Improved GB performance in mixed precision

platforms/cuda/src/CudaKernels.cpp

@@ -2794,6 +2794,7 @@ double CudaCalcGBSAOBCForceKernel::execute(ContextImpl& context, bool includeFor
         force1Args.push_back(&cu.getEnergyBuffer().getDevicePointer());
         force1Args.push_back(&cu.getPosq().getDevicePointer());
         force1Args.push_back(&bornRadii->getDevicePointer());
+        force1Args.push_back(NULL);
         if (nb.getUseCutoff()) {
             force1Args.push_back(&nb.getInteractingTiles().getDevicePointer());
             force1Args.push_back(&nb.getInteractionCount().getDevicePointer());
@@ -2813,13 +2814,14 @@ double CudaCalcGBSAOBCForceKernel::execute(ContextImpl& context, bool includeFor
         reduceBornSumKernel = cu.getKernel(module, "reduceBornSum");
         reduceBornForceKernel = cu.getKernel(module, "reduceBornForce");
     }
+    force1Args[5] = &includeEnergy;
     if (nb.getUseCutoff()) {
         if (maxTiles < nb.getInteractingTiles().getSize()) {
             maxTiles = nb.getInteractingTiles().getSize();
             computeSumArgs[3] = &nb.getInteractingTiles().getDevicePointer();
-            force1Args[5] = &nb.getInteractingTiles().getDevicePointer();
+            force1Args[6] = &nb.getInteractingTiles().getDevicePointer();
             computeSumArgs[13] = &nb.getInteractingAtoms().getDevicePointer();
-            force1Args[15] = &nb.getInteractingAtoms().getDevicePointer();
+            force1Args[16] = &nb.getInteractingAtoms().getDevicePointer();
         }
     }
     cu.executeKernel(computeBornSumKernel, &computeSumArgs[0], nb.getNumForceThreadBlocks()*nb.getForceThreadBlockSize(), nb.getForceThreadBlockSize());
@@ -3754,6 +3756,7 @@ double CudaCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeFo
         pairEnergyArgs.push_back(&cu.getPosq().getDevicePointer());
         pairEnergyArgs.push_back(&cu.getNonbondedUtilities().getExclusions().getDevicePointer());
         pairEnergyArgs.push_back(&cu.getNonbondedUtilities().getExclusionTiles().getDevicePointer());
+        pairEnergyArgs.push_back(NULL);
         if (nb.getUseCutoff()) {
             pairEnergyArgs.push_back(&nb.getInteractingTiles().getDevicePointer());
             pairEnergyArgs.push_back(&nb.getInteractionCount().getDevicePointer());
@@ -3832,13 +3835,14 @@ double CudaCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeFo
         if (changed)
             globals->upload(globalParamValues);
     }
+    pairEnergyArgs[5] = &includeEnergy;
     if (nb.getUseCutoff()) {
         if (maxTiles < nb.getInteractingTiles().getSize()) {
             maxTiles = nb.getInteractingTiles().getSize();
             pairValueArgs[4] = &nb.getInteractingTiles().getDevicePointer();
-            pairEnergyArgs[5] = &nb.getInteractingTiles().getDevicePointer();
+            pairEnergyArgs[6] = &nb.getInteractingTiles().getDevicePointer();
             pairValueArgs[14] = &nb.getInteractingAtoms().getDevicePointer();
-            pairEnergyArgs[15] = &nb.getInteractingAtoms().getDevicePointer();
+            pairEnergyArgs[16] = &nb.getInteractingAtoms().getDevicePointer();
         }
     }
     cu.executeKernel(pairValueKernel, &pairValueArgs[0], nb.getNumForceThreadBlocks()*nb.getForceThreadBlockSize(), nb.getForceThreadBlockSize());

