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37 * \brief Implements PME force gathering in CUDA.
39 * \author Aleksei Iupinov <a.yupinov@gmail.com>
46 #include "gromacs/gpu_utils/cuda_kernel_utils.cuh"
47 #include "gromacs/gpu_utils/typecasts.cuh"
50 #include "pme_gpu_calculate_splines.cuh"
54 * An inline CUDA function: unroll the dynamic index accesses to the constant grid sizes to avoid local memory operations.
56 __device__ __forceinline__ float read_grid_size(const float* realGridSizeFP, const int dimIndex)
60 case XX: return realGridSizeFP[XX];
61 case YY: return realGridSizeFP[YY];
62 case ZZ: return realGridSizeFP[ZZ];
68 /*! \brief Reduce the partial force contributions.
70 * \tparam[in] order The PME order (must be 4).
71 * \tparam[in] atomDataSize The number of partial force contributions for each atom (currently
72 * order^2 == 16) \tparam[in] blockSize The CUDA block size \param[out] sm_forces Shared
73 * memory array with the output forces (number of elements is number of atoms per block) \param[in]
74 * atomIndexLocal Local atom index \param[in] splineIndex Spline index \param[in]
75 * lineIndex Line index (same as threadLocalId) \param[in] realGridSizeFP Local grid
76 * size constant \param[in] fx Input force partial component X \param[in] fy Input
77 * force partial component Y \param[in] fz Input force partial component Z
79 template<const int order, const int atomDataSize, const int blockSize>
80 __device__ __forceinline__ void reduce_atom_forces(float3* __restrict__ sm_forces,
81 const int atomIndexLocal,
82 const int splineIndex,
84 const float* realGridSizeFP,
89 if (!(order & (order - 1))) // Only for orders of power of 2
91 const unsigned int activeMask = c_fullWarpMask;
93 // A tricky shuffle reduction inspired by reduce_force_j_warp_shfl
94 // TODO: find out if this is the best in terms of transactions count
95 static_assert(order == 4, "Only order of 4 is implemented");
96 static_assert(atomDataSize <= warp_size,
97 "TODO: rework for atomDataSize > warp_size (order 8 or larger)");
98 const int width = atomDataSize;
100 fx += __shfl_down_sync(activeMask, fx, 1, width);
101 fy += __shfl_up_sync(activeMask, fy, 1, width);
102 fz += __shfl_down_sync(activeMask, fz, 1, width);
109 fx += __shfl_down_sync(activeMask, fx, 2, width);
110 fz += __shfl_up_sync(activeMask, fz, 2, width);
117 // By now fx contains intermediate quad sums of all 3 components:
118 // splineIndex 0 1 2 and 3 4 5 6 and 7 8...
119 // sum of... fx0 to fx3 fy0 to fy3 fz0 to fz3 fx4 to fx7 fy4 to fy7 fz4 to fz7 etc.
121 // We have to just further reduce those groups of 4
122 for (int delta = 4; delta < atomDataSize; delta <<= 1)
124 fx += __shfl_down_sync(activeMask, fx, delta, width);
127 const int dimIndex = splineIndex;
130 const float n = read_grid_size(realGridSizeFP, dimIndex);
131 *((float*)(&sm_forces[atomIndexLocal]) + dimIndex) = fx * n;
136 // We use blockSize shared memory elements to read fx, or fy, or fz, and then reduce them to
137 // fit into smemPerDim elements which are stored separately (first 2 dimensions only)
138 const int smemPerDim = warp_size;
139 const int smemReserved = (DIM)*smemPerDim;
140 __shared__ float sm_forceReduction[smemReserved + blockSize];
141 __shared__ float* sm_forceTemp[DIM];
143 const int numWarps = blockSize / smemPerDim;
144 const int minStride =
145 max(1, atomDataSize / numWarps); // order 4: 128 threads => 4, 256 threads => 2, etc
148 for (int dimIndex = 0; dimIndex < DIM; dimIndex++)
150 int elementIndex = smemReserved + lineIndex;
151 // Store input force contributions
152 sm_forceReduction[elementIndex] = (dimIndex == XX) ? fx : (dimIndex == YY) ? fy : fz;
153 // sync here because two warps write data that the first one consumes below
155 // Reduce to fit into smemPerDim (warp size)
157 for (int redStride = atomDataSize / 2; redStride > minStride; redStride >>= 1)
159 if (splineIndex < redStride)
161 sm_forceReduction[elementIndex] += sm_forceReduction[elementIndex + redStride];
165 // Last iteration - packing everything to be nearby, storing convenience pointer
166 sm_forceTemp[dimIndex] = sm_forceReduction + dimIndex * smemPerDim;
167 int redStride = minStride;
168 if (splineIndex < redStride)
170 const int packedIndex = atomIndexLocal * redStride + splineIndex;
171 sm_forceTemp[dimIndex][packedIndex] =
172 sm_forceReduction[elementIndex] + sm_forceReduction[elementIndex + redStride];
177 assert((blockSize / warp_size) >= DIM);
178 // assert (atomsPerBlock <= warp_size);
180 const int warpIndex = lineIndex / warp_size;
181 const int dimIndex = warpIndex;
183 // First 3 warps can now process 1 dimension each
186 int sourceIndex = lineIndex % warp_size;
188 for (int redStride = minStride / 2; redStride > 1; redStride >>= 1)
190 if (!(splineIndex & redStride))
192 sm_forceTemp[dimIndex][sourceIndex] += sm_forceTemp[dimIndex][sourceIndex + redStride];
198 const float n = read_grid_size(realGridSizeFP, dimIndex);
199 const int atomIndex = sourceIndex / minStride;
201 if (sourceIndex == minStride * atomIndex)
203 *((float*)(&sm_forces[atomIndex]) + dimIndex) =
204 (sm_forceTemp[dimIndex][sourceIndex] + sm_forceTemp[dimIndex][sourceIndex + 1]) * n;
211 * A CUDA kernel which gathers the atom forces from the grid.
