/* -------------------------------------------------------------------------- * * OpenMM * * -------------------------------------------------------------------------- * * This is part of the OpenMM molecular simulation toolkit originating from * * Simbios, the NIH National Center for Physics-Based Simulation of * * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * * Portions copyright (c) 2009 Stanford University and the Authors. * * Authors: Erik Lindahl, Rossen Apostolov, Szilard Pall, Peter Eastman * * Contributors: * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU Lesser General Public License as published * * by the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU Lesser General Public License for more details. * * * * You should have received a copy of the GNU Lesser General Public License * * along with this program. If not, see . * * -------------------------------------------------------------------------- */ #include "gputypes.h" #include "bbsort.h" #include using namespace std; static __constant__ cudaGmxSimulation cSim; void SetCalculatePMESim(gpuContext gpu) { cudaError_t status; status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation)); RTERROR(status, "cudaMemcpyToSymbol: SetSim copy to cSim failed"); } void GetCalculatePMESim(gpuContext gpu) { cudaError_t status; status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation)); RTERROR(status, "cudaMemcpyFromSymbol: SetSim copy from cSim failed"); } inline __host__ __device__ int fast_mod(int a, int b) { return (b & (b - 1)) ? a % b : a & (b - 1); } inline __host__ __device__ float4 make_float4(float s) { return make_float4(s, s, s, s); } inline __host__ __device__ float4 operator-(float4 &a) { return make_float4(-a.x, -a.y, -a.z, -a.w); } inline __host__ __device__ float4 operator-(float4 a, float4 b) { return make_float4(a.x - b.x, a.y - b.y, a.z - b.z, a.w - b.w); } inline __host__ __device__ float4 operator+(float4 a, float4 b) { return make_float4(a.x + b.x, a.y + b.y, a.z + b.z, a.w + b.w); } inline __host__ __device__ float4 operator+(float4 a, float b) { return make_float4(a.x + b, a.y + b, a.z + b, a.w + b); } inline __host__ __device__ float4 operator+(float a, float4 b) { return make_float4(a + b.x, a + b.y, a + b.z, a + b.w); } inline __host__ __device__ float4 operator*(float s, float4 a) { return make_float4(a.x * s, a.y * s, a.z * s, a.w * s); } inline __host__ __device__ float4 operator*(float4 a, float4 b) { return make_float4(a.x * b.x, a.y * b.y, a.z * b.z, a.w + b.w); } inline __host__ __device__ float4 make_float4(int3 a) { return make_float4(a.x, a.y, a.z, 0); } __global__ void kUpdateGridIndexAndFraction_kernel() { unsigned int tnb = blockDim.x * gridDim.x; unsigned int tid = blockIdx.x * blockDim.x + threadIdx.x; for (int i = tid; i < cSim.atoms; i += tnb) { float4 ftmp = cSim.pPosq[i]; float3 t = make_float3((ftmp.x/cSim.periodicBoxSizeX+1.0f)*cSim.pmeGridSize.x, (ftmp.y/cSim.periodicBoxSizeY+1.0f)*cSim.pmeGridSize.y, (ftmp.z/cSim.periodicBoxSizeZ+1.0f)*cSim.pmeGridSize.z); float3 tix; ftmp.x = modff(t.x, &tix.x); ftmp.y = modff(t.y, &tix.y); ftmp.z = modff(t.z, &tix.z); cSim.pPmeParticleFraction[i] = ftmp; int4 itmp = make_int4(fast_mod(__float2int_rd(tix.x), cSim.pmeGridSize.x), fast_mod(__float2int_rd(tix.y), cSim.pmeGridSize.y), fast_mod(__float2int_rd(tix.z), cSim.pmeGridSize.z), 0); cSim.pPmeParticleIndex[i] = itmp; cSim.pPmeAtomGridIndex[i] = make_float2(i, itmp.x*cSim.pmeGridSize.y*cSim.pmeGridSize.z+itmp.y*cSim.pmeGridSize.z+itmp.z); } // // // Compute flags for which atoms affect which groups of grid points. // // const int3 numGroups = make_int3((cSim.pmeGridSize.x+cSim.pmeGroupSize.x-1)/cSim.pmeGroupSize.x, (cSim.pmeGridSize.y+cSim.pmeGroupSize.y-1)/cSim.pmeGroupSize.y, (cSim.pmeGridSize.z+cSim.pmeGroupSize.z-1)/cSim.pmeGroupSize.z); // const unsigned int totalGroups = numGroups.x*numGroups.y*numGroups.z; // const float3 gridScale = make_float3(cSim.pmeGridSize.x/cSim.periodicBoxSizeX, cSim.pmeGridSize.y/cSim.periodicBoxSizeY, cSim.pmeGridSize.z/cSim.periodicBoxSizeZ); // for (int group = tid; group < totalGroups; group += tnb) // { // int3 gridBase; // gridBase.x = group/(numGroups.y*numGroups.z); // int remainder = group-gridBase.x*numGroups.y*numGroups.z; // gridBase.y = remainder/numGroups.z; // gridBase.z = remainder-gridBase.y*numGroups.z; // gridBase.x *= cSim.pmeGroupSize.x; // gridBase.y *= cSim.pmeGroupSize.y; // gridBase.z *= cSim.pmeGroupSize.z; // unsigned int flags = 0; // unsigned int baseIndex = group*(cSim.paddedNumberOfAtoms/32); // for (int atomBlock = 0; atomBlock < cSim.paddedNumberOfAtoms>>GRIDBITS; atomBlock++) // { // // Decide if this block actually needs to be processed. // // int flagIndex = atomBlock%32; // if (flagIndex == 0) // flags = 0; // float4 boxSize = cSim.pGridBoundingBox[atomBlock]; // float4 center = cSim.pGridCenter[atomBlock]; // int maxx = (int) ceil((center.x+boxSize.x)*gridScale.x)+cSim.pmeGroupSize.x+PME_ORDER; // int maxy = (int) ceil((center.y+boxSize.y)*gridScale.y)+cSim.pmeGroupSize.y+PME_ORDER; // int maxz = (int) ceil((center.z+boxSize.z)*gridScale.z)+cSim.pmeGroupSize.z+PME_ORDER; // int minx = (int) floor((center.x-boxSize.x)*gridScale.x); // int miny = (int) floor((center.y-boxSize.y)*gridScale.y); // int minz = (int) floor((center.z-boxSize.z)*gridScale.z); // int x = minx+(gridBase.x-minx)%cSim.pmeGridSize.x; // int y = miny+(gridBase.y-miny)%cSim.pmeGridSize.y; // int z = minz+(gridBase.z-minz)%cSim.pmeGridSize.z; // if (maxx < x || maxy < y || maxz < z) // flags += 1<>GRIDBITS) // cSim.pPmeInteractionFlags[baseIndex+atomBlock/32] = flags; // } // } } /** * For each grid point, find the range of sorted atoms associated with that point. */ __global__ void kFindAtomRangeForGrid_kernel() { int thread = blockIdx.x*blockDim.x+threadIdx.x; int start = (cSim.atoms*thread)/(blockDim.x*gridDim.x); int end = (cSim.atoms*(thread+1))/(blockDim.x*gridDim.x); int last = (thread == 0 ? -1 : cSim.pPmeAtomGridIndex[start-1].y); for (int i = start; i < end; ++i) { float2 atomData = cSim.pPmeAtomGridIndex[i]; int gridIndex = atomData.y; if (gridIndex != last) { for (int j = last+1; j <= gridIndex; ++j) cSim.pPmeAtomRange[j] = i; last = gridIndex; } // The grid index won't be needed again. Reuse that component to hold the atom charge, thus saving // an extra load operation in the charge spreading kernel. cSim.pPmeAtomGridIndex[i].y = cSim.pPosq[(int) atomData.x].w; } // Fill in values beyond the last atom. if (thread == blockDim.x*gridDim.x-1) { int gridSize = cSim.pmeGridSize.x*cSim.pmeGridSize.y*cSim.pmeGridSize.z; for (int j = last+1; j <= gridSize; ++j) cSim.pPmeAtomRange[j] = cSim.atoms; } } __global__ void kUpdateBsplines_kernel() { unsigned int tnb = blockDim.x * gridDim.x; unsigned int tid = blockIdx.x * blockDim.x + threadIdx.x; extern __shared__ float4 bsplines_cache[]; // size = 2 * block_size * pme_order const float4 div_o = make_float4(1.0f/(PME_ORDER - 1)); for (int i = tid; i < cSim.atoms; i += tnb) { float4* data = &bsplines_cache[threadIdx.x*PME_ORDER]; float4* ddata = &bsplines_cache[threadIdx.x*PME_ORDER + blockDim.x*PME_ORDER]; for (int j = 0; j < PME_ORDER; j++) { data[j] = make_float4(0.0f); ddata[j] = make_float4(0.0f); } float4 dr = cSim.pPmeParticleFraction[i]; data[PME_ORDER - 1] = make_float4(0.0f); data[1] = dr; data[0] = make_float4(1.0f) - dr; for (int j = 3; j < PME_ORDER; j++) { float div = 1.0f / ((float)j - 1.0f); data[j - 1] = div * dr * data[j - 2]; for (int k = 1; k < (j - 1); k++) { data[j - k - 1] = div * ( (dr + float(k)) * data[j - k - 2] + (-dr + ((float)(j - k))) * data[j - k - 1]); } data[0] = div * (- dr + 1) * data[0]; } ddata[0] = -data[0]; for (int j = 1; j < PME_ORDER; j++) ddata[j] = data[j - 1] - data[j]; data[PME_ORDER - 1] = div_o * dr * data[PME_ORDER - 2]; for (int j = 1; j < (PME_ORDER - 1); j++) { data[PME_ORDER - j - 1] = div_o * ( (dr + (float)j) * data[PME_ORDER - j - 2] + (-dr + ((float)(PME_ORDER - j))) * data[PME_ORDER - j - 1] ); } data[0] = div_o * (-dr + 1.0f) * data[0]; for (int j = 0; j < PME_ORDER; j++) { cSim.pPmeBsplineTheta[i + j*cSim.atoms] = data[j]; cSim.pPmeBsplineDtheta[i + j*cSim.atoms] = ddata[j]; } } } //__global__ void kGridSpreadCharge_kernel() //{ // extern __shared__ float atomCharge[]; // int4* atomGridIndex = (int4*) &atomCharge[blockDim.x]; // const unsigned int totalWarps = gridDim.x*blockDim.x/GRID; // const unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/GRID; // const int3 numGroups = make_int3((cSim.pmeGridSize.x+cSim.pmeGroupSize.x-1)/cSim.pmeGroupSize.x, (cSim.pmeGridSize.y+cSim.pmeGroupSize.y-1)/cSim.pmeGroupSize.y, (cSim.pmeGridSize.z+cSim.pmeGroupSize.z-1)/cSim.pmeGroupSize.z); // const unsigned int totalGroups = numGroups.x*numGroups.y*numGroups.z; // unsigned int group = warp*totalGroups/totalWarps; // const unsigned int end = (warp+1)*totalGroups/totalWarps; // const unsigned int index = threadIdx.x & (GRID - 1); // // while (group < end) // { // // Process a group of grid points of size cSim.pmeGroupSize. First figure out the base index for the group, // // and the index of the specific point this thread will handle. // // int3 gridBase; // gridBase.x = group/(numGroups.y*numGroups.z); // int remainder = group-gridBase.x*numGroups.y*numGroups.z; // gridBase.y = remainder/numGroups.z; // gridBase.z = remainder-gridBase.y*numGroups.z; // gridBase.x *= cSim.pmeGroupSize.x; // gridBase.y *= cSim.pmeGroupSize.y; // gridBase.z *= cSim.pmeGroupSize.z; // int3 gridPoint; // gridPoint.x = index/(cSim.pmeGroupSize.y*cSim.pmeGroupSize.z); // remainder = index-gridPoint.x*cSim.pmeGroupSize.y*cSim.pmeGroupSize.z; // gridPoint.y = remainder/cSim.pmeGroupSize.z; // gridPoint.z = remainder-gridPoint.y*cSim.pmeGroupSize.z; // gridPoint.x += gridBase.x; // gridPoint.y += gridBase.y; // gridPoint.z += gridBase.z; // // // Loop over blocks of atoms. // // float result = 0.0f; // int flags = 0; // unsigned int baseIndex = group*(cSim.paddedNumberOfAtoms/32); // for (int atomBlock = 0; atomBlock < cSim.paddedNumberOfAtoms>>GRIDBITS; atomBlock++) // { // // Decide if this block actually needs to be processed. // // int flagIndex = atomBlock%32; // if (flagIndex == 0) // flags = cSim.pPmeInteractionFlags[baseIndex+atomBlock/32]; // if ((flags & (1<sim.blocks, gpu->sim.update_threads_per_block>>>(); LAUNCHERROR("kUpdateGridIndexAndFraction"); bbSort(gpu->psPmeAtomGridIndex->_pDevData, gpu->natoms); kFindAtomRangeForGrid_kernel<<sim.blocks, gpu->sim.update_threads_per_block>>>(); LAUNCHERROR("kFindAtomRangeForGrid"); unsigned int threads = 16380/(2*PME_ORDER*sizeof(float4)); kUpdateBsplines_kernel<<sim.blocks, threads, 2*threads*PME_ORDER*sizeof(float4)>>>(); LAUNCHERROR("kUpdateBsplines"); kGridSpreadCharge_kernel<<sim.blocks, 64, 64*(sizeof(float)+sizeof(int4))>>>(); LAUNCHERROR("kGridSpreadCharge"); // gpu->psPmeGrid->Download(); // for (int i = 0; i < gpu->psPmeGrid->_length; i += 100) // printf("%d %f %f\n", i, (*gpu->psPmeGrid)[i].x, (*gpu->psPmeGrid)[i].y); cufftExecC2C(gpu->fftplan, gpu->psPmeGrid->_pDevData, gpu->psPmeGrid->_pDevData, CUFFT_FORWARD); kReciprocalConvolution_kernel<<sim.blocks, gpu->sim.nonbond_threads_per_block>>>(); LAUNCHERROR("kReciprocalConvolution"); cufftExecC2C(gpu->fftplan, gpu->psPmeGrid->_pDevData, gpu->psPmeGrid->_pDevData, CUFFT_INVERSE); kGridInterpolateForce_kernel<<sim.blocks, gpu->sim.update_threads_per_block>>>(); LAUNCHERROR("kGridInterpolateForce"); }