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39 * CUDA non-bonded kernel used through preprocessor-based code generation
40 * of multiple kernel flavors, see nbnxn_cuda_kernels.cuh.
42 * NOTE: No include fence as it is meant to be included multiple times.
44 * \author Szilárd Páll <pall.szilard@gmail.com>
45 * \author Berk Hess <hess@kth.se>
46 * \ingroup module_nbnxm
49 #include "gromacs/gpu_utils/cuda_arch_utils.cuh"
50 #include "gromacs/gpu_utils/cuda_kernel_utils.cuh"
51 #include "gromacs/gpu_utils/typecasts.cuh"
52 #include "gromacs/math/utilities.h"
53 #include "gromacs/pbcutil/ishift.h"
54 /* Note that floating-point constants in CUDA code should be suffixed
55 * with f (e.g. 0.5f), to stop the compiler producing intermediate
56 * code that is in double precision.
59 #if defined EL_EWALD_ANA || defined EL_EWALD_TAB
60 /* Note: convenience macro, needs to be undef-ed at the end of the file. */
64 #if defined LJ_EWALD_COMB_GEOM || defined LJ_EWALD_COMB_LB
65 /* Note: convenience macro, needs to be undef-ed at the end of the file. */
69 #if defined EL_EWALD_ANY || defined EL_RF || defined LJ_EWALD \
70 || (defined EL_CUTOFF && defined CALC_ENERGIES)
71 /* Macro to control the calculation of exclusion forces in the kernel
72 * We do that with Ewald (elec/vdw) and RF. Cut-off only has exclusion
75 * Note: convenience macro, needs to be undef-ed at the end of the file.
77 # define EXCLUSION_FORCES
80 #if defined LJ_COMB_GEOM || defined LJ_COMB_LB
85 Kernel launch parameters:
86 - #blocks = #pair lists, blockId = pair list Id
87 - #threads = NTHREAD_Z * c_clSize^2
88 - shmem = see nbnxn_cuda.cu:calc_shmem_required_nonbonded()
90 Each thread calculates an i force-component taking one pair of i-j atoms.
94 /*! \brief Compute capability dependent definition of kernel launch configuration parameters.
96 * NTHREAD_Z controls the number of j-clusters processed concurrently on NTHREAD_Z
97 * warp-pairs per block.
99 * - On CC 3.0-3.5, and >=5.0 NTHREAD_Z == 1, translating to 64 th/block with 16
100 * blocks/multiproc, is the fastest even though this setup gives low occupancy
102 * NTHREAD_Z > 1 results in excessive register spilling unless the minimum blocks
103 * per multiprocessor is reduced proportionally to get the original number of max
104 * threads in flight (and slightly lower performance).
105 * - On CC 3.7 there are enough registers to double the number of threads; using
106 * NTHREADS_Z == 2 is fastest with 16 blocks (TODO: test with RF and other kernels
107 * with low-register use).
109 * Note that the current kernel implementation only supports NTHREAD_Z > 1 with
110 * shuffle-based reduction, hence CC >= 3.0.
113 * NOTEs on Volta / CUDA 9 extensions:
115 * - While active thread masks are required for the warp collectives
116 * (we use any and shfl), the kernel is designed such that all conditions
117 * (other than the inner-most distance check) including loop trip counts
118 * are warp-synchronous. Therefore, we don't need ballot to compute the
119 * active masks as these are all full-warp masks.
121 * - TODO: reconsider the use of __syncwarp(): its only role is currently to prevent
122 * WAR hazard due to the cj preload; we should try to replace it with direct
123 * loads (which may be faster given the improved L1 on Volta).
126 /* Kernel launch bounds for different compute capabilities. The value of NTHREAD_Z
127 * determines the number of threads per block and it is chosen such that
128 * 16 blocks/multiprocessor can be kept in flight.
129 * - CC 3.0,3.5, and >=5.0: NTHREAD_Z=1, (64, 16) bounds
130 * - CC 3.7: NTHREAD_Z=2, (128, 16) bounds
132 * Note: convenience macros, need to be undef-ed at the end of the file.
