#ifndef __OPENMM_OPENCLSORT_H__ #define __OPENMM_OPENCLSORT_H__ /* -------------------------------------------------------------------------- * * OpenMM * * -------------------------------------------------------------------------- * * This is part of the OpenMM molecular simulation toolkit originating from * * Simbios, the NIH National Center for Physics-Based Simulation of * * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * * Portions copyright (c) 2010-2018 Stanford University and the Authors. * * Authors: Peter Eastman * * Contributors: * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU Lesser General Public License as published * * by the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU Lesser General Public License for more details. * * * * You should have received a copy of the GNU Lesser General Public License * * along with this program. If not, see . * * -------------------------------------------------------------------------- */ #include "OpenCLArray.h" #include "OpenCLContext.h" #include "windowsExportOpenCL.h" namespace OpenMM { /** * This class sorts arrays of values. It supports any type of values, not just scalars, * so long as an appropriate sorting key can be defined by which to sort them. * * The sorting behavior is specified by a "trait" class that defines the type of data to * sort and the key for sorting it. Here is an example of a trait class for * sorting floats: * * class FloatTrait : public OpenCLSort::SortTrait { * int getDataSize() const {return 4;} * int getKeySize() const {return 4;} * const char* getDataType() const {return "float";} * const char* getKeyType() const {return "float";} * const char* getMinKey() const {return "-MAXFLOAT";} * const char* getMaxKey() const {return "MAXFLOAT";} * const char* getMaxValue() const {return "MAXFLOAT";} * const char* getSortKey() const {return "value";} * }; * * The algorithm used is a bucket sort, followed by a bitonic sort within each bucket * (in local memory when possible, in global memory otherwise). This is similar to * the algorithm described in * * Shifu Chen, Jing Qin, Yongming Xie, Junping Zhao, and Pheng-Ann Heng. "An Efficient * Sorting Algorithm with CUDA" Journal of the Chinese Institute of Engineers, 32(7), * pp. 915-921 (2009) * * but with many modifications and simplifications. In particular, this algorithm * involves much less communication between host and device, which is critical to get * good performance with the array sizes we typically work with (10,000 to 100,000 * elements). */ class OPENMM_EXPORT_OPENCL OpenCLSort { public: class SortTrait; /** * Create an OpenCLSort object for sorting data of a particular type. * * @param context the context in which to perform calculations * @param trait a SortTrait defining the type of data to sort. It should have been allocated * on the heap with the "new" operator. This object takes over ownership of it, * and deletes it when the OpenCLSort is deleted. * @param length the length of the arrays this object will be used to sort */ OpenCLSort(OpenCLContext& context, SortTrait* trait, unsigned int length); ~OpenCLSort(); /** * Sort an array. */ void sort(OpenCLArray& data); private: OpenCLContext& context; SortTrait* trait; OpenCLArray dataRange; OpenCLArray bucketOfElement; OpenCLArray offsetInBucket; OpenCLArray bucketOffset; OpenCLArray buckets; cl::Kernel shortListKernel, shortList2Kernel, computeRangeKernel, assignElementsKernel, computeBucketPositionsKernel, copyToBucketsKernel, sortBucketsKernel; unsigned int dataLength, rangeKernelSize, positionsKernelSize, sortKernelSize; bool isShortList, useShortList2; }; /** * A subclass of SortTrait defines the type of value to sort, and the key for sorting them. */ class OpenCLSort::SortTrait { public: virtual ~SortTrait() { } /** * Get the size of each data value in bytes. */ virtual int getDataSize() const = 0; /** * Get the size of each key value in bytes. */ virtual int getKeySize() const = 0; /** * Get the data type of the values to sort. */ virtual const char* getDataType() const = 0; /** * Get the data type of the sorting key. */ virtual const char* getKeyType() const = 0; /** * Get the minimum value a key can take. */ virtual const char* getMinKey() const = 0; /** * Get the maximum value a key can take. */ virtual const char* getMaxKey() const = 0; /** * Get a value whose key is guaranteed to equal getMaxKey(). */ virtual const char* getMaxValue() const = 0; /** * Get the CUDA code to select the key from the data value. */ virtual const char* getSortKey() const = 0; }; } // namespace OpenMM #endif // __OPENMM_OPENCLSORT_H__