platforms/cuda/src/kernels/customGBEnergyN2.cu

@@ -14,7 +14,7 @@ typedef struct {
  * Compute a force based on pair interactions.
  */
 extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forceBuffers, mixed* __restrict__ energyBuffer,
-        const real4* __restrict__ posq, const unsigned int* __restrict__ exclusions, const ushort2* __restrict__ exclusionTiles,
+        const real4* __restrict__ posq, const unsigned int* __restrict__ exclusions, const ushort2* __restrict__ exclusionTiles, bool needEnergy,
 #ifdef USE_CUTOFF
         const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize,
         real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, unsigned int maxTiles, const real4* __restrict__ blockCenter,
@@ -78,6 +78,7 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
                         COMPUTE_INTERACTION
                         dEdR /= -r;
                     }
+                    if (needEnergy)
                         energy += 0.5f*tempEnergy;
                     delta *= dEdR;
                     force.x -= delta.x;
@@ -130,6 +131,7 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
                         COMPUTE_INTERACTION
                         dEdR /= -r;
                     }
+                    if (needEnergy)
                         energy += tempEnergy;
                     delta *= dEdR;
                     force.x -= delta.x;
@@ -274,6 +276,7 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
                             COMPUTE_INTERACTION
                             dEdR /= -r;
                         }
+                        if (needEnergy)
                             energy += tempEnergy;
                         delta *= dEdR;
                         force.x -= delta.x;
@@ -318,6 +321,7 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
                             COMPUTE_INTERACTION
                             dEdR /= -r;
                         }
+                        if (needEnergy)
                             energy += tempEnergy;
                         delta *= dEdR;
                         force.x -= delta.x;

platforms/cuda/src/kernels/gbsaObc1.cu

@@ -400,7 +400,7 @@ typedef struct {
  */
 
 extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ forceBuffers, unsigned long long* __restrict__ global_bornForce,
-        mixed* __restrict__ energyBuffer, const real4* __restrict__ posq, const real* __restrict__ global_bornRadii,
+        mixed* __restrict__ energyBuffer, const real4* __restrict__ posq, const real* __restrict__ global_bornRadii, bool needEnergy,
 #ifdef USE_CUTOFF
         const int* __restrict__ tiles, const unsigned int* __restrict__ interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize,
         real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, unsigned int maxTiles, const real4* __restrict__ blockCenter,
@@ -465,6 +465,7 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
                         if (atom1 != y*TILE_SIZE+j)
                             tempEnergy -= scaledChargeProduct/CUTOFF;
 #endif
+                        if (needEnergy)
                             energy += 0.5f*tempEnergy;
                         delta *= dEdR;
                         force.x -= delta.x;
@@ -519,6 +520,7 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
 #ifdef USE_CUTOFF
                         tempEnergy -= scaledChargeProduct/CUTOFF;
 #endif
+                        if (needEnergy)
                             energy += tempEnergy;
                         delta *= dEdR;
                         force.x -= delta.x;
@@ -667,6 +669,7 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
 #ifdef USE_CUTOFF
                             tempEnergy -= scaledChargeProduct/CUTOFF;
 #endif
+                            if (needEnergy)
                                 energy += tempEnergy;
                             delta *= dEdR;
                             force.x -= delta.x;
@@ -716,6 +719,7 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
 #ifdef USE_CUTOFF
                             tempEnergy -= scaledChargeProduct/CUTOFF;
 #endif
+                            if (needEnergy)
                                 energy += tempEnergy;
                             delta *= dEdR;
                             force.x -= delta.x;

