Optimizations to updateParametersInContext() for CUDA

platforms/cuda/include/CudaContext.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2017 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -494,6 +494,10 @@ public:
     CudaNonbondedUtilities& getNonbondedUtilities() {
         return *nonbonded;
     }
+    /**
+     * Set the particle charges.  These are packed into the fourth element of the posq array.
+     */
+    void setCharges(const std::vector<double>& charges);
     /**
      * Get the thread used by this context for executing parallel computations.
      */
@@ -577,6 +581,12 @@ public:
      * and order to be revalidated.
      */
     void invalidateMolecules();
+    /**
+     * Mark that the current molecule definitions from one particular force (and hence the atom order)
+     * may be invalid.  This should be called whenever force field parameters change.  It will cause the
+     * definitions and order to be revalidated.
+     */
+    bool invalidateMolecules(CudaForceInfo* force);
 private:
     /**
      * Compute a sorted list of device indices in decreasing order of desirability
@@ -626,6 +636,7 @@ private:
     CUfunction clearFourBuffersKernel;
     CUfunction clearFiveBuffersKernel;
     CUfunction clearSixBuffersKernel;
+    CUfunction setChargesKernel;
     std::vector<CudaForceInfo*> forces;
     std::vector<Molecule> molecules;
     std::vector<MoleculeGroup> moleculeGroups;
@@ -638,6 +649,7 @@ private:
     CudaArray* energyBuffer;
     CudaArray* energyParamDerivBuffer;
     CudaArray* atomIndexDevice;
+    CudaArray* chargeBuffer;
     std::vector<std::string> energyParamDerivNames;
     std::map<std::string, double> energyParamDerivWorkspace;
     std::vector<int> atomIndex;

platforms/cuda/include/CudaKernels.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2017 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -292,9 +292,11 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const HarmonicBondForce& force);
 private:
+    class ForceInfo;
     int numBonds;
     bool hasInitializedKernel;
     CudaContext& cu;
+    ForceInfo* info;
     const System& system;
     CudaArray* params;
 };
@@ -332,9 +334,11 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const CustomBondForce& force);
 private:
+    class ForceInfo;
     int numBonds;
     bool hasInitializedKernel;
     CudaContext& cu;
+    ForceInfo* info;
     const System& system;
     CudaParameterSet* params;
     CudaArray* globals;
@@ -375,9 +379,11 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const HarmonicAngleForce& force);
 private:
+    class ForceInfo;
     int numAngles;
     bool hasInitializedKernel;
     CudaContext& cu;
+    ForceInfo* info;
     const System& system;
     CudaArray* params;
 };
@@ -415,9 +421,11 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const CustomAngleForce& force);
 private:
+    class ForceInfo;
     int numAngles;
     bool hasInitializedKernel;
     CudaContext& cu;
+    ForceInfo* info;
     const System& system;
     CudaParameterSet* params;
     CudaArray* globals;
@@ -458,9 +466,11 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const PeriodicTorsionForce& force);
 private:
+    class ForceInfo;
     int numTorsions;
     bool hasInitializedKernel;
     CudaContext& cu;
+    ForceInfo* info;
     const System& system;
     CudaArray* params;
 };
@@ -498,9 +508,11 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const RBTorsionForce& force);
 private:
+    class ForceInfo;
     int numTorsions;
     bool hasInitializedKernel;
     CudaContext& cu;
+    ForceInfo* info;
     const System& system;
     CudaArray* params1;
     CudaArray* params2;
@@ -539,9 +551,11 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force);
 private:
+    class ForceInfo;
     int numTorsions;
     bool hasInitializedKernel;
     CudaContext& cu;
+    ForceInfo* info;
     const System& system;
     std::vector<int2> mapPositionsVec;
     CudaArray* coefficients;
@@ -582,9 +596,11 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const CustomTorsionForce& force);
 private:
+    class ForceInfo;
     int numTorsions;
     bool hasInitializedKernel;
     CudaContext& cu;
+    ForceInfo* info;
     const System& system;
     CudaParameterSet* params;
     CudaArray* globals;
@@ -647,12 +663,14 @@ private:
         const char* getMaxValue() const {return "make_int2(2147483647, 2147483647)";}
         const char* getSortKey() const {return "value.y";}
     };
+    class ForceInfo;
     class PmeIO;
     class PmePreComputation;
     class PmePostComputation;
     class SyncStreamPreComputation;
     class SyncStreamPostComputation;
     CudaContext& cu;
+    ForceInfo* info;
     bool hasInitializedFFT;
     CudaArray* sigmaEpsilon;
     CudaArray* exceptionParams;
@@ -724,8 +742,10 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force);
 private:
+    class ForceInfo;
     void initInteractionGroups(const CustomNonbondedForce& force, const std::string& interactionSource, const std::vector<std::string>& tableTypes);
     CudaContext& cu;
+    ForceInfo* info;
     CudaParameterSet* params;
     CudaArray* globals;
     CudaArray* interactionGroupData;
@@ -775,10 +795,12 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const GBSAOBCForce& force);
 private:
+    class ForceInfo;
     double prefactor, surfaceAreaFactor, cutoff;
     bool hasCreatedKernels;
     int maxTiles;
     CudaContext& cu;
+    ForceInfo* info;
     CudaArray* params;
     CudaArray* bornSum;
     CudaArray* bornRadii;
@@ -825,10 +847,12 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const CustomGBForce& force);
 private:
+    class ForceInfo;
     double cutoff;
     bool hasInitializedKernels, needParameterGradient, needEnergyParamDerivs;
     int maxTiles, numComputedValues;
     CudaContext& cu;
+    ForceInfo* info;
     CudaParameterSet* params;
     CudaParameterSet* computedValues;
     CudaParameterSet* energyDerivs;
@@ -882,9 +906,11 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const CustomExternalForce& force);
 private:
+    class ForceInfo;
     int numParticles;
     bool hasInitializedKernel;
     CudaContext& cu;
+    ForceInfo* info;
     const System& system;
     CudaParameterSet* params;
     CudaArray* globals;
@@ -926,9 +952,11 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const CustomHbondForce& force);
 private:
+    class ForceInfo;
     int numDonors, numAcceptors;
     bool hasInitializedKernel;
     CudaContext& cu;
+    ForceInfo* info;
     CudaParameterSet* donorParams;
     CudaParameterSet* acceptorParams;
     CudaArray* globals;
@@ -978,9 +1006,11 @@ public:
     void copyParametersToContext(ContextImpl& context, const CustomCentroidBondForce& force);
 
 private:
+    class ForceInfo;
     int numGroups, numBonds;
     bool needEnergyParamDerivs;
     CudaContext& cu;
+    ForceInfo* info;
     CudaParameterSet* params;
     CudaArray* globals;
     CudaArray* groupParticles;
@@ -1031,8 +1061,10 @@ public:
     void copyParametersToContext(ContextImpl& context, const CustomCompoundBondForce& force);
 
 private:
+    class ForceInfo;
     int numBonds;
     CudaContext& cu;
+    ForceInfo* info;
     CudaParameterSet* params;
     CudaArray* globals;
     std::vector<std::string> globalParamNames;
@@ -1077,7 +1109,9 @@ public:
     void copyParametersToContext(ContextImpl& context, const CustomManyParticleForce& force);
 
 private:
+    class ForceInfo;
     CudaContext& cu;
+    ForceInfo* info;
     bool hasInitializedKernel;
     NonbondedMethod nonbondedMethod;
     int maxNeighborPairs, forceWorkgroupSize, findNeighborsWorkgroupSize;
@@ -1139,9 +1173,11 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const GayBerneForce& force);
 private:
+    class ForceInfo;
     class ReorderListener;
     void sortAtoms();
     CudaContext& cu;
+    ForceInfo* info;
     bool hasInitializedKernels;
     int numRealParticles, numExceptions, maxNeighborBlocks;
     GayBerneForce::NonbondedMethod nonbondedMethod;

platforms/cuda/src/CudaContext.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2017 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -108,7 +108,8 @@ static int executeInWindows(const string &command) {
 CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlockingSync, const string& precision, const string& compiler,
         const string& tempDir, const std::string& hostCompiler, CudaPlatform::PlatformData& platformData) : system(system), currentStream(0),
         time(0.0), platformData(platformData), stepCount(0), computeForceCount(0), stepsSinceReorder(99999), contextIsValid(false), atomsWereReordered(false), hasCompilerKernel(false), isNvccAvailable(false),
-        pinnedBuffer(NULL), posq(NULL), posqCorrection(NULL), velm(NULL), force(NULL), energyBuffer(NULL), energyParamDerivBuffer(NULL), atomIndexDevice(NULL), integration(NULL), expression(NULL), bonded(NULL), nonbonded(NULL), thread(NULL) {
+        pinnedBuffer(NULL), posq(NULL), posqCorrection(NULL), velm(NULL), force(NULL), energyBuffer(NULL), energyParamDerivBuffer(NULL), atomIndexDevice(NULL), chargeBuffer(NULL),
+        integration(NULL), expression(NULL), bonded(NULL), nonbonded(NULL), thread(NULL) {
     // Determine what compiler to use.
     
     this->compiler = "\""+compiler+"\"";
@@ -291,6 +292,7 @@ CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlocking
     clearFourBuffersKernel = getKernel(utilities, "clearFourBuffers");
     clearFiveBuffersKernel = getKernel(utilities, "clearFiveBuffers");
     clearSixBuffersKernel = getKernel(utilities, "clearSixBuffers");
+    setChargesKernel = getKernel(utilities, "setCharges");
 
     // Set defines based on the requested precision.
 
@@ -407,6 +409,8 @@ CudaContext::~CudaContext() {
         delete energyParamDerivBuffer;
     if (atomIndexDevice != NULL)
         delete atomIndexDevice;
+    if (chargeBuffer != NULL)
+        delete chargeBuffer;
     if (integration != NULL)
         delete integration;
     if (expression != NULL)
@@ -860,6 +864,25 @@ void CudaContext::clearAutoclearBuffers() {
     }
 }
 
+void CudaContext::setCharges(const vector<double>& charges) {
+    if (chargeBuffer == NULL)
+        chargeBuffer = new CudaArray(*this, numAtoms, useDoublePrecision ? sizeof(double) : sizeof(float), "chargeBuffer");
+    if (getUseDoublePrecision()) {
+        double* c = (double*) getPinnedBuffer();
+        for (int i = 0; i < charges.size(); i++)
+            c[i] = charges[i];
+        chargeBuffer->upload(c);
+    }
+    else {
+        float* c = (float*) getPinnedBuffer();
+        for (int i = 0; i < charges.size(); i++)
+            c[i] = (float) charges[i];
+        chargeBuffer->upload(c);
+    }
+    void* args[] = {&chargeBuffer->getDevicePointer(), &posq->getDevicePointer(), &atomIndexDevice->getDevicePointer(), &numAtoms};
+    executeKernel(setChargesKernel, args, numAtoms);
+}
+
 /**
  * This class ensures that atom reordering doesn't break virtual sites.
  */
@@ -1058,9 +1081,19 @@ void CudaContext::findMoleculeGroups() {
 }
 
 void CudaContext::invalidateMolecules() {
+    for (int i = 0; i < forces.size(); i++)
+        if (invalidateMolecules(forces[i]))
+            return;
+}
+
+bool CudaContext::invalidateMolecules(CudaForceInfo* force) {
     if (numAtoms == 0 || nonbonded == NULL || !nonbonded->getUseCutoff())
-        return;
+        return false;
     bool valid = true;
+    int forceIndex = -1;
+    for (int i = 0; i < forces.size(); i++)
+        if (forces[i] == force)
+            forceIndex = i;
     for (int group = 0; valid && group < (int) moleculeGroups.size(); group++) {
         MoleculeGroup& mol = moleculeGroups[group];
         vector<int>& instances = mol.instances;
@@ -1075,22 +1108,21 @@ void CudaContext::invalidateMolecules() {
             Molecule& m2 = molecules[instances[j]];
             int offset2 = offsets[j];
             for (int i = 0; i < (int) atoms.size() && valid; i++) {
-                for (int k = 0; k < (int) forces.size(); k++)
-                    if (!forces[k]->areParticlesIdentical(atoms[i]+offset1, atoms[i]+offset2))
-                        valid = false;
+                if (!force->areParticlesIdentical(atoms[i]+offset1, atoms[i]+offset2))
+                    valid = false;
             }
 
             // See if the force groups are identical.
 
-            for (int i = 0; i < (int) forces.size() && valid; i++) {
-                for (int k = 0; k < (int) m1.groups[i].size() && valid; k++)
-                    if (!forces[i]->areGroupsIdentical(m1.groups[i][k], m2.groups[i][k]))
+            if (valid && forceIndex > -1) {
+                for (int k = 0; k < (int) m1.groups[forceIndex].size() && valid; k++)
+                    if (!force->areGroupsIdentical(m1.groups[forceIndex][k], m2.groups[forceIndex][k]))
                         valid = false;
             }
         }
     }
     if (valid)
-        return;
+        return false;
 
     // The list of which molecules are identical is no longer valid.  We need to restore the
     // atoms to their original order, rebuild the list of identical molecules, and sort them
@@ -1158,6 +1190,7 @@ void CudaContext::invalidateMolecules() {
     for (int i = 0; i < (int) reorderListeners.size(); i++)
         reorderListeners[i]->execute();
     reorderAtoms();
+    return true;
 }
 
 void CudaContext::reorderAtoms() {

platforms/cuda/src/kernels/utilities.cu

@@ -73,4 +73,11 @@ __global__ void clearSixBuffers(int* __restrict__ buffer1, int size1, int* __res
     clearSingleBuffer(buffer6, size6);
 }
 
+/**
+ * Record the atomic charges into the posq array.
+ */
+__global__ void setCharges(real* __restrict__ charges, real4* __restrict__ posq, int* __restrict__ atomOrder, int numAtoms) {
+    for (int i = blockDim.x*blockIdx.x+threadIdx.x; i < numAtoms; i += blockDim.x*gridDim.x)
+        posq[i].w = charges[atomOrder[i]];
+}
 }
\ No newline at end of file