212 * The grid is assumed to be wrapped in dimension Z.
214 * \tparam[in] order The PME order (must be 4 currently).
215 * \tparam[in] wrapX Tells if the grid is wrapped in the X dimension.
216 * \tparam[in] wrapY Tells if the grid is wrapped in the Y dimension.
217 * \tparam[in] readGlobal Tells if we should read spline values from global memory
218 * \tparam[in] useOrderThreads Tells if we should use order threads per atom
219 * (order*order used if false)
220 * \param[in] kernelParams All the PME GPU data.
222 template<const int order, const bool wrapX, const bool wrapY, const bool readGlobal, const bool useOrderThreads>
223 __launch_bounds__(c_gatherMaxThreadsPerBlock, c_gatherMinBlocksPerMP) __global__
224 void pme_gather_kernel(const PmeGpuCudaKernelParams kernelParams)
226 /* Global memory pointers */
227 const float* __restrict__ gm_coefficients = kernelParams.atoms.d_coefficients;
228 const float* __restrict__ gm_grid = kernelParams.grid.d_realGrid;
229 float* __restrict__ gm_forces = kernelParams.atoms.d_forces;
231 /* Global memory pointers for readGlobal */
232 const float* __restrict__ gm_theta = kernelParams.atoms.d_theta;
233 const float* __restrict__ gm_dtheta = kernelParams.atoms.d_dtheta;
234 const int* __restrict__ gm_gridlineIndices = kernelParams.atoms.d_gridlineIndices;
240 const int atomsPerBlock =
241 useOrderThreads ? (c_gatherMaxThreadsPerBlock / c_pmeSpreadGatherThreadsPerAtom4ThPerAtom)
242 : (c_gatherMaxThreadsPerBlock / c_pmeSpreadGatherThreadsPerAtom);
243 const int blockIndex = blockIdx.y * gridDim.x + blockIdx.x;
245 /* Number of data components and threads for a single atom */
246 const int atomDataSize = useOrderThreads ? c_pmeSpreadGatherThreadsPerAtom4ThPerAtom
247 : c_pmeSpreadGatherThreadsPerAtom;
248 const int atomsPerWarp = useOrderThreads ? c_pmeSpreadGatherAtomsPerWarp4ThPerAtom
249 : c_pmeSpreadGatherAtomsPerWarp;
251 const int blockSize = atomsPerBlock * atomDataSize;
252 assert(blockSize == blockDim.x * blockDim.y * blockDim.z);
254 /* These are the atom indices - for the shared and global memory */
255 const int atomIndexLocal = threadIdx.z;
256 const int atomIndexOffset = blockIndex * atomsPerBlock;
257 const int atomIndexGlobal = atomIndexOffset + atomIndexLocal;
259 /* Early return for fully empty blocks at the end
260 * (should only happen for billions of input atoms)
262 if (atomIndexOffset >= kernelParams.atoms.nAtoms)
266 // 4 warps per block, 8 atoms per warp *3 *4
267 const int splineParamsSize = atomsPerBlock * DIM * order;
268 const int gridlineIndicesSize = atomsPerBlock * DIM;
269 __shared__ int sm_gridlineIndices[gridlineIndicesSize];
270 __shared__ float sm_theta[splineParamsSize];
271 __shared__ float sm_dtheta[splineParamsSize];
273 /* Spline Z coordinates */
274 const int ithz = threadIdx.x;
276 /* These are the spline contribution indices in shared memory */
277 const int splineIndex = threadIdx.y * blockDim.x + threadIdx.x;
278 const int lineIndex = (threadIdx.z * (blockDim.x * blockDim.y))
279 + splineIndex; /* And to all the block's particles */
281 const int threadLocalId =
282 (threadIdx.z * (blockDim.x * blockDim.y)) + blockDim.x * threadIdx.y + threadIdx.x;
283 const int threadLocalIdMax = blockDim.x * blockDim.y * blockDim.z;
288 const int localGridlineIndicesIndex = threadLocalId;
289 const int globalGridlineIndicesIndex = blockIndex * gridlineIndicesSize + localGridlineIndicesIndex;
290 const int globalCheckIndices = pme_gpu_check_atom_data_index(