platforms/opencl/src/OpenCLKernels.cpp

@@ -2872,6 +2872,7 @@ double OpenCLCalcGBSAOBCForceKernel::execute(ContextImpl& context, bool includeF
         force1Kernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
         force1Kernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
         force1Kernel.setArg<cl::Buffer>(index++, bornRadii->getDeviceBuffer());
+        index++; // Whether to include energy.
         if (nb.getUseCutoff()) {
             force1Kernel.setArg<cl::Buffer>(index++, nb.getInteractingTiles().getDeviceBuffer());
             force1Kernel.setArg<cl::Buffer>(index++, nb.getInteractionCount().getDeviceBuffer());
@@ -2907,17 +2908,18 @@ double OpenCLCalcGBSAOBCForceKernel::execute(ContextImpl& context, bool includeF
         reduceBornForceKernel.setArg<cl::Buffer>(index++, bornRadii->getDeviceBuffer());
         reduceBornForceKernel.setArg<cl::Buffer>(index++, obcChain->getDeviceBuffer());
     }
+    force1Kernel.setArg<cl_int>(5, includeEnergy);
     if (nb.getUseCutoff()) {
         setPeriodicBoxArgs(cl, computeBornSumKernel, 5);
-        setPeriodicBoxArgs(cl, force1Kernel, 7);
+        setPeriodicBoxArgs(cl, force1Kernel, 8);
         if (maxTiles < nb.getInteractingTiles().getSize()) {
             maxTiles = nb.getInteractingTiles().getSize();
             computeBornSumKernel.setArg<cl::Buffer>(3, nb.getInteractingTiles().getDeviceBuffer());
             computeBornSumKernel.setArg<cl_uint>(10, maxTiles);
             computeBornSumKernel.setArg<cl::Buffer>(13, nb.getInteractingAtoms().getDeviceBuffer());
-            force1Kernel.setArg<cl::Buffer>(5, nb.getInteractingTiles().getDeviceBuffer());
-            force1Kernel.setArg<cl_uint>(12, maxTiles);
-            force1Kernel.setArg<cl::Buffer>(15, nb.getInteractingAtoms().getDeviceBuffer());
+            force1Kernel.setArg<cl::Buffer>(6, nb.getInteractingTiles().getDeviceBuffer());
+            force1Kernel.setArg<cl_uint>(13, maxTiles);
+            force1Kernel.setArg<cl::Buffer>(16, nb.getInteractingAtoms().getDeviceBuffer());
         }
     }
     cl.executeKernel(computeBornSumKernel, nb.getNumForceThreadBlocks()*nb.getForceThreadBlockSize(), nb.getForceThreadBlockSize());
@@ -3933,6 +3935,7 @@ double OpenCLCalcCustomGBForceKernel::execute(ContextImpl& context, bool include
         pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*4*elementSize, NULL);
         pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusions().getDeviceBuffer());
         pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusionTiles().getDeviceBuffer());
+        index++; // Whether to include energy.
         if (nb.getUseCutoff()) {
             pairEnergyKernel.setArg<cl::Buffer>(index++, nb.getInteractingTiles().getDeviceBuffer());
             pairEnergyKernel.setArg<cl::Buffer>(index++, nb.getInteractionCount().getDeviceBuffer());
@@ -4029,17 +4032,18 @@ double OpenCLCalcCustomGBForceKernel::execute(ContextImpl& context, bool include
         if (changed)
             globals->upload(globalParamValues);
     }
+    pairEnergyKernel.setArg<cl_int>(7, includeEnergy);
     if (nb.getUseCutoff()) {
         setPeriodicBoxArgs(cl, pairValueKernel, 8);
-        setPeriodicBoxArgs(cl, pairEnergyKernel, 9);
+        setPeriodicBoxArgs(cl, pairEnergyKernel, 10);
         if (maxTiles < nb.getInteractingTiles().getSize()) {
             maxTiles = nb.getInteractingTiles().getSize();
             pairValueKernel.setArg<cl::Buffer>(6, nb.getInteractingTiles().getDeviceBuffer());
             pairValueKernel.setArg<cl_uint>(13, maxTiles);
             pairValueKernel.setArg<cl::Buffer>(16, nb.getInteractingAtoms().getDeviceBuffer());
-            pairEnergyKernel.setArg<cl::Buffer>(7, nb.getInteractingTiles().getDeviceBuffer());
-            pairEnergyKernel.setArg<cl_uint>(14, maxTiles);
-            pairEnergyKernel.setArg<cl::Buffer>(17, nb.getInteractingAtoms().getDeviceBuffer());
+            pairEnergyKernel.setArg<cl::Buffer>(8, nb.getInteractingTiles().getDeviceBuffer());
+            pairEnergyKernel.setArg<cl_uint>(15, maxTiles);
+            pairEnergyKernel.setArg<cl::Buffer>(18, nb.getInteractingAtoms().getDeviceBuffer());
         }
     }
     cl.executeKernel(pairValueKernel, nb.getNumForceThreadBlocks()*nb.getForceThreadBlockSize(), nb.getForceThreadBlockSize());

