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37 * \brief Implements helper routines for PME gather and spline routines.
39 * \author Aleksei Iupinov <a.yupinov@gmail.com>
46 #include "gromacs/gpu_utils/cuda_kernel_utils.cuh"
47 #include "gromacs/gpu_utils/vectype_ops.cuh"
53 * Gets a base of the unique index to an element in a spline parameter buffer (theta/dtheta),
54 * which is laid out for GPU spread/gather kernels. The base only corresponds to the atom index within the execution block.
55 * Feed the result into getSplineParamIndex() to get a full index.
56 * TODO: it's likely that both parameters can be just replaced with a single atom index, as they are derived from it.
57 * Do that, verifying that the generated code is not bloated, and/or revise the spline indexing scheme.
58 * Removing warp dependency would also be nice (and would probably coincide with removing c_pmeSpreadGatherAtomsPerWarp).
60 * \tparam order PME order
61 * \tparam atomsPerWarp Number of atoms processed by a warp
62 * \param[in] warpIndex Warp index wrt the block.
63 * \param[in] atomWarpIndex Atom index wrt the warp (from 0 to atomsPerWarp - 1).
65 * \returns Index into theta or dtheta array using GPU layout.
67 template<int order, int atomsPerWarp>
68 int __device__ __forceinline__ getSplineParamIndexBase(int warpIndex, int atomWarpIndex)
70 assert((atomWarpIndex >= 0) && (atomWarpIndex < atomsPerWarp));
71 const int dimIndex = 0;
72 const int splineIndex = 0;
73 // The zeroes are here to preserve the full index formula for reference
74 return (((splineIndex + order * warpIndex) * DIM + dimIndex) * atomsPerWarp + atomWarpIndex);
78 * Gets a unique index to an element in a spline parameter buffer (theta/dtheta),
79 * which is laid out for GPU spread/gather kernels. The index is wrt to the execution block,
80 * in range(0, atomsPerBlock * order * DIM).
81 * This function consumes result of getSplineParamIndexBase() and adjusts it for \p dimIndex and \p splineIndex.
83 * \tparam order PME order
84 * \tparam atomsPerWarp Number of atoms processed by a warp
85 * \param[in] paramIndexBase Must be result of getSplineParamIndexBase().
86 * \param[in] dimIndex Dimension index (from 0 to 2)
87 * \param[in] splineIndex Spline contribution index (from 0 to \p order - 1)
89 * \returns Index into theta or dtheta array using GPU layout.
91 template<int order, int atomsPerWarp>
92 int __device__ __forceinline__ getSplineParamIndex(int paramIndexBase, int dimIndex, int splineIndex)
94 assert((dimIndex >= XX) && (dimIndex < DIM));
95 assert((splineIndex >= 0) && (splineIndex < order));
96 return (paramIndexBase + (splineIndex * DIM + dimIndex) * atomsPerWarp);
100 * An inline CUDA function for skipping the zero-charge atoms.
102 * \returns Non-0 if atom should be processed, 0 otherwise.
103 * \param[in] coefficient The atom charge.
105 * This is called from the spline_and_spread and gather PME kernels.
107 bool __device__ __forceinline__ pme_gpu_check_atom_charge(const float coefficient)
109 assert(isfinite(coefficient));
110 return c_skipNeutralAtoms ? (coefficient != 0.0F) : true;
113 //! Controls if the atom and charge data is prefeched into shared memory or loaded per thread from global
114 static const bool c_useAtomDataPrefetch = true;
116 /*! \brief Asserts if the argument is finite.
118 * The function works for any data type, that can be casted to float. Note that there is also
119 * a specialized implementation for float3 data type.
121 * \param[in] arg Argument to check.
124 __device__ inline void assertIsFinite(T arg);
127 __device__ inline void assertIsFinite(float3 gmx_unused arg)
129 assert(isfinite(static_cast<float>(arg.x)));
130 assert(isfinite(static_cast<float>(arg.y)));
131 assert(isfinite(static_cast<float>(arg.z)));
135 __device__ inline void assertIsFinite(T gmx_unused arg)
137 assert(isfinite(static_cast<float>(arg)));
141 * General purpose function for loading atom-related data from global to shared memory.
143 * \tparam[in] T Data type (float/int/...)
144 * \tparam[in] atomsPerBlock Number of atoms processed by a block - should be accounted for in
145 * the size of the shared memory array.
146 * \tparam[in] dataCountPerAtom Number of data elements per single atom (e.g. DIM for an rvec
147 * coordinates array).
148 * \param[out] sm_destination Shared memory array for output.
149 * \param[in] gm_source Global memory array for input.
151 template<typename T, int atomsPerBlock, int dataCountPerAtom>
152 __device__ __forceinline__ void pme_gpu_stage_atom_data(T* __restrict__ sm_destination,
153 const T* __restrict__ gm_source)
155 const int blockIndex = blockIdx.y * gridDim.x + blockIdx.x;
156 const int threadLocalIndex = ((threadIdx.z * blockDim.y + threadIdx.y) * blockDim.x) + threadIdx.x;
157 const int localIndex = threadLocalIndex;
158 const int globalIndexBase = blockIndex * atomsPerBlock * dataCountPerAtom;
159 const int globalIndex = globalIndexBase + localIndex;
160 if (localIndex < atomsPerBlock * dataCountPerAtom)
162 assertIsFinite(gm_source[globalIndex]);
163 sm_destination[localIndex] = gm_source[globalIndex];
168 * PME GPU spline parameter and gridline indices calculation.
169 * This corresponds to the CPU functions calc_interpolation_idx() and make_bsplines().
170 * First stage of the whole kernel.
172 * \tparam[in] order PME interpolation order.
173 * \tparam[in] atomsPerBlock Number of atoms processed by a block - should be accounted for
174 * in the sizes of the shared memory arrays.
175 * \tparam[in] atomsPerWarp Number of atoms processed by a warp
176 * \tparam[in] writeSmDtheta Bool controlling if the theta derivative should be written to
177 * shared memory. Enables calculation of dtheta if set.
178 * \tparam[in] writeGlobal A boolean which tells if the theta values and gridlines should
179 * be written to global memory. Enables calculation of dtheta if
181 * \tparam[in] numGrids The number of grids using the splines.
182 * \param[in] kernelParams Input PME CUDA data in constant memory.
183 * \param[in] atomIndexOffset Starting atom index for the execution block w.r.t. global memory.
184 * \param[in] atomX Atom coordinate of atom processed by thread.
185 * \param[in] atomCharge Atom charge/coefficient of atom processed by thread.
186 * \param[out] sm_theta Atom spline values in the shared memory.
187 * \param[out] sm_dtheta Derivative of atom spline values in shared memory.
188 * \param[out] sm_gridlineIndices Atom gridline indices in the shared memory.
191 template<int order, int atomsPerBlock, int atomsPerWarp, bool writeSmDtheta, bool writeGlobal, int numGrids>
192 __device__ __forceinline__ void calculate_splines(const PmeGpuCudaKernelParams kernelParams,
193 const int atomIndexOffset,
195 const float atomCharge,
196 float* __restrict__ sm_theta,
197 float* __restrict__ sm_dtheta,
198 int* __restrict__ sm_gridlineIndices)
200 assert(numGrids == 1 || numGrids == 2);
201 assert(numGrids == 1 || c_skipNeutralAtoms == false);
203 /* Global memory pointers for output */
204 float* __restrict__ gm_theta = kernelParams.atoms.d_theta;
205 float* __restrict__ gm_dtheta = kernelParams.atoms.d_dtheta;
206 int* __restrict__ gm_gridlineIndices = kernelParams.atoms.d_gridlineIndices;
208 /* Fractional coordinates */
209 __shared__ float sm_fractCoords[atomsPerBlock * DIM];
211 /* Thread index w.r.t. block */
212 const int threadLocalId =
213 (threadIdx.z * (blockDim.x * blockDim.y)) + (threadIdx.y * blockDim.x) + threadIdx.x;
214 /* Warp index w.r.t. block - could probably be obtained easier? */
215 const int warpIndex = threadLocalId / warp_size;
216 /* Atom index w.r.t. warp - alternating 0 1 0 1 .. */
217 const int atomWarpIndex = threadIdx.z % atomsPerWarp;
218 /* Atom index w.r.t. block/shared memory */
219 const int atomIndexLocal = warpIndex * atomsPerWarp + atomWarpIndex;
221 /* Spline contribution index in one dimension */
222 const int threadLocalIdXY = (threadIdx.y * blockDim.x) + threadIdx.x;
223 const int orderIndex = threadLocalIdXY / DIM;
224 /* Dimension index */
225 const int dimIndex = threadLocalIdXY % DIM;
227 /* Multi-purpose index of rvec/ivec atom data */
228 const int sharedMemoryIndex = atomIndexLocal * DIM + dimIndex;
230 float splineData[order];
232 const int localCheck = (dimIndex < DIM) && (orderIndex < 1);
234 /* we have 4 threads per atom, but can only use 3 here for the dimensions */
237 /* Indices interpolation */
241 int tableIndex, tInt;
243 assert(atomIndexLocal < DIM * atomsPerBlock);
244 /* Accessing fields in fshOffset/nXYZ/recipbox/... with dimIndex offset
245 * puts them into local memory(!) instead of accessing the constant memory directly.
246 * That's the reason for the switch, to unroll explicitly.
247 * The commented parts correspond to the 0 components of the recipbox.
252 tableIndex = kernelParams.grid.tablesOffsets[XX];
253 n = kernelParams.grid.realGridSizeFP[XX];
254 t = atomX.x * kernelParams.current.recipBox[dimIndex][XX]
255 + atomX.y * kernelParams.current.recipBox[dimIndex][YY]
256 + atomX.z * kernelParams.current.recipBox[dimIndex][ZZ];
260 tableIndex = kernelParams.grid.tablesOffsets[YY];
261 n = kernelParams.grid.realGridSizeFP[YY];
262 t = /*atomX.x * kernelParams.current.recipBox[dimIndex][XX] + */ atomX.y
263 * kernelParams.current.recipBox[dimIndex][YY]
264 + atomX.z * kernelParams.current.recipBox[dimIndex][ZZ];
268 tableIndex = kernelParams.grid.tablesOffsets[ZZ];
269 n = kernelParams.grid.realGridSizeFP[ZZ];
270 t = /*atomX.x * kernelParams.current.recipBox[dimIndex][XX] + atomX.y * kernelParams.current.recipBox[dimIndex][YY] + */ atomX
272 * kernelParams.current.recipBox[dimIndex][ZZ];
275 const float shift = c_pmeMaxUnitcellShift;
276 /* Fractional coordinates along box vectors, adding a positive shift to ensure t is positive for triclinic boxes */
278 tInt = static_cast<int>(t);
279 assert(sharedMemoryIndex < atomsPerBlock * DIM);
280 sm_fractCoords[sharedMemoryIndex] = t - tInt;
283 assert(tInt < c_pmeNeighborUnitcellCount * n);
285 // TODO have shared table for both parameters to share the fetch, as index is always same?
286 // TODO compare texture/LDG performance
287 sm_fractCoords[sharedMemoryIndex] += fetchFromParamLookupTable(
288 kernelParams.grid.d_fractShiftsTable, kernelParams.fractShiftsTableTexture, tableIndex);
289 sm_gridlineIndices[sharedMemoryIndex] =
290 fetchFromParamLookupTable(kernelParams.grid.d_gridlineIndicesTable,
291 kernelParams.gridlineIndicesTableTexture,
295 gm_gridlineIndices[atomIndexOffset * DIM + sharedMemoryIndex] =
296 sm_gridlineIndices[sharedMemoryIndex];
300 /* B-spline calculation */
302 const int chargeCheck = pme_gpu_check_atom_charge(atomCharge);
303 /* With FEP (numGrids == 2), we might have 0 charge in state A, but !=0 in state B, so we always calculate splines */
304 if (numGrids == 2 || chargeCheck)
307 int o = orderIndex; // This is an index that is set once for PME_GPU_PARALLEL_SPLINE == 1
309 const float dr = sm_fractCoords[sharedMemoryIndex];
310 assert(isfinite(dr));
312 /* dr is relative offset from lower cell limit */
313 splineData[order - 1] = 0.0F;
315 splineData[0] = 1.0F - dr;
318 for (int k = 3; k < order; k++)
320 div = 1.0F / (k - 1.0F);
321 splineData[k - 1] = div * dr * splineData[k - 2];
323 for (int l = 1; l < (k - 1); l++)
325 splineData[k - l - 1] =
326 div * ((dr + l) * splineData[k - l - 2] + (k - l - dr) * splineData[k - l - 1]);
328 splineData[0] = div * (1.0F - dr) * splineData[0];
331 const int thetaIndexBase =
332 getSplineParamIndexBase<order, atomsPerWarp>(warpIndex, atomWarpIndex);
333 const int thetaGlobalOffsetBase = atomIndexOffset * DIM * order;
334 /* only calculate dtheta if we are saving it to shared or global memory */
335 if (writeSmDtheta || writeGlobal)
337 /* Differentiation and storing the spline derivatives (dtheta) */
339 for (o = 0; o < order; o++)
341 const int thetaIndex =
342 getSplineParamIndex<order, atomsPerWarp>(thetaIndexBase, dimIndex, o);
344 const float dtheta = ((o > 0) ? splineData[o - 1] : 0.0F) - splineData[o];
345 assert(isfinite(dtheta));
346 assert(thetaIndex < order * DIM * atomsPerBlock);
349 sm_dtheta[thetaIndex] = dtheta;
353 const int thetaGlobalIndex = thetaGlobalOffsetBase + thetaIndex;
354 gm_dtheta[thetaGlobalIndex] = dtheta;
359 div = 1.0F / (order - 1.0F);
360 splineData[order - 1] = div * dr * splineData[order - 2];
362 for (int k = 1; k < (order - 1); k++)
364 splineData[order - k - 1] = div
365 * ((dr + k) * splineData[order - k - 2]
366 + (order - k - dr) * splineData[order - k - 1]);
368 splineData[0] = div * (1.0F - dr) * splineData[0];
370 /* Storing the spline values (theta) */
372 for (o = 0; o < order; o++)
374 const int thetaIndex =
375 getSplineParamIndex<order, atomsPerWarp>(thetaIndexBase, dimIndex, o);
376 assert(thetaIndex < order * DIM * atomsPerBlock);
377 sm_theta[thetaIndex] = splineData[o];
378 assert(isfinite(sm_theta[thetaIndex]));
381 const int thetaGlobalIndex = thetaGlobalOffsetBase + thetaIndex;
382 gm_theta[thetaGlobalIndex] = splineData[o];