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*
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*/
/*! \internal \file
* \brief
* Implements classes in datastorage.h and paralleloptions.h.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
+#include "gmxpre.h"
+
#include "datastorage.h"
+#include <algorithm>
+#include <iterator>
#include <limits>
#include <vector>
#include "gromacs/analysisdata/abstractdata.h"
#include "gromacs/analysisdata/dataframe.h"
+#include "gromacs/analysisdata/datamodulemanager.h"
#include "gromacs/analysisdata/paralleloptions.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
/********************************************************************
- * AnalysisDataStorage::Impl
+ * AnalysisDataStorageImpl declaration
*/
+namespace internal
+{
+
+//! Smart pointer type for managing a storage frame builder.
+typedef gmx_unique_ptr<AnalysisDataStorageFrame>::type
+ AnalysisDataFrameBuilderPointer;
+
/*! \internal \brief
* Private implementation class for AnalysisDataStorage.
*
* \ingroup module_analysisdata
*/
-class AnalysisDataStorage::Impl
+class AnalysisDataStorageImpl
{
public:
//! Smart pointer type for managing a stored frame.
- typedef gmx_unique_ptr<AnalysisDataStorageFrame>::type FramePointer;
-
- /*! \brief
- * Stored information about a single stored frame.
- *
- * Methods in this class do not throw.
- */
- struct StoredFrame
- {
- //! Indicates what operations have been performed on a frame.
- enum Status
- {
- eMissing, //!< Frame has not yet been started.
- eStarted, //!< startFrame() has been called.
- eFinished, //!< finishFrame() has been called.
- eNotified //!< Appropriate notifications have been sent.
- };
-
- //! Constructs an object that manages a given frame object.
- explicit StoredFrame(AnalysisDataStorageFrame *frame)
- : frame(frame), status(eMissing)
- {
- }
- //! Whether the frame has been started with startFrame().
- bool isStarted() const { return status >= eStarted; }
- //! Whether the frame has been finished with finishFrame().
- bool isFinished() const { return status >= eFinished; }
- //! Whether all notifications have been sent.
- bool isNotified() const { return status >= eNotified; }
- //! Whether the frame is ready to be available outside the storage.
- bool isAvailable() const { return status >= eFinished; }
-
- /*! \brief
- * Actual frame data.
- *
- * Never NULL.
- */
- FramePointer frame;
- //! In what state the frame currently is.
- Status status;
- };
+ typedef gmx_unique_ptr<AnalysisDataStorageFrameData>::type FramePointer;
//! Shorthand for a list of data frames that are currently stored.
- typedef std::vector<StoredFrame> FrameList;
+ typedef std::vector<FramePointer> FrameList;
+ //! Shorthand for a list of currently unused storage frame builders.
+ typedef std::vector<AnalysisDataFrameBuilderPointer> FrameBuilderList;
- Impl();
+ AnalysisDataStorageImpl();
- //! Returns the number of columns in the attached data.
- int columnCount() const;
//! Returns whether the storage is set to use multipoint data.
bool isMultipoint() const;
/*! \brief
}
//! Returns the index of the oldest frame that may be currently stored.
int firstStoredIndex() const;
+ //! Returns the index of the first frame that is not fully notified.
+ int firstUnnotifiedIndex() const { return firstUnnotifiedIndex_; }
/*! \brief
* Computes index into \a frames_ for accessing frame \p index.
*
*
* \throws std::bad_alloc if out of memory.
*/
- void extendBuffer(AnalysisDataStorage *storage, size_t newSize);
+ void extendBuffer(size_t newSize);
/*! \brief
* Remove oldest frame from the storage to make space for a new one.
*
void rotateBuffer();
/*! \brief
- * Calls notification method in \a data_.
+ * Returns a frame builder object for use with a new frame.
+ *
+ * \throws std::bad_alloc if out of memory.
+ */
+ AnalysisDataFrameBuilderPointer getFrameBuilder();
+
+ /*! \brief
+ * Returns whether notifications should be immediately fired.
+ *
+ * This is used to optimize multipoint handling for non-parallel cases,
+ * where it is not necessary to store even a single frame.
+ *
+ * Does not throw.