134 #if GMX_PTX_ARCH == 370
135 # define NTHREAD_Z (2)
136 # define MIN_BLOCKS_PER_MP (16)
138 # define NTHREAD_Z (1)
139 # define MIN_BLOCKS_PER_MP (16)
140 #endif /* GMX_PTX_ARCH == 370 */
141 #define THREADS_PER_BLOCK (c_clSize * c_clSize * NTHREAD_Z)
143 #if GMX_PTX_ARCH >= 350
145 __launch_bounds__(THREADS_PER_BLOCK, MIN_BLOCKS_PER_MP)
147 __launch_bounds__(THREADS_PER_BLOCK)
148 #endif /* GMX_PTX_ARCH >= 350 */
150 # ifdef CALC_ENERGIES
151 __global__ void NB_KERNEL_FUNC_NAME(nbnxn_kernel, _VF_prune_cuda)
153 __global__ void NB_KERNEL_FUNC_NAME(nbnxn_kernel, _F_prune_cuda)
154 # endif /* CALC_ENERGIES */
156 # ifdef CALC_ENERGIES
157 __global__ void NB_KERNEL_FUNC_NAME(nbnxn_kernel, _VF_cuda)
159 __global__ void NB_KERNEL_FUNC_NAME(nbnxn_kernel, _F_cuda)
160 # endif /* CALC_ENERGIES */
161 #endif /* PRUNE_NBL */
162 (const NBAtomData atdat, const NBParamGpu nbparam, const Nbnxm::gpu_plist plist, bool bCalcFshift)
163 #ifdef FUNCTION_DECLARATION_ONLY
164 ; /* Only do function declaration, omit the function body. */
167 /* convenience variables */
168 const nbnxn_sci_t* pl_sci = plist.sci;
172 nbnxn_cj4_t* pl_cj4 = plist.cj4;
173 const nbnxn_excl_t* excl = plist.excl;
175 const int* atom_types = atdat.atomTypes;
176 int ntypes = atdat.numTypes;
178 const float2* lj_comb = atdat.ljComb;
179 float2 ljcp_i, ljcp_j;
181 const float4* xq = atdat.xq;
182 float3* f = asFloat3(atdat.f);
183 const float3* shift_vec = asFloat3(atdat.shiftVec);
184 float rcoulomb_sq = nbparam.rcoulomb_sq;
185 # ifdef VDW_CUTOFF_CHECK
186 float rvdw_sq = nbparam.rvdw_sq;
190 float lje_coeff2, lje_coeff6_6;
193 float two_k_rf = nbparam.two_k_rf;
196 float beta2 = nbparam.ewald_beta * nbparam.ewald_beta;
197 float beta3 = nbparam.ewald_beta * nbparam.ewald_beta * nbparam.ewald_beta;
200 float rlist_sq = nbparam.rlistOuter_sq;
203 # ifdef CALC_ENERGIES
205 float beta = nbparam.ewald_beta;
206 float ewald_shift = nbparam.sh_ewald;
208 float reactionFieldShift = nbparam.c_rf;
209 # endif /* EL_EWALD_ANY */
210 float* e_lj = atdat.eLJ;
211 float* e_el = atdat.eElec;
212 # endif /* CALC_ENERGIES */
214 /* thread/block/warp id-s */
215 unsigned int tidxi = threadIdx.x;
216 unsigned int tidxj = threadIdx.y;
217 unsigned int tidx = threadIdx.y * blockDim.x + threadIdx.x;
219 unsigned int tidxz = 0;
221 unsigned int tidxz = threadIdx.z;
223 unsigned int bidx = blockIdx.x;
224 unsigned int widx = tidx / warp_size; /* warp index */
226 int sci, ci, cj, ai, aj, cij4_start, cij4_end;
230 int i, jm, j4, wexcl_idx;
231 float qi, qj_f, r2, inv_r, inv_r2;
232 # if !defined LJ_COMB_LB || defined CALC_ENERGIES
233 float inv_r6, c6, c12;
236 float sigma, epsilon;
238 float int_bit, F_invr;
239 # ifdef CALC_ENERGIES
242 # if defined CALC_ENERGIES || defined LJ_POT_SWITCH
245 unsigned int wexcl, imask, mask_ji;
247 float3 xi, xj, rv, f_ij, fcj_buf;
248 float3 fci_buf[c_nbnxnGpuNumClusterPerSupercluster]; /* i force buffer */
251 /*! i-cluster interaction mask for a super-cluster with all c_nbnxnGpuNumClusterPerSupercluster=8 bits set */
252 const unsigned superClInteractionMask = ((1U << c_nbnxnGpuNumClusterPerSupercluster) - 1U);
254 /*********************************************************************
255 * Set up shared memory pointers.
