Detailed Description

Buffer for interprocessor communication.

A Buffer manages two blocks of raw memory, a send buffer and a receive buffer, that are used to communicate data between processors. The class provides a simple interace for:

Packing data into the send buffer on the processor that sends data (source processor)
Unpacking data from the receive buffer on a processor that receives the data (destination processor)
Sending, receiving, and broadcasting the data in these two buffers.

The functions that send, receive and broadcast data are relatively simple wrappers around MPI functions.

The send and receive buffers contain one or more blocks of data. Each block contains a prefix and data segment. The data segment contains a sequence of items of the same data type. The prefix contains information about the data segment, including the length of the buffer, the number of items, and the type of data.

Data types

Different possible types of data are enumerated by the public enum Buffer::BlockDataType. The allowed values of this enum are:

NONE : Default setting (between blocks)
ATOM : a full atom packed for exchange of ownership
GHOST : a ghost atom (position, id and typeId)
UPDATE : an update of a ghost atom position
FORCE : a force vector for use in a reverse update
GROUP2 : a Group<2> (bond)
GROUP3 : a Group<3> (angle)
GROUP4 : a Group<4> (dihedral)
SPECIAL : specialized nonstandard data type

The standard ATOM, GHOST, UPDATE, FORCE, and GROUP(2,3,4) types are used in the implementation of the Exchanger class.

The DdMd::Atom class and DdMd::Group class template provide provide member functions to pack and unpack individual items of standard types (atoms and groups). The pack and unpack functions in these classes each take a Buffer by reference as an argument. They are implemented using the primitive Buffer::pack<T>() and Buffer::unpack<T>() member function templates of the Buffer class, which a user to pack and unpack a single C variable of type T to or from a Buffer.

The SPECIAL BlockDataType value is a generic label for any specialized, non-standard data type. Code that uses an Buffer to communicate a specialized data type should provide functions to pack and unpack individual items of the required type. Like the pack and unpack functions for atoms and groups, these functions should be implemented using the Buffer::pack() and Buffer::unpack() function templates.

Packing a block of data

Example - packing a block of Group<2> objects:

Buffer buffer;
DArray< Group<2> > bonds;
// Clear buffer before packing
buffer.clear();   
// Pack data block
buffer.beginSendBlock(Buffer::GROUP2);
for (i = 0; i < bonds.size(); ++i) {
   bonds[i].pack(buffer);
   buffer.incrementSendSize();
}
bool isComplete = true;
endSendBlock(true);
// Pack subsequent blocks, if any.
buffer.send(communicator, destination);

Note:

Call beginSendBlock() and endSendBlock() before and after the loop over data items, respectively.
Call incrementSendSize() after packing each item to increment an internal counter of number of items in block.
The bool isComplete argument of endSendBlock(bool) indicates whether the block of data is complete, i.e., whether all data of this type is contained in this block (true), or whether the receiving processor should expect one or more further messages containing the rest of this block. This flag is sent as part of the block prefix.

Unpacking a block of data

Example - unpacking a block of Group<2> objects:

Buffer buffer;
DArray< Group<2> > bonds;
MPI::Intracomm communicator;
int source;
// Receive the buffer 
buffer.recv(communicator, source);
// Unpack a data block
bool isComplete;
int i = 0;
isComplete = buffer.beginRecvBlock();
while (buffer.recvSize()) {
   bonds[i].unpack(buffer);
   buffer.decrementRecvSize();
   ++i;
}
endRecvBlock();
// Subsequent blocks, if any

Note:

Call beginRecvBlock() and endRecvBlock() before and after the loop over items in the block, respectively. The return value of Buffer::recvSize() is equal to the total number of data items in the block after beginRecvBlock() returns, and must have reached zero when endRecvBlock() is called.
The return value of beginRecvBlock() is the value of the isComplete flag that was passed as an argument to the endSendBlock(bool) function on the source processor.
Call decrementRecvSize() after unpackingpacking each item to decrement the value recvSize counter by one.
This example does not include code to check the isComplete flag. More complete code would check this, and either throw an exception or prepare to receive another message if the flag was set false.

Sending a block in several messages

The above examples shows a simple case of packing and unpacking a complete block without any explicit checking of whether the message will fit in the buffer on the source processor or checking of the isComplete flag on the destination. Code that needs to send blocks that may exceed the buffer size can use the isComplete flag to break the a block of data into in several messages, by setting isComplete false in all but the last message of the sequence.

Here is an example of the code to receive an array of data that may have been split into several messages:

Buffer buffer;
DArray< Group<2> > bonds;
MPI::Intracomm communicator;
int source;
int i = 0;
bool isComplete = false;
while (!isComplete) {
   buffer.recv(communicator, source);
   isComplete = buffer.beginRecvBlock();
   while (buffer.recvSize()) {
      bonds[i].unpack(buffer);
      buffer.decrementRecvSize();
      ++i;
   }
   endRecvBlock();
}

The code required to avoid overfilling the send buffer on the source processor (not shown), requires knowledge of the packed size of one object. This is provided for Atom and Group objects by the Atom::packedAtomSize(), Atom::packedGhostSize() and Group::packedSize() static functions.

This idiom for dividing large blocks is used in the implementation of all the DdMd Distributor and Collector classes (AtomDistributor, AtomCollector, GroupDistributor and GroupCollector).

Definition at line 217 of file Buffer.h.

#include <Buffer.h>

Inheritance diagram for DdMd::Buffer:

Public Types
Public Types inherited from Util::Serializable
typedef BinaryFileOArchive	OArchive
	Type of output archive used by save method. More...

typedef BinaryFileIArchive	IArchive
	Type of input archive used by load method. More...

Public Member Functions
	Buffer ()
	Constructor. More...

virtual	~Buffer ()
	Destructor. More...

void	readParameters (std::istream &in)
	Read capacity and allocate buffers. More...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load internal state from an archive. More...

virtual void	save (Serializable::OArchive &ar)
	Save internal state to an archive. More...

void	allocate (int atomCapacity, int ghostCapacity)
	Allocate send and recv buffers. More...

Send Buffer Management
void	clearSendBuffer ()
	Clear the send buffer. More...

void	beginSendBlock (int sendType)
	Initialize a data block. More...

template<typename T >
void	pack (const T &data)
	Function template for packing one variable into the send buffer. More...

void	incrementSendSize ()
	Increment sendSize counter after packing an item (an Atom or Group). More...

void	endSendBlock (bool isComplete=true)
	Finalize a block in the send buffer. More...

Receive Buffer Management
bool	beginRecvBlock ()
	Begin to receive a block from the recv buffer. More...

template<typename T >
void	unpack (T &data)
	Function template unpacking one variable from the receive buffer. More...

void	decrementRecvSize ()
	Decrement recvSize counter after completely unpacking an item. More...

void	endRecvBlock ()
	Finish processing a block in the recv buffer. More...

Interprocessor Communication
void	sendRecv (MPI::Intracomm &comm, int source, int dest)
	Receive from processor send and send to processor recv. More...

void	send (MPI::Intracomm &comm, int dest)
	Send a complete buffer. More...

void	recv (MPI::Intracomm &comm, int source)
	Receive a buffer. More...

void	bcast (MPI::Intracomm &comm, int source)
	Broadcast a buffer. More...

Statistics
virtual void	computeStatistics (MPI::Intracomm &comm)
	Compute statistics (reduce from all processors). More...

void	outputStatistics (std::ostream &out)
	Output statistics. More...

void	clearStatistics ()
	Clear any accumulated usage statistics. More...

Accessors
int	sendSize () const
	Number of items in current send block. More...

int	recvSize () const
	Number of unread items left in current recv block. More...

bool	isAllocated () const
	Has memory been allocated for this Buffer? More...

bool	isInitialized () const
	Has this Buffer been initialized? More...

int	atomCapacity () const
	Maximum number of atoms for which space is available. More...

int	ghostCapacity () const
	Maximum number of ghost atoms for which space is available. More...

template<int N>
int	groupCapacity () const
	Maximum number of group<N> objects for which space is available. More...

Public Member Functions inherited from Util::ParamComposite
	ParamComposite ()
	Constructor. More...

