--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS 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 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS 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 GROMACS; if not, see
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+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
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+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Defines gmx::AnalysisDataFrameLocalData and supporting types.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_analysisdata
+ */
+#ifndef GMX_ANALYSISDATA_FRAMELOCALDATA_H
+#define GMX_ANALYSISDATA_FRAMELOCALDATA_H
+
+#include <algorithm>
+#include <numeric>
+#include <vector>
+
+#include "gromacs/analysisdata/paralleloptions.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/gmxassert.h"
+
+namespace gmx
+{
+
+//! \addtogroup module_analysisdata
+//! \{
+
+/*! \internal
+ * \brief
+ * Handle to a single data set within frame-local data array.
+ *
+ * Methods in this class do not throw.
+ *
+ * \see AnalysisDataFrameLocalData
+ */
+template<typename ValueType>
+class AnalysisDataFrameLocalDataSetHandle
+{
+ public:
+ //! Constructs a handle from an array of values.
+ explicit AnalysisDataFrameLocalDataSetHandle(ArrayRef<ValueType> values)
+ : values_(values)
+ {
+ }
+
+ //! Clears all values in the data set.
+ void clear()
+ {
+ std::fill(values_.begin(), values_.end(), ValueType());
+ }
+
+ //! Accesses a single value in the data set.
+ ValueType &value(int column)
+ {
+ GMX_ASSERT(column >= 0 && column < static_cast<int>(values_.size()),
+ "Invalid column index");
+ return values_[column];
+ }
+
+ private:
+ ArrayRef<ValueType> values_;
+};
+
+/*! \internal
+ * \brief
+ * Handle to a single frame data within frame-local data array.
+ *
+ * Methods in this class do not throw.
+ *
+ * \see AnalysisDataFrameLocalData
+ */
+template<typename ValueType>
+class AnalysisDataFrameLocalDataHandle
+{
+ public:
+ //! Shorthand for the internal array of values.
+ typedef std::vector<ValueType> ValueArray;
+ //! Shorthand for a handle to a single data set.
+ typedef AnalysisDataFrameLocalDataSetHandle<ValueType> DataSetHandle;
+
+ //! Constructs a handle from specified frame data.
+ AnalysisDataFrameLocalDataHandle(const std::vector<int> *dataSetIndices,
+ ValueArray *values)
+ : dataSetIndices_(dataSetIndices), values_(values)
+ {
+ }
+
+ //! Returns the number of data sets in the array.
+ int dataSetCount() const
+ {
+ return dataSetIndices_->size() - 1;
+ }
+ //! Clears all values in the frame.
+ void clear()
+ {
+ std::fill(values_->begin(), values_->end(), ValueType());
+ }
+
+ //! Returns a handle for a single data set.
+ DataSetHandle dataSet(int dataSet)
+ {
+ GMX_ASSERT(dataSet >= 0 && dataSet < dataSetCount(),
+ "Invalid data set index");
+ const int firstIndex = (*dataSetIndices_)[dataSet];
+ const int lastIndex = (*dataSetIndices_)[dataSet + 1];
+ typename ValueArray::iterator begin = values_->begin() + firstIndex;
+ typename ValueArray::iterator end = values_->begin() + lastIndex;
+ return DataSetHandle(arrayRefFromVector<ValueType>(begin, end));
+ }
+ //! Accesses a single value in the frame.
+ ValueType &value(int dataSet, int column)
+ {
+ GMX_ASSERT(dataSet >= 0 && dataSet < dataSetCount(),
+ "Invalid data set index");
+ const int firstIndex = (*dataSetIndices_)[dataSet];
+ GMX_ASSERT(column >= 0
+ && column < (*dataSetIndices_)[dataSet+1] - firstIndex,
+ "Invalid column index");
+ return (*values_)[firstIndex + column];
+ }
+
+ private:
+ const std::vector<int> *dataSetIndices_;
+ ValueArray *values_;
+};
+
+/*! \internal \brief
+ * Container for an array of frame-local values that supports parallel data
+ * processing.
+ *
+ * \tparam ValueType Type of values to store.
+ *
+ * This class provides a convenient interface to create an array of frame-local
+ * data for use in analysis data modules that support parallel processing.
+ * The object is initialized by setting the desired dimensionality with
+ * setDataSetCount() and setColumnCount(), followed by a call to init(),
+ * typically in AnalysisDataModuleInterface::parallelDataStarted(),
+ *
+ * After initialization, frameData() can be used to access the data for a given
+ * frame, independently from other frames. This works if the assumptions about
+ * parallelism hold: if `N` is the parallelization factor given for init() with
+ * AnalysisDataParallelOptions::parallelizationFactor(), then frame `i+N` must
+ * not be accessed before all processing for frame `i` is finished.
+ * Technically, the data for different frames is kept in a ring buffer of size
+ * `N`.
+ *
+ * The data for a frame is not cleared after it is reused for a new frame (but
+ * is initially cleared). This allows using the data for accumulating values
+ * over all frames in a lock-free manner.
+ *
+ * frameDataSet() is provided for convenience when only a single data set
+ * needs to be accessed (typically in AnalysisDataModuleInterface::pointsAdded()).
+ *
+ * Methods in this class do not throw except where indicated.
+ *
+ * \see AnalysisDataFrameLocalData
+ */
+template<typename ValueType>
+class AnalysisDataFrameLocalData
+{
+ public:
+ //! Shorthand for the internal array of values for a frame.
+ typedef std::vector<ValueType> ValueArray;
+ //! Shorthand for a handle to a single frame.
+ typedef AnalysisDataFrameLocalDataHandle<ValueType> FrameHandle;
+ //! Shorthand for a handle to a single data set.
+ typedef AnalysisDataFrameLocalDataSetHandle<ValueType> DataSetHandle;
+
+ //! Constructs an empty container with a single data set.
+ AnalysisDataFrameLocalData()
+ {
+ dataSetColumns_.resize(2);
+ }
+
+ //! Whether init() has been called.
+ bool isInitialized() const { return !values_.empty(); }
+ /*! \brief
+ * Returns number of independent data frames in this object.
+ *
+ * This supports looping over all the frame arrays to, e.g., sum them
+ * up at the end in accumulation scenarios.
+ */
+ int frameCount() const { return values_.size(); }
+
+ /*! \brief
+ * Sets the number of data sets stored for each frame.
+ *
+ * \throws std::bad_alloc if out of memory.
+ *
+ * If not called, there is a single data set in the object.
+ * Cannot be called after init().
+ */
+ void setDataSetCount(int dataSetCount)
+ {
+ GMX_RELEASE_ASSERT(!isInitialized(),
+ "Cannot change value count after init()");
+ GMX_RELEASE_ASSERT(dataSetCount >= 0,
+ "Invalid data set count");
+ dataSetColumns_.resize(dataSetCount + 1);
+ }
+ /*! \brief
+ * Sets the number of columns stored for a data set.
+ *
+ * Must be called for each data set that needs to have values,
+ * otherwise there will be zero columns for that data set.
+ * Cannot be called after init().
+ */
+ void setColumnCount(int dataSet, int columnCount)
+ {
+ GMX_RELEASE_ASSERT(!isInitialized(),
+ "Cannot change value count after init()");
+ GMX_RELEASE_ASSERT(dataSet >= 0 && dataSet < static_cast<int>(dataSetColumns_.size()) - 1,
+ "Invalid data set index");
+ GMX_RELEASE_ASSERT(columnCount >= 0,
+ "Invalid column count");
+ dataSetColumns_[dataSet + 1] = columnCount;
+ }
+
+ /*! \brief
+ * Initializes the storage to support specified parallelism.
+ *
+ * \throws std::bad_alloc if out of memory.
+ */
+ void init(const AnalysisDataParallelOptions &opt)
+ {
+ GMX_RELEASE_ASSERT(!isInitialized(), "init() called multiple times");
+ std::partial_sum(dataSetColumns_.begin(), dataSetColumns_.end(),
+ dataSetColumns_.begin());
+ values_.resize(opt.parallelizationFactor());
+ typename std::vector<ValueArray>::iterator i;
+ for (i = values_.begin(); i != values_.end(); ++i)
+ {
+ i->resize(dataSetColumns_.back());
+ }
+ }
+
+ //! Returns a handle to access data for a frame.
+ FrameHandle frameData(int frameIndex)
+ {
+ GMX_ASSERT(frameIndex >= 0, "Invalid frame index");
+ GMX_ASSERT(isInitialized(), "Cannot access data before init()");
+ return FrameHandle(&dataSetColumns_,
+ &values_[frameIndex % values_.size()]);
+ }
+ //! Returns a handle to access a single data set within a frame.
+ DataSetHandle frameDataSet(int frameIndex, int dataSet)
+ {
+ return frameData(frameIndex).dataSet(dataSet);
+ }
+
+ private:
+ /*! \brief
+ * Index to find data sets within a per-frame array in `values_`.
+ *
+ * The first entry is always zero, followed by one entry for each data
+ * set. Before init(), the data set entries hold the numbers set with
+ * setColumnCount(). After init(), the data set entries hold the
+ * indices of the first column for that data set in the per-frame
+ * arrays in `values_`.
+ */
+ std::vector<int> dataSetColumns_;
+ /*! \brief
+ * Data array for each frame.
+ *
+ * This is a ring buffer whose size is specified by the desired
+ * parallelism level. For each frame, there is a single array of
+ * values, where the individual data sets are indexed with
+ * `dataSetColumns_`.
+ */
+ std::vector<ValueArray> values_;
+};
+
+//! \}
+
+} // namespace gmx
+
+#endif
#include "gromacs/analysisdata/dataframe.h"
#include "gromacs/analysisdata/datastorage.h"
+#include "gromacs/analysisdata/framelocaldata.h"
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
{
for (int c = 0; c < columnCount(); ++c)
{
- real sum = 0;
+ double sum = 0;
for (int i = 0; i < rowCount(); ++i)
{
sum += value(i, c).value();
* BasicHistogramImpl
*/
-/*! \internal \brief
- * Private implementation class for AnalysisDataSimpleHistogramModule and
- * AnalysisDataWeightedHistogramModule.
+/*! \internal
+ * \brief
+ * Base class for private implementation classes for histogram modules.
+ *
+ * Actual implementation classes are derived from this and add an accumulation
+ * data member that is specific to the histogram type in question.
+ * This is done like this to keep implementation details out of the header, and
+ * to not unnecessarily duplicate code.
*
* \ingroup module_analysisdata
*/
BasicHistogramImpl();
//! Creates an histogram impl with defined bin parameters.
explicit BasicHistogramImpl(const AnalysisHistogramSettings &settings);
- ~BasicHistogramImpl();
+ // Virtual only for simplicity.
+ virtual ~BasicHistogramImpl();
/*! \brief
* (Re)initializes the histogram from settings.
*/
void init(const AnalysisHistogramSettings &settings);
- /*! \brief
- * Initializes data storage frame when a new frame starts.
- */
- void initFrame(int dataSetCount, AnalysisDataStorageFrame *frame);
//! Storage implementation object.
AnalysisDataStorage storage_;
averager_->init(settings);
}
-
-void
-BasicHistogramImpl::initFrame(int dataSetCount, AnalysisDataStorageFrame *frame)
-{
- for (int s = 0; s < dataSetCount; ++s)
- {
- frame->selectDataSet(s);
- for (int i = 0; i < frame->columnCount(); ++i)
- {
- frame->setValue(i, 0.0);
- }
- }
- frame->selectDataSet(0);
-}
-
} // namespace internal
* AnalysisDataSimpleHistogramModule
*/
+/*! \internal \brief
+ * Private implementation class for AnalysisDataSimpleHistogramModule.
+ *
+ * \ingroup module_analysisdata
+ */
+class AnalysisDataSimpleHistogramModule::Impl : public internal::BasicHistogramImpl
+{
+ public:
+ //! Shorthand for the per-frame accumulation data structure type.
+ typedef AnalysisDataFrameLocalData<gmx_int64_t> FrameLocalData;
+
+ Impl() {}
+ //! Creates an histogram impl with defined bin parameters.
+ explicit Impl(const AnalysisHistogramSettings &settings)
+ : BasicHistogramImpl(settings)
+ {
+ }
+
+ //! Accumulates the histogram within a frame.
+ FrameLocalData accumulator_;
+};
+
AnalysisDataSimpleHistogramModule::AnalysisDataSimpleHistogramModule()
- : impl_(new internal::BasicHistogramImpl())
+ : impl_(new Impl())
{
}
AnalysisDataSimpleHistogramModule::AnalysisDataSimpleHistogramModule(
const AnalysisHistogramSettings &settings)
- : impl_(new internal::BasicHistogramImpl(settings))
+ : impl_(new Impl(settings))
{
}
const AnalysisDataParallelOptions &options)
{
addModule(impl_->averager_);
- setDataSetCount(data->dataSetCount());
- for (int i = 0; i < data->dataSetCount(); ++i)
+ const int dataSetCount = data->dataSetCount();
+ const int columnCount = settings().binCount();
+ setDataSetCount(dataSetCount);
+ impl_->accumulator_.setDataSetCount(dataSetCount);
+ for (int i = 0; i < dataSetCount; ++i)
{
- setColumnCount(i, settings().binCount());
+ setColumnCount(i, columnCount);
+ impl_->accumulator_.setColumnCount(i, columnCount);
}
+ impl_->accumulator_.init(options);
impl_->storage_.startParallelDataStorage(this, &moduleManager(), options);
return true;
}
void
AnalysisDataSimpleHistogramModule::frameStarted(const AnalysisDataFrameHeader &header)
{
- AnalysisDataStorageFrame &frame = impl_->storage_.startFrame(header);
- impl_->initFrame(dataSetCount(), &frame);
+ impl_->accumulator_.frameData(header.index()).clear();
}
void
AnalysisDataSimpleHistogramModule::pointsAdded(const AnalysisDataPointSetRef &points)
{
- AnalysisDataStorageFrame &frame =
- impl_->storage_.currentFrame(points.frameIndex());
- frame.selectDataSet(points.dataSetIndex());
+ Impl::FrameLocalData::DataSetHandle handle
+ = impl_->accumulator_.frameDataSet(points.frameIndex(), points.dataSetIndex());
for (int i = 0; i < points.columnCount(); ++i)
{
if (points.present(i))
const int bin = settings().findBin(points.y(i));
if (bin != -1)
{
- frame.value(bin) += 1;
+ handle.value(bin) += 1;
}
}
}
void
AnalysisDataSimpleHistogramModule::frameFinished(const AnalysisDataFrameHeader &header)
{
- impl_->storage_.finishFrame(header.index());
+ Impl::FrameLocalData::FrameHandle handle
+ = impl_->accumulator_.frameData(header.index());
+ AnalysisDataStorageFrame &frame = impl_->storage_.startFrame(header);
+ const int columnCount = settings().binCount();
+ for (int s = 0; s < dataSetCount(); ++s)
+ {
+ Impl::FrameLocalData::DataSetHandle dataSet = handle.dataSet(s);
+ frame.selectDataSet(s);
+ for (int i = 0; i < columnCount; ++i)
+ {
+ frame.setValue(i, dataSet.value(i));
+ }
+ }
+ frame.finishFrame();
}
* AnalysisDataWeightedHistogramModule
*/
+/*! \internal \brief
+ * Private implementation class for AnalysisDataWeightedHistogramModule.
+ *
+ * \ingroup module_analysisdata
+ */
+class AnalysisDataWeightedHistogramModule::Impl : public internal::BasicHistogramImpl
+{
+ public:
+ //! Shorthand for the per-frame accumulation data structure type.
+ typedef AnalysisDataFrameLocalData<double> FrameLocalData;
+
+ Impl() {}
+ //! Creates an histogram impl with defined bin parameters.
+ explicit Impl(const AnalysisHistogramSettings &settings)
+ : BasicHistogramImpl(settings)
+ {
+ }
+
+ //! Accumulates the histogram within a frame.
+ FrameLocalData accumulator_;
+};
+
AnalysisDataWeightedHistogramModule::AnalysisDataWeightedHistogramModule()
- : impl_(new internal::BasicHistogramImpl())
+ : impl_(new Impl())
{
}
AnalysisDataWeightedHistogramModule::AnalysisDataWeightedHistogramModule(
const AnalysisHistogramSettings &settings)
- : impl_(new internal::BasicHistogramImpl(settings))
+ : impl_(new Impl(settings))
{
}
const AnalysisDataParallelOptions &options)
{
addModule(impl_->averager_);
- setDataSetCount(data->dataSetCount());
- for (int i = 0; i < data->dataSetCount(); ++i)
+ const int dataSetCount = data->dataSetCount();
+ const int columnCount = settings().binCount();
+ setDataSetCount(dataSetCount);
+ impl_->accumulator_.setDataSetCount(dataSetCount);
+ for (int i = 0; i < dataSetCount; ++i)
{
- setColumnCount(i, settings().binCount());
+ setColumnCount(i, columnCount);
+ impl_->accumulator_.setColumnCount(i, columnCount);
}
+ impl_->accumulator_.init(options);
impl_->storage_.startParallelDataStorage(this, &moduleManager(), options);
return true;
}
void
AnalysisDataWeightedHistogramModule::frameStarted(const AnalysisDataFrameHeader &header)
{
- AnalysisDataStorageFrame &frame = impl_->storage_.startFrame(header);
- impl_->initFrame(dataSetCount(), &frame);
+ impl_->accumulator_.frameData(header.index()).clear();
}
int bin = settings().findBin(points.y(0));
if (bin != -1)
{
- AnalysisDataStorageFrame &frame =
- impl_->storage_.currentFrame(points.frameIndex());
- frame.selectDataSet(points.dataSetIndex());
+ Impl::FrameLocalData::DataSetHandle handle
+ = impl_->accumulator_.frameDataSet(points.frameIndex(), points.dataSetIndex());
for (int i = 1; i < points.columnCount(); ++i)
{
- frame.value(bin) += points.y(i);
+ handle.value(bin) += points.y(i);
}
}
}
void
AnalysisDataWeightedHistogramModule::frameFinished(const AnalysisDataFrameHeader &header)
{
- impl_->storage_.finishFrame(header.index());
+ Impl::FrameLocalData::FrameHandle handle
+ = impl_->accumulator_.frameData(header.index());
+ AnalysisDataStorageFrame &frame = impl_->storage_.startFrame(header);
+ const int columnCount = settings().binCount();
+ for (int s = 0; s < dataSetCount(); ++s)
+ {
+ Impl::FrameLocalData::DataSetHandle dataSet = handle.dataSet(s);
+ frame.selectDataSet(s);
+ for (int i = 0; i < columnCount; ++i)
+ {
+ frame.setValue(i, dataSet.value(i));
+ }
+ }
+ frame.finishFrame();
}
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