nonbonded_nvidia.cl 12.7 KB
Newer Older
1
#define TILE_SIZE 32
2

3
typedef struct {
4
5
6
    float x, y, z;
    float q;
    float fx, fy, fz;
7
8
9
    ATOM_PARAMETER_DATA
} AtomData;

10
11
12
13
/**
 * Compute nonbonded interactions.
 */

14
15
__kernel __attribute__((reqd_work_group_size(WORK_GROUP_SIZE, 1, 1)))
void computeNonbonded(__global float4* forceBuffers, __global float* energyBuffer, __global float4* posq, __global unsigned int* exclusions,
16
        __global unsigned int* exclusionIndices, __global unsigned int* exclusionRowIndices, __local AtomData* localData, __local float* tempBuffer,
17
#ifdef USE_CUTOFF
18
        __global ushort2* tiles, __global unsigned int* interactionCount, float4 periodicBoxSize, float4 invPeriodicBoxSize, unsigned int maxTiles, __global unsigned int* interactionFlags
19
20
#else
        unsigned int numTiles
21
#endif
22
        PARAMETER_ARGUMENTS) {
23
24
    unsigned int totalWarps = get_global_size(0)/TILE_SIZE;
    unsigned int warp = get_global_id(0)/TILE_SIZE;
25
26
#ifdef USE_CUTOFF
    unsigned int numTiles = interactionCount[0];
27
28
    unsigned int pos = warp*(numTiles > maxTiles ? NUM_BLOCKS*(NUM_BLOCKS+1)/2 : numTiles)/totalWarps;
    unsigned int end = (warp+1)*(numTiles > maxTiles ? NUM_BLOCKS*(NUM_BLOCKS+1)/2 : numTiles)/totalWarps;
29
#else
30
31
    unsigned int pos = warp*numTiles/totalWarps;
    unsigned int end = (warp+1)*numTiles/totalWarps;
32
#endif
33
34
    float energy = 0.0f;
    unsigned int lasty = 0xFFFFFFFF;
35
36
    __local unsigned int exclusionRange[4];
    __local int exclusionIndex[2];
37
38

    while (pos < end) {
39
        // Extract the coordinates of this tile
40
        unsigned int x, y;
41
#ifdef USE_CUTOFF
42
        if (numTiles <= maxTiles) {
43
44
45
            ushort2 tileIndices = tiles[pos];
            x = tileIndices.x;
            y = tileIndices.y;
46
        }
47
        else
48
#endif
49
50
51
        {
            y = (unsigned int) floor(NUM_BLOCKS+0.5f-sqrt((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
            x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
52
53
            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                y += (x < y ? -1 : 1);
54
55
56
                x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
            }
        }
57
        unsigned int tgx = get_local_id(0) & (TILE_SIZE-1);
58
        unsigned int tbx = get_local_id(0) - tgx;
59
        unsigned int atom1 = x*TILE_SIZE + tgx;
60
        float4 force = 0.0f;
61
        float4 posq1 = posq[atom1];
62
        LOAD_ATOM1_PARAMETERS
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78

        // Locate the exclusion data for this tile.

#ifdef USE_EXCLUSIONS
        int localGroupIndex = get_local_id(0)/TILE_SIZE;
        if (tgx < 2)
            exclusionRange[2*localGroupIndex+tgx] = exclusionRowIndices[x+tgx];
        if (tgx == 0)
            exclusionIndex[localGroupIndex] = -1;
        for (int i = exclusionRange[2*localGroupIndex]+tgx; i < exclusionRange[2*localGroupIndex+1]; i += TILE_SIZE)
            if (exclusionIndices[i] == y)
                exclusionIndex[localGroupIndex] = i*TILE_SIZE;
        bool hasExclusions = (exclusionIndex[localGroupIndex] > -1);
#else
        bool hasExclusions = false;
#endif
79
        if (x == y) {
80
            // This tile is on the diagonal.
81

82
83
84
85
86
            const unsigned int localAtomIndex = get_local_id(0);
            localData[localAtomIndex].x = posq1.x;
            localData[localAtomIndex].y = posq1.y;
            localData[localAtomIndex].z = posq1.z;
            localData[localAtomIndex].q = posq1.w;
87
88
            LOAD_LOCAL_PARAMETERS_FROM_1
#ifdef USE_EXCLUSIONS
89
            unsigned int excl = exclusions[exclusionIndex[localGroupIndex]+tgx];
90
#endif
91
            for (unsigned int j = 0; j < TILE_SIZE; j++) {
92
#ifdef USE_EXCLUSIONS
93
                bool isExcluded = !(excl & 0x1);
94
#endif
95
96
                int atom2 = tbx+j;
                float4 posq2 = (float4) (localData[atom2].x, localData[atom2].y, localData[atom2].z, localData[atom2].q);
97
                float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
98
#ifdef USE_PERIODIC
99
100
101
                delta.x -= floor(delta.x*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
                delta.y -= floor(delta.y*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
                delta.z -= floor(delta.z*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
102
#endif
103
104
                float r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
                float r = sqrt(r2);
Peter Eastman's avatar
Peter Eastman committed
105
                float invR = RECIP(r);
106
                LOAD_ATOM2_PARAMETERS
107
                atom2 = y*TILE_SIZE+j;
108
#ifdef USE_SYMMETRIC
109
                float dEdR = 0.0f;
110
111
112
113
#else
                float4 dEdR1 = (float4) 0.0f;
                float4 dEdR2 = (float4) 0.0f;
#endif
114
115
                float tempEnergy = 0.0f;
                COMPUTE_INTERACTION
116
                energy += 0.5f*tempEnergy;
117
118
119
120
121
#ifdef USE_SYMMETRIC
                force.xyz -= delta.xyz*dEdR;
#else
                force.xyz -= dEdR1.xyz;
#endif
122
                excl >>= 1;
123
124
125
            }

