CUDA implementation of tabulated functions for CustomIntegrator

platforms/cuda/include/CudaKernels.h

@@ -1485,7 +1485,9 @@ private:
     class ReorderListener;
     class GlobalTarget;
     class DerivFunction;
-    std::string createPerDofComputation(const std::string& variable, const Lepton::ParsedExpression& expr, int component, CustomIntegrator& integrator, const std::string& forceName, const std::string& energyName);
+    std::string createPerDofComputation(const std::string& variable, const Lepton::ParsedExpression& expr, int component, CustomIntegrator& integrator,
+        const std::string& forceName, const std::string& energyName, std::vector<const TabulatedFunction*>& functions,
+        std::vector<std::pair<std::string, std::string> >& functionNames);
     void prepareForComputation(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid);
     Lepton::ExpressionTreeNode replaceDerivFunctions(const Lepton::ExpressionTreeNode& node, OpenMM::ContextImpl& context);
     void findExpressionsForDerivs(const Lepton::ExpressionTreeNode& node, std::vector<std::pair<Lepton::ExpressionTreeNode, std::string> >& variableNodes);
@@ -1504,6 +1506,7 @@ private:
     CudaArray* uniformRandoms;
     CudaArray* randomSeed;
     CudaArray* perDofEnergyParamDerivs;
+    std::vector<CudaArray*> tabulatedFunctions;
     std::map<int, CudaArray*> savedForces;
     std::set<int> validSavedForces;
     CudaParameterSet* perDofValues;

platforms/cuda/src/CudaKernels.cpp

@@ -48,6 +48,7 @@
 #include "lepton/Operation.h"
 #include "lepton/Parser.h"
 #include "lepton/ParsedExpression.h"
+#include "ReferenceTabulatedFunction.h"
 #include "SimTKOpenMMRealType.h"
 #include "SimTKOpenMMUtilities.h"
 #include <algorithm>
@@ -7061,6 +7062,8 @@ CudaIntegrateCustomStepKernel::~CudaIntegrateCustomStepKernel() {
         delete perDofEnergyParamDerivs;
     if (perDofValues != NULL)
         delete perDofValues;
+    for (auto function : tabulatedFunctions)
+        delete function;
     for (auto& f : savedForces)
         delete f.second;
 }
@@ -7078,7 +7081,8 @@ void CudaIntegrateCustomStepKernel::initialize(const System& system, const Custo
     SimTKOpenMMUtilities::setRandomNumberSeed(integrator.getRandomNumberSeed());
 }
 
-string CudaIntegrateCustomStepKernel::createPerDofComputation(const string& variable, const Lepton::ParsedExpression& expr, int component, CustomIntegrator& integrator, const string& forceName, const string& energyName) {
+string CudaIntegrateCustomStepKernel::createPerDofComputation(const string& variable, const Lepton::ParsedExpression& expr, int component, CustomIntegrator& integrator,
+        const string& forceName, const string& energyName, vector<const TabulatedFunction*>& functions, vector<pair<string, string> >& functionNames) {
     const string suffixes[] = {".x", ".y", ".z"};
     string suffix = suffixes[component];
     map<string, Lepton::ParsedExpression> expressions;
@@ -7111,8 +7115,6 @@ string CudaIntegrateCustomStepKernel::createPerDofComputation(const string& vari
         variables[integrator.getPerDofVariableName(i)] = "perDof"+suffix.substr(1)+perDofValues->getParameterSuffix(i);
     for (int i = 0; i < (int) parameterNames.size(); i++)
         variables[parameterNames[i]] = "globals["+cu.intToString(parameterVariableIndex[i])+"]";
-    vector<const TabulatedFunction*> functions;
-    vector<pair<string, string> > functionNames;
     vector<pair<ExpressionTreeNode, string> > variableNodes;
     findExpressionsForDerivs(expr.getRootNode(), variableNodes);
     for (auto& var : variables)
@@ -7149,13 +7151,34 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
         defines["PADDED_NUM_ATOMS"] = cu.intToString(cu.getPaddedNumAtoms());
         defines["WORK_GROUP_SIZE"] = cu.intToString(CudaContext::ThreadBlockSize);
         defines["SUM_BUFFER_SIZE"] = "0";
-        
+
+        // Record the tabulated functions.
+
+        map<string, Lepton::CustomFunction*> functions;
+        vector<pair<string, string> > functionNames;
+        vector<const TabulatedFunction*> functionList;
+        vector<string> tableTypes;
+        for (int i = 0; i < integrator.getNumTabulatedFunctions(); i++) {
+            functionList.push_back(&integrator.getTabulatedFunction(i));
+            string name = integrator.getTabulatedFunctionName(i);
+            string arrayName = "table"+cu.intToString(i);
+            functionNames.push_back(make_pair(name, arrayName));
+            functions[name] = createReferenceTabulatedFunction(integrator.getTabulatedFunction(i));
+            int width;
+            vector<float> f = cu.getExpressionUtilities().computeFunctionCoefficients(integrator.getTabulatedFunction(i), width);
+            tabulatedFunctions.push_back(CudaArray::create<float>(cu, f.size(), "TabulatedFunction"));
+            tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
+            if (width == 1)
+                tableTypes.push_back("float");
+            else
+                tableTypes.push_back("float"+cu.intToString(width));
+        }
+
         // Record information about all the computation steps.
 
         vector<string> variable(numSteps);
         vector<int> forceGroup;
         vector<vector<Lepton::ParsedExpression> > expression;
-        map<string, Lepton::CustomFunction*> functions;
         CustomIntegratorUtilities::analyzeComputations(context, integrator, expression, comparisons, blockEnd, invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy, forceGroup, functions);
         for (int step = 0; step < numSteps; step++) {
             string expr;
@@ -7327,7 +7350,7 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
                     if (numUniform > 0)
                         compute << "float4 uniform = uniformValues[uniformIndex+index];\n";
                     for (int i = 0; i < 3; i++)
-                        compute << createPerDofComputation(stepType[j] == CustomIntegrator::ComputePerDof ? variable[j] : "", expression[j][0], i, integrator, forceName[j], energyName[j]);
+                        compute << createPerDofComputation(stepType[j] == CustomIntegrator::ComputePerDof ? variable[j] : "", expression[j][0], i, integrator, forceName[j], energyName[j], functionList, functionNames);
                     if (variable[j] == "x") {
                         if (storePosAsDelta[j])
                             compute << "posDelta[index] = convertFromDouble4(position-convertToDouble4(loadPos(posq, posqCorrection, index)));\n";
@@ -7358,6 +7381,8 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
                     string valueName = "perDofValues"+cu.intToString(i+1);
                     args << ", " << buffer.getType() << "* __restrict__ " << valueName;
                 }
+                for (int i = 0; i < (int) tableTypes.size(); i++)
+                    args << ", const " << tableTypes[i]<< "* __restrict__ table" << i;
                 replacements["PARAMETER_ARGUMENTS"] = args.str();
                 if (loadPosAsDelta[step])
                     defines["LOAD_POS_AS_DELTA"] = "1";
@@ -7387,6 +7412,8 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
                 args1.push_back(&perDofEnergyParamDerivs->getDevicePointer());
                 for (auto& buffer : perDofValues->getBuffers())
                     args1.push_back(&buffer.getMemory());
+                for (auto array : tabulatedFunctions)
+                    args1.push_back(&array->getDevicePointer());
                 kernelArgs[step].push_back(args1);
                 if (stepType[step] == CustomIntegrator::ComputeSum) {
                     // Create a second kernel for this step that sums the values.
@@ -7449,7 +7476,7 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
         }
         Lepton::ParsedExpression keExpression = Lepton::Parser::parse(integrator.getKineticEnergyExpression()).optimize();
         for (int i = 0; i < 3; i++)
-            computeKE << createPerDofComputation("", keExpression, i, integrator, "f", "");
+            computeKE << createPerDofComputation("", keExpression, i, integrator, "f", "", functionList, functionNames);
         map<string, string> replacements;
         replacements["COMPUTE_STEP"] = computeKE.str();
         stringstream args;
@@ -7458,6 +7485,8 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
             string valueName = "perDofValues"+cu.intToString(i+1);
             args << ", " << buffer.getType() << "* __restrict__ " << valueName;
         }
+        for (int i = 0; i < (int) tableTypes.size(); i++)
+            args << ", const " << tableTypes[i]<< "* __restrict__ table" << i;
         replacements["PARAMETER_ARGUMENTS"] = args.str();
         defines["SUM_BUFFER_SIZE"] = cu.intToString(3*numAtoms);
         if (defines.find("LOAD_POS_AS_DELTA") != defines.end())
@@ -7482,6 +7511,8 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
         kineticEnergyArgs.push_back(&perDofEnergyParamDerivs->getDevicePointer());
         for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++)
             kineticEnergyArgs.push_back(&perDofValues->getBuffers()[i].getMemory());
+        for (auto array : tabulatedFunctions)
+            kineticEnergyArgs.push_back(&array->getDevicePointer());
         keNeedsForce = usesVariable(keExpression, "f");
 
         // Create a second kernel to sum the values.
@@ -7489,6 +7520,11 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
         defines["SUM_BUFFER_SIZE"] = cu.intToString(3*numAtoms);
         module = cu.createModule(CudaKernelSources::customIntegrator, defines);
         sumKineticEnergyKernel = cu.getKernel(module, useDouble ? "computeDoubleSum" : "computeFloatSum");
+
+        // Delete the custom functions.
+
+        for (auto& function : functions)
+            delete function.second;
     }
     
     // Make sure all values (variables, parameters, etc.) are up to date.

platforms/opencl/src/OpenCLKernels.cpp

@@ -7753,7 +7753,7 @@ void OpenCLIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
                 kernel.setArg<cl::Buffer>(index++, perDofEnergyParamDerivs->getDeviceBuffer());
                 for (auto& buffer : perDofValues->getBuffers())
                     kernel.setArg<cl::Memory>(index++, buffer.getMemory());
-                for (auto* array : tabulatedFunctions)
+                for (auto array : tabulatedFunctions)
                     kernel.setArg<cl::Buffer>(index++, array->getDeviceBuffer());
                 if (stepType[step] == CustomIntegrator::ComputeSum) {
                     // Create a second kernel for this step that sums the values.
@@ -7851,7 +7851,7 @@ void OpenCLIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
         kineticEnergyKernel.setArg<cl::Buffer>(index++, perDofEnergyParamDerivs->getDeviceBuffer());
         for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++)
             kineticEnergyKernel.setArg<cl::Memory>(index++, perDofValues->getBuffers()[i].getMemory());
-        for (auto* array : tabulatedFunctions)
+        for (auto array : tabulatedFunctions)
             kineticEnergyKernel.setArg<cl::Buffer>(index++, array->getDeviceBuffer());
         keNeedsForce = usesVariable(keExpression, "f");