256 * sm_nextSlotPtr should always be updated to point to the "next slot",
257 * that is past the last point where data has been stored.
259 extern __shared__ char sm_dynamicShmem[];
260 char* sm_nextSlotPtr = sm_dynamicShmem;
261 static_assert(sizeof(char) == 1,
262 "The shared memory offset calculation assumes that char is 1 byte");
264 /* shmem buffer for i x+q pre-loading */
265 float4* xqib = (float4*)sm_nextSlotPtr;
266 sm_nextSlotPtr += (c_nbnxnGpuNumClusterPerSupercluster * c_clSize * sizeof(*xqib));
268 /* shmem buffer for cj, for each warp separately */
269 int* cjs = (int*)(sm_nextSlotPtr);
270 /* the cjs buffer's use expects a base pointer offset for pairs of warps in the j-concurrent execution */
271 cjs += tidxz * c_nbnxnGpuClusterpairSplit * c_nbnxnGpuJgroupSize;
272 sm_nextSlotPtr += (NTHREAD_Z * c_nbnxnGpuClusterpairSplit * c_nbnxnGpuJgroupSize * sizeof(*cjs));
275 /* shmem buffer for i atom-type pre-loading */
276 int* atib = (int*)sm_nextSlotPtr;
277 sm_nextSlotPtr += (c_nbnxnGpuNumClusterPerSupercluster * c_clSize * sizeof(*atib));
279 /* shmem buffer for i-atom LJ combination rule parameters */
280 float2* ljcpib = (float2*)sm_nextSlotPtr;
281 sm_nextSlotPtr += (c_nbnxnGpuNumClusterPerSupercluster * c_clSize * sizeof(*ljcpib));
283 /*********************************************************************/
285 nb_sci = pl_sci[bidx]; /* my i super-cluster's index = current bidx */
286 sci = nb_sci.sci; /* super-cluster */
287 cij4_start = nb_sci.cj4_ind_start; /* first ...*/
288 cij4_end = nb_sci.cj4_ind_end; /* and last index of j clusters */
292 /* Pre-load i-atom x and q into shared memory */
293 ci = sci * c_nbnxnGpuNumClusterPerSupercluster + tidxj;
294 ai = ci * c_clSize + tidxi;
296 float* shiftptr = (float*)&shift_vec[nb_sci.shift];
297 xqbuf = xq[ai] + make_float4(LDG(shiftptr), LDG(shiftptr + 1), LDG(shiftptr + 2), 0.0f);
298 xqbuf.w *= nbparam.epsfac;
299 xqib[tidxj * c_clSize + tidxi] = xqbuf;
302 /* Pre-load the i-atom types into shared memory */
303 atib[tidxj * c_clSize + tidxi] = atom_types[ai];
305 /* Pre-load the LJ combination parameters into shared memory */
306 ljcpib[tidxj * c_clSize + tidxi] = lj_comb[ai];
311 for (i = 0; i < c_nbnxnGpuNumClusterPerSupercluster; i++)
313 fci_buf[i] = make_float3(0.0f);
317 /* TODO: we are trading registers with flops by keeping lje_coeff-s, try re-calculating it later */
318 lje_coeff2 = nbparam.ewaldcoeff_lj * nbparam.ewaldcoeff_lj;
319 lje_coeff6_6 = lje_coeff2 * lje_coeff2 * lje_coeff2 * c_oneSixth;
323 # ifdef CALC_ENERGIES
327 # ifdef EXCLUSION_FORCES /* Ewald or RF */
328 if (nb_sci.shift == CENTRAL && pl_cj4[cij4_start].cj[0] == sci * c_nbnxnGpuNumClusterPerSupercluster)
330 /* we have the diagonal: add the charge and LJ self interaction energy term */
331 for (i = 0; i < c_nbnxnGpuNumClusterPerSupercluster; i++)
333 # if defined EL_EWALD_ANY || defined EL_RF || defined EL_CUTOFF
334 qi = xqib[i * c_clSize + tidxi].w;
339 // load only the first 4 bytes of the parameter pair (equivalent with nbfp[idx].x)
340 E_lj += LDG((float*)&nbparam.nbfp[atom_types[(sci * c_nbnxnGpuNumClusterPerSupercluster + i) * c_clSize + tidxi]
345 /* divide the self term(s) equally over the j-threads, then multiply with the coefficients. */
347 E_lj /= c_clSize * NTHREAD_Z;
348 E_lj *= 0.5f * c_oneSixth * lje_coeff6_6;
351 # if defined EL_EWALD_ANY || defined EL_RF || defined EL_CUTOFF
352 /* Correct for epsfac^2 due to adding qi^2 */
353 E_el /= nbparam.epsfac * c_clSize * NTHREAD_Z;
354 # if defined EL_RF || defined EL_CUTOFF
355 E_el *= -0.5f * reactionFieldShift;
357 E_el *= -beta * M_FLOAT_1_SQRTPI; /* last factor 1/sqrt(pi) */
359 # endif /* EL_EWALD_ANY || defined EL_RF || defined EL_CUTOFF */
361 # endif /* EXCLUSION_FORCES */
363 # endif /* CALC_ENERGIES */
365 # ifdef EXCLUSION_FORCES
366 const int nonSelfInteraction = !(nb_sci.shift == CENTRAL & tidxj <= tidxi);
369 /* loop over the j clusters = seen by any of the atoms in the current super-cluster;
370 * The loop stride NTHREAD_Z ensures that consecutive warps-pairs are assigned
371 * consecutive j4's entries.
373 for (j4 = cij4_start + tidxz; j4 < cij4_end; j4 += NTHREAD_Z)
375 wexcl_idx = pl_cj4[j4].imei[widx].excl_ind;
376 imask = pl_cj4[j4].imei[widx].imask;
377 wexcl = excl[wexcl_idx].pair[(tidx) & (warp_size - 1)];
383 /* Pre-load cj into shared memory on both warps separately */
384 if ((tidxj == 0 | tidxj == 4) & (tidxi < c_nbnxnGpuJgroupSize))
386 cjs[tidxi + tidxj * c_nbnxnGpuJgroupSize / c_splitClSize] = pl_cj4[j4].cj[tidxi];
388 __syncwarp(c_fullWarpMask);
390 /* Unrolling this loop
391 - with pruning leads to register spilling;
392 - on Kepler and later it is much slower;
393 Tested with up to nvcc 7.5 */
394 for (jm = 0; jm < c_nbnxnGpuJgroupSize; jm++)
396 if (imask & (superClInteractionMask << (jm * c_nbnxnGpuNumClusterPerSupercluster)))
398 mask_ji = (1U << (jm * c_nbnxnGpuNumClusterPerSupercluster));
400 cj = cjs[jm + (tidxj & 4) * c_nbnxnGpuJgroupSize / c_splitClSize];
401 aj = cj * c_clSize + tidxj;
403 /* load j atom data */
405 xj = make_float3(xqbuf.x, xqbuf.y, xqbuf.z);
408 typej = atom_types[aj];
410 ljcp_j = lj_comb[aj];
413 fcj_buf = make_float3(0.0f);
415 # if !defined PRUNE_NBL
418 for (i = 0; i < c_nbnxnGpuNumClusterPerSupercluster; i++)
422 ci = sci * c_nbnxnGpuNumClusterPerSupercluster + i; /* i cluster index */
424 /* all threads load an atom from i cluster ci into shmem! */
425 xqbuf = xqib[i * c_clSize + tidxi];
426 xi = make_float3(xqbuf.x, xqbuf.y, xqbuf.z);