	ParamComposite (const ParamComposite &other)
	Copy constructor. More...

	ParamComposite (int capacity)
	Constructor. More...

virtual	~ParamComposite ()
	Virtual destructor. More...

void	resetParam ()
	Resets ParamComposite to its empty state. More...

virtual void	readParam (std::istream &in)
	Read the parameter file block. More...

virtual void	readParamOptional (std::istream &in)
	Read optional parameter file block. More...

virtual void	writeParam (std::ostream &out)
	Write all parameters to an output stream. More...

virtual void	load (Serializable::IArchive &ar)
	Load all parameters from an input archive. More...

virtual void	loadOptional (Serializable::IArchive &ar)
	Load an optional ParamComposite. More...

void	saveOptional (Serializable::OArchive &ar)
	Saves isActive flag, and then calls save() iff isActive is true. More...

void	readParamComposite (std::istream &in, ParamComposite &child, bool next=true)
	Add and read a required child ParamComposite. More...

void	readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true)
	Add and attempt to read an optional child ParamComposite. More...

template<typename Type >
ScalarParam< Type > &	read (std::istream &in, const char *label, Type &value)
	Add and read a new required ScalarParam < Type > object. More...

template<typename Type >
ScalarParam< Type > &	readOptional (std::istream &in, const char *label, Type &value)
	Add and read a new optional ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	readCArray (std::istream &in, const char label, Type value, int n)
	Add and read a required C array parameter. More...

template<typename Type >
CArrayParam< Type > &	readOptionalCArray (std::istream &in, const char label, Type value, int n)
	Add and read an optional C array parameter. More...

template<typename Type >
DArrayParam< Type > &	readDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
	Add and read a required DArray < Type > parameter. More...

template<typename Type >
DArrayParam< Type > &	readOptionalDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
	Add and read an optional DArray < Type > parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	readFArray (std::istream &in, const char *label, FArray< Type, N > &array)
	Add and read a required FArray < Type, N > array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	readOptionalFArray (std::istream &in, const char *label, FArray< Type, N > &array)
	Add and read an optional FArray < Type, N > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	readCArray2D (std::istream &in, const char label, Type value, int m, int n, int np)
	Add and read a required CArray2DParam < Type > 2D C-array. More...

template<typename Type >
CArray2DParam< Type > &	readOptionalCArray2D (std::istream &in, const char label, Type value, int m, int n, int np)
	Add and read an optional CArray2DParam < Type > 2D C-array parameter. More...

template<typename Type >
DMatrixParam< Type > &	readDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and read a required DMatrix < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	readOptionalDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and read an optional DMatrix < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	readDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read a required symmetrix DMatrix. More...

template<typename Type >
DSymmMatrixParam< Type > &	readOptionalDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read an optional DMatrix matrix parameter. More...

Begin &	readBegin (std::istream &in, const char *label, bool isRequired=true)
	Add and read a class label and opening bracket. More...

End &	readEnd (std::istream &in)
	Add and read the closing bracket. More...

Blank &	readBlank (std::istream &in)
	Add and read a new Blank object, representing a blank line. More...

void	loadParamComposite (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load a required child ParamComposite. More...

void	loadParamCompositeOptional (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load an optional child ParamComposite if isActive. More...

template<typename Type >
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value, bool isRequired)
	Add and load a new ScalarParam < Type > object. More...

template<typename Type >
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value)
	Add and load new required ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	loadCArray (Serializable::IArchive &ar, const char label, Type value, int n, bool isRequired)
	Add a C array parameter and load its elements. More...

template<typename Type >
CArrayParam< Type > &	loadCArray (Serializable::IArchive &ar, const char label, Type value, int n)
	Add and load a required CArrayParam< Type > array parameter. More...

template<typename Type >
DArrayParam< Type > &	loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n, bool isRequired)
	Add an load a DArray < Type > array parameter. More...

template<typename Type >
DArrayParam< Type > &	loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n)
	Add and load a required DArray< Type > array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array, bool isRequired)
	Add and load an FArray < Type, N > fixed-size array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array)
	Add and load a required FArray < Type > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	loadCArray2D (Serializable::IArchive &ar, const char label, Type value, int m, int n, int np, bool isRequired)
	Add and load a CArray2DParam < Type > C 2D array parameter. More...

