Merge pull request #1499 from peastman/reallocneighbors

Improved method for resizing neighbor list

platforms/opencl/src/kernels/nonbonded.cl

@@ -200,6 +200,8 @@ __kernel void computeNonbonded(
 
 #ifdef USE_CUTOFF
     unsigned int numTiles = interactionCount[0];
+    if (numTiles > maxTiles)
+        return; // There wasn't enough memory for the neighbor list.
     int pos = (int) (numTiles > maxTiles ? startTileIndex+warp*(long)numTileIndices/totalWarps : warp*(long)numTiles/totalWarps);
     int end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long)numTileIndices/totalWarps : (warp+1)*(long)numTiles/totalWarps);
 #else
@@ -223,42 +225,38 @@ __kernel void computeNonbonded(
         int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles) {
-            x = tiles[pos];
-            real4 blockSizeX = blockSize[x];
-            singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= MAX_CUTOFF &&
-                                  0.5f*periodicBoxSize.y-blockSizeX.y >= MAX_CUTOFF &&
-                                  0.5f*periodicBoxSize.z-blockSizeX.z >= MAX_CUTOFF);
-        }
-        else
-#endif
-        {
-            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+        x = tiles[pos];
+        real4 blockSizeX = blockSize[x];
+        singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= MAX_CUTOFF &&
+                              0.5f*periodicBoxSize.y-blockSizeX.y >= MAX_CUTOFF &&
+                              0.5f*periodicBoxSize.z-blockSizeX.z >= MAX_CUTOFF);
+#else
+        y = (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);
+        if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
+            y += (x < y ? -1 : 1);
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
-            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
-                y += (x < y ? -1 : 1);
-                x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
-            }
+        }
 
-            // Skip over tiles that have exclusions, since they were already processed.
+        // Skip over tiles that have exclusions, since they were already processed.
 
+        SYNC_WARPS;
+        while (skipTiles[tbx+TILE_SIZE-1] < pos) {
             SYNC_WARPS;
-            while (skipTiles[tbx+TILE_SIZE-1] < pos) {
-                SYNC_WARPS;
-                if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
-                    ushort2 tile = exclusionTiles[skipBase+tgx];
-                    skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
-                }
-                else
-                    skipTiles[get_local_id(0)] = end;
-                skipBase += TILE_SIZE;
-                currentSkipIndex = tbx;
-                SYNC_WARPS;
+            if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
+                ushort2 tile = exclusionTiles[skipBase+tgx];
+                skipTiles[get_local_id(0)] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
             }
-            while (skipTiles[currentSkipIndex] < pos)
-                currentSkipIndex++;
-            includeTile = (skipTiles[currentSkipIndex] != pos);
+            else
+                skipTiles[get_local_id(0)] = end;
+            skipBase += TILE_SIZE;
+            currentSkipIndex = tbx;
+            SYNC_WARPS;
         }
+        while (skipTiles[currentSkipIndex] < pos)
+            currentSkipIndex++;
+        includeTile = (skipTiles[currentSkipIndex] != pos);
+#endif
         if (includeTile) {
             unsigned int atom1 = x*TILE_SIZE + tgx;
 

platforms/opencl/src/kernels/nonbonded_cpu.cl

@@ -214,6 +214,8 @@ __kernel void computeNonbonded(
 
 #ifdef USE_CUTOFF
     const unsigned int numTiles = interactionCount[0];
+    if (numTiles > maxTiles)
+        return; // There wasn't enough memory for the neighbor list.
     int pos = (int) (numTiles > maxTiles ? (unsigned int) (startTileIndex+get_group_id(0)*(long)numTileIndices/get_num_groups(0)) : get_group_id(0)*(long)numTiles/get_num_groups(0));
     int end = (int) (numTiles > maxTiles ? (unsigned int) (startTileIndex+(get_group_id(0)+1)*(long)numTileIndices/get_num_groups(0)) : (get_group_id(0)+1)*(long)numTiles/get_num_groups(0));
 #else
@@ -234,35 +236,31 @@ __kernel void computeNonbonded(
         int x, y;
         bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles) {
-            x = tiles[pos];
-            real4 blockSizeX = blockSize[x];
-            singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= MAX_CUTOFF &&
-                                  0.5f*periodicBoxSize.y-blockSizeX.y >= MAX_CUTOFF &&
-                                  0.5f*periodicBoxSize.z-blockSizeX.z >= MAX_CUTOFF);
-        }
-        else
-#endif
-        {
-            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+        x = tiles[pos];
+        real4 blockSizeX = blockSize[x];
+        singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= MAX_CUTOFF &&
+                              0.5f*periodicBoxSize.y-blockSizeX.y >= MAX_CUTOFF &&
+                              0.5f*periodicBoxSize.z-blockSizeX.z >= MAX_CUTOFF);
+#else
+        y = (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);
+        if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
+            y += (x < y ? -1 : 1);
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
-            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
-                y += (x < y ? -1 : 1);
-                x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
-            }
+        }
 
-            // Skip over tiles that have exclusions, since they were already processed.
+        // Skip over tiles that have exclusions, since they were already processed.
 
-            while (nextToSkip < pos) {
-                if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
-                    ushort2 tile = exclusionTiles[currentSkipIndex++];
-                    nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
-                }
-                else
-                    nextToSkip = end;
+        while (nextToSkip < pos) {
+            if (currentSkipIndex < NUM_TILES_WITH_EXCLUSIONS) {
+                ushort2 tile = exclusionTiles[currentSkipIndex++];
+                nextToSkip = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
             }
-            includeTile = (nextToSkip != pos);
+            else
+                nextToSkip = end;
         }
+        includeTile = (nextToSkip != pos);
+#endif
         if (includeTile) {
             // Load the data for this tile.
 

plugins/amoeba/platforms/cuda/src/kernels/multipoleElectrostatics.cu

@@ -488,6 +488,8 @@ extern "C" __global__ void computeElectrostatics(
 
 #ifdef USE_CUTOFF
     const unsigned int numTiles = interactionCount[0];
+    if (numTiles > maxTiles)
+        return; // There wasn't enough memory for the neighbor list.
     int pos = (int) (numTiles > maxTiles ? startTileIndex+warp*(long long)numTileIndices/totalWarps : warp*(long long)numTiles/totalWarps);
     int end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long long)numTileIndices/totalWarps : (warp+1)*(long long)numTiles/totalWarps);
 #else
@@ -508,34 +510,31 @@ extern "C" __global__ void computeElectrostatics(
         
         int x, y;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles)
-            x = tiles[pos];
-        else
-#endif
-        {
-            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+        x = tiles[pos];
+#else
+        y = (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);
+        if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
+            y += (x < y ? -1 : 1);
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
-            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
-                y += (x < y ? -1 : 1);
-                x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
-            }
+        }
 
-            // Skip over tiles that have exclusions, since they were already processed.
+        // Skip over tiles that have exclusions, since they were already processed.
 
-            while (skipTiles[tbx+TILE_SIZE-1] < pos) {
-                if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
-                    ushort2 tile = exclusionTiles[skipBase+tgx];
-                    skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
-                }
-                else
-                    skipTiles[threadIdx.x] = end;
-                skipBase += TILE_SIZE;            
-                currentSkipIndex = tbx;
+        while (skipTiles[tbx+TILE_SIZE-1] < pos) {
+            if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
+                ushort2 tile = exclusionTiles[skipBase+tgx];
+                skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
             }
-            while (skipTiles[currentSkipIndex] < pos)
-                currentSkipIndex++;
-            includeTile = (skipTiles[currentSkipIndex] != pos);
+            else
+                skipTiles[threadIdx.x] = end;
+            skipBase += TILE_SIZE;            
+            currentSkipIndex = tbx;
         }
+        while (skipTiles[currentSkipIndex] < pos)
+            currentSkipIndex++;
+        includeTile = (skipTiles[currentSkipIndex] != pos);
+#endif
         if (includeTile) {
             unsigned int atom1 = x*TILE_SIZE + tgx;
 

plugins/amoeba/platforms/cuda/src/kernels/multipoleFixedField.cu

@@ -592,6 +592,8 @@ extern "C" __global__ void computeFixedField(
 
 #ifdef USE_CUTOFF
     const unsigned int numTiles = interactionCount[0];
+    if (numTiles > maxTiles)
+        return; // There wasn't enough memory for the neighbor list.
     int pos = (int) (numTiles > maxTiles ? startTileIndex+warp*(long long)numTileIndices/totalWarps : warp*(long long)numTiles/totalWarps);
     int end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long long)numTileIndices/totalWarps : (warp+1)*(long long)numTiles/totalWarps);
 #else
@@ -612,34 +614,31 @@ extern "C" __global__ void computeFixedField(
         
         int x, y;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles)
-            x = tiles[pos];
-        else
-#endif
-        {
-            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+        x = tiles[pos];
+#else
+        y = (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);
+        if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
+            y += (x < y ? -1 : 1);
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
-            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
-                y += (x < y ? -1 : 1);
-                x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
-            }
+        }
 
-            // Skip over tiles that have exclusions, since they were already processed.
+        // Skip over tiles that have exclusions, since they were already processed.
 
-            while (skipTiles[tbx+TILE_SIZE-1] < pos) {
-                if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
-                    ushort2 tile = exclusionTiles[skipBase+tgx];
-                    skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
-                }
-                else
-                    skipTiles[threadIdx.x] = end;
-                skipBase += TILE_SIZE;            
-                currentSkipIndex = tbx;
+        while (skipTiles[tbx+TILE_SIZE-1] < pos) {
+            if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
+                ushort2 tile = exclusionTiles[skipBase+tgx];
+                skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
             }
-            while (skipTiles[currentSkipIndex] < pos)
-                currentSkipIndex++;
-            includeTile = (skipTiles[currentSkipIndex] != pos);
+            else
+                skipTiles[threadIdx.x] = end;
+            skipBase += TILE_SIZE;            
+            currentSkipIndex = tbx;
         }
+        while (skipTiles[currentSkipIndex] < pos)
+            currentSkipIndex++;
+        includeTile = (skipTiles[currentSkipIndex] != pos);
+#endif
         if (includeTile) {
             unsigned int atom1 = x*TILE_SIZE + tgx;
 