platforms/opencl/src/kernels/customGBEnergyN2.cl

@@ -18,7 +18,7 @@ __kernel void computeN2Energy(
 #endif
         __global mixed* restrict energyBuffer, __local real4* restrict local_force,
         __global const real4* restrict posq, __local real4* restrict local_posq, __global const unsigned int* restrict exclusions,
-        __global const ushort2* exclusionTiles,
+        __global const ushort2* exclusionTiles, int needEnergy,
 #ifdef USE_CUTOFF
         __global const int* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize,
         real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, unsigned int maxTiles, __global const real4* restrict blockCenter,
@@ -82,6 +82,7 @@ __kernel void computeN2Energy(
                         COMPUTE_INTERACTION
                         dEdR /= -r;
                     }
+                    if (needEnergy)
                         energy += 0.5f*tempEnergy;
                     delta.xyz *= dEdR;
                     force.xyz -= delta.xyz;
@@ -133,6 +134,7 @@ __kernel void computeN2Energy(
                         COMPUTE_INTERACTION
                         dEdR /= -r;
                     }
+                    if (needEnergy)
                         energy += tempEnergy;
                     delta.xyz *= dEdR;
                     force.xyz -= delta.xyz;
@@ -289,6 +291,7 @@ __kernel void computeN2Energy(
                             COMPUTE_INTERACTION
                             dEdR /= -r;
                         }
+                        if (needEnergy)
                             energy += tempEnergy;
                         delta.xyz *= dEdR;
                         force.xyz -= delta.xyz;
@@ -328,6 +331,7 @@ __kernel void computeN2Energy(
                             COMPUTE_INTERACTION
                             dEdR /= -r;
                         }
+                        if (needEnergy)
                             energy += tempEnergy;
                         delta.xyz *= dEdR;
                         force.xyz -= delta.xyz;

platforms/opencl/src/kernels/gbsaObc.cl

@@ -385,7 +385,7 @@ __kernel void computeGBSAForce1(
 #else
         __global real4* restrict forceBuffers, __global real* restrict global_bornForce,
 #endif
-        __global mixed* restrict energyBuffer, __global const real4* restrict posq, __global const real* restrict global_bornRadii,
+        __global mixed* restrict energyBuffer, __global const real4* restrict posq, __global const real* restrict global_bornRadii, int needEnergy,
 #ifdef USE_CUTOFF
         __global const int* restrict tiles, __global const unsigned int* restrict interactionCount, real4 periodicBoxSize, real4 invPeriodicBoxSize, 
         real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, unsigned int maxTiles, __global const real4* restrict blockCenter,
@@ -452,6 +452,7 @@ __kernel void computeGBSAForce1(
                         if (atom1 != y*TILE_SIZE+j)
                             tempEnergy -= scaledChargeProduct/CUTOFF;
 #endif
+                        if (needEnergy)
                             energy += 0.5f*tempEnergy;
                         delta.xyz *= dEdR;
                         force.xyz -= delta.xyz;
@@ -506,6 +507,7 @@ __kernel void computeGBSAForce1(
 #ifdef USE_CUTOFF
                         tempEnergy -= scaledChargeProduct/CUTOFF;
 #endif
+                        if (needEnergy)
                             energy += tempEnergy;
                         delta.xyz *= dEdR;
                         force.xyz -= delta.xyz;
@@ -669,6 +671,7 @@ __kernel void computeGBSAForce1(
 #ifdef USE_CUTOFF
                             tempEnergy -= scaledChargeProduct/CUTOFF;
 #endif
+                            if (needEnergy)
                                 energy += tempEnergy;
                             delta.xyz *= dEdR;
                             force.xyz -= delta.xyz;
@@ -717,6 +720,7 @@ __kernel void computeGBSAForce1(
 #ifdef USE_CUTOFF
                             tempEnergy -= scaledChargeProduct/CUTOFF;
 #endif
+                            if (needEnergy)
                                 energy += tempEnergy;
                             delta.xyz *= dEdR;
                             force.xyz -= delta.xyz;