/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
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*
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*
- * GROningen MAchine for Chemical Simulations
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*
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-
- * This program is free software; you can redistribute it and/or
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+ * the research papers on the package. Check out http://www.gromacs.org.
*/
/*! \internal \file
* \brief
* Implements classes in analysisdata.h.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
-#include "gromacs/analysisdata/analysisdata.h"
+#include "gmxpre.h"
-#include <algorithm>
-#include <memory>
+#include "analysisdata.h"
#include "gromacs/analysisdata/dataframe.h"
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
-
-#include "abstractdata-impl.h"
-#include "analysisdata-impl.h"
+#include "gromacs/analysisdata/datastorage.h"
+#include "gromacs/analysisdata/paralleloptions.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/uniqueptr.h"
namespace gmx
{
/********************************************************************
- * AnalysisData::Impl
- ********************************************************************/
-
-static bool
-frame_index_gtr(AnalysisDataFrame *a, AnalysisDataFrame *b)
-{
- return a->_index > b->_index;
-}
-
-
-AnalysisData::Impl::Impl(AnalysisData *data)
- : _data(*data), _pstart(0)
-{
-}
-
+ * AnalysisDataHandleImpl
+ */
-AnalysisData::Impl::~Impl()
+namespace internal
{
- HandleList::const_iterator i;
- for (i = _handles.begin(); i != _handles.end(); ++i)
- {
- delete *i;
- }
-
- FrameList::const_iterator j;
- for (j = _pending.begin(); j != _pending.end(); ++j)
- {
- delete *j;
- }
-}
-
-void
-AnalysisData::Impl::addPendingFrame(AnalysisDataFrame *fr)
+/*! \internal \brief
+ * Private implementation class for AnalysisDataHandle.
+ *
+ * \ingroup module_analysisdata
+ */
+class AnalysisDataHandleImpl
{
- GMX_ASSERT(fr->_index >= _data.frameCount(),
- "addPendingFrame() called for too old frame");
- size_t pindex = fr->_index - _data.frameCount();
- if (pindex == 0)
- {
- // Just store our frame if it is the next one.
- _data.storeNextFrame(fr->_x, fr->_dx, fr->_y, fr->_dy, fr->_present);
- incrementPStart();
- }
- else
- {
- if (pindex >= _pending.size())
- {
- // TODO: We need to wait until earlier frames are ready...
- }
- // TODO: This is not thread-safe.
- pindex += _pstart;
- if (pindex > _pending.size())
+ public:
+ //! Creates a handle associated with the given data object.
+ explicit AnalysisDataHandleImpl(AnalysisData *data)
+ : data_(*data), currentFrame_(NULL)
{
- pindex -= _pending.size();
}
- int ncol = _data.columnCount();
- _pending[pindex]->_x = fr->_x;
- _pending[pindex]->_dx = fr->_dx;
- for (int i = 0; i < ncol; ++i)
- {
- _pending[pindex]->_y[i] = fr->_y[i];
- _pending[pindex]->_dy[i] = fr->_dy[i];
- _pending[pindex]->_present[i] = fr->_present[i];
- }
- _pending[pindex]->_index = fr->_index;
- }
- processPendingFrames();
-}
-
-
-void
-AnalysisData::Impl::processPendingFrames()
-{
- while (_pending[_pstart]->_index != -1)
- {
- AnalysisDataFrame *fr = _pending[_pstart];
+ //! The data object that this handle belongs to.
+ AnalysisData &data_;
+ //! Current storage frame object, or NULL if no current frame.
+ AnalysisDataStorageFrame *currentFrame_;
+};
- _data.storeNextFrame(fr->_x, fr->_dx, fr->_y, fr->_dy, fr->_present);
- fr->_index = -1;
- incrementPStart();
- }
-}
+} // namespace internal
+/********************************************************************
+ * AnalysisData::Impl
+ */
-void
-AnalysisData::Impl::incrementPStart()
+/*! \internal \brief
+ * Private implementation class for AnalysisData.
+ *
+ * \ingroup module_analysisdata
+ */
+class AnalysisData::Impl
{
- size_t val = _pstart;
-
- ++val;
- if (val >= _pending.size())
- {
- val -= _pending.size();
- }
- _pstart = val;
-}
-
+ public:
+ //! Smart pointer type to manage a data handle implementation.
+ typedef gmx_unique_ptr<internal::AnalysisDataHandleImpl>::type
+ HandlePointer;
+ //! Shorthand for a list of data handles.
+ typedef std::vector<HandlePointer> HandleList;
+
+ //! Storage implementation.
+ AnalysisDataStorage storage_;
+ /*! \brief
+ * List of handles for this data object.
+ *
+ * Note that AnalysisDataHandle objects also contain (raw) pointers
+ * to these objects.
