#include "openmm/internal/windowsExport.h"
#include "CudaPlatform.h"
namespace OpenMM {
class CudaArray;
class CudaForceInfo;
class CudaExpressionUtilities;
class CudaIntegrationUtilities;
class CudaBondedUtilities;
class CudaNonbondedUtilities;
class System;
/**
* This class contains the information associated with a Context by the CUDA Platform. Each CudaContext is
* specific to a particular device, and manages data structures and kernels for that device. When running a simulation
* in parallel on multiple devices, there is a separate CudaContext for each one. The list of all contexts is
* stored in the CudaPlatform::PlatformData.
*
* In addition, a worker thread is created for each CudaContext. This is used for parallel computations, so that
* blocking calls to one device will not block other devices. When only a single device is being used, the worker
* thread is not used and calculations are performed on the main application thread.
*/
class OPENMM_EXPORT CudaContext {
public:
class WorkTask;
class WorkThread;
class ReorderListener;
static const int ThreadBlockSize;
static const int TileSize;
CudaContext(const System& system, int deviceIndex, bool useBlockingSync, const std::string& precision,
const std::string& compiler, const std::string& tempDir, CudaPlatform::PlatformData& platformData);
~CudaContext();
/**
* This is called to initialize internal data structures after all Forces in the system
* have been initialized.
*/
void initialize();
/**
* Add a CudaForce to this context.
*/
void addForce(CudaForceInfo* force);
/**
* Get the CUcontext associated with this object.
*/
CUcontext getContext() {
return context;
}
/**
* Get whether the CUcontext associated with this object is currently a valid contex.
*/
bool getContextIsValid() const {
return contextIsValid;
}
/**
* Set the CUcontext associated with this object to be the current context. If the context is not
* valid, this returns without doing anything.
*/
void setAsCurrent();
/**
* Get the CUdevice associated with this object.
*/
CUdevice getDevice() {
return device;
}
/**
* Get the compute capability of the device associated with this object.
*/
double getComputeCapability() const {
return computeCapability;
}
/**
* Get the index of the CUdevice associated with this object.
*/
int getDeviceIndex() const {
return deviceIndex;
}
/**
* Get the PlatformData object this context is part of.
*/
CudaPlatform::PlatformData& getPlatformData() {
return platformData;
}
/**
* Get the index of this context in the list stored in the PlatformData.
*/
int getContextIndex() const {
return contextIndex;
}
/**
* Get the array which contains the position (the xyz components) and charge (the w component) of each atom.
*/
CudaArray& getPosq() {
return *posq;
}
/**
* Get the array which contains a correction to the position of each atom. This only exists if getUseMixedPrecision() returns true.
*/
CudaArray& getPosqCorrection() {
return *posqCorrection;
}
/**
* Get the array which contains the velocity (the xyz components) and inverse mass (the w component) of each atom.
*/
CudaArray& getVelm() {
return *velm;
}
/**
* Get the array which contains the force on each atom (represented as three long longs in 64 bit fixed point).
*/
CudaArray& getForce() {
return *force;
}
/**
* Get the array which contains the buffer in which energy is computed.
*/
CudaArray& getEnergyBuffer() {
return *energyBuffer;
}
/**
* Get a pointer to a block of pinned memory that can be used for efficient transfers between host and device.
* This is guaranteed to be at least as large as any of the arrays returned by methods of this class.
*/
void* getPinnedBuffer() {
return pinnedBuffer;
}
/**
* Get the host-side vector which contains the index of each atom.
*/
const std::vector& getAtomIndex() const {
return atomIndex;
}
/**
* Get the array which contains the index of each atom.
*/
CudaArray& getAtomIndexArray() {
return *atomIndexDevice;
}
/**
* Get the number of cells by which the positions are offset.
*/
std::vector& getPosCellOffsets() {
return posCellOffsets;
}
/**
* Replace all occurrences of a list of substrings.
*
* @param input a string to process
* @param replacements a set of strings that should be replaced with new strings wherever they appear in the input string
* @return a new string produced by performing the replacements
*/
std::string replaceStrings(const std::string& input, const std::map& replacements) const;
/**
* Create a CUDA module from source code.
*
* @param source the source code of the module
* @param optimizationFlags the optimization flags to pass to the CUDA compiler. If this is
* omitted, a default set of options will be used
*/
CUmodule createModule(const std::string source, const char* optimizationFlags = NULL);
/**
* Create a CUDA module from source code.
*
* @param source the source code of the module
* @param defines a set of preprocessor definitions (name, value) to define when compiling the program
* @param optimizationFlags the optimization flags to pass to the CUDA compiler. If this is
* omitted, a default set of options will be used
*/
CUmodule createModule(const std::string source, const std::map& defines, const char* optimizationFlags = NULL);
/**
* Get a kernel from a CUDA module.
*
* @param module the module to get the kernel from
* @param name the name of the kernel to get
*/
CUfunction getKernel(CUmodule& module, const std::string& name);
/**
* Execute a kernel.
*
* @param kernel the kernel to execute
* @param arguments an array of pointers to the kernel arguments
* @param threads the maximum number of threads that should be used
* @param blockSize the size of each thread block to use
* @param sharedSize the amount of dynamic shared memory to allocated for the kernel, in bytes
*/
void executeKernel(CUfunction kernel, void** arguments, int workUnits, int blockSize = -1, unsigned int sharedSize = 0);
/**
* Set all elements of an array to 0.
*/
void clearBuffer(CudaArray& array);
/**
* Set all elements of an array to 0.
*
* @param memory the memory to clear
* @param size the size of the buffer in bytes
*/
void clearBuffer(CUdeviceptr memory, int size);
/**
* Register a buffer that should be automatically cleared (all elements set to 0) at the start of each force or energy computation.
*/
void addAutoclearBuffer(CudaArray& array);
/**
* Register a buffer that should be automatically cleared (all elements set to 0) at the start of each force or energy computation.
*
* @param memory the memory to clear
* @param size the size of the buffer in bytes
*/
void addAutoclearBuffer(CUdeviceptr memory, int size);
/**
* Clear all buffers that have been registered with addAutoclearBuffer().
*/
void clearAutoclearBuffers();
/**
* Get the current simulation time.
*/
double getTime() {
return time;
}
/**
* Set the current simulation time.
*/
void setTime(double t) {
time = t;
}
/**
* Get the number of integration steps that have been taken.
*/
int getStepCount() {
return stepCount;
}
/**
* Set the number of integration steps that have been taken.
*/
void setStepCount(int steps) {
stepCount = steps;
}
/**
* Get the number of times forces or energy has been computed.
*/
int getComputeForceCount() {
return computeForceCount;
}
/**
* Set the number of times forces or energy has been computed.
*/
void setComputeForceCount(int count) {
computeForceCount = count;
}
/**
* Get the number of atoms.
*/
int getNumAtoms() const {
return numAtoms;
}
/**
* Get the number of atoms, rounded up to a multiple of TileSize. This is the actual size of
* most arrays with one element per atom.
*/
int getPaddedNumAtoms() const {
return paddedNumAtoms;
}
/**
* Get the number of blocks of TileSize atoms.
*/
int getNumAtomBlocks() const {
return numAtomBlocks;
}
/**
* Get the standard number of thread blocks to use when executing kernels.
*/
int getNumThreadBlocks() const {
return numThreadBlocks;
}
/**
* Get whether double precision is being used.
*/
bool getUseDoublePrecision() {
return useDoublePrecision;
}
/**
* Get whether mixed precision is being used.
*/
bool getUseMixedPrecision() {
return useMixedPrecision;
}
/**
* Convert a number to a string in a format suitable for including in a kernel.
* This takes into account whether the context uses single or double precision.
*/
std::string doubleToString(double value);
/**
* Convert a number to a string in a format suitable for including in a kernel.
*/
std::string intToString(int value);
/**
* Convert a CUDA result code to the corresponding string description.
*/
static std::string getErrorString(CUresult result);
/**
* Get the size of the periodic box.
*/
double4 getPeriodicBoxSize() const {
return periodicBoxSize;
}
/**
* Set the size of the periodic box.
*/
void setPeriodicBoxSize(double xsize, double ysize, double zsize) {
periodicBoxSize = make_double4(xsize, ysize, zsize, 0.0);
invPeriodicBoxSize = make_double4(1.0/xsize, 1.0/ysize, 1.0/zsize, 0.0);
periodicBoxSizeFloat = make_float4((float) xsize, (float) ysize, (float) zsize, 0.0f);
invPeriodicBoxSizeFloat = make_float4(1.0f/(float) xsize, 1.0f/(float) ysize, 1.0f/(float) zsize, 0.0f);
}
/**
* Get the inverse of the size of the periodic box.
*/
double4 getInvPeriodicBoxSize() const {
return invPeriodicBoxSize;
}
/**
* Get a pointer to the size of the periodic box, represented as either a float4 or double4 depending on
* this context's precision. This value is suitable for passing to kernels as an argument.
*/
void* getPeriodicBoxSizePointer() {
return (useDoublePrecision ? reinterpret_cast(&periodicBoxSize) : reinterpret_cast(&periodicBoxSizeFloat));
}
/**
* Get a pointer to the inverse of the size of the periodic box, represented as either a float4 or double4 depending on
* this context's precision. This value is suitable for passing to kernels as an argument.
*/
void* getInvPeriodicBoxSizePointer() {
return (useDoublePrecision ? reinterpret_cast(&invPeriodicBoxSize) : reinterpret_cast(&invPeriodicBoxSizeFloat));
}
/**
* Get the CudaIntegrationUtilities for this context.
*/
CudaIntegrationUtilities& getIntegrationUtilities() {
return *integration;
}
/**
* Get the CudaExpressionUtilities for this context.
*/
CudaExpressionUtilities& getExpressionUtilities() {
return *expression;
}
/**
* Get the CudaBondedUtilities for this context.
*/
CudaBondedUtilities& getBondedUtilities() {
return *bonded;
}
/**
* Get the CudaNonbondedUtilities for this context.
*/
CudaNonbondedUtilities& getNonbondedUtilities() {
return *nonbonded;
}
/**
* Get the thread used by this context for executing parallel computations.
*/
WorkThread& getWorkThread() {
return *thread;
}
/**
* Get whether atoms were reordered during the most recent force/energy computation.
*/
bool getAtomsWereReordered() const {
return atomsWereReordered;
}
/**
* Set whether atoms were reordered during the most recent force/energy computation.
*/
void setAtomsWereReordered(bool wereReordered) {
atomsWereReordered = wereReordered;
}
/**
* Reorder the internal arrays of atoms to try to keep spatially contiguous atoms close
* together in the arrays.
*
* @param enforcePeriodic if true, the atom positions may be altered to enforce periodic boundary conditions
*/
void reorderAtoms(bool enforcePeriodic);
/**
* Add a listener that should be called whenever atoms get reordered. The CudaContext
* assumes ownership of the object, and deletes it when the context itself is deleted.
*/
void addReorderListener(ReorderListener* listener);
/**
* Get the list of ReorderListeners.
*/
std::vector& getReorderListeners() {
return reorderListeners;
}
/**
* Mark that the current molecule definitions (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 the next to reorderAtoms() is called.
*/
void invalidateMolecules();
/**
* Get whether the current molecule definitions are valid.
*/
bool getMoleculesAreInvalid() {
return moleculesInvalid;
}
private:
struct Molecule;
struct MoleculeGroup;
class VirtualSiteInfo;
void findMoleculeGroups();
static void tagAtomsInMolecule(int atom, int molecule, std::vector& atomMolecule, std::vector >& atomBonds);
/**
* Ensure that all molecules marked as "identical" really are identical. This should be
* called whenever force field parameters change. If necessary, it will rebuild the list
* of molecules and resort the atoms.
*/
void validateMolecules();
/**
* This is the internal implementation of reorderAtoms(), templatized by the numerical precision in use.
*/
template
void reorderAtomsImpl(bool enforcePeriodic);
static bool hasInitializedCuda;
const System& system;
double time, computeCapability;
CudaPlatform::PlatformData& platformData;
int deviceIndex;
int contextIndex;
int stepCount;
int computeForceCount;
int numAtoms;
int paddedNumAtoms;
int numAtomBlocks;
int numThreadBlocks;
bool useBlockingSync, useDoublePrecision, useMixedPrecision, contextIsValid, atomsWereReordered, moleculesInvalid;
std::string compiler, tempDir, gpuArchitecture;
float4 periodicBoxSizeFloat, invPeriodicBoxSizeFloat;
double4 periodicBoxSize, invPeriodicBoxSize;
std::string defaultOptimizationOptions;
std::map compilationDefines;
CUcontext context;
CUdevice device;
CUfunction clearBufferKernel;
CUfunction clearTwoBuffersKernel;
CUfunction clearThreeBuffersKernel;
CUfunction clearFourBuffersKernel;
CUfunction clearFiveBuffersKernel;
CUfunction clearSixBuffersKernel;
std::vector forces;
std::vector molecules;
std::vector moleculeGroups;
std::vector posCellOffsets;
void* pinnedBuffer;
CudaArray* posq;
CudaArray* posqCorrection;
CudaArray* velm;
CudaArray* force;
CudaArray* energyBuffer;
CudaArray* atomIndexDevice;
std::vector atomIndex;
std::vector autoclearBuffers;
std::vector autoclearBufferSizes;
std::vector reorderListeners;
CudaIntegrationUtilities* integration;
CudaExpressionUtilities* expression;
CudaBondedUtilities* bonded;
CudaNonbondedUtilities* nonbonded;
WorkThread* thread;
};
struct CudaContext::Molecule {
std::vector atoms;
std::vector constraints;
std::vector > groups;
};
struct CudaContext::MoleculeGroup {
std::vector atoms;
std::vector instances;
std::vector offsets;
};
/**
* This abstract class defines a task to be executed on the worker thread.
*/
class CudaContext::WorkTask {
public:
virtual void execute() = 0;
virtual ~WorkTask() {
}
};
class CudaContext::WorkThread {
public:
struct ThreadData;
WorkThread();
~WorkThread();
/**
* Request that a task be executed on the worker thread. The argument should have been allocated on the
* heap with the "new" operator. After its execute() method finishes, the object will be deleted automatically.
*/
void addTask(CudaContext::WorkTask* task);
/**
* Get whether the worker thread is idle, waiting for a task to be added.
*/
bool isWaiting();
/**
* Get whether the worker thread has exited.
*/
bool isFinished();
/**
* Block until all tasks have finished executing and the worker thread is idle.
*/
void flush();
private:
std::queue tasks;
bool waiting, finished;
pthread_mutex_t queueLock;
pthread_cond_t waitForTaskCondition, queueEmptyCondition;
pthread_t thread;
};
/**
* This abstract class defines a function to be executed whenever atoms get reordered.
* Objects that need to know when reordering happens should create a reorderListener
* and register it by calling addReorderListener().
*/
class CudaContext::ReorderListener {
public:
virtual void execute() = 0;
virtual ~ReorderListener() {
}
};
} // namespace OpenMM
#endif /*OPENMM_CUDACONTEXT_H_*/