src/gromacs/analysisdata/framelocaldata.h

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  35 /*! \internal \file
  36  * \brief
  37  * Defines gmx::AnalysisDataFrameLocalData and supporting types.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_analysisdata
  41  */
  42 #ifndef GMX_ANALYSISDATA_FRAMELOCALDATA_H
  43 #define GMX_ANALYSISDATA_FRAMELOCALDATA_H
  44
  45 #include <algorithm>
  46 #include <numeric>
  47 #include <vector>
  48
  49 #include "gromacs/analysisdata/paralleloptions.h"
  50 #include "gromacs/utility/arrayref.h"
  51 #include "gromacs/utility/gmxassert.h"
  52
  53 namespace gmx
  54 {
  55
  56 //! \addtogroup module_analysisdata
  57 //! \{
  58
  59 /*! \internal
  60  * \brief
  61  * Handle to a single data set within frame-local data array.
  62  *
  63  * Methods in this class do not throw.
  64  *
  65  * \see AnalysisDataFrameLocalData
  66  */
  67 template<typename ValueType>
  68 class AnalysisDataFrameLocalDataSetHandle
  69 {
  70     public:
  71         //! Constructs a handle from an array of values.
  72         explicit AnalysisDataFrameLocalDataSetHandle(ArrayRef<ValueType> values)
  73             : values_(values)
  74         {
  75         }
  76
  77         //! Clears all values in the data set.
  78         void clear()
  79         {
  80             std::fill(values_.begin(), values_.end(), ValueType());
  81         }
  82
  83         //! Accesses a single value in the data set.
  84         ValueType &value(int column)
  85         {
  86             GMX_ASSERT(column >= 0 && column < static_cast<int>(values_.size()),
  87                        "Invalid column index");
  88             return values_[column];
  89         }
  90
  91     private:
  92         ArrayRef<ValueType>  values_;
  93 };
  94
  95 /*! \internal
  96  * \brief
  97  * Handle to a single frame data within frame-local data array.
  98  *
  99  * Methods in this class do not throw.
 100  *
 101  * \see AnalysisDataFrameLocalData
 102  */
 103 template<typename ValueType>
 104 class AnalysisDataFrameLocalDataHandle
 105 {
 106     public:
 107         //! Shorthand for the internal array of values.
 108         typedef std::vector<ValueType> ValueArray;
 109         //! Shorthand for a handle to a single data set.
 110         typedef AnalysisDataFrameLocalDataSetHandle<ValueType> DataSetHandle;
 111
 112         //! Constructs a handle from specified frame data.
 113         AnalysisDataFrameLocalDataHandle(const std::vector<int> *dataSetIndices,
 114                                          ValueArray             *values)
 115             : dataSetIndices_(dataSetIndices), values_(values)
 116         {
 117         }
 118
 119         //! Returns the number of data sets in the array.
 120         int dataSetCount() const
 121         {
 122             return dataSetIndices_->size() - 1;
 123         }
 124         //! Clears all values in the frame.
 125         void clear()
 126         {
 127             std::fill(values_->begin(), values_->end(), ValueType());
 128         }
 129
 130         //! Returns a handle for a single data set.
 131         DataSetHandle dataSet(int dataSet)
 132         {
 133             GMX_ASSERT(dataSet >= 0 && dataSet < dataSetCount(),
 134                        "Invalid data set index");
 135             const int firstIndex = (*dataSetIndices_)[dataSet];
 136             const int lastIndex  = (*dataSetIndices_)[dataSet + 1];
 137             typename ValueArray::iterator begin = values_->begin() + firstIndex;
 138             typename ValueArray::iterator end   = values_->begin() + lastIndex;
 139             return DataSetHandle(arrayRefFromVector<ValueType>(begin, end));
 140         }
 141         //! Accesses a single value in the frame.
 142         ValueType &value(int dataSet, int column)
 143         {
 144             GMX_ASSERT(dataSet >= 0 && dataSet < dataSetCount(),
 145                        "Invalid data set index");
 146             const int firstIndex = (*dataSetIndices_)[dataSet];
 147             GMX_ASSERT(column >= 0
 148                        && column < (*dataSetIndices_)[dataSet+1] - firstIndex,
 149                        "Invalid column index");
 150             return (*values_)[firstIndex + column];
 151         }
 152
 153     private:
 154         const std::vector<int> *dataSetIndices_;
 155         ValueArray             *values_;
 156 };
 157
 158 /*! \internal \brief
 159  * Container for an array of frame-local values that supports parallel data
 160  * processing.
 161  *
 162  * \tparam ValueType Type of values to store.
 163  *
 164  * This class provides a convenient interface to create an array of frame-local
 165  * data for use in analysis data modules that support parallel processing.
 166  * The object is initialized by setting the desired dimensionality with
 167  * setDataSetCount() and setColumnCount(), followed by a call to init(),
 168  * typically in IAnalysisDataModule::parallelDataStarted(),
 169  *
 170  * After initialization, frameData() can be used to access the data for a given
 171  * frame, independently from other frames.  This works if the assumptions about
 172  * parallelism hold: if `N` is the parallelization factor given for init() with
 173  * AnalysisDataParallelOptions::parallelizationFactor(), then frame `i+N` must
 174  * not be accessed before all processing for frame `i` is finished.
 175  * Technically, the data for different frames is kept in a ring buffer of size
 176  * `N`.
 177  *
 178  * The data for a frame is not cleared after it is reused for a new frame (but
 179  * is initially cleared).  This allows using the data for accumulating values
 180  * over all frames in a lock-free manner.
 181  *
 182  * frameDataSet() is provided for convenience when only a single data set
 183  * needs to be accessed (typically in IAnalysisDataModule::pointsAdded()).
 184  *
 185  * Methods in this class do not throw except where indicated.
 186  *
 187  * \see AnalysisDataFrameLocalData
 188  */
 189 template<typename ValueType>
 190 class AnalysisDataFrameLocalData
 191 {
 192     public:
 193         //! Shorthand for the internal array of values for a frame.
 194         typedef std::vector<ValueType> ValueArray;
 195         //! Shorthand for a handle to a single frame.
 196         typedef AnalysisDataFrameLocalDataHandle<ValueType> FrameHandle;
 197         //! Shorthand for a handle to a single data set.
 198         typedef AnalysisDataFrameLocalDataSetHandle<ValueType> DataSetHandle;
 199
 200         //! Constructs an empty container with a single data set.
 201         AnalysisDataFrameLocalData()
 202         {
 203             dataSetColumns_.resize(2);
 204         }
 205
 206         //! Whether init() has been called.
 207         bool isInitialized() const { return !values_.empty(); }
 208         /*! \brief
 209          * Returns number of independent data frames in this object.
 210          *
 211          * This supports looping over all the frame arrays to, e.g., sum them
 212          * up at the end in accumulation scenarios.
 213          */
 214         int frameCount() const { return values_.size(); }
 215
 216         /*! \brief
 217          * Sets the number of data sets stored for each frame.
 218          *
 219          * \throws std::bad_alloc if out of memory.
 220          *
 221          * If not called, there is a single data set in the object.
 222          * Cannot be called after init().
 223          */
 224         void setDataSetCount(int dataSetCount)
 225         {
 226             GMX_RELEASE_ASSERT(!isInitialized(),
 227                                "Cannot change value count after init()");
 228             GMX_RELEASE_ASSERT(dataSetCount >= 0,
 229                                "Invalid data set count");
 230             dataSetColumns_.resize(dataSetCount + 1);
 231         }
 232         /*! \brief
 233          * Sets the number of columns stored for a data set.
 234          *
 235          * Must be called for each data set that needs to have values,
 236          * otherwise there will be zero columns for that data set.
 237          * Cannot be called after init().
 238          */
 239         void setColumnCount(int dataSet, int columnCount)
 240         {
 241             GMX_RELEASE_ASSERT(!isInitialized(),
 242                                "Cannot change value count after init()");
 243             GMX_RELEASE_ASSERT(dataSet >= 0 && dataSet < static_cast<int>(dataSetColumns_.size()) - 1,
 244                                "Invalid data set index");
 245             GMX_RELEASE_ASSERT(columnCount >= 0,
 246                                "Invalid column count");
 247             dataSetColumns_[dataSet + 1] = columnCount;
 248         }
 249
 250         /*! \brief
 251          * Initializes the storage to support specified parallelism.
 252          *
 253          * \throws std::bad_alloc if out of memory.
 254          */
 255         void init(const AnalysisDataParallelOptions &opt)
 256         {
 257             GMX_RELEASE_ASSERT(!isInitialized(), "init() called multiple times");
 258             std::partial_sum(dataSetColumns_.begin(), dataSetColumns_.end(),
 259                              dataSetColumns_.begin());
 260             values_.resize(opt.parallelizationFactor());
 261             typename std::vector<ValueArray>::iterator i;
 262             for (i = values_.begin(); i != values_.end(); ++i)
 263             {
 264                 i->resize(dataSetColumns_.back());
 265             }
 266         }
 267
 268         //! Returns a handle to access data for a frame.
 269         FrameHandle frameData(int frameIndex)
 270         {
 271             GMX_ASSERT(frameIndex >= 0, "Invalid frame index");
 272             GMX_ASSERT(isInitialized(), "Cannot access data before init()");
 273             return FrameHandle(&dataSetColumns_,
 274                                &values_[frameIndex % values_.size()]);
 275         }
 276         //! Returns a handle to access a single data set within a frame.
 277         DataSetHandle frameDataSet(int frameIndex, int dataSet)
 278         {
 279             return frameData(frameIndex).dataSet(dataSet);
 280         }
 281
 282     private:
 283         /*! \brief
 284          * Index to find data sets within a per-frame array in `values_`.
 285          *
 286          * The first entry is always zero, followed by one entry for each data
 287          * set.  Before init(), the data set entries hold the numbers set with
 288          * setColumnCount().  After init(), the data set entries hold the
 289          * indices of the first column for that data set in the per-frame
 290          * arrays in `values_`.
 291          */
 292         std::vector<int>         dataSetColumns_;
 293         /*! \brief
 294          * Data array for each frame.
 295          *
 296          * This is a ring buffer whose size is specified by the desired
 297          * parallelism level.  For each frame, there is a single array of
 298          * values, where the individual data sets are indexed with
 299          * `dataSetColumns_`.
 300          */
 301         std::vector<ValueArray>  values_;
 302 };
 303
 304 //! \}
 305
 306 } // namespace gmx
 307
 308 #endif