428 /* distance between i and j atoms */
433 /* If _none_ of the atoms pairs are in cutoff range,
434 the bit corresponding to the current
435 cluster-pair in imask gets set to 0. */
436 if (!__any_sync(c_fullWarpMask, r2 < rlist_sq))
442 int_bit = (wexcl & mask_ji) ? 1.0f : 0.0f;
444 /* cutoff & exclusion check */
445 # ifdef EXCLUSION_FORCES
446 if ((r2 < rcoulomb_sq) * (nonSelfInteraction | (ci != cj)))
448 if ((r2 < rcoulomb_sq) * int_bit)
451 /* load the rest of the i-atom parameters */
455 /* LJ 6*C6 and 12*C12 */
456 typei = atib[i * c_clSize + tidxi];
457 fetch_nbfp_c6_c12(c6, c12, nbparam, ntypes * typei + typej);
459 ljcp_i = ljcpib[i * c_clSize + tidxi];
461 c6 = ljcp_i.x * ljcp_j.x;
462 c12 = ljcp_i.y * ljcp_j.y;
464 /* LJ 2^(1/6)*sigma and 12*epsilon */
465 sigma = ljcp_i.x + ljcp_j.x;
466 epsilon = ljcp_i.y * ljcp_j.y;
467 # if defined CALC_ENERGIES || defined LJ_FORCE_SWITCH || defined LJ_POT_SWITCH
468 convert_sigma_epsilon_to_c6_c12(sigma, epsilon, &c6, &c12);
470 # endif /* LJ_COMB_GEOM */
471 # endif /* LJ_COMB */
473 // Ensure distance do not become so small that r^-12 overflows
474 r2 = max(r2, c_nbnxnMinDistanceSquared);
477 inv_r2 = inv_r * inv_r;
478 # if !defined LJ_COMB_LB || defined CALC_ENERGIES
479 inv_r6 = inv_r2 * inv_r2 * inv_r2;
480 # ifdef EXCLUSION_FORCES
481 /* We could mask inv_r2, but with Ewald
482 * masking both inv_r6 and F_invr is faster */
484 # endif /* EXCLUSION_FORCES */
486 F_invr = inv_r6 * (c12 * inv_r6 - c6) * inv_r2;
487 # if defined CALC_ENERGIES || defined LJ_POT_SWITCH
489 * (c12 * (inv_r6 * inv_r6 + nbparam.repulsion_shift.cpot) * c_oneTwelveth
490 - c6 * (inv_r6 + nbparam.dispersion_shift.cpot) * c_oneSixth);
492 # else /* !LJ_COMB_LB || CALC_ENERGIES */
493 float sig_r = sigma * inv_r;
494 float sig_r2 = sig_r * sig_r;
495 float sig_r6 = sig_r2 * sig_r2 * sig_r2;
496 # ifdef EXCLUSION_FORCES
498 # endif /* EXCLUSION_FORCES */
500 F_invr = epsilon * sig_r6 * (sig_r6 - 1.0f) * inv_r2;
501 # endif /* !LJ_COMB_LB || CALC_ENERGIES */
503 # ifdef LJ_FORCE_SWITCH
504 # ifdef CALC_ENERGIES
505 calculate_force_switch_F_E(nbparam, c6, c12, inv_r, r2, &F_invr, &E_lj_p);
507 calculate_force_switch_F(nbparam, c6, c12, inv_r, r2, &F_invr);
508 # endif /* CALC_ENERGIES */
509 # endif /* LJ_FORCE_SWITCH */
513 # ifdef LJ_EWALD_COMB_GEOM
514 # ifdef CALC_ENERGIES
515 calculate_lj_ewald_comb_geom_F_E(
516 nbparam, typei, typej, r2, inv_r2, lje_coeff2, lje_coeff6_6, int_bit, &F_invr, &E_lj_p);
518 calculate_lj_ewald_comb_geom_F(
519 nbparam, typei, typej, r2, inv_r2, lje_coeff2, lje_coeff6_6, &F_invr);
520 # endif /* CALC_ENERGIES */
521 # elif defined LJ_EWALD_COMB_LB
522 calculate_lj_ewald_comb_LB_F_E(nbparam,
529 # ifdef CALC_ENERGIES
537 # endif /* CALC_ENERGIES */
539 # endif /* LJ_EWALD_COMB_GEOM */
540 # endif /* LJ_EWALD */
542 # ifdef LJ_POT_SWITCH
543 # ifdef CALC_ENERGIES
544 calculate_potential_switch_F_E(nbparam, inv_r, r2, &F_invr, &E_lj_p);
546 calculate_potential_switch_F(nbparam, inv_r, r2, &F_invr, &E_lj_p);
547 # endif /* CALC_ENERGIES */
548 # endif /* LJ_POT_SWITCH */
550 # ifdef VDW_CUTOFF_CHECK
551 /* Separate VDW cut-off check to enable twin-range cut-offs
552 * (rvdw < rcoulomb <= rlist)
554 vdw_in_range = (r2 < rvdw_sq) ? 1.0f : 0.0f;
555 F_invr *= vdw_in_range;
556 # ifdef CALC_ENERGIES
557 E_lj_p *= vdw_in_range;
559 # endif /* VDW_CUTOFF_CHECK */
561 # ifdef CALC_ENERGIES
567 # ifdef EXCLUSION_FORCES
568 F_invr += qi * qj_f * int_bit * inv_r2 * inv_r;
570 F_invr += qi * qj_f * inv_r2 * inv_r;
574 F_invr += qi * qj_f * (int_bit * inv_r2 * inv_r - two_k_rf);
576 # if defined EL_EWALD_ANA
578 * (int_bit * inv_r2 * inv_r + pmecorrF(beta2 * r2) * beta3);
579 # elif defined EL_EWALD_TAB
582 - interpolate_coulomb_force_r(nbparam, r2 * inv_r))
584 # endif /* EL_EWALD_ANA/TAB */
586 # ifdef CALC_ENERGIES
588 E_el += qi * qj_f * (int_bit * inv_r - reactionFieldShift);
592 * (int_bit * inv_r + 0.5f * two_k_rf * r2 - reactionFieldShift);
595 /* 1.0f - erff is faster than erfcf */
597 * (inv_r * (int_bit - erff(r2 * inv_r * beta)) - int_bit * ewald_shift);
598 # endif /* EL_EWALD_ANY */
602 /* accumulate j forces in registers */
605 /* accumulate i forces in registers */
610 /* shift the mask bit by 1 */
614 /* reduce j forces */
615 reduce_force_j_warp_shfl(fcj_buf, f, tidxi, aj, c_fullWarpMask);
619 /* Update the imask with the new one which does not contain the
620 out of range clusters anymore. */
621 pl_cj4[j4].imei[widx].imask = imask;
624 // avoid shared memory WAR hazards between loop iterations
625 __syncwarp(c_fullWarpMask);
628 /* skip central shifts when summing shift forces */
629 if (nb_sci.shift == CENTRAL)
634 float fshift_buf = 0.0f;
636 /* reduce i forces */
637 for (i = 0; i < c_nbnxnGpuNumClusterPerSupercluster; i++)
639 ai = (sci * c_nbnxnGpuNumClusterPerSupercluster + i) * c_clSize + tidxi;
640 reduce_force_i_warp_shfl(fci_buf[i], f, &fshift_buf, bCalcFshift, tidxj, ai, c_fullWarpMask);
643 /* add up local shift forces into global mem, tidxj indexes x,y,z */
644 if (bCalcFshift && (tidxj & 3) < 3)
646 float3* fShift = asFloat3(atdat.fShift);
647 atomicAdd(&(fShift[nb_sci.shift].x) + (tidxj & 3), fshift_buf);
650 # ifdef CALC_ENERGIES
651 /* reduce the energies over warps and store into global memory */
652 reduce_energy_warp_shfl(E_lj, E_el, e_lj, e_el, tidx, c_fullWarpMask);
655 #endif /* FUNCTION_DECLARATION_ONLY */
658 #undef MIN_BLOCKS_PER_MP
659 #undef THREADS_PER_BLOCK
662 #undef EXCLUSION_FORCES