template<typename Type >
CArray2DParam< Type > &	loadCArray2D (Serializable::IArchive &ar, const char label, Type value, int m, int n, int np)
	Add and load a required < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired)
	Add and load a DMatrixParam < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and load a required DMatrixParam < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n, bool isRequired)
	Add and load a symmetric DSymmMatrixParam < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n)
	Add and load a required DSymmMatrixParam < Type > matrix parameter. More...

void	addParamComposite (ParamComposite &child, bool next=true)
	Add a child ParamComposite object to the format array. More...

Begin &	addBegin (const char *label)
	Add a Begin object representing a class name and bracket. More...

End &	addEnd ()
	Add a closing bracket. More...

Blank &	addBlank ()
	Create and add a new Blank object, representing a blank line. More...

std::string	className () const
	Get class name string. More...

bool	isRequired () const
	Is this ParamComposite required in the input file? More...

bool	isActive () const
	Is this parameter active? More...

Public Member Functions inherited from Util::ParamComponent
virtual	~ParamComponent ()
	Destructor. More...

void	setIndent (const ParamComponent &parent, bool next=true)
	Set indent level. More...

std::string	indent () const
	Return indent string for this object (string of spaces). More...

template<class Archive >
void	serialize (Archive &ar, const unsigned int version)
	Serialize this ParamComponent as a string. More...

Public Member Functions inherited from Util::Serializable
virtual	~Serializable ()
	Destructor. More...

Public Member Functions inherited from Util::MpiFileIo
	MpiFileIo ()
	Constructor. More...

	MpiFileIo (const MpiFileIo &other)
	Copy constructor. More...

bool	isIoProcessor () const
	Can this processor do file I/O ? More...

void	setIoCommunicator (MPI::Intracomm &communicator)
	Set the communicator. More...

void	clearCommunicator ()
	Clear (nullify) the communicator. More...

bool	hasIoCommunicator () const
	Does this object have an associated MPI communicator? More...

MPI::Intracomm &	ioCommunicator () const
	Get the MPI communicator by reference. More...

Additional Inherited Members
Static Public Member Functions inherited from Util::ParamComponent
static void	initStatic ()
	Initialize static echo member to false. More...

static void	setEcho (bool echo=true)
	Enable or disable echoing for all subclasses of ParamComponent. More...

static bool	echo ()
	Get echo parameter. More...

Protected Member Functions inherited from Util::ParamComposite
void	setClassName (const char *className)
	Set class name string. More...

void	setIsRequired (bool isRequired)
	Set or unset the isActive flag. More...

void	setIsActive (bool isActive)
	Set or unset the isActive flag. More...

void	setParent (ParamComponent &param, bool next=true)
	Set this to the parent of a child component. More...

void	addComponent (ParamComponent &param, bool isLeaf=true)
	Add a new ParamComponent object to the format array. More...

template<typename Type >
ScalarParam< Type > &	add (std::istream &in, const char *label, Type &value, bool isRequired=true)
	Add a new required ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	addCArray (std::istream &in, const char label, Type value, int n, bool isRequired=true)
	Add (but do not read) a required C array parameter. More...

template<typename Type >
DArrayParam< Type > &	addDArray (std::istream &in, const char *label, DArray< Type > &array, int n, bool isRequired=true)
	Add (but do not read) a DArray < Type > parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	addFArray (std::istream &in, const char *label, FArray< Type, N > &array, bool isRequired=true)
	Add (but do not read) a FArray < Type, N > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	addCArray2D (std::istream &in, const char label, Type value, int m, int n, int np, bool isRequired=true)
	Add (but do not read) a CArray2DParam < Type > 2D C-array. More...

template<typename Type >
DMatrixParam< Type > &	addDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired=true)
	Add and read a required DMatrix < Type > matrix parameter. More...

Protected Member Functions inherited from Util::ParamComponent
	ParamComponent ()
	Constructor. More...

	ParamComponent (const ParamComponent &other)
	Copy constructor. More...

Member Enumeration Documentation

enum DdMd::Buffer::BlockDataType

Enumeration of types of data to be sent in blocks.

Definition at line 225 of file Buffer.h.

Constructor & Destructor Documentation

DdMd::Buffer::Buffer ( )

Constructor.

Definition at line 22 of file Buffer.cpp.

References Util::ParamComposite::setClassName().

DdMd::Buffer::~Buffer ( )

virtual

Destructor.

Definition at line 49 of file Buffer.cpp.

Member Function Documentation

void DdMd::Buffer::readParameters ( std::istream & in )

virtual

Read capacity and allocate buffers.

Parameters

in	input parameter stream

Reimplemented from Util::ParamComposite.

Definition at line 86 of file Buffer.cpp.

References allocate(), and UTIL_THROW.

void DdMd::Buffer::loadParameters ( Serializable::IArchive & ar )

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Definition at line 112 of file Buffer.cpp.

References allocate(), and UTIL_THROW.

void DdMd::Buffer::save ( Serializable::OArchive & ar )

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from Util::ParamComposite.

Definition at line 137 of file Buffer.cpp.

void DdMd::Buffer::allocate	(	int	atomCapacity,
		int	ghostCapacity
	)

Allocate send and recv buffers.

Calculate amounts of memory required to accommodate specified number of local atoms (atomCapacity), or the specified number of ghosts (ghostCapacity), and allocate send and receive buffers large enough to hold the larger value.

Parameters

atomCapacity	max expected number of local atoms.
ghostCapacity	max expected number of ghost atoms.

Definition at line 62 of file Buffer.cpp.

References allocate(), atomCapacity(), ghostCapacity(), and UTIL_THROW.

Referenced by allocate(), loadParameters(), and readParameters().

void DdMd::Buffer::clearSendBuffer ( )

Clear the send buffer.

Definition at line 212 of file Buffer.cpp.

Referenced by DdMd::AtomDistributor::addAtom(), DdMd::Exchanger::exchange(), DdMd::AtomDistributor::newAtomPtr(), DdMd::GroupDistributor< N >::newPtr(), DdMd::Exchanger::reverseUpdate(), DdMd::AtomCollector::send(), DdMd::GroupCollector< N >::send(), DdMd::GroupDistributor< N >::send(), DdMd::AtomDistributor::send(), DdMd::GroupDistributor< N >::setup(), DdMd::AtomDistributor::setup(), and DdMd::Exchanger::update().

void DdMd::Buffer::beginSendBlock ( int sendType )

Initialize a data block.

Sets sendSize() to zero and sets the sendType.

Parameters

sendType BlockDataType value for type of data to be sent

Definition at line 223 of file Buffer.cpp.

References UTIL_THROW.

Referenced by DdMd::AtomDistributor::addAtom(), DdMd::Exchanger::exchange(), DdMd::AtomDistributor::newAtomPtr(), DdMd::GroupDistributor< N >::newPtr(), DdMd::GroupStorage< N >::pack(), DdMd::Exchanger::reverseUpdate(), DdMd::AtomCollector::send(), DdMd::GroupCollector< N >::send(), DdMd::AtomDistributor::send(), DdMd::GroupDistributor< N >::setup(), DdMd::AtomDistributor::setup(), and DdMd::Exchanger::update().

template<typename T >

void DdMd::Buffer::pack ( const T & data )

inline

Function template for packing one variable into the send buffer.

This template is used to implement the pack functions provided by the DdMd::Atom and DdMd::Group classes. It is designed to pack a single primitive C variable into the send buffer. It will also work on any plain old data type T for which assignment (=) does a straight bitwise copy.

Parameters

data	variable to be packed into the send buffer.

Definition at line 563 of file Buffer.h.

References UTIL_THROW.

Referenced by DdMd::Group< N >::pack(), DdMd::Atom::packAtom(), DdMd::Atom::packForce(), DdMd::Atom::packGhost(), and DdMd::Atom::packUpdate().

void DdMd::Buffer::incrementSendSize ( )

inline

Increment sendSize counter after packing an item (an Atom or Group).

Definition at line 604 of file Buffer.h.

Referenced by DdMd::Group< N >::pack(), DdMd::Atom::packAtom(), DdMd::Atom::packForce(), DdMd::Atom::packGhost(), and DdMd::Atom::packUpdate().

void DdMd::Buffer::endSendBlock ( bool isComplete = true )

Finalize a block in the send buffer.

This method writes the "prefix" section at the beginning of a data block. The descriptor specifies the length of the block, the type of data, and whether the block is "complete".

A block should be marked as incomplete iff the required data of the relevant sendtype did not fit into the buffer. This tells the receiving processor to expect one or more other buffers containing the remaining data of the same type type.

Parameters

isComplete false if data block is incomplete, true otherwise

Definition at line 247 of file Buffer.cpp.

Referenced by DdMd::AtomDistributor::addAtom(), DdMd::Exchanger::exchange(), DdMd::AtomDistributor::newAtomPtr(), DdMd::GroupDistributor< N >::newPtr(), DdMd::GroupStorage< N >::pack(), DdMd::Exchanger::reverseUpdate(), DdMd::AtomCollector::send(), DdMd::GroupCollector< N >::send(), DdMd::GroupDistributor< N >::send(), DdMd::AtomDistributor::send(), and DdMd::Exchanger::update().

bool DdMd::Buffer::beginRecvBlock ( )

Begin to receive a block from the recv buffer.

This method reads the descriptor section at the beginning of a block, and sets the receive cursor to be ready to unpack the first item.

Returns: false if this block is complete, false otherwise.

Definition at line 271 of file Buffer.cpp.

References UTIL_THROW.

Referenced by DdMd::Exchanger::exchange(), DdMd::AtomCollector::nextPtr(), DdMd::GroupCollector< N >::nextPtr(), DdMd::GroupDistributor< N >::receive(), DdMd::AtomDistributor::receive(), DdMd::Exchanger::reverseUpdate(), DdMd::GroupStorage< N >::unpack(), and DdMd::Exchanger::update().

template<typename T >

void DdMd::Buffer::unpack ( T & data )

inline

Function template unpacking one variable from the receive buffer.

This template is used to implement the unpack functions provided by the DdMd::Atom and DdMd::Group classes. It is designed to unpack a single primitive C variable from the buffer. It will work on any plain old data type T for which the assignment (=) operator does a straight bitwise copy.

Parameters

data	variable into which data should be copied from buffer.

Definition at line 578 of file Buffer.h.

References UTIL_THROW.

Referenced by DdMd::Group< N >::unpack(), DdMd::Atom::unpackAtom(), DdMd::Atom::unpackForce(), DdMd::Atom::unpackGhost(), and DdMd::Atom::unpackUpdate().

void DdMd::Buffer::decrementRecvSize ( )

inline

Decrement recvSize counter after completely unpacking an item.

Definition at line 610 of file Buffer.h.

Referenced by DdMd::Group< N >::unpack(), DdMd::Atom::unpackAtom(), DdMd::Atom::unpackForce(), DdMd::Atom::unpackGhost(), and DdMd::Atom::unpackUpdate().

void DdMd::Buffer::endRecvBlock ( )

Finish processing a block in the recv buffer.

This method checks that the recvSize() is zero at the end of a block, and that the receive buffer cursor is at the expected positon, and throws an exception if any suprises occur. It also nullifies the recvSize counter.

Definition at line 301 of file Buffer.cpp.

References UTIL_THROW.

Referenced by DdMd::Exchanger::exchange(), DdMd::AtomCollector::nextPtr(), DdMd::AtomDistributor::receive(), DdMd::Exchanger::reverseUpdate(), DdMd::GroupStorage< N >::unpack(), and DdMd::Exchanger::update().

void DdMd::Buffer::sendRecv	(	MPI::Intracomm &	comm,
		int	source,
		int	dest
	)

Receive from processor send and send to processor recv.

After transmission, clears the send buffer for reuse, by calling clearSend(), and sets the receive buffer for unpacking, by setting recvSize() to the total number of atoms recieved and setting the receive pointer to first atom to be unpacked.

Throws an Exception if atomType() == NONE or sendSize() == 0.

Parameters