+ */
+ bool shouldNotifyImmediately() const
+ {
+ return isMultipoint() && storageLimit_ == 0 && pendingLimit_ == 1;
+ }
+ /*! \brief
+ * Returns whether data needs to be stored at all.
+ *
+ * This is used to optimize multipoint handling for parallel cases
+ * (where shouldNotifyImmediately() returns false),
+ * where it is not necessary to store even a single frame.
*
- * \throws unspecified Any exception thrown by
- * AbstractAnalysisData::notifyPointsAdd().
+ * \todo
+ * This could be extended to non-multipoint data as well.
+ *
+ * Does not throw.
*/
- void notifyPointSet(const AnalysisDataPointSetRef &points);
+ bool needStorage() const
+ {
+ return storageLimit_ > 0 || (pendingLimit_ > 1 && modules_->hasSerialModules());
+ }
/*! \brief
* Calls notification methods for new frames.
*
* Also rotates the \a frames_ buffer as necessary.
*/
void notifyNextFrames(size_t firstLocation);
+ //! Implementation for AnalysisDataStorage::finishFrame().
+ void finishFrame(int index);
- //! Data object to use for notification calls.
- AbstractAnalysisData *data_;
- /*! \brief
- * Whether the storage has been set to allow multipoint.
- *
- * Should be possible to remove once full support for multipoint data
- * has been implemented; isMultipoint() can simply return
- * \c data_->isMultipoint() in that case.
- */
- bool bMultipoint_;
+
+ //! Parent data object to access data dimensionality etc.
+ const AbstractAnalysisData *data_;
+ //! Manager to use for notification calls.
+ AnalysisDataModuleManager *modules_;
/*! \brief
* Number of past frames that need to be stored.
*
*
* Should always be at least one.
*
+ * \todo
+ * Get rid of this alltogether, as it is no longer used much.
+ *
* \see AnalysisDataStorage::startFrame()
*/
int pendingLimit_;
FrameList frames_;
//! Location of oldest frame in \a frames_.
size_t firstFrameLocation_;
+ //! Index of the first frame that is not fully notified.
+ int firstUnnotifiedIndex_;
+ /*! \brief
+ * Currently unused frame builders.
+ *
+ * The builders are cached to avoid repeatedly allocating memory for
+ * them. Typically, there are as many builders as there are concurrent
+ * users of the storage object. Whenever a frame is started, a builder
+ * is pulled from this pool by getFrameBuilder() (a new one is created
+ * if none are available), and assigned for that frame. When that
+ * frame is finished, the builder is returned to this pool.
+ */
+ FrameBuilderList builders_;
/*! \brief
* Index of next frame that will be added to \a frames_.
*
int nextIndex_;
};
-AnalysisDataStorage::Impl::Impl()
- : data_(NULL), bMultipoint_(false),
- storageLimit_(0), pendingLimit_(1), firstFrameLocation_(0), nextIndex_(0)
+/********************************************************************
+ * AnalysisDataStorageFrameImpl declaration
+ */
+
+/*! \internal
+ * \brief
+ * Internal representation for a single stored frame.
+ *
+ * It is implemented such that the frame header is always valid, i.e.,
+ * header().isValid() returns always true.
+ *
+ * Methods in this class do not throw unless otherwise indicated.
+ *
+ * \ingroup module_analysisdata
+ */
+class AnalysisDataStorageFrameData
{
-}
+ public:
+ //! Shorthand for a iterator into storage value containers.
+ typedef std::vector<AnalysisDataValue>::const_iterator ValueIterator;
+
+ //! Indicates what operations have been performed on a frame.
+ enum Status
+ {
+ eMissing, //!< Frame has not yet been started.
+ eStarted, //!< startFrame() has been called.
+ eFinished, //!< finishFrame() has been called.
+ eNotified //!< Appropriate notifications have been sent.
+ };
+ /*! \brief
+ * Create a new storage frame.
+ *
+ * \param storageImpl Storage object this frame belongs to.
+ * \param[in] index Zero-based index for the frame.
+ */
+ AnalysisDataStorageFrameData(AnalysisDataStorageImpl *storageImpl,
+ int index);
+
+ //! Whether the frame has been started with startFrame().
+ bool isStarted() const { return status_ >= eStarted; }
+ //! Whether the frame has been finished with finishFrame().
+ bool isFinished() const { return status_ >= eFinished; }
+ //! Whether all notifications have been sent.
+ bool isNotified() const { return status_ >= eNotified; }
+ //! Whether the frame is ready to be available outside the storage.
+ bool isAvailable() const { return status_ >= eFinished; }
+
+ //! Marks the frame as notified.
+ void markNotified() { status_ = eNotified; }
+
+ //! Returns the storage implementation object.
+ AnalysisDataStorageImpl &storageImpl() const { return storageImpl_; }
+ //! Returns the underlying data object (for data dimensionalities etc.).
+ const AbstractAnalysisData &baseData() const { return *storageImpl().data_; }
+
+ //! Returns header for the frame.
+ const AnalysisDataFrameHeader &header() const { return header_; }
+ //! Returns zero-based index of the frame.
+ int frameIndex() const { return header().index(); }
+ //! Returns the number of point sets for the frame.
+ int pointSetCount() const { return pointSets_.size(); }
+
+ //! Clears the frame for reusing as a new frame.
+ void clearFrame(int newIndex);
+ /*! \brief
+ * Initializes the frame during AnalysisDataStorage::startFrame().
+ *
+ * \param[in] header Header to use for the new frame.
+ * \param[in] builder Builder object to use.
+ */
+ void startFrame(const AnalysisDataFrameHeader &header,
+ AnalysisDataFrameBuilderPointer builder);
+ //! Returns the builder for this frame.
+ AnalysisDataStorageFrame &builder() const
+ {
+ GMX_ASSERT(builder_, "Accessing builder for not-in-progress frame");
+ return *builder_;
+ }
+ /*! \brief
+ * Adds a new point set to this frame.
+ */
+ void addPointSet(int dataSetIndex, int firstColumn,
+ ValueIterator begin, ValueIterator end);
+ /*! \brief
+ * Finalizes the frame during AnalysisDataStorage::finishFrame().
+ *
+ * \returns The builder object used by the frame, for reusing it for
+ * other frames.
+ */
+ AnalysisDataFrameBuilderPointer finishFrame(bool bMultipoint);
-int
-AnalysisDataStorage::Impl::columnCount() const
+ //! Returns frame reference to this frame.
+ AnalysisDataFrameRef frameReference() const
+ {
+ return AnalysisDataFrameRef(header_, values_, pointSets_);
+ }
+ //! Returns point set reference to a given point set.
+ AnalysisDataPointSetRef pointSet(int index) const;
+
+ private:
+ //! Storage object that contains this frame.
+ AnalysisDataStorageImpl &storageImpl_;
+ //! Header for the frame.
+ AnalysisDataFrameHeader header_;
+ //! Values for the frame.
+ std::vector<AnalysisDataValue> values_;
+ //! Information about each point set in the frame.
+ std::vector<AnalysisDataPointSetInfo> pointSets_;
+ /*! \brief
+ * Builder object for the frame.
+ *
+ * Non-NULL when the frame is in progress, i.e., has been started but
+ * not yet finished.
+ */
+ AnalysisDataFrameBuilderPointer builder_;
+ //! In what state the frame currently is.
+ Status status_;
+
+ GMX_DISALLOW_COPY_AND_ASSIGN(AnalysisDataStorageFrameData);
+};
+
+/********************************************************************
+ * AnalysisDataStorageImpl implementation
+ */
+
+AnalysisDataStorageImpl::AnalysisDataStorageImpl()
+ : data_(NULL), modules_(NULL),
+ storageLimit_(0), pendingLimit_(1),
+ firstFrameLocation_(0), firstUnnotifiedIndex_(0), nextIndex_(0)
{
- GMX_ASSERT(data_ != NULL, "columnCount() called too early");
- return data_->columnCount();
}
bool
-AnalysisDataStorage::Impl::isMultipoint() const
+AnalysisDataStorageImpl::isMultipoint() const
{
- return bMultipoint_;
+ GMX_ASSERT(data_ != NULL, "isMultipoint() called too early");
+ return data_->isMultipoint();
}
int
-AnalysisDataStorage::Impl::firstStoredIndex() const
+AnalysisDataStorageImpl::firstStoredIndex() const
{
- return frames_[firstFrameLocation_].frame->frameIndex();
+ return frames_[firstFrameLocation_]->frameIndex();
}
int
-AnalysisDataStorage::Impl::computeStorageLocation(int index) const
+AnalysisDataStorageImpl::computeStorageLocation(int index) const
{
if (index < firstStoredIndex() || index >= nextIndex_)
{
size_t
-AnalysisDataStorage::Impl::endStorageLocation() const
+AnalysisDataStorageImpl::endStorageLocation() const
{
if (storeAll())
{
return frames_.size();
}
- if (frames_[0].frame->frameIndex() == 0 || firstFrameLocation_ == 0)
+ if (frames_[0]->frameIndex() == 0 || firstFrameLocation_ == 0)
{
return frames_.size() - 1;
}
void
-AnalysisDataStorage::Impl::extendBuffer(AnalysisDataStorage *storage,
- size_t newSize)
+AnalysisDataStorageImpl::extendBuffer(size_t newSize)
{
frames_.reserve(newSize);
while (frames_.size() < newSize)
{
- frames_.push_back(StoredFrame(
- new AnalysisDataStorageFrame(storage, columnCount(), nextIndex_)));
+ frames_.push_back(FramePointer(new AnalysisDataStorageFrameData(this, nextIndex_)));
++nextIndex_;
}
// The unused frame should not be included in the count.
void
-AnalysisDataStorage::Impl::rotateBuffer()
+AnalysisDataStorageImpl::rotateBuffer()
{
GMX_ASSERT(!storeAll(),
"No need to rotate internal buffer if everything is stored");
nextFirst = 0;
}
firstFrameLocation_ = nextFirst;
- StoredFrame &prevFrame = frames_[prevFirst];
- prevFrame.status = StoredFrame::eMissing;
- prevFrame.frame->header_ = AnalysisDataFrameHeader(nextIndex_ + 1, 0.0, 0.0);
- prevFrame.frame->clearValues();
+ frames_[prevFirst]->clearFrame(nextIndex_ + 1);
++nextIndex_;
}
-void
-AnalysisDataStorage::Impl::notifyPointSet(const AnalysisDataPointSetRef &points)
+AnalysisDataFrameBuilderPointer
+AnalysisDataStorageImpl::getFrameBuilder()
{
- data_->notifyPointsAdd(points);
+ if (builders_.empty())
+ {
+ return AnalysisDataFrameBuilderPointer(new AnalysisDataStorageFrame(*data_));
+ }
+ AnalysisDataFrameBuilderPointer builder(move(builders_.back()));
+ builders_.pop_back();
+ return move(builder);
}
void
-AnalysisDataStorage::Impl::notifyNextFrames(size_t firstLocation)
+AnalysisDataStorageImpl::notifyNextFrames(size_t firstLocation)
{
- if (firstLocation != firstFrameLocation_)
+ if (frames_[firstLocation]->frameIndex() != firstUnnotifiedIndex_)
{
- // firstLocation can only be zero here if !storeAll() because
- // firstFrameLocation_ is always zero for storeAll()
- int prevIndex =
- (firstLocation == 0 ? frames_.size() - 1 : firstLocation - 1);
- if (!frames_[prevIndex].isNotified())
- {
- return;
- }
+ return;
}
- size_t i = firstLocation;
+ size_t i = firstLocation;
size_t end = endStorageLocation();
while (i != end)
{
- Impl::StoredFrame &storedFrame = frames_[i];
+ AnalysisDataStorageFrameData &storedFrame = *frames_[i];
if (!storedFrame.isFinished())
{
break;
}
- if (storedFrame.status == StoredFrame::eFinished)
+ if (!storedFrame.isNotified())
{
- data_->notifyFrameStart(storedFrame.frame->header());
- data_->notifyPointsAdd(storedFrame.frame->currentPoints());
- data_->notifyFrameFinish(storedFrame.frame->header());
- storedFrame.status = StoredFrame::eNotified;
- if (storedFrame.frame->frameIndex() >= storageLimit_)
+ // Increment before the notifications to make the frame available
+ // in the module callbacks.
+ ++firstUnnotifiedIndex_;
+ modules_->notifyFrameStart(storedFrame.header());
+ for (int j = 0; j < storedFrame.pointSetCount(); ++j)
+ {
+ modules_->notifyPointsAdd(storedFrame.pointSet(j));
+ }
+ modules_->notifyFrameFinish(storedFrame.header());
+ storedFrame.markNotified();
+ if (storedFrame.frameIndex() >= storageLimit_)
{
rotateBuffer();
}
}
+void
+AnalysisDataStorageImpl::finishFrame(int index)
+{
+ const int storageIndex = computeStorageLocation(index);
+ GMX_RELEASE_ASSERT(storageIndex >= 0, "Out of bounds frame index");
+
+ AnalysisDataStorageFrameData &storedFrame = *frames_[storageIndex];
+ GMX_RELEASE_ASSERT(storedFrame.isStarted(),
+ "finishFrame() called for frame before startFrame()");
+ GMX_RELEASE_ASSERT(!storedFrame.isFinished(),
+ "finishFrame() called twice for the same frame");
+ GMX_RELEASE_ASSERT(storedFrame.frameIndex() == index,
+ "Inconsistent internal frame indexing");
+ builders_.push_back(storedFrame.finishFrame(isMultipoint()));
+ modules_->notifyParallelFrameFinish(storedFrame.header());
+ if (shouldNotifyImmediately())
+ {
+ ++firstUnnotifiedIndex_;
+ modules_->notifyFrameFinish(storedFrame.header());
+ if (storedFrame.frameIndex() >= storageLimit_)
+ {
+ rotateBuffer();
+ }
+ }
+ else
+ {
+ notifyNextFrames(storageIndex);
+ }
+}
+
+
/********************************************************************
- * AnalysisDataStorageFrame
+ * AnalysisDataStorageFrame implementation
*/
-AnalysisDataStorageFrame::AnalysisDataStorageFrame(AnalysisDataStorage *storage,
- int columnCount, int index)
- : storage_(*storage), header_(index, 0.0, 0.0), values_(columnCount)
+AnalysisDataStorageFrameData::AnalysisDataStorageFrameData(
+ AnalysisDataStorageImpl *storageImpl,
+ int index)
+ : storageImpl_(*storageImpl), header_(index, 0.0, 0.0), status_(eMissing)
+{
+ GMX_RELEASE_ASSERT(storageImpl->data_ != NULL,
+ "Storage frame constructed before data started");
+ // With non-multipoint data, the point set structure is static,
+ // so initialize it only once here.
+ if (!baseData().isMultipoint())
+ {
+ int offset = 0;
+ for (int i = 0; i < baseData().dataSetCount(); ++i)
+ {
+ int columnCount = baseData().columnCount(i);
+ pointSets_.push_back(
+ AnalysisDataPointSetInfo(offset, columnCount, i, 0));
+ offset += columnCount;
+ }
+ }
+}
+
+
+void
+AnalysisDataStorageFrameData::clearFrame(int newIndex)
{
+ GMX_RELEASE_ASSERT(!builder_, "Should not clear an in-progress frame");
+ status_ = eMissing;
+ header_ = AnalysisDataFrameHeader(newIndex, 0.0, 0.0);
+ values_.clear();
+ if (baseData().isMultipoint())
+ {
+ pointSets_.clear();
+ }
}
-AnalysisDataStorageFrame::~AnalysisDataStorageFrame()
+void
+AnalysisDataStorageFrameData::startFrame(
+ const AnalysisDataFrameHeader &header,
+ AnalysisDataFrameBuilderPointer builder)
{
+ status_ = eStarted;
+ header_ = header;
+ builder_ = move(builder);
+ builder_->data_ = this;
+ builder_->selectDataSet(0);
}
-AnalysisDataPointSetRef
-AnalysisDataStorageFrame::currentPoints() const
+void
+AnalysisDataStorageFrameData::addPointSet(int dataSetIndex, int firstColumn,
+ ValueIterator begin, ValueIterator end)
{
- std::vector<AnalysisDataValue>::const_iterator begin = values_.begin();
- std::vector<AnalysisDataValue>::const_iterator end = values_.end();
- while (begin != end && !begin->isSet())
+ const int valueCount = end - begin;
+ AnalysisDataPointSetInfo pointSetInfo(0, valueCount,
+ dataSetIndex, firstColumn);
+ AnalysisDataPointSetRef pointSet(header(), pointSetInfo,
+ constArrayRefFromVector<AnalysisDataValue>(begin, end));
+ storageImpl().modules_->notifyParallelPointsAdd(pointSet);
+ if (storageImpl().shouldNotifyImmediately())
+ {
+ storageImpl().modules_->notifyPointsAdd(pointSet);
+ }
+ else if (storageImpl().needStorage())
+ {
+ pointSets_.push_back(
+ AnalysisDataPointSetInfo(values_.size(), valueCount,
+ dataSetIndex, firstColumn));
+ std::copy(begin, end, std::back_inserter(values_));
+ }
+}
+
+
+AnalysisDataFrameBuilderPointer
+AnalysisDataStorageFrameData::finishFrame(bool bMultipoint)
+{
+ status_ = eFinished;
+ if (!bMultipoint)
+ {
+ GMX_RELEASE_ASSERT(static_cast<int>(pointSets_.size()) == baseData().dataSetCount(),
+ "Point sets created for non-multipoint data");
+ values_ = builder_->values_;
+ builder_->clearValues();
+ for (int i = 0; i < pointSetCount(); ++i)
+ {
+ storageImpl().modules_->notifyParallelPointsAdd(pointSet(i));
+ }
+ }
+ else
{
- ++begin;
+ GMX_RELEASE_ASSERT(!builder_->bPointSetInProgress_,
+ "Unfinished point set");
}
- while (end != begin && !(end-1)->isSet())
+ AnalysisDataFrameBuilderPointer builder(move(builder_));
+ builder_.reset();
+ return move(builder);
+}
+
+
+AnalysisDataPointSetRef
+AnalysisDataStorageFrameData::pointSet(int index) const
+{
+ GMX_ASSERT(index >= 0 && index < pointSetCount(),
+ "Invalid point set index");
+ return AnalysisDataPointSetRef(
+ header_, pointSets_[index],
+ constArrayRefFromVector<AnalysisDataValue>(values_.begin(), values_.end()));
+}
+
+} // namespace internal
+
+/********************************************************************
+ * AnalysisDataStorageFrame
+ */
+
+AnalysisDataStorageFrame::AnalysisDataStorageFrame(
+ const AbstractAnalysisData &data)
+ : data_(NULL), currentDataSet_(0), currentOffset_(0),
+ columnCount_(data.columnCount(0)), bPointSetInProgress_(false)
+{
+ int totalColumnCount = 0;
+ for (int i = 0; i < data.dataSetCount(); ++i)
{
- --end;
+ totalColumnCount += data.columnCount(i);
}
- int firstColumn = (begin != end) ? begin - values_.begin() : 0;
- return AnalysisDataPointSetRef(header_, firstColumn,
- AnalysisDataValuesRef(begin, end));
+ values_.resize(totalColumnCount);
+}
+
+
+AnalysisDataStorageFrame::~AnalysisDataStorageFrame()
+{
}
void
AnalysisDataStorageFrame::clearValues()
{
- std::vector<AnalysisDataValue>::iterator i;
- for (i = values_.begin(); i != values_.end(); ++i)
+ if (bPointSetInProgress_)
+ {
+ std::vector<AnalysisDataValue>::iterator i;
+ for (i = values_.begin(); i != values_.end(); ++i)
+ {
+ i->clear();
+ }
+ }
+ bPointSetInProgress_ = false;
+}
+
+
+void
+AnalysisDataStorageFrame::selectDataSet(int index)
+{
+ GMX_RELEASE_ASSERT(data_ != NULL, "Invalid frame accessed");
+ const AbstractAnalysisData &baseData = data_->baseData();
+ GMX_RELEASE_ASSERT(index >= 0 && index < baseData.dataSetCount(),
+ "Out of range data set index");
+ GMX_RELEASE_ASSERT(!baseData.isMultipoint() || !bPointSetInProgress_,
+ "Point sets in multipoint data cannot span data sets");
+ currentDataSet_ = index;
+ currentOffset_ = 0;
+ // TODO: Consider precalculating.