plugins/amoeba/platforms/cuda/src/kernels/multipoleInducedField.cu

@@ -454,6 +454,8 @@ extern "C" __global__ void computeInducedField(
 
 #ifdef USE_CUTOFF
     const unsigned int numTiles = interactionCount[0];
+    if (numTiles > maxTiles)
+        return; // There wasn't enough memory for the neighbor list.
     int pos = (int) (numTiles > maxTiles ? startTileIndex+warp*(long long)numTileIndices/totalWarps : warp*(long long)numTiles/totalWarps);
     int end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long long)numTileIndices/totalWarps : (warp+1)*(long long)numTiles/totalWarps);
 #else
@@ -474,34 +476,31 @@ extern "C" __global__ void computeInducedField(
         
         int x, y;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles)
-            x = tiles[pos];
-        else
-#endif
-        {
-            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+        x = tiles[pos];
+#else
+        y = (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);
+        if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
+            y += (x < y ? -1 : 1);
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
-            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
-                y += (x < y ? -1 : 1);
-                x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
-            }
+        }
 
-            // Skip over tiles that have exclusions, since they were already processed.
+        // Skip over tiles that have exclusions, since they were already processed.
 
-            while (skipTiles[tbx+TILE_SIZE-1] < pos) {
-                if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
-                    ushort2 tile = exclusionTiles[skipBase+tgx];
-                    skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
-                }
-                else
-                    skipTiles[threadIdx.x] = end;
-                skipBase += TILE_SIZE;            
-                currentSkipIndex = tbx;
+        while (skipTiles[tbx+TILE_SIZE-1] < pos) {
+            if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
+                ushort2 tile = exclusionTiles[skipBase+tgx];
+                skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
             }
-            while (skipTiles[currentSkipIndex] < pos)
-                currentSkipIndex++;
-            includeTile = (skipTiles[currentSkipIndex] != pos);
+            else
+                skipTiles[threadIdx.x] = end;
+            skipBase += TILE_SIZE;            
+            currentSkipIndex = tbx;
         }
+        while (skipTiles[currentSkipIndex] < pos)
+            currentSkipIndex++;
+        includeTile = (skipTiles[currentSkipIndex] != pos);
+#endif
         if (includeTile) {
             unsigned int atom1 = x*TILE_SIZE + tgx;
 

plugins/amoeba/platforms/cuda/src/kernels/pmeMultipoleElectrostatics.cu

@@ -555,6 +555,8 @@ extern "C" __global__ void computeElectrostatics(
 
 #ifdef USE_CUTOFF
     const unsigned int numTiles = interactionCount[0];
+    if (numTiles > maxTiles)
+        return; // There wasn't enough memory for the neighbor list.
     int pos = (int) (numTiles > maxTiles ? startTileIndex+warp*(long long)numTileIndices/totalWarps : warp*(long long)numTiles/totalWarps);
     int end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long long)numTileIndices/totalWarps : (warp+1)*(long long)numTiles/totalWarps);
 #else
@@ -575,34 +577,31 @@ extern "C" __global__ void computeElectrostatics(
         
         int x, y;
 #ifdef USE_CUTOFF
-        if (numTiles <= maxTiles)
-            x = tiles[pos];
-        else
-#endif
-        {
-            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+        x = tiles[pos];
+#else
+        y = (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);
+        if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
+            y += (x < y ? -1 : 1);
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
-            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
-                y += (x < y ? -1 : 1);
-                x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
-            }
+        }
 
-            // Skip over tiles that have exclusions, since they were already processed.
+        // Skip over tiles that have exclusions, since they were already processed.
 
-            while (skipTiles[tbx+TILE_SIZE-1] < pos) {
-                if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
-                    ushort2 tile = exclusionTiles[skipBase+tgx];
-                    skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
-                }
-                else
-                    skipTiles[threadIdx.x] = end;
-                skipBase += TILE_SIZE;            
-                currentSkipIndex = tbx;
+        while (skipTiles[tbx+TILE_SIZE-1] < pos) {
+            if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
+                ushort2 tile = exclusionTiles[skipBase+tgx];
+                skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
             }
-            while (skipTiles[currentSkipIndex] < pos)
-                currentSkipIndex++;
-            includeTile = (skipTiles[currentSkipIndex] != pos);
+            else
+                skipTiles[threadIdx.x] = end;
+            skipBase += TILE_SIZE;            
+            currentSkipIndex = tbx;
         }
+        while (skipTiles[currentSkipIndex] < pos)
+            currentSkipIndex++;
+        includeTile = (skipTiles[currentSkipIndex] != pos);
+#endif
         if (includeTile) {
             unsigned int atom1 = x*TILE_SIZE + tgx;