            // Write results
126
#ifdef USE_OUTPUT_BUFFER_PER_BLOCK
127
            unsigned int offset = x*TILE_SIZE + tgx + x*PADDED_NUM_ATOMS;
128
#else
129
            unsigned int offset = x*TILE_SIZE + tgx + warp*PADDED_NUM_ATOMS;
130
#endif
131
            forceBuffers[offset].xyz += force.xyz;
132
133
        }
        else {
134
135
            // This is an off-diagonal tile.

136
            const unsigned int localAtomIndex = get_local_id(0);
137
            if (lasty != y) {
138
                unsigned int j = y*TILE_SIZE + tgx;
139
                float4 tempPosq = posq[j];
140
141
142
143
                localData[localAtomIndex].x = tempPosq.x;
                localData[localAtomIndex].y = tempPosq.y;
                localData[localAtomIndex].z = tempPosq.z;
                localData[localAtomIndex].q = tempPosq.w;
144
                LOAD_LOCAL_PARAMETERS_FROM_GLOBAL
145
            }
146
147
148
            localData[localAtomIndex].fx = 0.0f;
            localData[localAtomIndex].fy = 0.0f;
            localData[localAtomIndex].fz = 0.0f;
149
#ifdef USE_CUTOFF
150
            unsigned int flags = (numTiles <= maxTiles ? interactionFlags[pos] : 0xFFFFFFFF);
151
            if (!hasExclusions && flags != 0xFFFFFFFF) {
152
153
154
155
156
157
                if (flags == 0) {
                    // No interactions in this tile.
                }
                else {
                    // Compute only a subset of the interactions in this tile.

158
                    for (unsigned int j = 0; j < TILE_SIZE; j++) {
159
160
                        if ((flags&(1<<j)) != 0) {
                            bool isExcluded = false;
161
162
                            int atom2 = tbx+j;
                            float4 posq2 = (float4) (localData[atom2].x, localData[atom2].y, localData[atom2].z, localData[atom2].q);
163
                            float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
164
#ifdef USE_PERIODIC
165
166
167
                            delta.x -= floor(delta.x*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
                            delta.y -= floor(delta.y*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
                            delta.z -= floor(delta.z*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
168
#endif
169
                            float r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
170
171
                            float invR = RSQRT(r2);
                            float r = RECIP(invR);
172
                            LOAD_ATOM2_PARAMETERS
173
                            atom2 = y*TILE_SIZE+j;
174
#ifdef USE_SYMMETRIC
175
                            float dEdR = 0.0f;
176
177
178
179
#else
                            float4 dEdR1 = (float4) 0.0f;
                            float4 dEdR2 = (float4) 0.0f;
#endif
180
181
                            float tempEnergy = 0.0f;
                            COMPUTE_INTERACTION
182
			    energy += tempEnergy;
183
                            int bufferIndex = 3*get_local_id(0);
184
#ifdef USE_SYMMETRIC
185
                            delta.xyz *= dEdR;
186
                            force.xyz -= delta.xyz;
187
188
189
                            tempBuffer[bufferIndex] = delta.x;
                            tempBuffer[bufferIndex+1] = delta.y;
                            tempBuffer[bufferIndex+2] = delta.z;
190
191
#else
                            force.xyz -= dEdR1.xyz;
192
193
194
                            tempBuffer[bufferIndex] = dEdR2.x;
                            tempBuffer[bufferIndex+1] = dEdR2.y;
                            tempBuffer[bufferIndex+2] = dEdR2.z;
195
#endif
196

197
                            // Sum the forces on atom2.
198

199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
                            if (tgx % 2 == 0) {
                                tempBuffer[bufferIndex] += tempBuffer[bufferIndex+3];
                                tempBuffer[bufferIndex+1] += tempBuffer[bufferIndex+4];
                                tempBuffer[bufferIndex+2] += tempBuffer[bufferIndex+5];
                            }
                            if (tgx % 4 == 0) {
                                tempBuffer[bufferIndex] += tempBuffer[bufferIndex+6];
                                tempBuffer[bufferIndex+1] += tempBuffer[bufferIndex+7];
                                tempBuffer[bufferIndex+2] += tempBuffer[bufferIndex+8];
                            }
                            if (tgx % 8 == 0) {
                                tempBuffer[bufferIndex] += tempBuffer[bufferIndex+12];
                                tempBuffer[bufferIndex+1] += tempBuffer[bufferIndex+13];
                                tempBuffer[bufferIndex+2] += tempBuffer[bufferIndex+14];
                            }
                            if (tgx % 16 == 0) {
                                tempBuffer[bufferIndex] += tempBuffer[bufferIndex+24];
                                tempBuffer[bufferIndex+1] += tempBuffer[bufferIndex+25];
                                tempBuffer[bufferIndex+2] += tempBuffer[bufferIndex+26];
                            }
219
                            if (tgx == 0) {
220
221
222
                                localData[tbx+j].fx += tempBuffer[bufferIndex] + tempBuffer[bufferIndex+48];
                                localData[tbx+j].fy += tempBuffer[bufferIndex+1] + tempBuffer[bufferIndex+49];
                                localData[tbx+j].fz += tempBuffer[bufferIndex+2] + tempBuffer[bufferIndex+50];
223
                            }
224
225
226
227
                        }
                    }
                }
            }
228
            else
229
230
#endif
            {
231
232
                // Compute the full set of interactions in this tile.

233
#ifdef USE_EXCLUSIONS
234
                unsigned int excl = (hasExclusions ? exclusions[exclusionIndex[localGroupIndex]+tgx] : 0xFFFFFFFF);
235
                excl = (excl >> tgx) | (excl << (TILE_SIZE - tgx));
236
#endif
237
                unsigned int tj = tgx;
238
                for (unsigned int j = 0; j < TILE_SIZE; j++) {
239
#ifdef USE_EXCLUSIONS
240
                    bool isExcluded = !(excl & 0x1);
241
#endif
242
243
                    int atom2 = tbx+tj;
                    float4 posq2 = (float4) (localData[atom2].x, localData[atom2].y, localData[atom2].z, localData[atom2].q);
244
                    float4 delta = (float4) (posq2.xyz - posq1.xyz, 0.0f);
245
#ifdef USE_PERIODIC
246
247
248
                    delta.x -= floor(delta.x*invPeriodicBoxSize.x+0.5f)*periodicBoxSize.x;
                    delta.y -= floor(delta.y*invPeriodicBoxSize.y+0.5f)*periodicBoxSize.y;
                    delta.z -= floor(delta.z*invPeriodicBoxSize.z+0.5f)*periodicBoxSize.z;
249
#endif
250
                    float r2 = delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
251
252
                    float invR = RSQRT(r2);
                    float r = RECIP(invR);
253
                    LOAD_ATOM2_PARAMETERS
254
                    atom2 = y*TILE_SIZE+tj;
255
#ifdef USE_SYMMETRIC
256
                    float dEdR = 0.0f;
257
258
259
260
#else
                    float4 dEdR1 = (float4) 0.0f;
                    float4 dEdR2 = (float4) 0.0f;
#endif
261
262
                    float tempEnergy = 0.0f;
                    COMPUTE_INTERACTION
263
		    energy += tempEnergy;
264
#ifdef USE_SYMMETRIC
265
                    delta.xyz *= dEdR;
266
                    force.xyz -= delta.xyz;
267
268
269
                    localData[tbx+tj].fx += delta.x;
                    localData[tbx+tj].fy += delta.y;
                    localData[tbx+tj].fz += delta.z;
270
271
272
273
274
275
#else
                    force.xyz -= dEdR1.xyz;
                    localData[tbx+tj].fx += dEdR2.x;
                    localData[tbx+tj].fy += dEdR2.y;
                    localData[tbx+tj].fz += dEdR2.z;
#endif
276
#ifdef USE_EXCLUSIONS
277
                    excl >>= 1;
Peter Eastman's avatar
Bug fix  
Peter Eastman committed
278
#endif
279
                    tj = (tj + 1) & (TILE_SIZE - 1);
280
281
282
283
                }
            }

            // Write results
284
#ifdef USE_OUTPUT_BUFFER_PER_BLOCK
285
286
            unsigned int offset1 = x*TILE_SIZE + tgx + y*PADDED_NUM_ATOMS;
            unsigned int offset2 = y*TILE_SIZE + tgx + x*PADDED_NUM_ATOMS;
287
#else
288
289
            unsigned int offset1 = x*TILE_SIZE + tgx + warp*PADDED_NUM_ATOMS;
            unsigned int offset2 = y*TILE_SIZE + tgx + warp*PADDED_NUM_ATOMS;
290
#endif
291
            forceBuffers[offset1].xyz += force.xyz;
292
            forceBuffers[offset2] += (float4) (localData[get_local_id(0)].fx, localData[get_local_id(0)].fy, localData[get_local_id(0)].fz, 0.0f);
293
        }
294
        lasty = y;
295
296
297
298
        pos++;
    }
    energyBuffer[get_global_id(0)] += energy;
}