+ */
+ HandleList handles_;
+};
/********************************************************************
* AnalysisData
*/
AnalysisData::AnalysisData()
- : _impl(new Impl(this))
+ : impl_(new Impl)
{
}
AnalysisData::~AnalysisData()
{
- delete _impl;
}
void
-AnalysisData::setColumns(int ncol, bool multipoint)
+AnalysisData::setDataSetCount(int dataSetCount)
{
- GMX_RELEASE_ASSERT(ncol > 0, "Number of columns must be positive");
- GMX_RELEASE_ASSERT(_impl->_handles.empty(),
+ GMX_RELEASE_ASSERT(impl_->handles_.empty(),
"Cannot change data dimensionality after creating handles");
- setColumnCount(ncol);
- setMultipoint(multipoint);
+ AbstractAnalysisData::setDataSetCount(dataSetCount);
}
-AnalysisDataHandle *
-AnalysisData::startData(AnalysisDataParallelOptions opt)
+void
+AnalysisData::setColumnCount(int dataSet, int columnCount)
{
- if (_impl->_handles.empty())
- {
- startDataStore();
- }
- else if (isMultipoint())
- {
- GMX_THROW(NotImplementedError("Parallelism not supported for multipoint data"));
- }
+ GMX_RELEASE_ASSERT(impl_->handles_.empty(),
+ "Cannot change data dimensionality after creating handles");
+ AbstractAnalysisData::setColumnCount(dataSet, columnCount);
+}
+
+
+void
+AnalysisData::setMultipoint(bool bMultipoint)
+{
+ GMX_RELEASE_ASSERT(impl_->handles_.empty(),
+ "Cannot change data type after creating handles");
+ AbstractAnalysisData::setMultipoint(bMultipoint);
+}
- std::auto_ptr<AnalysisDataHandle> handle(new AnalysisDataHandle(this));
- _impl->_handles.push_back(handle.get());
- size_t oldSize = _impl->_pending.size();
- _impl->_pending.resize(2 * _impl->_handles.size() - 1);
- Impl::FrameList::iterator i;
- for (i = _impl->_pending.begin() + oldSize; i != _impl->_pending.end(); ++i)
+int
+AnalysisData::frameCount() const
+{
+ return impl_->storage_.frameCount();
+}
+
+
+AnalysisDataHandle
+AnalysisData::startData(const AnalysisDataParallelOptions &opt)
+{
+ GMX_RELEASE_ASSERT(impl_->handles_.size() < static_cast<unsigned>(opt.parallelizationFactor()),
+ "Too many calls to startData() compared to provided options");
+ if (impl_->handles_.empty())
{
- *i = new AnalysisDataFrame(columnCount());
- (*i)->_index = -1;
+ impl_->storage_.startParallelDataStorage(this, &moduleManager(), opt);
}
- return handle.release();
+ Impl::HandlePointer handle(new internal::AnalysisDataHandleImpl(this));
+ impl_->handles_.push_back(move(handle));
+ return AnalysisDataHandle(impl_->handles_.back().get());
}
void
-AnalysisData::finishData(AnalysisDataHandle *handle)
+AnalysisData::finishData(AnalysisDataHandle handle)
{
Impl::HandleList::iterator i;
- i = std::find(_impl->_handles.begin(), _impl->_handles.end(), handle);
- GMX_RELEASE_ASSERT(i != _impl->_handles.end(),
+ for (i = impl_->handles_.begin(); i != impl_->handles_.end(); ++i)
+ {
+ if (i->get() == handle.impl_)
+ {
+ break;
+ }
+ }
+ GMX_RELEASE_ASSERT(i != impl_->handles_.end(),
"finishData() called for an unknown handle");
- _impl->_handles.erase(i);
- delete handle;
+ impl_->handles_.erase(i);
- if (_impl->_handles.empty())
+ if (impl_->handles_.empty())
{
- notifyDataFinish();
+ impl_->storage_.finishDataStorage();
}
}
-/********************************************************************
- * AnalysisDataHandle::Impl
- */
-
-AnalysisDataHandle::Impl::Impl(AnalysisData *data)
- : _data(*data)
+AnalysisDataFrameRef
+AnalysisData::tryGetDataFrameInternal(int index) const
{
- if (!_data.isMultipoint())
- {
- _frame.reset(new AnalysisDataFrame(_data.columnCount()));
- }
+ return impl_->storage_.tryGetDataFrame(index);
}
-AnalysisDataHandle::Impl::~Impl()
+bool
+AnalysisData::requestStorageInternal(int nframes)
{
+ return impl_->storage_.requestStorage(nframes);
}
* AnalysisDataHandle
*/
-AnalysisDataHandle::AnalysisDataHandle(AnalysisData *data)
- : _impl(new Impl(data))
+AnalysisDataHandle::AnalysisDataHandle()
+ : impl_(NULL)
{
}
-AnalysisDataHandle::~AnalysisDataHandle()
+AnalysisDataHandle::AnalysisDataHandle(internal::AnalysisDataHandleImpl *impl)
+ : impl_(impl)
{
- delete _impl;
}
void
AnalysisDataHandle::startFrame(int index, real x, real dx)
{
- if (_impl->_data.isMultipoint())
- {
- _impl->_data.notifyFrameStart(AnalysisDataFrameHeader(index, x, dx));
- }
- else
- {
- _impl->_frame->_index = index;
- _impl->_frame->_x = x;
- _impl->_frame->_dx = dx;
- for (int i = 0; i < _impl->_data.columnCount(); ++i)
- {
- _impl->_frame->_y[i] = 0.0;
- _impl->_frame->_dy[i] = 0.0;
- _impl->_frame->_present[i] = false;
- }
- }
+ GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
+ GMX_RELEASE_ASSERT(impl_->currentFrame_ == NULL,
+ "startFrame() called twice without calling finishFrame()");
+ impl_->currentFrame_ =
+ &impl_->data_.impl_->storage_.startFrame(index, x, dx);
}
void
-AnalysisDataHandle::addPoint(int col, real y, real dy, bool present)
+AnalysisDataHandle::selectDataSet(int index)
{
- if (_impl->_data.isMultipoint())
- {
- _impl->_data.notifyPointsAdd(col, 1, &y, &dy, &present);
- }
- else
- {
- GMX_ASSERT(!_impl->_frame->_present[col],
- "Data for a column set multiple times");
- _impl->_frame->_y[col] = y;
- _impl->_frame->_dy[col] = dy;
- _impl->_frame->_present[col] = present;
- }
+ GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
+ GMX_RELEASE_ASSERT(impl_->currentFrame_ != NULL,
+ "selectDataSet() called without calling startFrame()");
+ impl_->currentFrame_->selectDataSet(index);
}
void
-AnalysisDataHandle::addPoints(int firstcol, int n,
- const real *y, const real *dy,
- const bool *present)
+AnalysisDataHandle::setPoint(int column, real value, bool bPresent)
{
- if (_impl->_data.isMultipoint())
- {
- _impl->_data.notifyPointsAdd(firstcol, n, y, dy, present);
- }
- else
- {
- for (int i = 0; i < n; ++i)
- {
- addPoint(firstcol + i, y[i], dy ? dy[i] : 0.0,
- present ? present[i] : true);
- }
- }
+ GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
+ GMX_RELEASE_ASSERT(impl_->currentFrame_ != NULL,
+ "setPoint() called without calling startFrame()");
+ impl_->currentFrame_->setValue(column, value, bPresent);
}
void
-AnalysisDataHandle::finishFrame()
+AnalysisDataHandle::setPoint(int column, real value, real error, bool bPresent)
{
- if (_impl->_data.isMultipoint())
- {
- _impl->_data.notifyFrameFinish();
- }
- else
+ GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
+ GMX_RELEASE_ASSERT(impl_->currentFrame_ != NULL,
+ "setPoint() called without calling startFrame()");
+ impl_->currentFrame_->setValue(column, value, error, bPresent);
+}
+
+
+void
+AnalysisDataHandle::setPoints(int firstColumn, int count, const real *values)
+{
+ GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
+ GMX_RELEASE_ASSERT(impl_->currentFrame_ != NULL,
+ "setPoints() called without calling startFrame()");
+ for (int i = 0; i < count; ++i)
{
- _impl->_data._impl->addPendingFrame(_impl->_frame.get());
+ impl_->currentFrame_->setValue(firstColumn + i, values[i]);
}
}
void
-AnalysisDataHandle::addFrame(int index, real x, const real *y, const real *dy,
- const bool *present)
+AnalysisDataHandle::finishPointSet()
{
- addFrame(index, x, 0.0, y, dy, present);
+ GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
+ GMX_RELEASE_ASSERT(impl_->data_.isMultipoint(),
+ "finishPointSet() called for non-multipoint data");
+ GMX_RELEASE_ASSERT(impl_->currentFrame_ != NULL,
+ "finishPointSet() called without calling startFrame()");
+ impl_->currentFrame_->finishPointSet();
}
void
-AnalysisDataHandle::addFrame(int index, real x, real dx,
- const real *y, const real *dy,
- const bool *present)
+AnalysisDataHandle::finishFrame()
{
- startFrame(index, x, dx);
- addPoints(0, _impl->_data.columnCount(), y, dy, present);
- finishFrame();
+ GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
+ GMX_RELEASE_ASSERT(impl_->currentFrame_ != NULL,
+ "finishFrame() called without calling startFrame()");
+ AnalysisDataStorageFrame *frame = impl_->currentFrame_;
+ impl_->currentFrame_ = NULL;
+ frame->finishFrame();
}
void
AnalysisDataHandle::finishData()
{
- // Calls delete this
- _impl->_data.finishData(this);
+ GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
+ // Deletes the implementation pointer.
+ impl_->data_.finishData(*this);
+ impl_ = NULL;
}
} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff