ObjId OneToOneDataIndexMsg::findOtherEnd( ObjId f ) const
{
if ( f.element() == e1() )
return ObjId( e2()->id(), f.dataIndex );
else if ( f.element() == e2() )
return ObjId( e1()->id(), f.dataIndex );
return ObjId( 0, BADINDEX );
}
void EndoMesh::setSurround( const Eref& e, ObjId v )
{
if ( !v.element()->cinfo()->isA( "ChemCompt" ) ) {
cout << "Warning: 'surround' may only be set to an object of class 'ChemCompt'\n";
cout << v.path() << " is of class " << v.element()->cinfo()->name() << endl;
return;
}
surround_ = v;
parent_ = reinterpret_cast< const MeshCompt* >( v.data() );
}
ObjId OneToAllMsg::findOtherEnd( ObjId f ) const
{
if ( f.element() == e1() ) {
if ( f.dataIndex == i1_ )
return ObjId( e2()->id(), 0 );
} else if ( f.element() == e2() ) {
return ObjId( e1()->id(), i1_ );
}
return ObjId( 0, BADINDEX );
}
/**
Populates the vector of event data buffers (vectors), vector of
event source objects, vector of event source fields and the vector
of event datasets by querying the messages on InputVariables.
*/
void NSDFWriter::openEventData(const Eref &eref)
{
if (filehandle_ <= 0){
return;
}
for (unsigned int ii = 0; ii < eventInputs_.size(); ++ii){
stringstream path;
path << eref.objId().path() << "/" << "eventInput[" << ii << "]";
ObjId inputObj = ObjId(path.str());
Element * el = inputObj.element();
const DestFinfo * dest = static_cast<const DestFinfo*>(el->cinfo()->findFinfo("input"));
vector < ObjId > src;
vector < string > srcFields;
el->getMsgSourceAndSender(dest->getFid(), src, srcFields);
if (src.size() > 1){
cerr << "NSDFWriter::openEventData - only one source can be connected to an eventInput" <<endl;
} else if (src.size() == 1){
eventSrcFields_.push_back(srcFields[0]);
eventSrc_.push_back(src[0].path());
events_.resize(eventSrc_.size());
stringstream path;
path << src[0].path() << "." << srcFields[0];
hid_t dataSet = getEventDataset(src[0].path(), srcFields[0]);
eventDatasets_.push_back(dataSet);
} else {
cerr <<"NSDFWriter::openEventData - cannot handle multiple connections at single input." <<endl;
}
}
}
void Shell::doMove( Id orig, ObjId newParent )
{
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 );
}
void Shell::recvGet( const Eref& e, const Qinfo* q, PrepackedBuffer pb )
{
if ( myNode_ == 0 ) {
if ( gettingVector_ ) {
ObjId tgt = q->src();
// unsigned int linearIndex = q->src().eref().index().value();
unsigned int linearIndex =
tgt.element()->dataHandler()->linearIndex( tgt.dataId );
if ( linearIndex >= getBuf_.size() ) {
if ( linearIndex >= getBuf_.capacity() )
getBuf_.reserve( linearIndex * 2 );
getBuf_.resize( linearIndex + 1 );
}
assert ( linearIndex < getBuf_.size() );
double*& c = getBuf_[ linearIndex ];
c = new double[ pb.dataSize() ];
memcpy( c, pb.data(), pb.dataSize() * sizeof( double ) );
// cout << myNode_ << ":" << q->threadNum() << ": Shell::recvGet[" << linearIndex << "]= (" << pb.dataSize() << ", " << *c << ")\n";
} else {
assert ( getBuf_.size() == 1 );
double*& c = getBuf_[ 0 ];
c = new double[ pb.dataSize() ];
memcpy( c, pb.data(), pb.dataSize() * sizeof( double ) );
handleAck( 0, OkStatus );
}
++numGetVecReturns_;
}
}
// Utility function: return the compartment in which the specified
// object is located.
// Simply traverses the tree toward the root till it finds a
// compartment. Pools use a special msg, but this works for reacs too.
ObjId getCompt( Id id )
{
ObjId pa = Neutral::parent( id.eref() ).id;
if ( pa == ObjId() )
return pa;
else if ( pa.element()->cinfo()->isA( "ChemCompt" ) )
return pa;
return getCompt( pa );
}
/// non-static func. Returns the Id found by traversing the specified path.
ObjId Shell::doFind( const string& path ) const
{
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;
}
ObjId SparseMsg::findOtherEnd( ObjId f ) const
{
if ( f.element() == e1() ) {
const unsigned int* entry;
const unsigned int* colIndex;
unsigned int num = matrix_.getRow( f.dataIndex, &entry, &colIndex );
if ( num > 0 ) { // Return the first matching entry.
return ObjId( e2()->id(), colIndex[0] );
}
return ObjId( 0, BADINDEX );
} else if ( f.element() == e2() ) { // Bad! Slow! Avoid!
vector< unsigned int > entry;
vector< unsigned int > rowIndex;
unsigned int num = matrix_.getColumn( f.dataIndex, entry, rowIndex );
if ( num > 0 ) { // Return the first matching entry.
return ObjId( e1()->id(), DataId( rowIndex[0] ) );
}
}
return ObjId( 0, BADINDEX );
}
bool Shell::innerMove( Id orig, ObjId newParent )
{
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;
}
/**
* 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.
*/
bool Shell::adopt( ObjId parent, Id child, unsigned int msgIndex ) {
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;
}
ObjId Neutral::parent( ObjId oid )
{
static const Finfo* pf = neutralCinfo->findFinfo( "parentMsg" );
static const DestFinfo* pf2 = dynamic_cast< const DestFinfo* >( pf );
static const FuncId pafid = pf2->getFid();
if ( oid.id == Id() ) {
cout << "Warning: Neutral::parent: tried to take parent of root\n";
return Id();
}
ObjId mid = oid.element()->findCaller( pafid );
assert( mid != ObjId() );
ObjId pa = Msg::getMsg( mid )->findOtherEnd( oid );
return pa;
}
/**
* 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.
*
*/
Id Shell::doCreate( string type, ObjId parent, string name,
unsigned int numData,
NodePolicy nodePolicy,
unsigned int preferredNode )
{
#ifdef ENABLE_LOGGER
clock_t t = clock();
#endif
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();
}
if ( Neutral::child( parent.eref(), name ) != Id() ) {
stringstream ss;
ss << "Shell::doCreate: Object with same name already present: '"
<< parent.path() << "/" << name << "'. No Element created";
warning( 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 );
#ifdef ENABLE_LOGGER
logger.creationTime.push_back((float(clock() - t)/CLOCKS_PER_SEC));
#endif
return ret;
} else {
stringstream ss;
ss << "Shell::doCreate: Class '" << type << "' not known. No Element created";
warning( ss.str() );
}
#ifdef ENABLE_LOGGER
logger.creationTime.push_back((float(clock() - t)/CLOCKS_PER_SEC));
#endif
return Id();
}