGEOM: vdwkt = vdwktLJCUT_COMBGEOM; break;
206 case ljcrLB: vdwkt = vdwktLJCUT_COMBLB; break;
207 case ljcrNONE: vdwkt = vdwktLJCUT_COMBNONE; break;
208 default: GMX_RELEASE_ASSERT(false, "Unknown combination rule");
211 case eintmodFORCESWITCH: vdwkt = vdwktLJFORCESWITCH; break;
212 case eintmodPOTSWITCH: vdwkt = vdwktLJPOTSWITCH; break;
213 default: GMX_RELEASE_ASSERT(false, "Unsupported VdW interaction modifier");
216 else if (ic.vdwtype == evdwPME)
218 if (ic.ljpme_comb_rule == eljpmeGEOM)
220 vdwkt = vdwktLJEWALDCOMBGEOM;
224 vdwkt = vdwktLJEWALDCOMBLB;
225 /* At setup we (should have) selected the C reference kernel */
226 GMX_RELEASE_ASSERT(kernelSetup.kernelType == Nbnxm::KernelType::Cpu4x4_PlainC,
227 "Only the C reference nbnxn SIMD kernel supports LJ-PME with LB "
228 "combination rules");
233 GMX_RELEASE_ASSERT(false, "Unsupported VdW interaction type");
236 gmx::ArrayRef<const NbnxnPairlistCpu> pairlists = pairlistSet.cpuLists();
238 int gmx_unused nthreads = gmx_omp_nthreads_get(emntNonbonded);
239 wallcycle_sub_start(wcycle, ewcsNONBONDED_CLEAR);
240 #pragma omp parallel for schedule(static) num_threads(nthreads)
241 for (gmx::index nb = 0; nb < pairlists.ssize(); nb++)
243 // Presently, the kernels do not call C++ code that can throw,
244 // so no need for a try/catch pair in this OpenMP region.
245 nbnxn_atomdata_output_t* out = &nbat->out[nb];
247 if (clearF == enbvClearFYes)
249 clearForceBuffer(nbat, nb);
251 clear_fshift(out->fshift.data());
256 wallcycle_sub_stop(wcycle, ewcsNONBONDED_CLEAR);
257 wallcycle_sub_start(wcycle, ewcsNONBONDED_KERNEL);
260 // TODO: Change to reference
261 const NbnxnPairlistCpu* pairlist = &pairlists[nb];
263 if (!stepWork.computeEnergy)
265 /* Don't calculate energies */
266 switch (kernelSetup.kernelType)
268 case Nbnxm::KernelType::Cpu4x4_PlainC:
269 nbnxn_kernel_noener_ref[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
271 #ifdef GMX_NBNXN_SIMD_2XNN
272 case Nbnxm::KernelType::Cpu4xN_Simd_2xNN:
273 nbnxm_kernel_noener_simd_2xmm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
276 #ifdef GMX_NBNXN_SIMD_4XN
277 case Nbnxm::KernelType::Cpu4xN_Simd_4xN:
278 nbnxm_kernel_noener_simd_4xm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
281 default: GMX_RELEASE_ASSERT(false, "Unsupported kernel architecture");
284 else if (out->Vvdw.size() == 1)
286 /* A single energy group (pair) */
290 switch (kernelSetup.kernelType)
292 case Nbnxm::KernelType::Cpu4x4_PlainC:
293 nbnxn_kernel_ener_ref[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
295 #ifdef GMX_NBNXN_SIMD_2XNN
296 case Nbnxm::KernelType::Cpu4xN_Simd_2xNN:
297 nbnxm_kernel_ener_simd_2xmm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
300 #ifdef GMX_NBNXN_SIMD_4XN
301 case Nbnxm::KernelType::Cpu4xN_Simd_4xN:
302 nbnxm_kernel_ener_simd_4xm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
305 default: GMX_RELEASE_ASSERT(false, "Unsupported kernel architecture");
310 /* Calculate energy group contributions */
311 clearGroupEnergies(out);
315 switch (kernelSetup.kernelType)
317 case Nbnxm::KernelType::Cpu4x4_PlainC:
318 unrollj = c_nbnxnCpuIClusterSize;
319 nbnxn_kernel_energrp_ref[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
321 #ifdef GMX_NBNXN_SIMD_2XNN
322 case Nbnxm::KernelType::Cpu4xN_Simd_2xNN:
323 unrollj = GMX_SIMD_REAL_WIDTH / 2;
324 nbnxm_kernel_energrp_simd_2xmm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
327 #ifdef GMX_NBNXN_SIMD_4XN
328 case Nbnxm::KernelType::Cpu4xN_Simd_4xN:
329 unrollj = GMX_SIMD_REAL_WIDTH;
330 nbnxm_kernel_energrp_simd_4xm[coulkt][vdwkt](pairlist, nbat, &ic, shiftVectors, out);
333 default: GMX_RELEASE_ASSERT(false, "Unsupported kernel architecture");
336 if (kernelSetup.kernelType != Nbnxm::KernelType::Cpu4x4_PlainC)
341 reduceGroupEnergySimdBuffers<2>(nbatParams.nenergrp, nbatParams.neg_2log, out);
344 reduceGroupEnergySimdBuffers<4>(nbatParams.nenergrp, nbatParams.neg_2log, out);
347 reduceGroupEnergySimdBuffers<8>(nbatParams.nenergrp, nbatParams.neg_2log, out);
349 default: GMX_RELEASE_ASSERT(false, "Unsupported j-unroll size");
354 wallcycle_sub_stop(wcycle, ewcsNONBONDED_KERNEL);
356 if (stepWork.computeEnergy)
358 reduce_energies_over_lists(nbat, pairlists.ssize(), vVdw, vCoulomb);
362 static void accountFlops(t_nrnb* nrnb,
363 const PairlistSet& pairlistSet,
364 const nonbonded_verlet_t& nbv,
365 const interaction_const_t& ic,
366 const gmx::StepWorkload& stepWork)
368 const bool usingGpuKernels = nbv.useGpu();
370 int enr_nbnxn_kernel_ljc;
371 if (EEL_RF(ic.eeltype) || ic.eeltype == eelCUT)
373 enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_RF;
375 else if ((!usingGpuKernels && nbv.kernelSetup().ewaldExclusionType == Nbnxm::EwaldExclusionType::Analytical)
376 || (usingGpuKernels && Nbnxm::gpu_is_kernel_ewald_analytical(nbv.gpu_nbv)))
378 enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_EWALD;
382 enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_TAB;
384 int enr_nbnxn_kernel_lj = eNR_NBNXN_LJ;
385 if (stepWork.computeEnergy)
387 /* In eNR_??? the nbnxn F+E kernels are always the F kernel + 1 */
388 enr_nbnxn_kernel_ljc += 1;
389 enr_nbnxn_kernel_lj += 1;
392 inc_nrnb(nrnb, enr_nbnxn_kernel_ljc, pairlistSet.natpair_ljq_);
393 inc_nrnb(nrnb, enr_nbnxn_kernel_lj, pairlistSet.natpair_lj_);
394 /* The Coulomb-only kernels are offset -eNR_NBNXN_LJ_RF+eNR_NBNXN_RF */
395 inc_nrnb(nrnb, enr_nbnxn_kernel_ljc - eNR_NBNXN_LJ_RF + eNR_NBNXN_RF, pairlistSet.natpair_q_);
397 if (ic.vdw_modifier == eintmodFORCESWITCH)
399 /* We add up the switch cost separately */
400 inc_nrnb(nrnb, eNR_NBNXN_ADD_LJ_FSW + (stepWork.computeEnergy ? 1 : 0),
401 pairlistSet.natpair_ljq_ + pairlistSet.natpair_lj_);
403 if (ic.vdw_modifier == eintmodPOTSWITCH)
405 /* We add up the switch cost separately */
406 inc_nrnb(nrnb, eNR_NBNXN_ADD_LJ_PSW + (stepWork.computeEnergy ? 1 : 0),
407 pairlistSet.natpair_ljq_ + pairlistSet.natpair_lj_);
409 if (ic.vdwtype == evdwPME)
411 /* We add up the LJ Ewald cost separately */
412 inc_nrnb(nrnb, eNR_NBNXN_ADD_LJ_EWALD + (stepWork.computeEnergy ? 1 : 0),
413 pairlistSet.natpair_ljq_ + pairlistSet.natpair_lj_);
417 void nonbonded_verlet_t::dispatchNonbondedKernel(gmx::InteractionLocality iLocality,
418 const interaction_const_t& ic,
419 const gmx::StepWorkload& stepWork,
421 const t_forcerec& fr,
422 gmx_enerdata_t* enerd,
425 const PairlistSet& pairlistSet = pairlistSets().pairlistSet(iLocality);
427 switch (kernelSetup().kernelType)
429 case Nbnxm::KernelType::Cpu4x4_PlainC:
430 case Nbnxm::KernelType::Cpu4xN_Simd_4xN:
431 case Nbnxm::KernelType::Cpu4xN_Simd_2xNN:
432 nbnxn_kernel_cpu(pairlistSet, kernelSetup(), nbat.get(), ic, fr.shift_vec, stepWork,
433 clearF, enerd->grpp.ener[egCOULSR].data(),
434 fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data(),
438 case Nbnxm::KernelType::Gpu8x8x8:
439 Nbnxm::gpu_launch_kernel(gpu_nbv, stepWork, iLocality);
442 case Nbnxm::KernelType::Cpu8x8x8_PlainC:
443 nbnxn_kernel_gpu_ref(
444 pairlistSet.gpuList(), nbat.get(), &ic, fr.shift_vec, stepWork, clearF,
445 nbat->out[0].f, nbat->out[0].fshift.data(), enerd->grpp.ener[egCOULSR].data(),
446 fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data());
449 default: GMX_RELEASE_ASSERT(false, "Invalid nonbonded kernel type passed!");
452 accountFlops(nrnb, pairlistSet, *this, ic, stepWork);
455 void nonbonded_verlet_t::dispatchFreeEnergyKernel(gmx::InteractionLocality iLocality,
456 const t_forcerec* fr,
458 gmx::ForceWithShiftForces* forceWithShiftForces,
459 const t_mdatoms& mdatoms,
462 gmx_enerdata_t* enerd,
463 const gmx::StepWorkload& stepWork,
466 const auto nbl_fep = pairlistSets().pairlistSet(iLocality).fepLists();
468 /* When the first list is empty, all are empty and there is nothing to do */
469 if (!pairlistSets().params().haveFep || nbl_fep[0]->nrj == 0)
475 /* Add short-range interactions */
476 donb_flags |= GMX_NONBONDED_DO_SR;
478 if (stepWork.computeForces)
480 donb_flags |= GMX_NONBONDED_DO_FORCE;
482 if (stepWork.computeVirial)
484 donb_flags |= GMX_NONBONDED_DO_SHIFTFORCE;
486 if (stepWork.computeEnergy)
488 donb_flags |= GMX_NONBONDED_DO_POTENTIAL;
491 nb_kernel_data_t kernel_data;
492 real dvdl_nb[efptNR] = { 0 };
493 kernel_data.flags = donb_flags;
494 kernel_data.lambda = lambda;
495 kernel_data.dvdl = dvdl_nb;
497 kernel_data.energygrp_elec = enerd->grpp.ener[egCOULSR].data();
498 kernel_data.energygrp_vdw = enerd->grpp.ener[egLJSR].data();
500 GMX_ASSERT(gmx_omp_nthreads_get(emntNonbonded) == nbl_fep.ssize(),
501 "Number of lists should be same as number of NB threads");
503 wallcycle_sub_start(wcycle_, ewcsNONBONDED_FEP);
504 #pragma omp parallel for schedule(static) num_threads(nbl_fep.ssize())
505 for (gmx::index th = 0; th < nbl_fep.ssize(); th++)
509 gmx_nb_free_energy_kernel(nbl_fep[th].get(), x, forceWithShiftForces, fr, &mdatoms,
512 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
515 if (fepvals->sc_alpha != 0)
517 enerd->dvdl_nonlin[efptVDW] += dvdl_nb[efptVDW];
518 enerd->dvdl_nonlin[efptCOUL] += dvdl_nb[efptCOUL];
522 enerd->dvdl_lin[efptVDW] += dvdl_nb[efptVDW];
523 enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
526 /* If we do foreign lambda and we have soft-core interactions
527 * we have to recalculate the (non-linear) energies contributions.
529 if (fepvals->n_lambda > 0 && stepWork.computeDhdl && fepvals->sc_alpha != 0)
532 kernel_data.flags = (donb_flags & ~(GMX_NONBONDED_DO_FORCE | GMX_NONBONDED_DO_SHIFTFORCE))
533 | GMX_NONBONDED_DO_FOREIGNLAMBDA;
534 kernel_data.lambda = lam_i;
535 kernel_data.energygrp_elec = enerd->foreign_grpp.ener[egCOULSR].data();
536 kernel_data.energygrp_vdw = enerd->foreign_grpp.ener[egLJSR].data();
537 /* Note that we add to kernel_data.dvdl, but ignore the result */
539 for (size_t i = 0; i < enerd->enerpart_lambda.size(); i++)
541 for (int j = 0; j < efptNR; j++)
543 lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i - 1]);
545 reset_foreign_enerdata(enerd);
546 #pragma omp parallel for schedule(static) num_threads(nbl_fep.ssize())
547 for (gmx::index th = 0; th < nbl_fep.ssize(); th++)
551 gmx_nb_free_energy_kernel(nbl_fep[th].get(), x, forceWithShiftForces, fr,
552 &mdatoms, &kernel_data, nrnb);
554 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
557 sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
558 enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
561 wallcycle_sub_stop(wcycle_, ewcsNONBONDED_FEP);