Shell Class Reference

#include <Shell.h>

Collaboration diagram for Shell:

Public Member Functions
void	addClockMsgs (const vector< ObjId > &list, const string &field, unsigned int tick, unsigned int msgIndex)
void	destroy (const Eref &e, ObjId oid)
ObjId	doAddMsg (const string &msgType, ObjId src, const string &srcField, ObjId dest, const string &destField)
Id	doCopy (Id orig, ObjId newParent, string newName, unsigned int n, bool toGlobal, bool copyExtMsgs)
	Returns the Id of the root of the copied tree upon success. More...
Id	doCreate (string type, ObjId parent, string name, unsigned int numData, NodePolicy nodePolicy=MooseBlockBalance, unsigned int preferredNode=1)
bool	doDelete (ObjId oid)
ObjId	doFind (const string &path) const
Id	doLoadModel (const string &fname, const string &modelpath, const string &solverClass="")
	Returns the Id of the loaded model. More...
void	doMove (Id orig, ObjId newParent)
void	doNonBlockingStart (double runtime)
void	doQuit ()
void	doReacDiffMesh (Id baseCompartment)
void	doReinit ()
void	doSaveModel (Id model, const string &fileName, bool qflag=0) const
void	doSetClock (unsigned int tickNum, double dt)
void	doSetParserIdleFlag (bool isParserIdle)
void	doStart (double runtime, bool notify=false)
void	doStop ()
void	doSyncDataHandler (Id tgt)
void	doTerminate ()
void	doUseClock (string path, string field, unsigned int tick)
string	doVersion ()
void	error (const string &text)
void	expectVector (bool flag)
ObjId	getCwe () const
const ProcInfo *	getProcInfo (unsigned int index) const
void	handleAck (unsigned int ackNode, unsigned int status)
void	handleAddMsg (const Eref &e, string msgType, ObjId src, string srcField, ObjId dest, string destField, unsigned int msgIndex)
void	handleCopy (const Eref &e, vector< ObjId > args, string newName, unsigned int n, bool toGlobal, bool copyExtMsgs)
void	handleCreate (const Eref &e, string type, ObjId parent, Id newElm, string name, NodeBalance nb, unsigned int parentMsgIndex)
void	handleMove (const Eref &e, Id orig, ObjId newParent)
void	handleQuit ()
	This function is NOT called when simulation ends normally. More...
void	handleSync (const Eref &e, Id elm, FuncId fid)
void	handleUseClock (const Eref &e, string path, string field, unsigned int tick, unsigned int msgIndex)
void	initAck ()
const Msg *	innerAddMsg (string msgType, ObjId src, string srcField, ObjId dest, string destField, unsigned int msgIndex)
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. More...
void	innerCreate (string type, ObjId parent, Id newElm, string name, const NodeBalance &nb, unsigned int parentMsgIndex)
bool	innerMove (Id orig, ObjId newParent)
bool	innerUseClock (string path, string field, unsigned int tick, unsigned int msgIndex)
bool	isAckPending () const
bool	isRunning () const
void	setCwe (ObjId cwe)
void	setShellElement (Element *shelle)
	Shell ()
void	start (double runTime)
void	waitForAck ()
void	warning (const string &text)
	~Shell ()

Static Public Member Functions
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. More...
static bool	chopPath (const string &path, vector< string > &ret, vector< unsigned int > &index)
static bool	chopString (const string &path, vector< string > &ret, char separator= '/')
static void	cleanSimulation ()
	Clean-up MOOSE before shutting down. This function is called whenever keyboard interrupt terminates the simulation. More...
static void	clearRestructuringQ ()
static void	dropClockMsgs (const vector< ObjId > &list, const string &field)
static bool	inBlockingParserCall ()
static const Cinfo *	initCinfo ()
static bool	isNameValid (const string &name)
static bool	isParserIdle ()
static bool	isSingleThreaded ()
static bool	keepLooping ()
static void	launchParser ()
static void	launchThreads ()
static void	loadBalance ()
static unsigned int	myNode ()
static unsigned int	numCores ()
static unsigned int	numNodes ()
static unsigned int	numProcessThreads ()
static const ProcInfo *	procInfo ()
	Static func for returning the ProcInfo of the shell. More...
static unsigned int	reduceInt (unsigned int val)
static void	setHardware (unsigned int numCores, unsigned int numNodes, unsigned int myNode)

Static Public Attributes
static const unsigned int	ErrorStatus = ~1
static const unsigned int	OkStatus = ~0

Private Attributes
ObjId	cwe_
	Current working Element. More...
vector< double * >	getBuf_
bool	gettingVector_
unsigned int	numGetVecReturns_
Element *	shelle_

Static Private Attributes
static vector< unsigned int >	acked_
static bool	doReinit_
static bool	isBlockedOnParser_ = 0
static bool	isParserIdle_
static bool	keepLooping_ = 1
static unsigned int	myNode_
static unsigned int	numAcks_ = 0
static unsigned int	numCores_
static unsigned int	numNodes_
static unsigned int	numProcessThreads_
static ProcInfo	p_
static double	runtime_
static vector< ProcInfo >	threadProcs_

Detailed Description

Definition at line 43 of file Shell.h.

Constructor & Destructor Documentation

Shell::Shell

(

)

Definition at line 152 of file Shell.cpp.

References getBuf_.

    :
    gettingVector_( 0 ),
    numGetVecReturns_( 0 ),
    cwe_( ObjId() )
{
    getBuf_.resize( 1, 0 );
}

Shell::~Shell

(

)

Definition at line 161 of file Shell.cpp.

{
    ;
}

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

Definition at line 924 of file Shell.cpp.

References dropClockMsgs(), and innerAddMsg().

Referenced by innerUseClock().

{
    if ( !Id( 1 ).element() )
        return;
    ObjId clockId( 1 );
    dropClockMsgs( list, field ); // Forbid duplicate PROCESS actions.
    for ( vector< ObjId >::const_iterator i = list.begin();
            i != list.end(); ++i )
    {
        if ( i->element() )
        {
            stringstream ss;
            ss << "proc" << tick;
            const Msg* m = innerAddMsg( "OneToAll",
                                        clockId, ss.str(),
                                        *i, field, msgIndex++ );
            if ( m )
                i->element()->innerSetTick( tick );
        }
    }
}

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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.

Definition at line 654 of file Shell.cpp.

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

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

{
    static const Finfo* pf = Neutral::initCinfo()->findFinfo( "parentMsg" );
    // static const DestFinfo* pf2 = dynamic_cast< const DestFinfo* >( pf );
    // static const FuncId pafid = pf2->getFid();
    static const Finfo* f1 = Neutral::initCinfo()->findFinfo( "childOut" );

    assert( !( child.element() == 0 ) );
    assert( !( child == Id() ) );
    assert( !( parent.element() == 0 ) );

    Msg* m = new OneToAllMsg( parent.eref(), child.element(), msgIndex );
    assert( m );

    // cout << myNode_ << ", Shell::adopt: mid = " << m->mid() << ", pa =" << parent << "." << parent()->getName() << ", kid=" << child << "." << child()->getName() << "\n";

    if ( !f1->addMsg( pf, m->mid(), parent.element() ) )
    {
        cout << "move: Error: unable to add parent->child msg from " <<
             parent.element()->getName() << " to " <<
             child.element()->getName() << "\n";
        return 0;
    }
    return 1;
}

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bool Shell::adopt ( Id  parent, Id  child, unsigned int  msgIndex  )

static

Adaptor for above function. Also static function.

Definition at line 681 of file Shell.cpp.

References adopt().

{
    return adopt( ObjId( parent ), child, msgIndex );
}

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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} }

static func.

Example: /foo/bar[10]/zod[3] would return: ret: {"foo", "bar", "zod" } index: { 0, 10, 3 }

Definition at line 512 of file Shell.cpp.

References chopString(), and extractIndex().

Referenced by doFind(), and testChopPath().

{
    bool isAbsolute = chopString( path, ret, '/' );
    if ( isAbsolute )
    {
        index.clear();
    }
    else
    {
        index.clear();
    }
    for ( unsigned int i = 0; i < ret.size(); ++i )
    {
        index.push_back( 0 );
        if ( ret[i] == "." )
            continue;
        if ( ret[i] == ".." )
        {
            continue;
        }
        if ( !extractIndex( ret[i], index[i] ) )
        {
            cout << "Error: Shell::chopPath: Failed to parse indices in path '" <<
                 path << "'\n";
            ret.resize( 0 );
            index.resize( 0 );
            return isAbsolute;
        }
        size_t pos = ret[i].find_first_of( '[' );
        if ( ret[i].find_first_of( '[' ) != string::npos )
            ret[i] = ret[i].substr( 0, pos );
    }

    return isAbsolute;
}

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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.

Static func to subdivide a string at the specified separator.

Definition at line 459 of file Shell.cpp.

References path.

Referenced by chopPath(), findBraceContent(), innerFind(), matchBeforeBrace(), simpleWildcardFind(), and testChopString().

{
    // /foo/bar/zod
    // foo/bar/zod
    // ./foo/bar/zod
    // ../foo/bar/zod
    // .
    // /
    // ..
    ret.resize( 0 );
    if ( path.length() == 0 )
        return 1; // Treat it as an absolute path

    bool isAbsolute = 0;
    string temp = path;
    if ( path[0] == separator )
    {
        isAbsolute = 1;
        if ( path.length() == 1 )
            return 1;
        temp = temp.substr( 1 );
    }

    string::size_type pos = temp.find_first_of( separator );
    ret.push_back( temp.substr( 0, pos ) );
    while ( pos != string::npos )
    {
        temp = temp.substr( pos + 1 );
        if ( temp.length() == 0 )
            break;
        pos = temp.find_first_of( separator );
        ret.push_back( temp.substr( 0, pos ) );
    }
    return isAbsolute;
}

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void Shell::cleanSimulation ( )

static

Clean-up MOOSE before shutting down. This function is called whenever keyboard interrupt terminates the simulation.

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

Definition at line 1015 of file Shell.cpp.

References Neutral::children(), Eref::data(), moose::debug, doDelete(), Id::eref(), moose::info, and LOG.

Referenced by handle_keyboard_interrupts().

{
    Eref sheller = Id().eref();
    Shell* s = reinterpret_cast< Shell* >( sheller.data() );
    vector< Id > kids;
    Neutral::children( sheller, kids );
    for ( vector< Id >::iterator i = kids.begin(); i != kids.end(); ++i )
    {
        if ( i->value() > 4 )                   /* These are created by users */
        {
            LOG( moose::debug
                    , "Shell::cleanSimulation: deleted cruft at " <<
                 i->value() << ": " << i->path());
            s->doDelete( *i );
        }
    }
    LOG( moose::info, "Cleaned up!");
}

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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
	)

Definition at line 722 of file Shell.cpp.

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

Referenced by initCinfo().

{
    Neutral *n = reinterpret_cast< Neutral* >( e.data() );
    assert( n );
    // cout << myNode_ << ": Shell::destroy done for element id: " << eid << ", name = " << eid.element()->getName() << endl;
    n->destroy( oid.eref(), 0 );
    if ( cwe_.id == oid.id )
        cwe_ = ObjId();
}

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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.

Definition at line 269 of file Shell.cpp.

References BADINDEX, Finfo::checkTarget(), Element::cinfo(), ObjId::dataIndex, Id::element(), Cinfo::findFinfo(), Cinfo::finfoMap(), Element::getName(), ObjId::id, innerAddMsg(), Msg::mid(), myNode_, and SetGet6< A1, A2, A3, A4, A5, A6 >::set().

Referenced by ReadCell::addCanonicalChannel(), ReadKkit::addmsg(), ReadCell::addSpikeGen(), addSpine(), benchmarkMsg(), ReadSwc::build(), ReadCell::buildCompartment(), ReadKkit::buildEnz(), ReadKkit::buildSumTotal(), doClassSpecificMessaging(), ReadCspace::expandEnzyme(), ReadCspace::expandReaction(), ReadKkit::innerAddMsg(), makeCompt(), ReadCspace::makePlots(), makeReacTest(), Stoich::setElist(), testAssortedMsg(), testCalcJunction(), testClock(), testCopyMsgOps(), testGetMsg(), testGetMsgs(), testMMenzProcess(), testMpiFibonacci(), testMsgElementListing(), testPoolVolumeScaling(), testReacVolumeScaling(), testShellAddMsg(), testStats(), and testTwoReacGetNeighbors().

{

    if ( !src.id.element() )
    {
        cout << myNode_ << ": Error: Shell::doAddMsg: src not found" << endl;
        return ObjId();
    }
    if ( !dest.id.element() )
    {
        cout << myNode_ << ": Error: Shell::doAddMsg: dest not found" << endl;
        return ObjId(0, BADINDEX );
    }
    const Finfo* f1 = src.id.element()->cinfo()->findFinfo( srcField );
    if ( !f1 )
    {
        cout << myNode_ << ": Shell::doAddMsg: Error: Failed to find field " << srcField <<
             " on src: " << src.id.element()->getName() << endl;
        return ObjId(0, BADINDEX );
    }
    const Finfo* f2 = dest.id.element()->cinfo()->findFinfo( destField );
    if ( !f2 )
    {
        cout << myNode_ << ": Shell::doAddMsg: Error: Failed to find field " << destField <<
             " on dest: " << dest.id.element()->getName() << endl;
        cout << "Available fields are : " << endl
             << moose::mapToString<string, Finfo*>(dest.id.element()->cinfo()->finfoMap());

        return ObjId( 0, BADINDEX );
    }
    if ( ! f1->checkTarget( f2 ) )
    {
        cout << myNode_ << ": Shell::doAddMsg: Error: Src/Dest Msg type mismatch: " << srcField << "/" << destField << endl;
        return ObjId( 0, BADINDEX );
    }

    const Msg* m = innerAddMsg( msgType, src, srcField, dest, destField, 0 );

    SetGet6< string, ObjId, string, ObjId, string, unsigned int >::set(
        ObjId(), // Apply command to Shell
        "addMsg",   // Function to call.
        msgType,
        src,
        srcField,
        dest,
        destField,
        m->mid().dataIndex
    );

    return m->mid();

    // const Msg* m = innerAddMsg( msgType, src, srcField, dest, destField );
    // return m->mid();
    // return Msg::lastMsg()->mid();
}

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

Returns the Id of the root of the copied tree upon success.

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.

Definition at line 16 of file ShellCopy.cpp.

References Neutral::child(), ObjId::eref(), Neutral::isDescendant(), isNameValid(), Id::nextId(), ObjId::path(), Id::path(), and shelle_.

Referenced by ReadCell::addChannel(), addSpine(), ReadCell::buildCompartment(), buildFromProto(), testCopy(), testCopyFieldElement(), testCopyMsgOps(), and testGetMsg().

{
    if ( newName.length() > 0 && !isNameValid( newName ) ) {
        cout << "Error: Shell::doCopy: Illegal name for copy.\n";
        return Id();
    }

    if ( Neutral::isDescendant( newParent, orig ) ) {
        cout << "Error: Shell::doCopy: Cannot copy object to descendant in tree\n";
        return Id();
    }
    if ( n < 1 ) {
        cout << "Warning: Shell::doCopy( " << orig.path() << " to " <<
            newParent.path() << " ) : numCopies must be > 0, using 1 \n";
        return Id();
    }
    if ( Neutral::child( newParent.eref(), newName ) != Id() ) {
        cout << "Error: Shell::doCopy: Cannot copy object '" << newName <<
               "' onto '" << newParent.path() <<
               "' since object with same name already present.\n";
        return Id();
    }

    Eref sheller( shelle_, 0 );
    Id newElm = Id::nextId();
    vector< ObjId > args;
    args.push_back( orig );
    args.push_back( newParent );
    args.push_back( newElm );
    SetGet5< vector < ObjId >, string, unsigned int, bool, bool >::set(
            ObjId(), "copy",
            args, newName, n, toGlobal, copyExtMsg );
    /*
    if ( innerCopy( args, newName, n, toGlobal, copyExtMsg ) )
        return newElm;
    else
        return Id();
    */
    return newElm;
}

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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.

This is the version used by the parser. Acts as a blocking, serial-like interface to a potentially multithread, multinode call. Returns the new Id index upon success, otherwise returns Id(). The data of the new Element is not necessarily allocated at this point, that can be deferred till the global Instantiate or Reset calls. Idea is that the model should be fully defined before load balancing.

Definition at line 181 of file Shell.cpp.

References Cinfo::banCreation(), Neutral::child(), ObjId::element(), ObjId::eref(), Cinfo::find(), isNameValid(), name, Id::nextId(), OneToAllMsg::numMsg(), ObjId::path(), SetGet6< A1, A2, A3, A4, A5, A6 >::set(), moose::showWarn(), and warning().

Referenced by ReadKkit::assignPoolCompartments(), benchmarkMsg(), ReadKkit::buildChan(), ReadCell::buildCompartment(), ReadKkit::buildEnz(), ReadKkit::buildGraph(), ReadKkit::buildGroup(), ReadKkit::buildInfo(), ReadKkit::buildPlot(), ReadKkit::buildPool(), ReadKkit::buildReac(), ReadKkit::buildStim(), ReadKkit::buildSumTotal(), ReadKkit::buildTable(), doLoadModel(), ReadCspace::expandEnzyme(), ReadCspace::expandReaction(), makeCompt(), ReadCspace::makeMolecule(), ReadCspace::makePlots(), makeReacTest(), makeStandardElements(), ReadCell::read(), ReadKkit::read(), ReadCell::startGraftCell(), test_to_py(), testAssortedMsg(), testBuildStoich(), testCalcJunction(), testCellDiffn(), testChildren(), testClockMessaging(), testCopy(), testCopyFieldElement(), testCopyMsgOps(), testCylDiffn(), testCylDiffnWithStoich(), testDescendant(), testFilterOffNodeTargets(), testFindModelParent(), testGetMsg(), testGetMsgs(), testInterNodeOps(), testMMenz(), testMMenzProcess(), testMove(), testMpiFibonacci(), testMsgElementListing(), testObjIdToAndFromPath(), testPoolVolumeScaling(), testReacVolumeScaling(), testReMesh(), testRunGsolve(), testRunKsolve(), testShellAddMsg(), testShellParserCreateDelete(), testShellParserStart(), testShellSetGet(), testSmallCellDiffn(), testStats(), testSyncSynapseSize(), testTable(), testTaperingCylDiffn(), testTreeTraversal(), testTwoReacGetNeighbors(), testVolScaling(), and testWildcard().

{

    const Cinfo* c = Cinfo::find( type );
    if ( !isNameValid( name ) )
    {
        stringstream ss;
        ss << "Shell::doCreate: bad character in name'" << name <<
           "'. No Element created";
        warning( ss.str() );
        return Id();
    }

    if ( c )
    {
        if ( c->banCreation() )
        {
            stringstream ss;
            ss << "Shell::doCreate: Cannot create an object of class '" <<
               type << "' because it is an abstract base class or a FieldElement.\n";
            warning( ss.str() );
            return Id();
        }
        Element* pa = parent.element();
        if ( !pa )
        {
            stringstream ss;
            ss << "Shell::doCreate: Parent Element'" << parent << "' not found. No Element created";
            warning( ss.str() );
            return Id();
        }

        // TODO: This should be an error in future.
        // This logic of handling already existing path is now handled in
        // melements.cpp . Calling this section should become an error in
        // future.
        if ( Neutral::child( parent.eref(), name ) != Id() )
        {
            stringstream ss;
            ss << "Object with same path already present : " << parent.path()
                << "/" << name;
            moose::showWarn( ss.str() );
            return Id();
        }
        // Get the new Id ahead of time and pass to all nodes.
        Id ret = Id::nextId();
        NodeBalance nb( numData, nodePolicy, preferredNode );
        // Get the parent MsgIndex ahead of time and pass to all nodes.
        unsigned int parentMsgIndex = OneToAllMsg::numMsg();

        SetGet6< string, ObjId, Id, string, NodeBalance, unsigned int >::set(
            ObjId(), // Apply command to Shell
            "create",   // Function to call.
            type,       // class of new object
            parent,     // Parent
            ret,        // id of new object
            name,       // name of new object
            nb,         // Node balance configuration
            parentMsgIndex  // Message index of child-parent msg.
        );

        // innerCreate( type, parent, ret, name, numData, isGlobal );

        return ret;
    }
    else
    {
        stringstream ss;
        ss << "Shell::doCreate: Class '" << type << "' not known. No Element created";
        warning( ss.str() );
    }

    return Id();
}

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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.

Definition at line 259 of file Shell.cpp.

References SetGet1< A >::set().

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

{
    SetGet1< ObjId >::set( ObjId(), "delete", oid );
    /*
       Neutral n;
       n.destroy( i.eref(), 0 );
       */
    return true;
}

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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

Definition at line 549 of file Shell.cpp.

References BADINDEX, Neutral::child(), chopPath(), cwe_, ObjId::dataIndex, ObjId::element(), ObjId::eref(), ObjId::fieldIndex, Element::hasFields(), Element::numData(), and Neutral::parent().

Referenced by ReadKkit::buildChan(), ReadKkit::buildEnz(), ReadKkit::buildGraph(), ReadKkit::buildGroup(), ReadKkit::buildPlot(), ReadKkit::buildPool(), ReadKkit::buildReac(), ReadKkit::buildStim(), ReadKkit::buildTable(), Id::Id(), and testTreeTraversal().

{
    if ( path == "/" || path == "/root" )
        return ObjId();

    ObjId curr;
    vector< string > names;
    vector< unsigned int > indices;
    bool isAbsolute = chopPath( path, names, indices );
    assert( names.size() == indices.size() );

    if ( !isAbsolute )
        curr = cwe_;

    for ( unsigned int i = 0; i < names.size(); ++i )
    {
        if ( names[i] == "." )
        {
        }
        else if ( names[i] == ".." )
        {
            curr = Neutral::parent( curr.eref() );
        }
        else
        {
            ObjId pa = curr;
            curr = Neutral::child( curr.eref(), names[i] );
            if ( curr == ObjId() ) // Neutral::child returned Id(), ie, bad.
                return ObjId( 0, BADINDEX );
            if ( curr.element()->hasFields() )
            {
                curr.dataIndex = pa.dataIndex;
                curr.fieldIndex = indices[i];
            }
            else
            {
                curr.dataIndex = indices[i];
                if ( curr.element()->numData() <= curr.dataIndex  )
                    return ObjId( 0, BADINDEX );
            }
        }
    }

    assert( curr.element() );
    if ( curr.element()->numData() <= curr.dataIndex )
        return ObjId( 0, BADINDEX );
    if ( curr.fieldIndex > 0 && !curr.element()->hasFields() )
        return ObjId( 0, BADINDEX );

    return curr;
}

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

Returns the Id of the loaded model.

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

Definition at line 132 of file LoadModels.cpp.

References ReadSwc::build(), Element::cinfo(), CSPACE, cwe_, doCreate(), DOTP, Id::element(), moose::failed, findModelParent(), findModelType(), moose::info, Cinfo::isA(), KKIT, LOG, ReadCspace::makePlots(), ReadCell::read(), ReadKkit::read(), ReadCspace::readModelString(), SWC, and UNKNOWN.

{
    ifstream fin( fileName.c_str() );
    if ( !fin )
    {
        LOG( moose::failed, "Shell::doLoadModel: could not open file " << fileName );
        return Id();
    }

    string modelName;
    Id parentId;

    if ( !( findModelParent ( cwe_, modelPath, parentId, modelName ) ) )
        return Id();

    string line;
    switch ( findModelType( fileName, fin, line ) )
    {
    case DOTP:
    {
        ReadCell rc;
        return rc.read( fileName, modelName, parentId );
        return Id();
    }
    case SWC:
    {
        LOG( moose::info, "In doLoadModel for SWC" );
        ReadSwc rs( fileName );
        Id model = parentId;
        if ( !parentId.element()->cinfo()->isA( "Neuron" ) )
        {
            model = doCreate( "Neuron", parentId, modelName, 1 );
        }
        rs.build( model, 0.5e-3, 1.0, 1.0, 0.01 );
        return model;
    }
    case KKIT:
    {
        string sc = solverClass;
        ReadKkit rk;
        Id ret = rk.read( fileName, modelName, parentId, sc);
        return ret;
    }
    break;
    case CSPACE:
    {
        string sc = solverClass;
        ReadCspace rc;
        Id ret = rc.readModelString( line, modelName, parentId, sc);
        rc.makePlots( 1.0 );
        return ret;
    }
    case UNKNOWN:
    default:
        cout << "Error: Shell::doLoadModel: File type of '" <<
             fileName << "' is unknown\n";
    }
    return Id();
}

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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.

Definition at line 390 of file Shell.cpp.

References Neutral::child(), ObjId::element(), Id::element(), ObjId::eref(), Element::getName(), Neutral::isDescendant(), name, ObjId::path(), SetGet2< A1, A2 >::set(), and warning().

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

{
    if ( orig == Id() )
    {
        cout << "Error: Shell::doMove: Cannot move root Element\n";
        return;
    }

    if ( newParent.element() == 0 )
    {
        cout << "Error: Shell::doMove: Cannot move object to null parent \n";
        return;
    }
    if ( Neutral::isDescendant( newParent, orig ) )
    {
        cout << "Error: Shell::doMove: Cannot move object to descendant in tree\n";
        return;

    }
    const string& name = orig.element()->getName();
    if ( Neutral::child( newParent.eref(), name ) != Id() )
    {
        stringstream ss;
        ss << "Shell::doMove: Object with same name already present: '"
           << newParent.path() << "/" << name << "'. Move failed.";
        warning( ss.str() );
        return;
    }

    SetGet2< Id, ObjId >::set( ObjId(), "move", orig, newParent );
    // innerMove( orig, newParent );
}

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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.

Definition at line 327 of file Shell.cpp.

References SetGet0::set().

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

{
    SetGet0::set( ObjId(), "quit" );
}

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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.

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.

Definition at line 362 of file Shell.cpp.

References SetGet0::set().

Referenced by benchmarkMsg(), ReadKkit::read(), ReadKkit::run(), testCalcJunction(), testCellDiffn(), testCopyMsgOps(), testCylDiffn(), testCylDiffnWithStoich(), testGetMsg(), testMMenzProcess(), testRunGsolve(), testRunKsolve(), testSetupReac(), testSmallCellDiffn(), testStats(), and testTaperingCylDiffn().

{

    Id clockId( 1 );
    SetGet0::set( clockId, "reinit" );

}

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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

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

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

Definition at line 31 of file SaveModels.cpp.

References writeKkit().

{
    // string modelFamily = Field< string >::get( model, "modelFamily" );
    // if ( modelFamily != "kinetic" ) {
    //  cout << "Warning: Shell::doSaveModel: Do not know how to save "
    //          "model of family '" << modelFamily << "'.\n";
    //  return;
    // }

    size_t pos = fileName.find( "." );
    string fileType = fileName.substr( pos );

    if ( fileType == ".g" ) { // kkit model requested.
            // cout << "Cannot write kkit model at this point\n";
            writeKkit( model, fileName );
    } else if (fileType == ".cspace"){
            // writeCspace( model, fileName );
            cout << "Cannot write cspace model at this point\n";
    } else {
        cout << "Warning: Shell::doSaveModel: Do not know how to save "
                "model of file type '" << fileType << "'.\n";
    }
}

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

Definition at line 377 of file Shell.cpp.

References LookupField< L, A >::set().

Referenced by benchmarkMsg(), getShell(), initCinfo(), main(), makeReacTest(), ReadKkit::run(), setMethod(), testCalcJunction(), testCellDiffn(), testCopyMsgOps(), testCylDiffn(), testCylDiffnWithStoich(), testFibonacci(), testGetMsg(), testMMenzProcess(), testMpiFibonacci(), testRunGsolve(), testRunKsolve(), testShellAddMsg(), testShellParserStart(), testSmallCellDiffn(), testStats(), and testTaperingCylDiffn().

{
    LookupField< unsigned int, double >::set( ObjId( 1 ), "tickDt", tickNum, dt );
}

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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,
		bool	notify = false
	)

Starts off simulation, to run for 'runtime' more than current time. This version is blocking, and returns only when the simulation is done. If `nofity = true' then also notify user whenever 10% of simulation is over.

Definition at line 332 of file Shell.cpp.

References Streamer::cleanUp(), SetGet2< A1, A2 >::set(), and wildcardFind().

Referenced by benchmarkMsg(), ReadKkit::run(), testCalcJunction(), testCellDiffn(), testCopyMsgOps(), testCylDiffn(), testCylDiffnWithStoich(), testFibonacci(), testGetMsg(), testMMenzProcess(), testMpiFibonacci(), testRunGsolve(), testRunKsolve(), testSetupReac(), testShellAddMsg(), testShellParserStart(), testSmallCellDiffn(), testStats(), and testTaperingCylDiffn().

{
    Id clockId( 1 );
    SetGet2< double, bool >::set( clockId, "start", runtime, notify );

    /*-----------------------------------------------------------------------------
     *  Now that simulation is over, call cleanUp function of Streamer class
     *  objects. The purpose of this is to write whatever is left in tables to
     *  the output file.
     *-----------------------------------------------------------------------------*/
    vector< ObjId > streamers;
    wildcardFind( "/##[TYPE=Streamer]", streamers );
    // LOG( moose::debug,  "total streamers " << streamers.size( ) );
    for( vector<ObjId>::const_iterator itr = streamers.begin()
            ; itr != streamers.end(); itr++ )
    {
        Streamer* pStreamer = reinterpret_cast<Streamer*>( itr->data( ) );
        pStreamer->cleanUp( );
    }
}

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void Shell::doStop

(

)

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

Definition at line 370 of file Shell.cpp.

References SetGet0::set().

{
    Id clockId( 1 );
    SetGet0::set( clockId, "stop" );
}

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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
	)

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'

Definition at line 382 of file Shell.cpp.

References OneToAllMsg::numMsg(), and SetGet4< A1, A2, A3, A4 >::set().

Referenced by benchmarkMsg(), getShell(), main(), setMethod(), testCalcJunction(), testCellDiffn(), testCopyMsgOps(), testCylDiffn(), testCylDiffnWithStoich(), testGetMsg(), testMMenzProcess(), testMpiFibonacci(), testRunGsolve(), testRunKsolve(), testShellAddMsg(), testShellParserStart(), testSmallCellDiffn(), testStats(), and testTaperingCylDiffn().

{
    unsigned int msgIndex = OneToAllMsg::numMsg();
    SetGet4< string, string, unsigned int, unsigned int >::set( ObjId(),
            "useClock", path, field, tick, msgIndex );
    // innerUseClock( path, field, tick);
}

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string Shell::doVersion

(

)

Returns version number of the software.

Definition at line 605 of file Shell.cpp.

References MOOSE_VERSION.

{
    return MOOSE_VERSION;
}

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'

Definition at line 886 of file Shell.cpp.

References Msg::deleteMsg(), DestFinfo::getFid(), and insertSharedMsgs().

Referenced by addClockMsgs().

{
    vector< ObjId > msgs; // These are the messages to delete.
    for ( vector< ObjId >::const_iterator
            i = list.begin(); i != list.end(); ++i )
    {
        // Sanity check: shouldn't try to operate on already deleted objects
        if ( i->element() )
        {
            const Finfo* f = i->element()->cinfo()->findFinfo( field );
            const DestFinfo* df = dynamic_cast< const DestFinfo *>( f );
            if ( df )
            {
                FuncId fid = df->getFid();

                // These are the messages to be zapped
                vector< ObjId > caller;
                if ( i->element()->getInputMsgs( caller, fid ) > 0 )
                {
                    msgs.insert( msgs.end(), caller.begin(), caller.end() );
                }
            }
            else
            {
                insertSharedMsgs( f, i->element(), msgs );
            }
        }
    }
    // Do the unique/erase bit. My favourite example of C++ hideousity.
    sort( msgs.begin(), msgs.end() );
    msgs.erase( unique( msgs.begin(), msgs.end() ), msgs.end() );
    // Delete them.
    for( vector< ObjId >::iterator i = msgs.begin(); i != msgs.end(); ++i )
        Msg::deleteMsg( *i );
}

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void Shell::error

(

const string &

text

)

Definition at line 1006 of file Shell.cpp.

{
    cout << "Error: Shell:: " << text << endl;
}

void Shell::expectVector

(

bool

flag

)

set the gettingVector_ flag

ObjId Shell::getCwe

(

)

const

Returns the current working Element of the Shell

Definition at line 615 of file Shell.cpp.

References cwe_.

Referenced by Neuron::buildElist(), Neuron::getExprElist(), Neuron::getExprVal(), initCinfo(), and innerFind().

{
    return cwe_;
}

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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.

Wrapper function, that does the ack. Other functions also use the inner function to build message trees, so we don't want it to emit multiple acks.

Definition at line 738 of file Shell.cpp.

References innerAddMsg(), and myNode().

Referenced by initCinfo().

{
    // Node 0 will have already called innerAddMsg to get the msgIndex
    if ( myNode() != 0 )
        innerAddMsg( msgType, src, srcField, dest, destField, msgIndex );
    /*
    if ( innerAddMsg( msgType, src, srcField, dest, destField ) )
        ack()->send( Eref( shelle_, 0 ), Shell::myNode(), OkStatus );
    else
        ack()->send( Eref( shelle_, 0), Shell::myNode(), ErrorStatus );
    */
}

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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.

Definition at line 162 of file ShellCopy.cpp.

References innerCopy().

Referenced by initCinfo().

{
    if ( !innerCopy( args, newName, n, toGlobal, copyExtMsgs ) ) {
        cout << "Error on Shell::myNode()::Shell::handleCopy for " <<
                newName << ", " << n << endl;
    }
    /*
    static const Finfo* ackf =
        Shell::initCinfo()->findFinfo( "ack" );
    static const SrcFinfo2< unsigned int, unsigned int >*
        ack = dynamic_cast< const SrcFinfo2< unsigned int, unsigned int >* >( ackf );
    assert( ackf );
    assert( ack );

    if ( innerCopy( args, newName, n, toGlobal, copyExtMsgs ) )
        ack->send( Eref( shelle_, 0 ), Shell::myNode(), ErrorStatus );
    else
        ack->send( Eref( shelle_, 0 ), Shell::myNode(), OkStatus );
    */
}

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

This function handles the message request to create an Element. This request specifies the Id of the new Element and is handled on all nodes.

In due course we also have to set up the node decomposition of the Element, but for now the num indicates the total # of array entries. This gets a bit complicated if the Element is a multidim array.

Definition at line 638 of file Shell.cpp.

References innerCreate().

Referenced by initCinfo().

{
    innerCreate( type, parent, newElm, name, nb, parentMsgIndex );
}

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

Handler to move Element orig onto the newParent.

Definition at line 851 of file Shell.cpp.

References innerMove().

Referenced by initCinfo().

{

    innerMove( orig, newParent );
    /*
    if ( innerMove( orig, newParent ) )
        ack()->send( Eref( shelle_, 0 ), Shell::myNode(), OkStatus );
    else
        ack()->send( Eref( shelle_, 0 ), Shell::myNode(), ErrorStatus );
        */
}

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void Shell::handleQuit

(

)

This function is NOT called when simulation ends normally.

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

Definition at line 990 of file Shell.cpp.

References keepLooping_.

Referenced by initCinfo().

{
    Shell::keepLooping_ = 0;
}

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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
	)

Definition at line 972 of file Shell.cpp.

References innerUseClock().

Referenced by initCinfo().

{
    // cout << q->getProcInfo()->threadIndexInGroup << ": in Shell::handleUseClock with path " << path << endl << flush;
    innerUseClock( path, field, tick, msgIndex );
    /*
    if ( innerUseClock( path, field, tick ) )
        ack()->send( Eref( shelle_, 0 ),
            Shell::myNode(), OkStatus );
    else
        ack()->send( Eref( shelle_, 0 ),
            Shell::myNode(), ErrorStatus );
            */
}

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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.

Definition at line 86 of file ShellThreads.cpp.

References isBlockedOnParser_.

{
    return isBlockedOnParser_;
}

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

Definition at line 46 of file Shell.cpp.

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

Referenced by init().

{

// Value Finfos
    static ReadOnlyValueFinfo< Shell, bool > isRunning(
        "isRunning",
        "Flag: Checks if simulation is in progress",
        &Shell::isRunning );

    static ValueFinfo< Shell, ObjId > cwe(
        "cwe",
        "Current working Element",
        &Shell::setCwe,
        &Shell::getCwe );

// Dest Finfos: Functions handled by Shell
    static DestFinfo handleUseClock( "useClock",
                                     "Deals with assignment of path to a given clock."
                                     " Arguments: path, field, tick number. ",
                                     new EpFunc4< Shell, string, string, unsigned int, unsigned int >(
                                         &Shell::handleUseClock )
                                   );
    static DestFinfo handleCreate( "create",
                                   "create( class, parent, newElm, name, numData, isGlobal )",
                                   new EpFunc6< Shell, string, ObjId, Id, string, NodeBalance, unsigned int >( &Shell::handleCreate ) );

    static DestFinfo handleDelete( "delete",
                                   "When applied to a regular object, this function operates "
                                   "on the Id (element) specified by the ObjId argument. "
                                   "The function deletes the entire object "
                                   "array on this Id, including all dataEntries on it,"
                                   "all its messages, and all its children. The DataIndex here "
                                   "is ignored, and all dataEntries are destroyed. \n"
                                   "When applied to a message: Destroys only that one specific "
                                   "message identified by the full ObjId. \n"
                                   "Args: ObjId\n",
                                   new EpFunc1< Shell, ObjId >( & Shell::destroy ) );

    static DestFinfo handleAddMsg( "addMsg",
                                   "Makes a msg. Arguments are:"
                                   " msgtype, src object, src field, dest object, dest field",
                                   new EpFunc6< Shell, string, ObjId, string, ObjId, string, unsigned int >
                                   ( & Shell::handleAddMsg ) );
    static DestFinfo handleQuit( "quit",
                                 "Stops simulation running and quits the simulator",
                                 new OpFunc0< Shell >( & Shell::handleQuit ) );
    static DestFinfo handleMove( "move",
                                 "handleMove( Id orig, Id newParent ): "
                                 "moves an Element to a new parent",
                                 new EpFunc2< Shell, Id, ObjId >( & Shell::handleMove ) );
    static DestFinfo handleCopy( "copy",
                                 "handleCopy( vector< Id > args, string newName, unsigned int nCopies, bool toGlobal, bool copyExtMsgs ): "
                                 " The vector< Id > has Id orig, Id newParent, Id newElm. "
                                 "This function copies an Element and all its children to a new parent."
                                 " May also expand out the original into nCopies copies."
                                 " Normally all messages within the copy tree are also copied. "
                                 " If the flag copyExtMsgs is true, then all msgs going out are also copied.",
                                 new EpFunc5< Shell, vector< ObjId >, string, unsigned int, bool, bool >(
                                     & Shell::handleCopy ) );

    static DestFinfo setclock( "setclock",
                               "Assigns clock ticks. Args: tick#, dt",
                               new OpFunc2< Shell, unsigned int, double >( & Shell::doSetClock ) );

    static Finfo* shellFinfos[] =
    {
        &setclock,
//  Shared msg
        // &master,
        // &worker,
        &handleCreate,
        &handleDelete,
        &handleCopy,
        &handleMove,
        &handleAddMsg,
        &handleQuit,
        &handleUseClock,
    };

    static Dinfo< Shell > d;
    static Cinfo shellCinfo (
        "Shell",
        Neutral::initCinfo(),
        shellFinfos,
        sizeof( shellFinfos ) / sizeof( Finfo* ),
        &d
        //new Dinfo< Shell >()
    );

#ifdef ENABLE_LOGGER
    float time = (float(clock() - t)/CLOCKS_PER_SEC);
    logger.initializationTime.push_back( time );
#endif

    return &shellCinfo;
}

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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

The actual function that adds messages. Does NOT send an ack. The msgIndex specifies the index on which to place this message. If the value is zero it does an automatic placement. Returns zero on failure.

Definition at line 759 of file Shell.cpp.

References Finfo::addMsg(), Finfo::checkTarget(), Element::cinfo(), Id::element(), ObjId::eref(), Cinfo::findFinfo(), Element::getName(), ObjId::id, and myNode_.

Referenced by addClockMsgs(), doAddMsg(), and handleAddMsg().

{
    /*
    cout << myNode_ << ", Shell::handleAddMsg: " <<
        msgType << ", " << mid <<
        ", src =" << src << "." << srcField <<
        ", dest =" << dest << "." << destField << "\n";
        */
    const Finfo* f1 = src.id.element()->cinfo()->findFinfo( srcField );
    if ( f1 == 0 ) return 0;
    const Finfo* f2 = dest.id.element()->cinfo()->findFinfo( destField );
    if ( f2 == 0 ) return 0;

    // Should have been done before msgs request went out.
    assert( f1->checkTarget( f2 ) );

    Msg *m = 0;
    if ( msgType == "diagonal" || msgType == "Diagonal" )
    {
        m = new DiagonalMsg( src.id.element(), dest.id.element(),
                             msgIndex );
    }
    else if ( msgType == "sparse" || msgType == "Sparse" )
    {
        m = new SparseMsg( src.id.element(), dest.id.element(), msgIndex );
    }
    else if ( msgType == "Single" || msgType == "single" )
    {
        m = new SingleMsg( src.eref(), dest.eref(), msgIndex );
    }
    else if ( msgType == "OneToAll" || msgType == "oneToAll" )
    {
        m = new OneToAllMsg( src.eref(), dest.id.element(), msgIndex );
    }
    else if ( msgType == "AllToOne" || msgType == "allToOne" )
    {
        m = new OneToAllMsg( dest.eref(), src.id.element(), msgIndex ); // Little hack.
    }
    else if ( msgType == "OneToOne" || msgType == "oneToOne" )
    {
        m = new OneToOneMsg( src.eref(), dest.eref(), msgIndex );
    }
    else
    {
        cout << myNode_ <<
             ": Error: Shell::handleAddMsg: msgType not known: "
             << msgType << endl;
        return m;
    }
    if ( m )
    {
        if ( f1->addMsg( f2, m->mid(), src.id.element() ) )
        {
            return m;
        }
        delete m;
        m = 0;
    }
    cout << myNode_ <<
         ": Error: Shell::handleAddMsg: Unable to make/connect Msg: "
         << msgType << " from " << src.id.element()->getName() <<
         " to " << dest.id.element()->getName() << endl;
    return m;
}

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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.

Definition at line 144 of file ShellCopy.cpp.

References innerCopyElements(), and innerCopyMsgs().

Referenced by handleCopy().

{
    map< Id, Id > tree;
    // args are orig, newParent, newElm.
    assert( args.size() == 3 );
    Element* e = innerCopyElements( args[0], args[1], args[2],
                    n, toGlobal, tree );
    if ( !e ) {
        return 0;
    }
    if ( newName != "" )
        e->setName( newName );
    //innerCopyData( orig, newParent );
    innerCopyMsgs( tree, n, copyExtMsgs );
    return 1;
}

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

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.

This function actually creates the object. Runs on all nodes. Assumes we've already done all the argument checking.

Definition at line 690 of file Shell.cpp.

References adopt(), Cinfo::find(), Clock::lookupDefaultTick(), MooseBlockBalance, MooseGlobal, MooseSingleNode, Cinfo::name(), NodeBalance::numData, NodeBalance::policy, and Element::setTick().

Referenced by handleCreate(), and Cell::setupSolver().

{
    const Cinfo* c = Cinfo::find( type );
    if ( c )
    {
        Element* ret = 0;
        switch ( nb.policy )
        {
        case MooseGlobal:
            ret = new GlobalDataElement( newElm, c, name, nb.numData );
            break;
        case MooseBlockBalance:
            ret = new LocalDataElement( newElm, c, name, nb.numData );
            break;
        case MooseSingleNode:
            cout << "Error: Shell::innerCreate: Yet to implement SingleNodeDataElement. Making BlockBalance.\n";
            ret = new LocalDataElement( newElm, c, name, nb.numData );
            // ret = new SingleNodeDataElement( newElm, c, name, numData, nb.preferredNode );
            break;
        };
        assert( ret );
        adopt( parent, newElm, msgIndex );
        ret->setTick( Clock::lookupDefaultTick( c->name() ) );
    }
    else
    {
        assert( 0 );
    }
}

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

Moves Element orig onto the newParent.

Definition at line 826 of file Shell.cpp.

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

Referenced by handleMove().

{
    static const Finfo* pf = Neutral::initCinfo()->findFinfo( "parentMsg" );
    static const DestFinfo* pf2 = dynamic_cast< const DestFinfo* >( pf );
    static const FuncId pafid = pf2->getFid();
    static const Finfo* f1 = Neutral::initCinfo()->findFinfo( "childOut" );

    assert( !( orig == Id() ) );
    assert( !( newParent.element() == 0 ) );

    ObjId mid = orig.element()->findCaller( pafid );
    Msg::deleteMsg( mid );

    Msg* m = new OneToAllMsg( newParent.eref(), orig.element(), 0 );
    assert( m );
    if ( !f1->addMsg( pf, m->mid(), newParent.element() ) )
    {
        cout << "move: Error: unable to add parent->child msg from " <<
             newParent.element()->getName() << " to " <<
             orig.element()->getName() << "\n";
        return 0;
    }
    return 1;
}

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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.

Definition at line 948 of file Shell.cpp.

References addClockMsgs(), and wildcardFind().

Referenced by handleUseClock().

{
    vector< ObjId > list;
    wildcardFind( path, list ); // By default scans only Elements.
    if ( list.size() == 0 )
    {
        // cout << "Warning: Shell::innerUseClock: no Elements found on path " << path << endl;
        return 0;
    }
    // string tickField = "proc";
    // Hack to get around a common error.
    if ( field.substr( 0, 4 ) == "proc" || field.substr( 0, 4 ) == "Proc" )
        field = "proc";
    if ( field.substr( 0, 4 ) == "init" || field.substr( 0, 4 ) == "Init" )
        field = "init";

    addClockMsgs( list, field, tick, msgIndex );
    for ( vector< ObjId >::iterator
            i = list.begin(); i != list.end(); ++i )
        i->id.element()->innerSetTick( tick );
    return 1;
}

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bool Shell::isAckPending

(

)

const

Test for receipt of acks from all nodes

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 func to check if an object name is legal. True if legal.

Definition at line 499 of file Shell.cpp.

Referenced by doCopy(), doCreate(), and Neutral::setName().

{
    return ( name.length() > 0 &&
             name.find_first_of( "[] #?\"/\\" ) == string::npos );
}

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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

Definition at line 620 of file Shell.cpp.

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

Referenced by initCinfo().

{
    static Id clockId( 1 );
    assert( clockId.element() != 0 );

    return ( reinterpret_cast< const Clock* >( clockId.eref().data() ) )->isRunning();
}

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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

Definition at line 996 of file Shell.cpp.

References keepLooping_.

Referenced by main().

{
    return keepLooping_;
}

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void Shell::launchParser ( )

static

Launches Parser. Blocking when the parser blocks.

Definition at line 28 of file ShellThreads.cpp.

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

Referenced by main().

{
    Id shellId;
    Shell* s = reinterpret_cast< Shell* >( shellId.eref().data() );
    bool quit = 0;

    cout << "moose : " << flush;
    while ( !quit ) {
        string temp;
        cin >> temp;
        if ( temp == "quit" || temp == "q" ) {
            s->doQuit();
            quit = 1;
        }
    }
    cout << "\nQuitting Moose\n" << flush;
}

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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

Definition at line 60 of file ShellThreads.cpp.

Referenced by init().

{
    // Need more info here on how to set up groups distributed over
    // nodes. In fact this will have to be computed _after_ the
    // simulation is loaded. Will also need quite a bit of juggling between
    // nodes when things get really scaled up.
    //
    // Note that the messages have to be rebuilt after this call.
    // Note that this function is called independently on each node.
}

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unsigned int Shell::myNode ( )

static

Definition at line 81 of file ShellThreads.cpp.

References myNode_.

Referenced by PostMaster::addToSendBuf(), PostMaster::addToSetBuf(), PostMaster::clearPendingRecv(), PostMaster::dispatchSetBuf(), PostMaster::getMyNode(), LocalDataElement::getNode(), GlobalDataElement::getNode(), MsgElement::getNode(), FieldElement::getNumOnNode(), getShell(), handleAddMsg(), ObjId::isDataHere(), Eref::isDataHere(), ObjId::isOffNode(), main(), mooseMyNode(), nonMpiTests(), PostMaster::PostMaster(), TestSched::process(), PostMaster::process(), Element::putTargetsInDigest(), PostMaster::reinit(), PostMaster::remoteFieldGetVec(), PostMaster::remoteGet(), PostMaster::remoteGetVec(), LocalDataElement::setDataSize(), setHardware(), SetGet::strGet(), SetGet::strSet(), testInterNodeOps(), and testShellParserStart().

{
    return myNode_;
}

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unsigned int Shell::numCores ( )

static

Definition at line 71 of file ShellThreads.cpp.

References numCores_.

Referenced by nonMpiTests(), and setHardware().

{
    return numCores_;
}

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unsigned int Shell::numNodes ( )

static

Definition at line 76 of file ShellThreads.cpp.

References numNodes_.

Referenced by PostMaster::clearPending(), PostMaster::clearPendingRecv(), Element::digestMessages(), dispatchBuffers(), PostMaster::dispatchSetBuf(), filterOffNodeTargets(), PostMaster::finalizeSends(), PostMaster::getNumNodes(), getShell(), ObjId::isOffNode(), main(), mooseNumNodes(), nonMpiTests(), PostMaster::PostMaster(), PostMaster::process(), Element::putOffNodeTargetsInDigest(), Element::putTargetsInDigest(), PostMaster::reinit(), PostMaster::remoteGetVec(), LocalDataElement::setDataSize(), setHardware(), testFibonacci(), testFilterOffNodeTargets(), and testSyncSynapseSize().

{
    return numNodes_;
}

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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

Definition at line 610 of file Shell.cpp.

References cwe_.

Referenced by Neuron::buildElist(), Neuron::getExprElist(), Neuron::getExprVal(), initCinfo(), and testTreeTraversal().

{
    cwe_ = val;
}

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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.

Definition at line 47 of file ShellThreads.cpp.

References acked_, myNode(), myNode_, numCores(), numCores_, numNodes(), and numNodes_.

Referenced by init(), and nonMpiTests().

{
    numCores_ = numCores;
    numNodes_ = numNodes;
    myNode_ = myNode;
    acked_.resize( numNodes, 0 );
}

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void Shell::setShellElement

(

Element *

shelle

)

Definition at line 166 of file Shell.cpp.

References shelle_.

Referenced by init().

{
    shelle_ = shelle;
}

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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

)

Definition at line 1001 of file Shell.cpp.

References moose::showWarn().

Referenced by doCreate(), and doMove().

{
    moose::showWarn( text  );
}

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Member Data Documentation

vector< unsigned int > Shell::acked_

staticprivate

Definition at line 622 of file Shell.h.

Referenced by setHardware().

ObjId Shell::cwe_

private

Current working Element.

Definition at line 639 of file Shell.h.

Referenced by destroy(), doFind(), doLoadModel(), getCwe(), and setCwe().

bool Shell::doReinit_

staticprivate

Flag to tell system to reinitialize. We use this to defer the actual operation to the 'process' call for a clean reinit.

Definition at line 629 of file Shell.h.

const unsigned int Shell::ErrorStatus = ~1

static

Definition at line 493 of file Shell.h.

vector< double* > Shell::getBuf_

private

Buffer into which return values from the 'get' command are placed Only index 0 is used for any single-value 'get' call. If it was the 'getVec' command then the array is filled up

Definition at line 558 of file Shell.h.

Referenced by Shell().

bool Shell::gettingVector_

private

Flag, used by the 'get' subsystem which maintains a buffer for returned value. True when the returned value is a vector.

Definition at line 564 of file Shell.h.

bool Shell::isBlockedOnParser_ = 0

staticprivate

Flag: True when the parser thread is blocked waiting for some system call to be handled by the threading and the MPI connected nodes.

Definition at line 577 of file Shell.h.

Referenced by inBlockingParserCall().

bool Shell::isParserIdle_

staticprivate

Definition at line 636 of file Shell.h.

bool Shell::keepLooping_ = 1

staticprivate

Flag: Tells the ProcessLoop to keep on going. Should only be altered during a barrier.

Definition at line 583 of file Shell.h.

Referenced by handleQuit(), and keepLooping().

unsigned int Shell::myNode_

staticprivate

Identifier for current node

Definition at line 606 of file Shell.h.

Referenced by doAddMsg(), innerAddMsg(), myNode(), and setHardware().

unsigned int Shell::numAcks_ = 0

staticprivate

Array of threads, initialized in launchThreads.

Definition at line 621 of file Shell.h.

unsigned int Shell::numCores_

staticprivate

Number of CPU cores in system.

Definition at line 588 of file Shell.h.

Referenced by numCores(), and setHardware().

unsigned int Shell::numGetVecReturns_

private

Counter, used by the 'get' subsystem in order to keep track of number of returned values, especially for getVec.

Definition at line 570 of file Shell.h.

unsigned int Shell::numNodes_

staticprivate

Number of nodes in MPI-based system. Each node may have many threads.

Definition at line 601 of file Shell.h.

Referenced by numNodes(), and setHardware().

unsigned int Shell::numProcessThreads_

staticprivate

Number of threads dedicated to the ProcessLoop. The parser thread is the master thread. Additional threads may be created for graphics, but not now.

Definition at line 595 of file Shell.h.

const unsigned int Shell::OkStatus = ~0

static

Definition at line 492 of file Shell.h.

ProcInfo Shell::p_

staticprivate

Shell owns its own ProcInfo, has global thread/node info. Used to talk to parser and for thread specification in setup operations.

Definition at line 613 of file Shell.h.

double Shell::runtime_

staticprivate

Simulation run time

Definition at line 634 of file Shell.h.

Element* Shell::shelle_

private

Definition at line 551 of file Shell.h.

Referenced by doCopy(), and setShellElement().

vector< ProcInfo > Shell::threadProcs_

staticprivate

Definition at line 615 of file Shell.h.

---

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

• moose-core/shell/Shell.h
• moose-core/shell/LoadModels.cpp
• moose-core/shell/SaveModels.cpp
• moose-core/shell/Shell.cpp
• moose-core/shell/ShellCopy.cpp
• moose-core/shell/ShellThreads.cpp