291 globalGridlineIndicesIndex, kernelParams.atoms.nAtoms * DIM);
292 if ((localGridlineIndicesIndex < gridlineIndicesSize) & globalCheckIndices)
294 sm_gridlineIndices[localGridlineIndicesIndex] = gm_gridlineIndices[globalGridlineIndicesIndex];
295 assert(sm_gridlineIndices[localGridlineIndicesIndex] >= 0);
297 /* The loop needed for order threads per atom to make sure we load all data values, as each thread must load multiple values
298 with order*order threads per atom, it is only required for each thread to load one data value */
301 const int iMax = useOrderThreads ? 3 : 1;
303 for (int i = iMin; i < iMax; i++)
305 int localSplineParamsIndex =
307 + i * threadLocalIdMax; /* i will always be zero for order*order threads per atom */
308 int globalSplineParamsIndex = blockIndex * splineParamsSize + localSplineParamsIndex;
309 int globalCheckSplineParams = pme_gpu_check_atom_data_index(
310 globalSplineParamsIndex, kernelParams.atoms.nAtoms * DIM * order);
311 if ((localSplineParamsIndex < splineParamsSize) && globalCheckSplineParams)
313 sm_theta[localSplineParamsIndex] = gm_theta[globalSplineParamsIndex];
314 sm_dtheta[localSplineParamsIndex] = gm_dtheta[globalSplineParamsIndex];
315 assert(isfinite(sm_theta[localSplineParamsIndex]));
316 assert(isfinite(sm_dtheta[localSplineParamsIndex]));
323 const float3* __restrict__ gm_coordinates = asFloat3(kernelParams.atoms.d_coordinates);
324 /* Recaclulate Splines */
325 if (c_useAtomDataPrefetch)
328 __shared__ float sm_coefficients[atomsPerBlock];
330 __shared__ float3 sm_coordinates[atomsPerBlock];
331 /* Staging coefficients/charges */
332 pme_gpu_stage_atom_data<float, atomsPerBlock, 1>(kernelParams, sm_coefficients, gm_coefficients);
334 /* Staging coordinates */
335 pme_gpu_stage_atom_data<float3, atomsPerBlock, 1>(kernelParams, sm_coordinates, gm_coordinates);
337 atomX = sm_coordinates[atomIndexLocal];
338 atomCharge = sm_coefficients[atomIndexLocal];
342 atomX = gm_coordinates[atomIndexGlobal];
343 atomCharge = gm_coefficients[atomIndexGlobal];
345 calculate_splines<order, atomsPerBlock, atomsPerWarp, true, false>(
346 kernelParams, atomIndexOffset, atomX, atomCharge, sm_theta, sm_dtheta, sm_gridlineIndices);
353 const int globalCheck = pme_gpu_check_atom_data_index(atomIndexGlobal, kernelParams.atoms.nAtoms);
354 const int chargeCheck = pme_gpu_check_atom_charge(gm_coefficients[atomIndexGlobal]);
356 if (chargeCheck & globalCheck)
358 const int nx = kernelParams.grid.realGridSize[XX];
359 const int ny = kernelParams.grid.realGridSize[YY];
360 const int nz = kernelParams.grid.realGridSize[ZZ];
361 const int pny = kernelParams.grid.realGridSizePadded[YY];
362 const int pnz = kernelParams.grid.realGridSizePadded[ZZ];
364 const int atomWarpIndex = atomIndexLocal % atomsPerWarp;
365 const int warpIndex = atomIndexLocal / atomsPerWarp;
367 const int splineIndexBase = getSplineParamIndexBase<order, atomsPerWarp>(warpIndex, atomWarpIndex);
368 const int splineIndexZ = getSplineParamIndex<order, atomsPerWarp>(splineIndexBase, ZZ, ithz);
369 const float2 tdz = make_float2(sm_theta[splineIndexZ], sm_dtheta[splineIndexZ]);
371 int iz = sm_gridlineIndices[atomIndexLocal * DIM + ZZ] + ithz;
372 const int ixBase = sm_gridlineIndices[atomIndexLocal * DIM + XX];
380 const int ithyMin = useOrderThreads ? 0 : threadIdx.y;
381 const int ithyMax = useOrderThreads ? order : threadIdx.y + 1;
382 for (int ithy = ithyMin; ithy < ithyMax; ithy++)
384 const int splineIndexY = getSplineParamIndex<order, atomsPerWarp>(splineIndexBase, YY, ithy);
385 const float2 tdy = make_float2(sm_theta[splineIndexY], sm_dtheta[splineIndexY]);
387 iy = sm_gridlineIndices[atomIndexLocal * DIM + YY] + ithy;
388 if (wrapY & (iy >= ny))
392 constOffset = iy * pnz + iz;
395 for (int ithx = 0; (ithx < order); ithx++)
397 int ix = ixBase + ithx;
398 if (wrapX & (ix >= nx))
402 const int gridIndexGlobal = ix * pny * pnz + constOffset;
403 assert(gridIndexGlobal >= 0);
404 const float gridValue = gm_grid[gridIndexGlobal];
405 assert(isfinite(gridValue));
406 const int splineIndexX =
407 getSplineParamIndex<order, atomsPerWarp>(splineIndexBase, XX, ithx);
408 const float2 tdx = make_float2(sm_theta[splineIndexX], sm_dtheta[splineIndexX]);
409 const float fxy1 = tdz.x * gridValue;
410 const float fz1 = tdz.y * gridValue;
411 fx += tdx.y * tdy.x * fxy1;
412 fy += tdx.x * tdy.y * fxy1;
413 fz += tdx.x * tdy.x * fz1;
418 // Reduction of partial force contributions
419 __shared__ float3 sm_forces[atomsPerBlock];
420 reduce_atom_forces<order, atomDataSize, blockSize>(sm_forces, atomIndexLocal, splineIndex, lineIndex,
421 kernelParams.grid.realGridSizeFP, fx, fy, fz);
424 /* Calculating the final forces with no component branching, atomsPerBlock threads */
425 const int forceIndexLocal = threadLocalId;
426 const int forceIndexGlobal = atomIndexOffset + forceIndexLocal;
427 const int calcIndexCheck = pme_gpu_check_atom_data_index(forceIndexGlobal, kernelParams.atoms.nAtoms);
428 if ((forceIndexLocal < atomsPerBlock) & calcIndexCheck)
430 const float3 atomForces = sm_forces[forceIndexLocal];
431 const float negCoefficient = -gm_coefficients[forceIndexGlobal];
433 result.x = negCoefficient * kernelParams.current.recipBox[XX][XX] * atomForces.x;
434 result.y = negCoefficient
435 * (kernelParams.current.recipBox[XX][YY] * atomForces.x
436 + kernelParams.current.recipBox[YY][YY] * atomForces.y);
437 result.z = negCoefficient
438 * (kernelParams.current.recipBox[XX][ZZ] * atomForces.x
439 + kernelParams.current.recipBox[YY][ZZ] * atomForces.y
440 + kernelParams.current.recipBox[ZZ][ZZ] * atomForces.z);
441 sm_forces[forceIndexLocal] = result;
445 assert(atomsPerBlock <= warp_size);
447 /* Writing or adding the final forces component-wise, single warp */
448 const int blockForcesSize = atomsPerBlock * DIM;
449 const int numIter = (blockForcesSize + warp_size - 1) / warp_size;
450 const int iterThreads = blockForcesSize / numIter;
451 if (threadLocalId < iterThreads)
454 for (int i = 0; i < numIter; i++)
456 int outputIndexLocal = i * iterThreads + threadLocalId;
457 int outputIndexGlobal = blockIndex * blockForcesSize + outputIndexLocal;
458 const int globalOutputCheck =
459 pme_gpu_check_atom_data_index(outputIndexGlobal, kernelParams.atoms.nAtoms * DIM);
460 if (globalOutputCheck)
462 const float outputForceComponent = ((float*)sm_forces)[outputIndexLocal];
463 gm_forces[outputIndexGlobal] = outputForceComponent;
469 //! Kernel instantiations
470 template __global__ void pme_gather_kernel<4, true, true, true, true>(const PmeGpuCudaKernelParams);
471 template __global__ void pme_gather_kernel<4, true, true, true, false>(const PmeGpuCudaKernelParams);
472 template __global__ void pme_gather_kernel<4, true, true, false, true>(const PmeGpuCudaKernelParams);
473 template __global__ void pme_gather_kernel<4, true, true, false, false>(const PmeGpuCudaKernelParams);