#include <gromacs/analysisdata/analysisdata.h>

Inheritance diagram for gmx::AnalysisData:

Collaboration diagram for gmx::AnalysisData:

Description

Parallelizable data container for raw data.

This is the main class used to implement parallelizable data processing in analysis tools. It is used by first creating an object and setting its properties using setDataSetCount(), setColumnCount() and setMultipoint(), and attaching necessary modules using addModule() etc. Then one or more AnalysisDataHandle objects can be created using startData(). Each data handle can then be independently used to provide data frames (each frame must be provided by a single handle, but different frames can be freely mixed between the handles). The finishFrameSerial() method must be called in serial for each frame, after one of the handles has been used to provide the data for that frame. When all data has been provided, the handles are destroyed using finishData() (or AnalysisDataHandle::finishData()).

When used through the trajectory analysis framework, calls to startData(), finishFrameSerial(), and finishData() are handled by the framework.

Todo:: Parallel implementation is not complete.

Special note for MPI implementation: assuming that the initialization of data objects is identical in all processes, associating the data objects in different MPI processes should be possible without changes in the interface. Alternative, more robust implementation could get a unique ID as parameter to the constructor or a separate function, but would require all tools to provide it. With the current registration mechanism in TrajectoryAnalysisModule, this should be straightforward.

Examples:: template.cpp.

Classes
class	Impl
	Private implementation class for AnalysisData. More...

Public Member Functions
	AnalysisData ()
	Creates an empty analysis data object. More...

void	setDataSetCount (int dataSetCount)
	Sets the number of data sets. More...

void	setColumnCount (int dataSet, int columnCount)
	Sets the number of columns in a data set. More...

void	setMultipoint (bool bMultipoint)
	Sets whether the data contains multiple points per column per frame. More...

int	frameCount () const override
	Returns the total number of frames in the data. More...

AnalysisDataHandle	startData (const AnalysisDataParallelOptions &opt)
	Creates a handle for adding data. More...

void	finishFrameSerial (int frameIndex)
	Performs in-order sequential processing for the next frame. More...

void	finishData (AnalysisDataHandle handle)
	Destroys a handle after all data has been added. More...

Public Member Functions inherited from gmx::AbstractAnalysisData
bool	isMultipoint () const
	Whether the data can have multiple points in the same column in the same frame. More...

int	dataSetCount () const
	Returns the number of data sets in the data object. More...

int	columnCount (int dataSet) const
	Returns the number of columns in a data set. More...

int	columnCount () const
	Returns the number of columns in the data. More...

AnalysisDataFrameRef	tryGetDataFrame (int index) const
	Access stored data. More...

AnalysisDataFrameRef	getDataFrame (int index) const
	Access stored data. More...

bool	requestStorage (int nframes)
	Request storage of frames. More...

void	addModule (const AnalysisDataModulePointer &module)
	Adds a module to process the data. More...

void	addColumnModule (int col, int span, const AnalysisDataModulePointer &module)
	Adds a module that processes only a subset of the columns. More...

void	applyModule (IAnalysisDataModule *module)
	Applies a module to process data that is ready. More...

Friends
class	AnalysisDataHandle

Additional Inherited Members
Protected Member Functions inherited from gmx::AbstractAnalysisData
	AbstractAnalysisData ()
	Initializes a new analysis data object. More...

void	setDataSetCount (int dataSetCount)
	Sets the number of data sets. More...

void	setColumnCount (int dataSet, int columnCount)
	Sets the number of columns for a data set. More...

void	setMultipoint (bool bMultipoint)
	Sets whether the data has multiple points per column in a frame. More...

AnalysisDataModuleManager &	moduleManager ()
	Returns the module manager to use for calling notification methods.

const AnalysisDataModuleManager &	moduleManager () const
	Returns the module manager to use for calling notification methods.

Constructor & Destructor Documentation

gmx::AnalysisData::AnalysisData ( )

Creates an empty analysis data object.

Exceptions

std::bad_alloc if out of memory.

Member Function Documentation

void gmx::AnalysisData::finishData ( AnalysisDataHandle handle )

Destroys a handle after all data has been added.

Parameters

[in] handle Handle to destroy.

Exceptions

unspecified Any exception thrown by attached data modules in IAnalysisDataModule::dataFinished().

handle must have been obtained from startData() of this object. The order of the calls with respect to the corresponding startData() calls is not important.

The handle (and any copies) are invalid after the call.

void gmx::AnalysisData::finishFrameSerial ( int frameIndex )

Performs in-order sequential processing for the next frame.

Parameters

[in] frameIndex Index of the frame that has been finished.

Exceptions

unspecified Any exception thrown by attached data modules in IAnalysisDataModule::frameFinishedSerial().

This method should be called sequentially for each frame, after data for that frame has been produced. It is not necessary to call this method if there is no parallelism, i.e., if only a single data handle is created and the parallelization options provided at that time do not indicate parallelism.

int gmx::AnalysisData::frameCount ( ) const

overridevirtual

Returns the total number of frames in the data.

Returns: The total number of frames in the data.

This function returns the number of frames that the object has produced. If requestStorage() has been successfully called, tryGetDataframe() or getDataFrame() can be used to access some or all of these frames.

Does not throw.

Derived classes should implement this to return the number of frames. The frame count should not be incremented before tryGetDataFrameInternal() can return the new frame. The frame count must be incremented before AnalysisDataModuleManager::notifyFrameFinish() is called.

Implements gmx::AbstractAnalysisData.

void gmx::AnalysisData::setColumnCount	(	int	dataSet,
		int	columnCount
	)

Sets the number of columns in a data set.

Parameters

[in]	dataSet	Zero-based data set index.
[in]	columnCount	Number of columns in the data (must be > 0).

Exceptions

APIError if modules have been added that are not compatible with the new column count.

Must be called before startData() for each data set. Must not be called after startData() has been called. If called multiple times for a data set, the last call takes effect.

Examples:: template.cpp.

void gmx::AnalysisData::setDataSetCount ( int dataSetCount )

Sets the number of data sets.

Parameters

[in] dataSetCount Number of data sets (must be > 0).

Exceptions

std::bad_alloc	if out of memory.
APIError	if modules have been added that are not compatible with the new data set count.

Must not be called after startData() has been called. If not called, a single data set is assumed. If called multiple times, the last call takes effect.

void gmx::AnalysisData::setMultipoint ( bool bMultipoint )

Sets whether the data contains multiple points per column per frame.

Parameters

[in] bMultipoint Whether the data will allow multiple points per column within a single frame.

Exceptions

APIError if modules have been added that are not compatible with the new setting.

If this method is not called, the data is not multipoint.

Must not be called after startData() has been called.

See Also: isMultipoint()

AnalysisDataHandle gmx::AnalysisData::startData ( const AnalysisDataParallelOptions & opt )

Creates a handle for adding data.

Parameters

[in] opt Options for setting how this handle will be used.

Returns: The created handle.

Exceptions

std::bad_alloc	if out of memory.
APIError	if any attached data module is not compatible.
unspecified	Any exception thrown by attached data modules in IAnalysisDataModule::dataStarted().

The caller should retain the returned handle (or a copy of it), and pass it to finishData() after successfully adding all data. The caller should discard the returned handle if an error occurs; memory allocated for the handle will be freed when the AnalysisData object is destroyed.

The opt options should be the same for all calls to this method, and the number of calls should match the parallelization factor defined in opt.

The documentation for this class was generated from the following files:

api/legacy/include/gromacs/analysisdata/analysisdata.h
src/gromacs/analysisdata/analysisdata.cpp

Description

Classes

Public Member Functions

Friends

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation