Fixed potential invalid memory access (#3428)

* Fixed potential invalid memory access

* Fixed exception

platforms/common/include/openmm/common/ArrayInterface.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) 2019-2021 Stanford University and the Authors.      *
+ * Portions copyright (c) 2019-2022 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -51,7 +51,7 @@ public:
      * @param elementSize       the size of each element in bytes
      * @param name              the name of the array
      */
-    virtual void initialize(ComputeContext& context, int size, int elementSize, const std::string& name) = 0;
+    virtual void initialize(ComputeContext& context, size_t size, int elementSize, const std::string& name) = 0;
     /**
      * Initialize this object.  The template argument is the data type of each array element.
      *
@@ -60,13 +60,13 @@ public:
      * @param name              the name of the array
      */
     template <class T>
-    void initialize(ComputeContext& context, int size, const std::string& name) {
+    void initialize(ComputeContext& context, size_t size, const std::string& name) {
         initialize(context, size, sizeof(T), name);
     }
     /**
      * Recreate the internal storage to have a different size.
      */
-    virtual void resize(int size) = 0;
+    virtual void resize(size_t size) = 0;
     /**
      * Get whether this array has been initialized.
      */
@@ -74,7 +74,7 @@ public:
     /**
      * Get the number of elements in the array.
      */
-    virtual int getSize() const = 0;
+    virtual size_t getSize() const = 0;
     /**
      * Get the size of each element in bytes.
      */

platforms/common/include/openmm/common/ComputeArray.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) 2019-2021 Stanford University and the Authors.      *
+ * Portions copyright (c) 2019-2022 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -60,7 +60,7 @@ public:
      * @param elementSize       the size of each element in bytes
      * @param name              the name of the array
      */
-    void initialize(ComputeContext& context, int size, int elementSize, const std::string& name);
+    void initialize(ComputeContext& context, size_t size, int elementSize, const std::string& name);
     /**
      * Initialize this object.  The template argument is the data type of each array element.
      *
@@ -69,13 +69,13 @@ public:
      * @param name              the name of the array
      */
     template <class T>
-    void initialize(ComputeContext& context, int size, const std::string& name) {
+    void initialize(ComputeContext& context, size_t size, const std::string& name) {
         initialize(context, size, sizeof(T), name);
     }
     /**
      * Recreate the internal storage to have a different size.
      */
-    void resize(int size);
+    void resize(size_t size);
     /**
      * Get whether this array has been initialized.
      */
@@ -83,7 +83,7 @@ public:
     /**
      * Get the number of elements in the array.
      */
-    int getSize() const;
+    size_t getSize() const;
     /**
      * Get the size of each element in bytes.
      */

platforms/common/src/CommonKernels.cpp

@@ -4734,7 +4734,7 @@ double CommonCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bo
             startIndicesKernel->execute(256, 256);
             copyPairsKernel->execute(maxNeighborPairs);
         }
-        int maxThreads = min(cc.getNumAtoms()*forceWorkgroupSize, cc.getEnergyBuffer().getSize());
+        int maxThreads = min(cc.getNumAtoms()*forceWorkgroupSize, (int) cc.getEnergyBuffer().getSize());
         forceKernel->execute(maxThreads, forceWorkgroupSize);
         if (nonbondedMethod != NoCutoff) {
             // Make sure there was enough memory for the neighbor list.
@@ -5290,7 +5290,7 @@ void CommonCalcCustomCVForceKernel::initialize(const System& system, const Custo
     copyForcesKernel->addArg(cc.getPaddedNumAtoms());
     addForcesKernel = program->createKernel("addForces");
     addForcesKernel->addArg(cc.getLongForceBuffer());
-    addForcesKernel->addArg(cc.getLongForceBuffer().getSize());
+    addForcesKernel->addArg((int) cc.getLongForceBuffer().getSize());
     for (int i = 0; i < numCVs; i++) {
         addForcesKernel->addArg();
         addForcesKernel->addArg();
@@ -6143,7 +6143,7 @@ std::pair<double, double> CommonIntegrateNoseHooverStepKernel::computeMaskedKine
 
         reduceEnergyKernel->addArg(energyBuffer);
         reduceEnergyKernel->addArg(kineticEnergyBuffer);
-        reduceEnergyKernel->addArg(energyBuffer.getSize());
+        reduceEnergyKernel->addArg((int) energyBuffer.getSize());
     }
 
     cc.clearBuffer(energyBuffer);
@@ -6507,7 +6507,7 @@ void CommonIntegrateVariableLangevinStepKernel::initialize(const System& system,
     selectSizeKernel = program->createKernel("selectLangevinStepSize");
     params.initialize(cc, 3, cc.getUseDoublePrecision() || cc.getUseMixedPrecision() ? sizeof(double) : sizeof(float), "langevinParams");
     blockSize = min(256, system.getNumParticles());
-    blockSize = max(blockSize, params.getSize());
+    blockSize = max(blockSize, (int) params.getSize());
 }
 
 double CommonIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime) {

platforms/common/src/ComputeArray.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) 2019-2021 Stanford University and the Authors.      *
+ * Portions copyright (c) 2019-2022 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -43,14 +43,14 @@ ArrayInterface& ComputeArray::getArray() {
     return *impl;
 }
 
-void ComputeArray::initialize(ComputeContext& context, int size, int elementSize, const std::string& name) {
+void ComputeArray::initialize(ComputeContext& context, size_t size, int elementSize, const std::string& name) {
     if (impl != NULL)
         throw OpenMMException("The array "+getName()+" has already been initialized");
     impl = context.createArray();
     impl->initialize(context, size, elementSize, name);
 }
 
-void ComputeArray::resize(int size) {
+void ComputeArray::resize(size_t size) {
     if (impl == NULL)
         throw OpenMMException("ComputeArray has not been initialized");
     impl->resize(size);
@@ -60,7 +60,7 @@ bool ComputeArray::isInitialized() const {
     return (impl != NULL);
 }
 
-int ComputeArray::getSize() const {
+size_t ComputeArray::getSize() const {
     if (impl == NULL)
         throw OpenMMException("ComputeArray has not been initialized");
     return impl->getSize();

platforms/common/src/IntegrationUtilities.cpp

@@ -602,7 +602,7 @@ IntegrationUtilities::IntegrationUtilities(ComputeContext& context, const System
     // Set arguments for constraint kernels.
 
     if (settleAtoms.isInitialized()) {
-        settlePosKernel->addArg(settleAtoms.getSize());
+        settlePosKernel->addArg((int) settleAtoms.getSize());
         settlePosKernel->addArg();
         settlePosKernel->addArg(context.getPosq());
         settlePosKernel->addArg(posDelta);
@@ -611,7 +611,7 @@ IntegrationUtilities::IntegrationUtilities(ComputeContext& context, const System
         settlePosKernel->addArg(settleParams);
         if (context.getUseMixedPrecision())
             settlePosKernel->addArg(context.getPosqCorrection());
-        settleVelKernel->addArg(settleAtoms.getSize());
+        settleVelKernel->addArg((int) settleAtoms.getSize());
         settleVelKernel->addArg();
         settleVelKernel->addArg(context.getPosq());
         settleVelKernel->addArg(posDelta);
@@ -622,7 +622,7 @@ IntegrationUtilities::IntegrationUtilities(ComputeContext& context, const System
             settleVelKernel->addArg(context.getPosqCorrection());
     }
     if (shakeAtoms.isInitialized()) {
-        shakePosKernel->addArg(shakeAtoms.getSize());
+        shakePosKernel->addArg((int) shakeAtoms.getSize());
         shakePosKernel->addArg();
         shakePosKernel->addArg(context.getPosq());
         shakePosKernel->addArg(posDelta);
@@ -630,7 +630,7 @@ IntegrationUtilities::IntegrationUtilities(ComputeContext& context, const System
         shakePosKernel->addArg(shakeParams);
         if (context.getUseMixedPrecision())
             shakePosKernel->addArg(context.getPosqCorrection());
-        shakeVelKernel->addArg(shakeAtoms.getSize());
+        shakeVelKernel->addArg((int) shakeAtoms.getSize());
         shakeVelKernel->addArg();
         shakeVelKernel->addArg(context.getPosq());
         shakeVelKernel->addArg(context.getVelm());
@@ -755,7 +755,7 @@ void IntegrationUtilities::initRandomNumberGenerator(unsigned int randomNumberSe
     random.initialize<mm_float4>(context, 4*context.getPaddedNumAtoms(), "random");
     randomSeed.initialize<mm_int4>(context, context.getNumThreadBlocks()*64, "randomSeed");
     randomPos = random.getSize();
-    randomKernel->addArg(random.getSize());
+    randomKernel->addArg((int) random.getSize());
     randomKernel->addArg(random);
     randomKernel->addArg(randomSeed);
 

platforms/cuda/include/CudaArray.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) 2009-2021 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2022 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -55,7 +55,7 @@ public:
      * @param name              the name of the array
      */
     template <class T>
-    static CudaArray* create(CudaContext& context, int size, const std::string& name) {
+    static CudaArray* create(CudaContext& context, size_t size, const std::string& name) {
         return new CudaArray(context, size, sizeof(T), name);
     }
     /**
@@ -71,7 +71,7 @@ public:
      * @param elementSize       the size of each element in bytes
      * @param name              the name of the array
      */
-    CudaArray(CudaContext& context, int size, int elementSize, const std::string& name);
+    CudaArray(CudaContext& context, size_t size, int elementSize, const std::string& name);
     ~CudaArray();
     /**
      * Initialize this object.
@@ -81,7 +81,7 @@ public:
      * @param elementSize       the size of each element in bytes
      * @param name              the name of the array
      */
-    void initialize(ComputeContext& context, int size, int elementSize, const std::string& name);
+    void initialize(ComputeContext& context, size_t size, int elementSize, const std::string& name);
     /**
      * Initialize this object.  The template argument is the data type of each array element.
      *
@@ -90,13 +90,13 @@ public:
      * @param name              the name of the array
      */
     template <class T>
-    void initialize(ComputeContext& context, int size, const std::string& name) {
+    void initialize(ComputeContext& context, size_t size, const std::string& name) {
         initialize(context, size, sizeof(T), name);
     }
     /**
      * Recreate the internal storage to have a different size.
      */
-    void resize(int size);
+    void resize(size_t size);
     /**
      * Get whether this array has been initialized.
      */
@@ -106,7 +106,7 @@ public:
     /**
      * Get the number of elements in the array.
      */
-    int getSize() const {
+    size_t getSize() const {
         return size;
     }
     /**
@@ -182,7 +182,8 @@ public:
 private:
     CudaContext* context;
     CUdeviceptr pointer;
-    int size, elementSize;
+    size_t size;
+    int elementSize;
     bool ownsMemory;
     std::string name;
 };

platforms/cuda/include/CudaNonbondedUtilities.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) 2009-2019 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2022 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -338,7 +338,7 @@ private:
     CudaArray rebuildNeighborList;
     CudaSort* blockSorter;
     CUevent downloadCountEvent;
-    int* pinnedCountBuffer;
+    unsigned int* pinnedCountBuffer;
     std::vector<void*> forceArgs, findBlockBoundsArgs, sortBoxDataArgs, findInteractingBlocksArgs;
     std::vector<std::vector<int> > atomExclusions;
     std::vector<ParameterInfo> parameters;
@@ -348,7 +348,8 @@ private:
     std::map<int, std::string> groupKernelSource;
     double lastCutoff;
     bool useCutoff, usePeriodic, anyExclusions, usePadding, forceRebuildNeighborList, canUsePairList;
-    int startTileIndex, startBlockIndex, numBlocks, maxTiles, maxSinglePairs, maxExclusions, numForceThreadBlocks, forceThreadBlockSize, numAtoms, groupFlags;
+    int startTileIndex, startBlockIndex, numBlocks, maxExclusions, numForceThreadBlocks, forceThreadBlockSize, numAtoms, groupFlags;
+    unsigned int maxTiles, maxSinglePairs;
     long long numTiles;
     std::string kernelSource;
 };

platforms/cuda/src/CudaArray.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) 2012-2021 Stanford University and the Authors.      *
+ * Portions copyright (c) 2012-2022 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,7 +36,7 @@ using namespace OpenMM;
 CudaArray::CudaArray() : pointer(0), ownsMemory(false) {
 }
 
-CudaArray::CudaArray(CudaContext& context, int size, int elementSize, const std::string& name) : pointer(0) {
+CudaArray::CudaArray(CudaContext& context, size_t size, int elementSize, const std::string& name) : pointer(0) {
     initialize(context, size, elementSize, name);
 }
 
@@ -52,7 +52,7 @@ CudaArray::~CudaArray() {
     }
 }
 
-void CudaArray::initialize(ComputeContext& context, int size, int elementSize, const std::string& name) {
+void CudaArray::initialize(ComputeContext& context, size_t size, int elementSize, const std::string& name) {
     if (this->pointer != 0)
         throw OpenMMException("CudaArray has already been initialized");
     this->context = &dynamic_cast<CudaContext&>(context);
@@ -69,7 +69,7 @@ void CudaArray::initialize(ComputeContext& context, int size, int elementSize, c
     }
 }
 
-void CudaArray::resize(int size) {
+void CudaArray::resize(size_t size) {
     if (pointer == 0)
         throw OpenMMException("CudaArray has not been initialized");
     if (!ownsMemory)

platforms/cuda/src/CudaNonbondedUtilities.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) 2009-2018 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2022 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -71,7 +71,7 @@ CudaNonbondedUtilities::CudaNonbondedUtilities(CudaContext& context) : context(c
     int multiprocessors;
     CHECK_RESULT(cuDeviceGetAttribute(&multiprocessors, CU_DEVICE_ATTRIBUTE_MULTIPROCESSOR_COUNT, context.getDevice()));
     CHECK_RESULT(cuEventCreate(&downloadCountEvent, 0));
-    CHECK_RESULT(cuMemHostAlloc((void**) &pinnedCountBuffer, 2*sizeof(int), CU_MEMHOSTALLOC_PORTABLE));
+    CHECK_RESULT(cuMemHostAlloc((void**) &pinnedCountBuffer, 2*sizeof(unsigned int), CU_MEMHOSTALLOC_PORTABLE));
     numForceThreadBlocks = 4*multiprocessors;
     forceThreadBlockSize = (context.getComputeCapability() < 2.0 ? 128 : 256);
     setKernelSource(CudaKernelSources::nonbonded);
@@ -430,12 +430,13 @@ bool CudaNonbondedUtilities::updateNeighborListSize() {
     // this from happening in the future.
 
     if (pinnedCountBuffer[0] > maxTiles) {
-        maxTiles = (int) (1.2*pinnedCountBuffer[0]);
-        int totalTiles = context.getNumAtomBlocks()*(context.getNumAtomBlocks()+1)/2;
+        maxTiles = (unsigned int) (1.2*pinnedCountBuffer[0]);
+        unsigned int numBlocks = context.getNumAtomBlocks();
+        int totalTiles = numBlocks*(numBlocks+1)/2;
         if (maxTiles > totalTiles)
             maxTiles = totalTiles;
         interactingTiles.resize(maxTiles);
-        interactingAtoms.resize(CudaContext::TileSize*maxTiles);
+        interactingAtoms.resize(CudaContext::TileSize*(size_t) maxTiles);
         if (forceArgs.size() > 0)
             forceArgs[7] = &interactingTiles.getDevicePointer();
         findInteractingBlocksArgs[6] = &interactingTiles.getDevicePointer();
@@ -444,7 +445,7 @@ bool CudaNonbondedUtilities::updateNeighborListSize() {
         findInteractingBlocksArgs[7] = &interactingAtoms.getDevicePointer();
     }
     if (pinnedCountBuffer[1] > maxSinglePairs) {
-        maxSinglePairs = (int) (1.2*pinnedCountBuffer[1]);
+        maxSinglePairs = (unsigned int) (1.2*pinnedCountBuffer[1]);
         singlePairs.resize(maxSinglePairs);
         if (forceArgs.size() > 0)
             forceArgs[19] = &singlePairs.getDevicePointer();

platforms/cuda/src/kernels/findInteractingBlocks.cu

@@ -76,7 +76,7 @@ extern "C" __global__ void sortBoxData(const real2* __restrict__ sortedBlock, co
     }
 }
 
-__device__ int saveSinglePairs(int x, int* atoms, int* flags, int length, unsigned int maxSinglePairs, unsigned int* singlePairCount, int2* singlePairs, int* sumBuffer, volatile int& pairStartIndex) {
+__device__ int saveSinglePairs(int x, int* atoms, int* flags, int length, unsigned int maxSinglePairs, unsigned int* singlePairCount, int2* singlePairs, int* sumBuffer, volatile unsigned int& pairStartIndex) {
     // Record interactions that should be computed as single pairs rather than in blocks.
     
     const int indexInWarp = threadIdx.x%32;
@@ -95,7 +95,7 @@ __device__ int saveSinglePairs(int x, int* atoms, int* flags, int length, unsign
         pairStartIndex = atomicAdd(singlePairCount,(unsigned int) sum);
     __syncwarp();
     int prevSum = __shfl_up_sync(0xffffffff, sum, 1);
-    int pairIndex = pairStartIndex + (indexInWarp > 0 ? prevSum : 0);
+    unsigned int pairIndex = pairStartIndex + (indexInWarp > 0 ? prevSum : 0);
     for (int i = indexInWarp; i < length; i += 32) {
         int count = __popc(flags[i]);
         if (count <= MAX_BITS_FOR_PAIRS && pairIndex+count <= maxSinglePairs) {
@@ -196,14 +196,14 @@ extern "C" __global__ __launch_bounds__(GROUP_SIZE,3) void findBlocksWithInterac
     __shared__ int workgroupFlagsBuffer[BUFFER_SIZE*(GROUP_SIZE/32)];
     __shared__ int warpExclusions[MAX_EXCLUSIONS*(GROUP_SIZE/32)];
     __shared__ real4 posBuffer[GROUP_SIZE];
-    __shared__ volatile int workgroupTileIndex[GROUP_SIZE/32];
-    __shared__ int worksgroupPairStartIndex[GROUP_SIZE/32];
+    __shared__ volatile unsigned int workgroupTileIndex[GROUP_SIZE/32];
+    __shared__ unsigned int workgroupPairStartIndex[GROUP_SIZE/32];
     int* sumBuffer = (int*) posBuffer; // Reuse the same buffer to save memory
     int* buffer = workgroupBuffer+BUFFER_SIZE*(warpStart/32);
     int* flagsBuffer = workgroupFlagsBuffer+BUFFER_SIZE*(warpStart/32);
     int* exclusionsForX = warpExclusions+MAX_EXCLUSIONS*(warpStart/32);
-    volatile int& tileStartIndex = workgroupTileIndex[warpStart/32];
-    volatile int& pairStartIndex = worksgroupPairStartIndex[warpStart/32];
+    volatile unsigned int& tileStartIndex = workgroupTileIndex[warpStart/32];
+    volatile unsigned int& pairStartIndex = workgroupPairStartIndex[warpStart/32];
 
     // Loop over blocks.
     
@@ -342,11 +342,11 @@ extern "C" __global__ __launch_bounds__(GROUP_SIZE,3) void findBlocksWithInterac
 #if MAX_BITS_FOR_PAIRS > 0
                     neighborsInBuffer = saveSinglePairs(x, buffer, flagsBuffer, neighborsInBuffer, maxSinglePairs, &interactionCount[1], singlePairs, sumBuffer+warpStart, pairStartIndex);
 #endif
-                    int tilesToStore = neighborsInBuffer/TILE_SIZE;
+                    unsigned int tilesToStore = neighborsInBuffer/TILE_SIZE;
                     if (tilesToStore > 0) {
                         if (indexInWarp == 0)
                             tileStartIndex = atomicAdd(&interactionCount[0], tilesToStore);
-                        int newTileStartIndex = tileStartIndex;
+                        unsigned int newTileStartIndex = tileStartIndex;
                         if (newTileStartIndex+tilesToStore <= maxTiles) {
                             if (indexInWarp < tilesToStore)
                                 interactingTiles[newTileStartIndex+indexInWarp] = x;
@@ -369,10 +369,10 @@ extern "C" __global__ __launch_bounds__(GROUP_SIZE,3) void findBlocksWithInterac
             neighborsInBuffer = saveSinglePairs(x, buffer, flagsBuffer, neighborsInBuffer, maxSinglePairs, &interactionCount[1], singlePairs, sumBuffer+warpStart, pairStartIndex);
 #endif
         if (neighborsInBuffer > 0) {
-            int tilesToStore = (neighborsInBuffer+TILE_SIZE-1)/TILE_SIZE;
+            unsigned int tilesToStore = (neighborsInBuffer+TILE_SIZE-1)/TILE_SIZE;
             if (indexInWarp == 0)
                 tileStartIndex = atomicAdd(&interactionCount[0], tilesToStore);
-            int newTileStartIndex = tileStartIndex;
+            unsigned int newTileStartIndex = tileStartIndex;
             if (newTileStartIndex+tilesToStore <= maxTiles) {
                 if (indexInWarp < tilesToStore)
                     interactingTiles[newTileStartIndex+indexInWarp] = x;

platforms/opencl/include/OpenCLArray.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) 2009-2021 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2022 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -59,7 +59,7 @@ public:
      * @param flags             the set of flags to specify when creating the OpenCL Buffer
      */
     template <class T>
-    static OpenCLArray* create(OpenCLContext& context, int size, const std::string& name, cl_int flags = CL_MEM_READ_WRITE) {
+    static OpenCLArray* create(OpenCLContext& context, size_t size, const std::string& name, cl_int flags = CL_MEM_READ_WRITE) {
         return new OpenCLArray(context, size, sizeof(T), name, flags);
     }
     /**
@@ -72,7 +72,7 @@ public:
      * @param name              the name of the array
      */
     template <class T>
-    static OpenCLArray* create(OpenCLContext& context, cl::Buffer* buffer, int size, const std::string& name) {
+    static OpenCLArray* create(OpenCLContext& context, cl::Buffer* buffer, size_t size, const std::string& name) {
         return new OpenCLArray(context, buffer, size, sizeof(T), name);
     }
     /**
@@ -89,7 +89,7 @@ public:
      * @param name              the name of the array
      * @param flags             the set of flags to specify when creating the OpenCL Buffer
      */
-    OpenCLArray(OpenCLContext& context, int size, int elementSize, const std::string& name, cl_int flags = CL_MEM_READ_WRITE);
+    OpenCLArray(OpenCLContext& context, size_t size, int elementSize, const std::string& name, cl_int flags = CL_MEM_READ_WRITE);
     /**
      * Create an OpenCLArray object that uses a preexisting Buffer.
      *
@@ -99,7 +99,7 @@ public:
      * @param elementSize       the size of each element in bytes
      * @param name              the name of the array
      */
-    OpenCLArray(OpenCLContext& context, cl::Buffer* buffer, int size, int elementSize, const std::string& name);
+    OpenCLArray(OpenCLContext& context, cl::Buffer* buffer, size_t size, int elementSize, const std::string& name);
     ~OpenCLArray();
     /**
      * Initialize this array.
@@ -109,7 +109,7 @@ public:
      * @param elementSize       the size of each element in bytes
      * @param name              the name of the array
      */
-    void initialize(ComputeContext& context, int size, int elementSize, const std::string& name);
+    void initialize(ComputeContext& context, size_t size, int elementSize, const std::string& name);
     /**
      * Initialize this object.
      *
@@ -119,7 +119,7 @@ public:
      * @param name              the name of the array
      * @param flags             the set of flags to specify when creating the OpenCL Buffer
      */
-    void initialize(OpenCLContext& context, int size, int elementSize, const std::string& name, cl_int flags);
+    void initialize(OpenCLContext& context, size_t size, int elementSize, const std::string& name, cl_int flags);
     /**
      * Initialize this object to use a preexisting Buffer.
      *
@@ -129,7 +129,7 @@ public:
      * @param elementSize       the size of each element in bytes
      * @param name              the name of the array
      */
-    void initialize(OpenCLContext& context, cl::Buffer* buffer, int size, int elementSize, const std::string& name);
+    void initialize(OpenCLContext& context, cl::Buffer* buffer, size_t size, int elementSize, const std::string& name);
     /**
      * Initialize this object.  The template argument is the data type of each array element.
      *
@@ -139,7 +139,7 @@ public:
      * @param flags             the set of flags to specify when creating the OpenCL Buffer
      */
     template <class T>
-    void initialize(OpenCLContext& context, int size, const std::string& name, cl_int flags = CL_MEM_READ_WRITE) {
+    void initialize(OpenCLContext& context, size_t size, const std::string& name, cl_int flags = CL_MEM_READ_WRITE) {
         initialize(context, size, sizeof(T), name, flags);
     }
     /**
@@ -152,13 +152,13 @@ public:
      * @param name              the name of the array
      */
     template <class T>
-    void initialize(OpenCLContext& context, cl::Buffer* buffer, int size, const std::string& name) {
+    void initialize(OpenCLContext& context, cl::Buffer* buffer, size_t size, const std::string& name) {
         initialize(context, buffer, size, sizeof(T), name);
     }
     /**
      * Recreate the internal storage to have a different size.
      */
-    void resize(int size);
+    void resize(size_t size);
     /**
      * Get whether this array has been initialized.
      */
@@ -168,7 +168,7 @@ public:
     /**
      * Get the size of the array.
      */
-    int getSize() const {
+    size_t getSize() const {
         return size;
     }
     /**
@@ -241,7 +241,8 @@ public:
 private:
     OpenCLContext* context;
     cl::Buffer* buffer;
-    int size, elementSize;
+    size_t size;
+    int elementSize;
     cl_int flags;
     bool ownsBuffer;
     std::string name;

platforms/opencl/include/OpenCLNonbondedUtilities.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) 2009-2019 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2022 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -322,7 +322,7 @@ private:
     OpenCLSort* blockSorter;
     cl::Event downloadCountEvent;
     cl::Buffer* pinnedCountBuffer;
-    int* pinnedCountMemory;
+    unsigned int* pinnedCountMemory;
     std::vector<std::vector<int> > atomExclusions;
     std::vector<ParameterInfo> parameters;
     std::vector<ParameterInfo> arguments;

platforms/opencl/src/OpenCLArray.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) 2012-2021 Stanford University and the Authors.      *
+ * Portions copyright (c) 2012-2022 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -35,11 +35,11 @@ using namespace OpenMM;
 OpenCLArray::OpenCLArray() : buffer(NULL), ownsBuffer(false) {
 }
 
-OpenCLArray::OpenCLArray(OpenCLContext& context, int size, int elementSize, const std::string& name, cl_int flags) : buffer(NULL) {
+OpenCLArray::OpenCLArray(OpenCLContext& context, size_t size, int elementSize, const std::string& name, cl_int flags) : buffer(NULL) {
     initialize(context, size, elementSize, name, flags);
 }
 
-OpenCLArray::OpenCLArray(OpenCLContext& context, cl::Buffer* buffer, int size, int elementSize, const std::string& name) : buffer(NULL) {
+OpenCLArray::OpenCLArray(OpenCLContext& context, cl::Buffer* buffer, size_t size, int elementSize, const std::string& name) : buffer(NULL) {
     initialize(context, buffer, size, elementSize, name);
 }
 
@@ -48,11 +48,11 @@ OpenCLArray::~OpenCLArray() {
         delete buffer;
 }
 
-void OpenCLArray::initialize(ComputeContext& context, int size, int elementSize, const std::string& name) {
+void OpenCLArray::initialize(ComputeContext& context, size_t size, int elementSize, const std::string& name) {
     initialize(dynamic_cast<OpenCLContext&>(context), size, elementSize, name, CL_MEM_READ_WRITE);
 }
 
-void OpenCLArray::initialize(OpenCLContext& context, int size, int elementSize, const std::string& name, cl_int flags) {
+void OpenCLArray::initialize(OpenCLContext& context, size_t size, int elementSize, const std::string& name, cl_int flags) {
     if (buffer != NULL)
         throw OpenMMException("OpenCLArray has already been initialized");
     this->context = &context;
@@ -71,7 +71,7 @@ void OpenCLArray::initialize(OpenCLContext& context, int size, int elementSize,
     }
 }
 
-void OpenCLArray::initialize(OpenCLContext& context, cl::Buffer* buffer, int size, int elementSize, const std::string& name) {
+void OpenCLArray::initialize(OpenCLContext& context, cl::Buffer* buffer, size_t size, int elementSize, const std::string& name) {
     if (this->buffer != NULL)
         throw OpenMMException("OpenCLArray has already been initialized");
     this->context = &context;
@@ -82,7 +82,7 @@ void OpenCLArray::initialize(OpenCLContext& context, cl::Buffer* buffer, int siz
     ownsBuffer = false;
 }
 
-void OpenCLArray::resize(int size) {
+void OpenCLArray::resize(size_t size) {
     if (buffer == NULL)
         throw OpenMMException("OpenCLArray has not been initialized");
     if (!ownsBuffer)

platforms/opencl/src/OpenCLContext.cpp

@@ -532,9 +532,9 @@ void OpenCLContext::initialize() {
             energyParamDerivBuffer.initialize<cl_float>(*this, numEnergyParamDerivs*energyBufferSize, "energyParamDerivBuffer");
         addAutoclearBuffer(energyParamDerivBuffer);
     }
-    int bufferBytes = max(max(velm.getSize()*velm.getElementSize(),
+    int bufferBytes = max(max((int) velm.getSize()*velm.getElementSize(),
             energyBufferSize*energyBuffer.getElementSize()),
-            longForceBuffer.getSize()*longForceBuffer.getElementSize());
+            (int) longForceBuffer.getSize()*longForceBuffer.getElementSize());
     pinnedBuffer = new cl::Buffer(context, CL_MEM_ALLOC_HOST_PTR, bufferBytes);
     pinnedMemory = currentQueue.enqueueMapBuffer(*pinnedBuffer, CL_TRUE, CL_MAP_READ | CL_MAP_WRITE, 0, bufferBytes);
     for (int i = 0; i < numAtoms; i++) {

platforms/opencl/src/OpenCLNonbondedUtilities.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) 2009-2020 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2022 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -89,8 +89,8 @@ OpenCLNonbondedUtilities::OpenCLNonbondedUtilities(OpenCLContext& context) : con
             numForceBuffers = numForceThreadBlocks*forceThreadBlockSize/OpenCLContext::TileSize;
         }
     }
-    pinnedCountBuffer = new cl::Buffer(context.getContext(), CL_MEM_ALLOC_HOST_PTR, sizeof(int));
-    pinnedCountMemory = (int*) context.getQueue().enqueueMapBuffer(*pinnedCountBuffer, CL_TRUE, CL_MAP_READ, 0, sizeof(int));
+    pinnedCountBuffer = new cl::Buffer(context.getContext(), CL_MEM_ALLOC_HOST_PTR, sizeof(unsigned int));
+    pinnedCountMemory = (unsigned int*) context.getQueue().enqueueMapBuffer(*pinnedCountBuffer, CL_TRUE, CL_MAP_READ, 0, sizeof(int));
     setKernelSource(deviceIsCpu ? OpenCLKernelSources::nonbonded_cpu : OpenCLKernelSources::nonbonded);
 }
 
@@ -395,18 +395,19 @@ void OpenCLNonbondedUtilities::computeInteractions(int forceGroups, bool include
 bool OpenCLNonbondedUtilities::updateNeighborListSize() {
     if (!useCutoff)
         return false;
-    if (pinnedCountMemory[0] <= (unsigned int) interactingTiles.getSize())
+    if (pinnedCountMemory[0] <= interactingTiles.getSize())
         return false;
 
     // The most recent timestep had too many interactions to fit in the arrays.  Make the arrays bigger to prevent
     // this from happening in the future.
 
-    int maxTiles = (int) (1.2*pinnedCountMemory[0]);
-    int totalTiles = context.getNumAtomBlocks()*(context.getNumAtomBlocks()+1)/2;
+    unsigned int maxTiles = (unsigned int) (1.2*pinnedCountMemory[0]);
+    unsigned int numBlocks = context.getNumAtomBlocks();
+    int totalTiles = numBlocks*(numBlocks+1)/2;
     if (maxTiles > totalTiles)
         maxTiles = totalTiles;
     interactingTiles.resize(maxTiles);
-    interactingAtoms.resize(OpenCLContext::TileSize*maxTiles);
+    interactingAtoms.resize(OpenCLContext::TileSize*(size_t) maxTiles);
     for (map<int, KernelSet>::iterator iter = groupKernels.begin(); iter != groupKernels.end(); ++iter) {
         KernelSet& kernels = iter->second;
         if (*reinterpret_cast<cl_kernel*>(&kernels.forceKernel) != NULL) {

platforms/opencl/src/kernels/findInteractingBlocks.cl

@@ -97,12 +97,12 @@ __kernel void findBlocksWithInteractions(real4 periodicBoxSize, real4 invPeriodi
     __local int workgroupBuffer[BUFFER_SIZE*(GROUP_SIZE/32)];
     __local int warpExclusions[MAX_EXCLUSIONS*(GROUP_SIZE/32)];
     __local real3 posBuffer[GROUP_SIZE];
-    __local volatile int workgroupTileIndex[GROUP_SIZE/32];
+    __local volatile unsigned int workgroupTileIndex[GROUP_SIZE/32];
     __local bool includeBlockFlags[GROUP_SIZE];
     __local volatile short2 atomCountBuffer[GROUP_SIZE];
     __local int* buffer = workgroupBuffer+BUFFER_SIZE*(warpStart/32);
     __local int* exclusionsForX = warpExclusions+MAX_EXCLUSIONS*(warpStart/32);
-    __local volatile int* tileStartIndex = workgroupTileIndex+(warpStart/32);
+    __local volatile unsigned int* tileStartIndex = workgroupTileIndex+(warpStart/32);
 
     // Loop over blocks.
 
@@ -233,11 +233,11 @@ __kernel void findBlocksWithInteractions(real4 periodicBoxSize, real4 invPeriodi
                     if (neighborsInBuffer > BUFFER_SIZE-TILE_SIZE) {
                         // Store the new tiles to memory.
 
-                        int tilesToStore = neighborsInBuffer/TILE_SIZE;
+                        unsigned int tilesToStore = neighborsInBuffer/TILE_SIZE;
                         if (indexInWarp == 0)
                             *tileStartIndex = atom_add(interactionCount, tilesToStore);
                         SYNC_WARPS;
-                        int newTileStartIndex = *tileStartIndex;
+                        unsigned int newTileStartIndex = *tileStartIndex;
                         if (newTileStartIndex+tilesToStore <= maxTiles) {
                             if (indexInWarp < tilesToStore)
                                 interactingTiles[newTileStartIndex+indexInWarp] = x;
@@ -255,11 +255,11 @@ __kernel void findBlocksWithInteractions(real4 periodicBoxSize, real4 invPeriodi
         // If we have a partially filled buffer,  store it to memory.
         
         if (neighborsInBuffer > 0) {
-            int tilesToStore = (neighborsInBuffer+TILE_SIZE-1)/TILE_SIZE;
+            unsigned int tilesToStore = (neighborsInBuffer+TILE_SIZE-1)/TILE_SIZE;
             if (indexInWarp == 0)
                 *tileStartIndex = atom_add(interactionCount, tilesToStore);
             SYNC_WARPS;
-            int newTileStartIndex = *tileStartIndex;
+            unsigned int newTileStartIndex = *tileStartIndex;
             if (newTileStartIndex+tilesToStore <= maxTiles) {
                 if (indexInWarp < tilesToStore)
                     interactingTiles[newTileStartIndex+indexInWarp] = x;

plugins/amoeba/platforms/common/src/AmoebaCommonKernels.cpp

@@ -1255,7 +1255,7 @@ void CommonCalcAmoebaMultipoleForceKernel::computeInducedField() {
     computeInducedFieldKernel->setArg(7, numTileIndices);
     if (usePME) {
         setPeriodicBoxArgs(cc, computeInducedFieldKernel, 10);
-        computeInducedFieldKernel->setArg(15, nb.getInteractingTiles().getSize());
+        computeInducedFieldKernel->setArg(15, (int) nb.getInteractingTiles().getSize());
     }
     cc.clearBuffer(inducedField);
     cc.clearBuffer(inducedFieldPolar);