+ for (int i = 0; i < index; ++i)
{
- i->clear();
+ currentOffset_ += baseData.columnCount(i);
}
+ columnCount_ = baseData.columnCount(index);
}
void
AnalysisDataStorageFrame::finishPointSet()
{
- storage_.impl_->notifyPointSet(currentPoints());
+ GMX_RELEASE_ASSERT(data_ != NULL, "Invalid frame accessed");
+ GMX_RELEASE_ASSERT(data_->baseData().isMultipoint(),
+ "Should not be called for non-multipoint data");
+ if (bPointSetInProgress_)
+ {
+ std::vector<AnalysisDataValue>::const_iterator begin
+ = values_.begin() + currentOffset_;
+ std::vector<AnalysisDataValue>::const_iterator end
+ = begin + columnCount_;
+ int firstColumn = 0;
+ while (begin != end && !begin->isSet())
+ {
+ ++begin;
+ ++firstColumn;
+ }
+ while (end != begin && !(end-1)->isSet())
+ {
+ --end;
+ }
+ if (begin == end)
+ {
+ firstColumn = 0;
+ }
+ data_->addPointSet(currentDataSet_, firstColumn, begin, end);
+ }
clearValues();
}
+void
+AnalysisDataStorageFrame::finishFrame()
+{
+ GMX_RELEASE_ASSERT(data_ != NULL, "Invalid frame accessed");
+ data_->storageImpl().finishFrame(data_->frameIndex());
+}
+
+
/********************************************************************
* AnalysisDataStorage
*/
}
-void
-AnalysisDataStorage::setMultipoint(bool bMultipoint)
-{
- if (bMultipoint && impl_->storageLimit_ > 0)
- {
- GMX_THROW(APIError("Storage of multipoint data not supported"));
- }
- impl_->bMultipoint_ = bMultipoint;
-}
-
-
-void
-AnalysisDataStorage::setParallelOptions(const AnalysisDataParallelOptions &opt)
+int
+AnalysisDataStorage::frameCount() const
{
- impl_->pendingLimit_ = 2 * opt.parallelizationFactor() - 1;
+ return impl_->firstUnnotifiedIndex();
}
AnalysisDataFrameRef
AnalysisDataStorage::tryGetDataFrame(int index) const
{
- if (impl_->isMultipoint())
- {
- return AnalysisDataFrameRef();
- }
int storageIndex = impl_->computeStorageLocation(index);
if (storageIndex == -1)
{
return AnalysisDataFrameRef();
}
- const Impl::StoredFrame &storedFrame = impl_->frames_[storageIndex];
+ const internal::AnalysisDataStorageFrameData &storedFrame
+ = *impl_->frames_[storageIndex];
if (!storedFrame.isAvailable())
{
return AnalysisDataFrameRef();
}
- const Impl::FramePointer &frame = storedFrame.frame;
- return AnalysisDataFrameRef(frame->header(), frame->values_);
+ return storedFrame.frameReference();
}
bool
AnalysisDataStorage::requestStorage(int nframes)
{
- if (impl_->isMultipoint())
- {
- return false;
- }
-
// Handle the case when everything needs to be stored.
if (nframes == -1)
{
void
-AnalysisDataStorage::startDataStorage(AbstractAnalysisData *data)
+AnalysisDataStorage::startDataStorage(AbstractAnalysisData *data,
+ AnalysisDataModuleManager *modules)
+{
+ modules->notifyDataStart(data);
+ // Data needs to be set before calling extendBuffer()
+ impl_->data_ = data;
+ impl_->modules_ = modules;
+ if (!impl_->storeAll())
+ {
+ // 2 = pending limit (1) + 1
+ impl_->extendBuffer(impl_->storageLimit_ + 2);
+ }
+}
+
+
+void
+AnalysisDataStorage::startParallelDataStorage(
+ AbstractAnalysisData *data,
+ AnalysisDataModuleManager *modules,
+ const AnalysisDataParallelOptions &options)
{
+ const int pendingLimit = options.parallelizationFactor();
+ impl_->pendingLimit_ = pendingLimit;
+ modules->notifyParallelDataStart(data, options);
// Data needs to be set before calling extendBuffer()
- impl_->data_ = data;
- setMultipoint(data->isMultipoint());
+ impl_->data_ = data;
+ impl_->modules_ = modules;
if (!impl_->storeAll())
{
- impl_->extendBuffer(this, impl_->storageLimit_ + impl_->pendingLimit_ + 1);
+ impl_->extendBuffer(impl_->storageLimit_ + pendingLimit + 1);
}
}
AnalysisDataStorage::startFrame(const AnalysisDataFrameHeader &header)
{
GMX_ASSERT(header.isValid(), "Invalid header");
- Impl::StoredFrame *storedFrame;
+ internal::AnalysisDataStorageFrameData *storedFrame;
if (impl_->storeAll())
{
size_t size = header.index() + 1;
if (impl_->frames_.size() < size)
{
- impl_->extendBuffer(this, size);
+ impl_->extendBuffer(size);
}
- storedFrame = &impl_->frames_[header.index()];
+ storedFrame = impl_->frames_[header.index()].get();
}
else
{
{
GMX_THROW(APIError("Out of bounds frame index"));
}
- storedFrame = &impl_->frames_[storageIndex];
+ storedFrame = impl_->frames_[storageIndex].get();
}
GMX_RELEASE_ASSERT(!storedFrame->isStarted(),
"startFrame() called twice for the same frame");
- GMX_RELEASE_ASSERT(storedFrame->frame->frameIndex() == header.index(),
+ GMX_RELEASE_ASSERT(storedFrame->frameIndex() == header.index(),
"Inconsistent internal frame indexing");
- storedFrame->status = Impl::StoredFrame::eStarted;
- storedFrame->frame->header_ = header;
- if (impl_->isMultipoint())
+ storedFrame->startFrame(header, impl_->getFrameBuilder());
+ impl_->modules_->notifyParallelFrameStart(header);
+ if (impl_->shouldNotifyImmediately())
{
- impl_->data_->notifyFrameStart(header);
+ impl_->modules_->notifyFrameStart(header);
}
- return *storedFrame->frame;
+ return storedFrame->builder();
}
AnalysisDataStorageFrame &
AnalysisDataStorage::currentFrame(int index)
{
- int storageIndex = impl_->computeStorageLocation(index);
+ const int storageIndex = impl_->computeStorageLocation(index);
GMX_RELEASE_ASSERT(storageIndex >= 0, "Out of bounds frame index");
- Impl::StoredFrame &storedFrame = impl_->frames_[storageIndex];
+
+ internal::AnalysisDataStorageFrameData &storedFrame = *impl_->frames_[storageIndex];
GMX_RELEASE_ASSERT(storedFrame.isStarted(),
"currentFrame() called for frame before startFrame()");
GMX_RELEASE_ASSERT(!storedFrame.isFinished(),
"currentFrame() called for frame after finishFrame()");
- GMX_RELEASE_ASSERT(storedFrame.frame->frameIndex() == index,
+ GMX_RELEASE_ASSERT(storedFrame.frameIndex() == index,
"Inconsistent internal frame indexing");
- return *storedFrame.frame;
+ return storedFrame.builder();
}
void
AnalysisDataStorage::finishFrame(int index)
{
- int storageIndex = impl_->computeStorageLocation(index);
- GMX_RELEASE_ASSERT(storageIndex >= 0, "Out of bounds frame index");
- Impl::StoredFrame &storedFrame = impl_->frames_[storageIndex];
- GMX_RELEASE_ASSERT(storedFrame.isStarted(),
- "finishFrame() called for frame before startFrame()");
- GMX_RELEASE_ASSERT(!storedFrame.isFinished(),
- "finishFrame() called twice for the same frame");
- GMX_RELEASE_ASSERT(storedFrame.frame->frameIndex() == index,
- "Inconsistent internal frame indexing");
- storedFrame.status = Impl::StoredFrame::eFinished;
- if (impl_->isMultipoint())
- {
- // TODO: Check that the last point set has been finished
- impl_->data_->notifyFrameFinish(storedFrame.frame->header());
- if (storedFrame.frame->frameIndex() >= impl_->storageLimit_)
- {
- impl_->rotateBuffer();
- }
- }
- else
- {
- impl_->notifyNextFrames(storageIndex);
- }
+ impl_->finishFrame(index);
}
-
void
-AnalysisDataStorage::finishFrame(const AnalysisDataStorageFrame &frame)
+AnalysisDataStorage::finishDataStorage()
{
- finishFrame(frame.frameIndex());
+ // TODO: Check that all frames have been finished etc.
+ impl_->builders_.clear();
+ impl_->modules_->notifyDataFinish();
}
} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff