Shell Class Reference

#include <Shell.h>

Collaboration diagram for Shell:

Public Member Functions
	Shell ()
	~Shell ()
string	doVersion ()
string	doRevision ()
void	setCwe (ObjId cwe)
ObjId	getCwe () const
bool	isRunning () const
Id	doCreate (string type, ObjId parent, string name, unsigned int numData, NodePolicy nodePolicy=MooseBlockBalance, unsigned int preferredNode=1)
bool	doDelete (ObjId oid)
ObjId	doAddMsg (const string &msgType, ObjId src, const string &srcField, ObjId dest, const string &destField)
void	doQuit ()
void	doStart (double runtime)
void	doNonBlockingStart (double runtime)
void	doReinit ()
void	doStop ()
void	doTerminate ()
void	doMove (Id orig, ObjId newParent)
Id	doCopy (Id orig, ObjId newParent, string newName, unsigned int n, bool toGlobal, bool copyExtMsgs)
ObjId	doFind (const string &path) const
void	doUseClock (string path, string field, unsigned int tick)
Id	doLoadModel (const string &fname, const string &modelpath, const string &solverClass="")
void	doSaveModel (Id model, const string &fileName, bool qflag=0) const
int	doWriteSBML (const string &fname, const string &modelpath)
Id	doReadSBML (const string &fname, const string &modelpath, const string &solverclass="")
void	doSyncDataHandler (Id tgt)
void	doReacDiffMesh (Id baseCompartment)
void	doSetParserIdleFlag (bool isParserIdle)
void	start (double runTime)
void	initAck ()
void	waitForAck ()
void	handleAck (unsigned int ackNode, unsigned int status)
bool	isAckPending () const
void	handleQuit ()
void	handleCreate (const Eref &e, string type, ObjId parent, Id newElm, string name, NodeBalance nb, unsigned int parentMsgIndex)
void	destroy (const Eref &e, ObjId oid)
void	innerCreate (string type, ObjId parent, Id newElm, string name, const NodeBalance &nb, unsigned int parentMsgIndex)
bool	innerCopy (const vector< ObjId > &args, const string &newName, unsigned int n, bool toGlobal, bool copyExtMsgs)
	Does actual work of copying. Returns true on success.
const Msg *	innerAddMsg (string msgType, ObjId src, string srcField, ObjId dest, string destField, unsigned int msgIndex)
void	handleAddMsg (const Eref &e, string msgType, ObjId src, string srcField, ObjId dest, string destField, unsigned int msgIndex)
bool	innerMove (Id orig, ObjId newParent)
void	handleMove (const Eref &e, Id orig, ObjId newParent)
void	handleSync (const Eref &e, Id elm, FuncId fid)
void	handleCopy (const Eref &e, vector< ObjId > args, string newName, unsigned int n, bool toGlobal, bool copyExtMsgs)
bool	innerUseClock (string path, string field, unsigned int tick, unsigned int msgIndex)
void	handleUseClock (const Eref &e, string path, string field, unsigned int tick, unsigned int msgIndex)
void	addClockMsgs (const vector< ObjId > &list, const string &field, unsigned int tick, unsigned int msgIndex)
void	doSetClock (unsigned int tickNum, double dt)
void	warning (const string &text)
void	error (const string &text)
void	setShellElement (Element *shelle)
const ProcInfo *	getProcInfo (unsigned int index) const
void	expectVector (bool flag)
Static Public Member Functions
static void	clearRestructuringQ ()
static void	dropClockMsgs (const vector< ObjId > &list, const string &field)
static void	setHardware (unsigned int numCores, unsigned int numNodes, unsigned int myNode)
static unsigned int	myNode ()
static unsigned int	numNodes ()
static unsigned int	numCores ()
static unsigned int	numProcessThreads ()
static void	loadBalance ()
static void	launchParser ()
static bool	inBlockingParserCall ()
static bool	isSingleThreaded ()
static bool	keepLooping ()
static bool	isParserIdle ()
static void	launchThreads ()
static unsigned int	reduceInt (unsigned int val)
static const Cinfo *	initCinfo ()
static bool	adopt (ObjId parent, Id child, unsigned int msgIndex)
static bool	adopt (Id parent, Id child, unsigned int msgIndex)
	Adaptor for above function. Also static function.
static const ProcInfo *	procInfo ()
	Static func for returning the ProcInfo of the shell.
static bool	chopString (const string &path, vector< string > &ret, char separator= '/')
static bool	isNameValid (const string &name)
static bool	chopPath (const string &path, vector< string > &ret, vector< unsigned int > &index)
static void	cleanSimulation ()
Static Public Attributes
static const unsigned int	OkStatus = ~0
static const unsigned int	ErrorStatus = ~1

Constructor & Destructor Documentation

Shell::Shell ( )

Shell::~Shell ( )

Member Function Documentation

void Shell::addClockMsgs	(	const vector< ObjId > &	list,
		const string &	field,
		unsigned int	tick,
		unsigned int	msgIndex
	)

Utility function to set up messages to schedule a list of Ids using the specified field and tick

bool Shell::adopt	(	Id	parent,
		Id	child,
		unsigned int	msgIndex
	)			`[static]`

Adaptor for above function. Also static function.

References adopt().

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bool Shell::adopt	(	ObjId	parent,
		Id	child,
		unsigned int	msgIndex
	)			`[static]`

Static utility function. Attaches child element to parent element. Must only be called from functions executing in parallel on all nodes, as it does a local message addition MsgIndex is needed to be sure that the same msg identifies parent-child connection on all nodes.

References Finfo::addMsg(), ObjId::element(), Id::element(), ObjId::eref(), Cinfo::findFinfo(), Element::getName(), initCinfo(), and Msg::mid().

Referenced by adopt(), buildFinfoElement(), init(), Msg::initMsgManagers(), innerCopyElements(), Cinfo::makeCinfoElements(), testSetGetExtField(), and testStrSet().

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static bool Shell::chopPath	(	const string &	path,
		vector< string > &	ret,
		vector< unsigned int > &	index
	)			`[static]`

Chop up the path into a vector of Element names, and also fills out a matching vector of indices. If at any level of the path there are no indices or the index is zero, the index entry * remains empty. Otherwise the entry contains a vector with index values for this level of the path. The zeroth position of this index vector is the slowest varying, i.e., most significant. Returns true if it starts at '/'.

Example: /foo/bar[10]/zod[3][4][5] would return: ret: {"foo", "bar", "zod" } index: { {}, {10}, {3,4,5} }

Referenced by testChopPath().

static bool Shell::chopString	(	const string &	path,
		vector< string > &	ret,
		char	separator = `'/'`
	)			`[static]`

Chops up the names in the string into the vector of strings, using the specified separator. Returns true if it is an absolute path, that is, starts with the separator.

Referenced by simpleWildcardFind(), and testChopString().

void Shell::cleanSimulation ( ) [static]

Cleans up all Elements except /root itself, /clock, /classes, and /Msgs. In due course will also do suitable reinitialization of tick and other values.

References Neutral::children(), Eref::data(), and doDelete().

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static void Shell::clearRestructuringQ ( ) [static]

Works through internal queue of operations that modify the structure of the simulation. These operations have to be carefully separated from any other functions or messaging, so this happens while all other threads are blocked.

void Shell::destroy	(	const Eref &	e,
		ObjId	oid
	)

References Eref::data(), Neutral::destroy(), ObjId::eref(), and ObjId::id.

Referenced by initCinfo().

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ObjId Shell::doAddMsg	(	const string &	msgType,
		ObjId	src,
		const string &	srcField,
		ObjId	dest,
		const string &	destField
	)

Sets up a Message of specified type. Later need to consider doing this through MsgSpecs only. Here the 'args' vector handles whatever arguments we may need to pass to the specified msgType.

Referenced by benchmarkMsg(), ReadSwc::build(), ReadCspace::expandEnzyme(), ReadCspace::expandReaction(), makeCompt(), ReadCspace::makePlots(), makeReacTest(), testAssortedMsg(), testClock(), testCopyMsgOps(), testGetMsg(), testGetMsgs(), testMMenzProcess(), testMpiFibonacci(), testMsgElementListing(), testPoolVolumeScaling(), testReacVolumeScaling(), testShellAddMsg(), testStats(), and testTwoReacGetNeighbors().

Id Shell::doCopy	(	Id	orig,
		ObjId	newParent,
		string	newName,
		unsigned int	n,
		bool	toGlobal,
		bool	copyExtMsgs
	)

Copies orig Element to newParent. n specifies how many copies are made. copyExtMsgs specifies whether to also copy messages from orig to objects outside the copy tree. Usually we don't do this.

Referenced by testCopy(), testCopyFieldElement(), testCopyMsgOps(), and testGetMsg().

Id Shell::doCreate	(	string	type,
		ObjId	parent,
		string	name,
		unsigned int	numData,
		NodePolicy	nodePolicy = `MooseBlockBalance`,
		unsigned int	preferredNode = `1`
	)

Create an Element. Returns its id. type: Specifies classname of Objects in Element. parent: Id of parent element name: Name to be used for identifying Element. numData: Size of array.

Referenced by ReadKkit::assignPoolCompartments(), benchmarkMsg(), ReadCspace::expandEnzyme(), ReadCspace::expandReaction(), makeCompt(), ReadCspace::makeMolecule(), ReadCspace::makePlots(), makeReacTest(), makeStandardElements(), setMethod(), testAssortedMsg(), testBuildStoich(), testChildren(), testClockMessaging(), testCopy(), testCopyFieldElement(), testCopyMsgOps(), testDescendant(), testFilterOffNodeTargets(), testFindModelParent(), testGetMsg(), testGetMsgs(), testInterNodeOps(), testMMenz(), testMMenzProcess(), testMove(), testMpiFibonacci(), testMsgElementListing(), testObjIdToAndFromPath(), testPoolVolumeScaling(), testReacVolumeScaling(), testReMesh(), testRunGsolve(), testRunKsolve(), testShellAddMsg(), testShellParserCreateDelete(), testShellParserStart(), testShellSetGet(), testStats(), testSyncSynapseSize(), testTable(), testTreeTraversal(), testTwoReacGetNeighbors(), testVolScaling(), and testWildcard().

bool Shell::doDelete ( ObjId oid )

Delete specified Element and all its children and all Msgs connected to it. This also works for Msgs, which are also identified by an ObjId. Unlike regular objects, only the one Msg entry specified by the DataIndex part of the ObjId argument is deleted.

Referenced by benchmarkMsg(), cleanSimulation(), testAssortedMsg(), testBuildStoich(), testChildren(), testClockMessaging(), testCopy(), testCopyFieldElement(), testCopyMsgOps(), testDescendant(), testFilterOffNodeTargets(), testFindModelParent(), testGetMsg(), testGetMsgs(), testInterNodeOps(), testMMenz(), testMMenzProcess(), testMove(), testMsgElementListing(), testObjIdToAndFromPath(), testPoolVolumeScaling(), testReacVolumeScaling(), testReadKkit(), ReadCspace::testReadModel(), testReMesh(), testRunGsolve(), testRunKsolve(), testSetupReac(), testShellAddMsg(), testShellParserCreateDelete(), testShellSetGet(), testStats(), testSyncSynapseSize(), testTable(), testTreeTraversal(), testTwoReacGetNeighbors(), testVolScaling(), and testWildcard().

ObjId Shell::doFind ( const string & path ) const

Looks up the Id specified by the given path. May include relative references and the internal cwe (current working Element) on the shell

Referenced by Id::Id(), and testTreeTraversal().

Id Shell::doLoadModel	(	const string &	fname,
		const string &	modelpath,
		const string &	solverClass = `""`
	)

Loads in a model to a specified path. Tries to figure out model type from fname or contents of file. Currently knows about kkit, cspace. Soon to learn .p, SBML, NeuroML. Later to learn NineML

void Shell::doMove	(	Id	orig,
		ObjId	newParent
	)

shifts orig Element (including offspring) to newParent. All old hierarchy, data, Msgs etc are preserved below the orig.

References Neutral::child(), Id::element(), ObjId::element(), ObjId::eref(), Element::getName(), Neutral::isDescendant(), ObjId::path(), and warning().

Referenced by ReadKkit::assignPoolCompartments(), ReadKkit::assignReacCompartments(), testMove(), and testObjIdToAndFromPath().

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void Shell::doNonBlockingStart ( double runtime )

Starts off simulation, to run for 'runtime' more than current time. This version returns at once, and the parser can go on to do other things. It has to check with the Shell::isRunning function (accessible as a MOOSE field) to find out if it is finished. Can call 'doStop', 'doTerminate' or 'doReinit' at any time to stop the run with increasing levels of prejudice.

void Shell::doQuit ( )

Cleanly quits simulation, wrapping up all nodes and threads.

References logger, and SetGet0::set().

Referenced by launchParser(), main(), and testShellParserQuit().

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void Shell::doReacDiffMesh ( Id baseCompartment )

This function builds a reac-diffusion mesh starting at the specified ChemCompt, which houses MeshEntry FieldElements. Assumes that the dimensions of the baseCompartment have just been redefined, and we now need to go through and update the child reaction system.

Id Shell::doReadSBML	(	const string &	fname,
		const string &	modelpath,
		const string &	solverclass = `""`
	)

void Shell::doReinit ( )

Reinitializes simulation: time goes to zero, all scheduled objects are set to initial conditions. If simulation is already running, first stops it.

References logger, and SetGet0::set().

Referenced by benchmarkMsg(), ReadKkit::run(), testCopyMsgOps(), testGetMsg(), testMMenzProcess(), testRunGsolve(), testRunKsolve(), testSetupReac(), and testStats().

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string Shell::doRevision ( )

Returns SVN revision number of the software. This information is useful for developers. In release versions it defaults to "0".

References SVN_REVISION.

void Shell::doSaveModel	(	Id	model,
		const string &	fileName,
		bool	qflag = `0`
	)			const

Saves specified model to specified file, using filetype identified by filename extension. Currently known filetypes are: .g: Kkit model

Still to come: .p: GENESIS neuron morphology and channel spec file .sbml: SBML file .nml: NeuroML file .9ml: NineML file .snml: SigNeurML

void Shell::doSetClock	(	unsigned int	tickNum,
		double	dt
	)

Referenced by benchmarkMsg(), initCinfo(), main(), makeReacTest(), ReadKkit::run(), setMethod(), testCopyMsgOps(), testFibonacci(), testGetMsg(), testMMenzProcess(), testMpiFibonacci(), testRunGsolve(), testRunKsolve(), testShellAddMsg(), testShellParserStart(), and testStats().

void Shell::doSetParserIdleFlag ( bool isParserIdle )

This function is called by the parser to tell the ProcessLoop to wait a bit between cycles. Used when we are waiting for user input and there is no point in having the ProcessLoop go at full speed. When flag is true, then the ProcessLoop will sleep a bit, when false it will work at full speed.

void Shell::doStart ( double runtime )

Starts off simulation, to run for 'runtime' more than current time. This version is blocking, and returns only when the simulation is done.

References logger.

Referenced by benchmarkMsg(), ReadKkit::run(), testCopyMsgOps(), testFibonacci(), testGetMsg(), testMMenzProcess(), testMpiFibonacci(), testRunGsolve(), testRunKsolve(), testSetupReac(), testShellAddMsg(), testShellParserStart(), and testStats().

void Shell::doStop ( )

Cleanly stops simulation, ready to take up again from where the stop occurred. Waits till current operations are done.

References SetGet0::set().

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void Shell::doSyncDataHandler ( Id tgt )

This function synchronizes fieldDimension on the DataHandler across nodes. Used after function calls that might alter the number of Field entries in the table.. The tgt is the FieldElement whose fieldDimension needs updating.

void Shell::doTerminate ( )

Terminate ongoing simulation, with prejudice. Uncleanly stops simulation. Things may be in a mess with different objects at different times, but it stops at once.

void Shell::doUseClock	(	string	path,
		string	field,
		unsigned int	tick
	)

Deprecated. Fallback Find function which treats index brackets as part of name string, and does not try to extract integer indices. ObjId doFindWithoutIndexing( const string& path ) const; Connects up process messages from the specified Tick to the targets on the path. Does so for whole Elements, not individual entries in the Element array. The target on the path usually has the 'process' field but other options are allowed, like 'init'

Referenced by benchmarkMsg(), main(), setMethod(), testCopyMsgOps(), testGetMsg(), testMMenzProcess(), testMpiFibonacci(), testRunGsolve(), testRunKsolve(), testShellAddMsg(), testShellParserStart(), and testStats().

string Shell::doVersion ( )

Returns version number of the software.

References MOOSE_VERSION.

int Shell::doWriteSBML	(	const string &	fname,
		const string &	modelpath
	)

Write given model to SBML file. Returns success value.

static void Shell::dropClockMsgs	(	const vector< ObjId > &	list,
		const string &	field
	)			`[static]`

Utility function to unschedule the specified elist operating on the specified field, typically 'process'

void Shell::error ( const string & text )

void Shell::expectVector ( bool flag )

set the gettingVector_ flag

ObjId Shell::getCwe ( ) const

Returns the current working Element of the Shell

Referenced by initCinfo().

const ProcInfo* Shell::getProcInfo ( unsigned int index ) const

void Shell::handleAck	(	unsigned int	ackNode,
		unsigned int	status
	)

Generic handler for ack msgs from various nodes. Keeps track of which nodes have responded.

void Shell::handleAddMsg	(	const Eref &	e,
		string	msgType,
		ObjId	src,
		string	srcField,
		ObjId	dest,
		string	destField,
		unsigned int	msgIndex
	)

Connects src to dest on appropriate fields, with specified msgType. This wrapper function sends the ack back to the master node.

Referenced by initCinfo().

void Shell::handleCopy	(	const Eref &	e,
		vector< ObjId >	args,
		string	newName,
		unsigned int	n,
		bool	toGlobal,
		bool	copyExtMsgs
	)

Deep copy of source element to target, renaming it to newName. The Args are orig, newParent, newElm where the newElm is the Id passed in for the root of the copy. All subsequent created Elements should have successive Ids. The copy may generate an array with n entries. Normally only copies msgs within the tree, but if the flag copyExtMsgs is true then it copies external Msgs too.

Referenced by initCinfo().

void Shell::handleCreate	(	const Eref &	e,
		string	type,
		ObjId	parent,
		Id	newElm,
		string	name,
		NodeBalance	nb,
		unsigned int	parentMsgIndex
	)

Referenced by initCinfo().

void Shell::handleMove	(	const Eref &	e,
		Id	orig,
		ObjId	newParent
	)

Handler to move Element orig onto the newParent.

References innerMove().

Referenced by initCinfo().

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void Shell::handleQuit ( )

Wraps up operations. Doesn't quit instantly, completes the current process cycle first.

Referenced by initCinfo().

void Shell::handleSync	(	const Eref &	e,
		Id	elm,
		FuncId	fid
	)

Handles sync of DataHandler indexing across nodes

void Shell::handleUseClock	(	const Eref &	e,
		string	path,
		string	field,
		unsigned int	tick,
		unsigned int	msgIndex
	)

Referenced by initCinfo().

bool Shell::inBlockingParserCall ( ) [static]

True when the parser is in a call which is being blocked because it requires the event loop to complete some actions.

void Shell::initAck ( )

Initialize acks. This call should be done before the 'send' goes out, because with the wonders of threading we might get a response to the 'send' before this call is executed. This MUST be followed by a waitForAck call.

const Cinfo * Shell::initCinfo ( ) [static]

References d, destroy(), doSetClock(), getCwe(), handleAddMsg(), handleCopy(), handleCreate(), handleMove(), handleQuit(), handleUseClock(), Neutral::initCinfo(), isRunning(), logger, and setCwe().

Referenced by adopt(), init(), and innerMove().

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const Msg* Shell::innerAddMsg	(	string	msgType,
		ObjId	src,
		string	srcField,
		ObjId	dest,
		string	destField,
		unsigned int	msgIndex
	)

Connects src to dest on appropriate fields, with specified msgType. This inner function does NOT send an ack. Returns true on success

bool Shell::innerCopy	(	const vector< ObjId > &	args,
		const string &	newName,
		unsigned int	n,
		bool	toGlobal,
		bool	copyExtMsgs
	)

Does actual work of copying. Returns true on success.

void Shell::innerCreate	(	string	type,
		ObjId	parent,
		Id	newElm,
		string	name,
		const NodeBalance &	nb,
		unsigned int	parentMsgIndex
	)

Function that does the actual work of creating a new Element. The Class of the Moose objects formed is specified by type. The NodeBalance specifies how many entries and how they are distributed across nodes. The parentMsgIndex specifies the index for the parent-child message.

bool Shell::innerMove	(	Id	orig,
		ObjId	newParent
	)

Moves Element orig onto the newParent.

References Finfo::addMsg(), Msg::deleteMsg(), Id::element(), ObjId::element(), ObjId::eref(), Element::findCaller(), Cinfo::findFinfo(), DestFinfo::getFid(), Element::getName(), initCinfo(), and Msg::mid().

Referenced by handleMove().

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bool Shell::innerUseClock	(	string	path,
		string	field,
		unsigned int	tick,
		unsigned int	msgIndex
	)

Sets up scheduling for elements on the path.

bool Shell::isAckPending ( ) const

Test for receipt of acks from all nodes

static bool Shell::isNameValid ( const string & name ) [static]

Checks that the provided name is valid for an object. This returns false if it finds the reserved path chars /#[]

static bool Shell::isParserIdle ( ) [static]

Flag to indicate if the parser is idle. If so, the main ProcessLoop should also slow down to avoid pounding on the CPUs

bool Shell::isRunning ( ) const

Returns flag to indicate whether simulation is still running

References Eref::data(), Id::element(), and Id::eref().

Referenced by initCinfo().

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static bool Shell::isSingleThreaded ( ) [static]

True in single-threaded mode. This is a special mode of the system in which it does not start up the event loop at all, and the whole thing operates on one thread, which is ultimately under the control of the parser. Note that this is distinct from running on one core. It is possible, and even recommended, to run in multithread mode even when the system has just one core to run it on.

bool Shell::keepLooping ( ) [static]

True as long as the main process loop is looping

Referenced by main().

void Shell::launchParser ( ) [static]

Launches Parser. Blocking when the parser blocks.

References Eref::data(), doQuit(), and Id::eref().

Referenced by main().

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static void Shell::launchThreads ( ) [static]

This function sets up the threading for the entire system. It creates all the worker threads and the threads for handling MPI and handling shell requests.

void Shell::loadBalance ( ) [static]

Stub for eventual function to handle load balancing. This must be called to set up default groups.

Regular shell function that requires that the information about the hardware have been loaded in. For now the function just assigns SimGroups

Referenced by init().

unsigned int Shell::myNode ( ) [static]

Referenced by MsgElement::getNode(), LocalDataElement::getNode(), GlobalDataElement::getNode(), FieldElement::getNumOnNode(), ObjId::isDataHere(), Eref::isDataHere(), ObjId::isOffNode(), main(), mooseMyNode(), nonMpiTests(), TestSched::process(), LocalDataElement::setDataSize(), testInterNodeOps(), and testShellParserStart().

unsigned int Shell::numCores ( ) [static]

Referenced by nonMpiTests().

unsigned int Shell::numNodes ( ) [static]

Referenced by Element::digestMessages(), dispatchBuffers(), filterOffNodeTargets(), ObjId::isOffNode(), main(), mooseNumNodes(), nonMpiTests(), LocalDataElement::setDataSize(), testFibonacci(), testFilterOffNodeTargets(), and testSyncSynapseSize().

static unsigned int Shell::numProcessThreads ( ) [static]

static const ProcInfo* Shell::procInfo ( ) [static]

Static func for returning the ProcInfo of the shell.

static unsigned int Shell::reduceInt ( unsigned int val ) [static]

Checks for highest 'val' on all nodes

void Shell::setCwe ( ObjId cwe )

Assigns the current working Element of the Shell

Referenced by initCinfo(), and testTreeTraversal().

void Shell::setHardware	(	unsigned int	numCores,
		unsigned int	numNodes,
		unsigned int	myNode
	)			`[static]`

Assigns the hardware availability. Assumes that each node will have the same number of cores available.

Referenced by init(), and nonMpiTests().

void Shell::setShellElement ( Element * shelle )

Referenced by init().

void Shell::start ( double runTime )

Sets of a simulation for duration runTime. Handles cases including single-thread, multithread, and multinode

void Shell::waitForAck ( )

test for completion of request. This MUST be preceded by an initAck call.

void Shell::warning ( const string & text )

Referenced by doMove().

Member Data Documentation

const unsigned int Shell::ErrorStatus = ~1 [static]

const unsigned int Shell::OkStatus = ~0 [static]

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

shell/Shell.h
shell/Shell.cpp
shell/ShellThreads.cpp

Shell Class Reference

Public Member Functions

Static Public Member Functions

Static Public Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation