void OneToOneMsg::targets( vector< vector< Eref > > & v) const
{
unsigned int n = e1_->numData();
v.resize( e1_->numData() );
if ( e2_->hasFields() ) {
if ( Eref( e2_, i2_ ).isDataHere() ) {
assert( i2_ > e2_->localDataStart() );
unsigned int nf = e2_->numField( i2_ - e2_->localDataStart() );
if ( n > nf )
n = nf;
for ( unsigned int i = 0; i < n; ++i )
v[i].resize( 1, Eref( e2_, i2_, i ) );
} else { // Don't know target node # of entries, so send all.
unsigned int start = e1_->localDataStart();
unsigned int end = start + e1_->numLocalData();
for ( unsigned int i = start; i < end; ++i ) {
v[i].resize( 1, Eref( e2_, i2_, i ) );
}
}
} else {
if ( n > e2_->numData() )
n = e2_->numData();
for ( unsigned int i = 0; i < n; ++i ) {
v[i].resize( 1, Eref( e2_, i ) );
}
}
}
void ZombieHandler::forall( const OpFunc* f, Element* e, const Qinfo* q,
const double* arg, unsigned int argSize, unsigned int numArgs ) const
{ // This should be relevant. But I still have to define threadStart_
// Find which thread parent is willing to handle
// I still don't know how to get at the parent DataId. I need it.
if ( parent_->execThread( q->threadNum(), 0 ) ) {
// On this thread, figure out which index range we should use.
// We have start and end, so that is fine.
// Iterate through the opfunc for all of these.
if ( numArgs <= 1 ) {
for( unsigned int i = start_; i != end_; ++i ) {
f->op( Eref( e, i ), q, arg );
}
} else {
unsigned int argOffset = argSize * start_;
unsigned int maxOffset = argSize * numArgs;
for( unsigned int i = start_; i != end_; ++i ) {
f->op( Eref( e, i ), q, arg + argOffset );
argOffset += argSize;
if ( argOffset >= maxOffset )
argOffset = 0;
}
}
}
}
Eref OneToAllMsg::firstTgt( const Eref& src ) const
{
if ( src.element() == e1_ )
return Eref( e2_, 0 );
else if ( src.element() == e2_ )
return Eref( e1_, i1_ );
return Eref( 0, 0 );
}
Eref SingleMsg::firstTgt( const Eref& src ) const
{
if ( src.element() == e1_ )
return Eref( e2_, i2_, f2_ );
else if ( src.element() == e2_ )
return Eref( e1_, i1_ );
return Eref( 0, 0 );
}
/**
* This is a little tricky because we might be mapping between
* data entries and field entries here.
* May wish also to apply to exec operations.
* At this point, the effect of trying to go between regular
* data entries and field entries is undefined.
*/
Eref OneToOneDataIndexMsg::firstTgt( const Eref& src ) const
{
if ( src.element() == e1_ ) {
return Eref( e2_, src.dataIndex(), 0 );
} else if ( src.element() == e2_ ) {
return Eref( e1_, src.dataIndex() );
}
return Eref( 0, 0 );
}
/**
* This is a little tricky because we might be mapping between
* data entries and field entries here.
* May wish also to apply to exec operations.
* At this point, the effect of trying to go between regular
* data entries and field entries is undefined.
*/
Eref OneToOneMsg::firstTgt( const Eref& src ) const
{
if ( src.element() == e1_ ) {
if ( e2_->hasFields() )
return Eref( e2_, i2_, src.dataIndex() );
else
return Eref( e2_, src.dataIndex(), 0 );
} else if ( src.element() == e2_ ) {
return Eref( e1_, src.dataIndex() );
}
return Eref( 0, 0 );
}
// This puts the special HopFuncs into the MsgDigest. Furthermore, the
// Erefs to which they point are the originating Eref instance on the
// remote node. This Eref will then invoke its own send call to complete
// the message transfer.
void Element::putOffNodeTargetsInDigest(
unsigned int srcNum, vector< vector< bool > >& targetNodes )
// targetNodes[srcDataId][node]
{
if ( msgBinding_[ srcNum ].size() == 0 )
return;
const MsgFuncBinding& mfb = msgBinding_[ srcNum ][0];
const Msg* msg = Msg::getMsg( mfb.mid );
const OpFunc* func;
if ( msg->e1() == this ) {
func = msg->e2()->cinfo()->getOpFunc( mfb.fid );
} else {
func = msg->e1()->cinfo()->getOpFunc( mfb.fid );
}
assert( func );
// How do I eventually destroy these?
const OpFunc* hop = func->makeHopFunc( srcNum );
for ( unsigned int i = 0; i < numData(); ++i ) {
vector< Eref > tgts;
for ( unsigned int j = 0; j < Shell::numNodes(); ++j ) {
if ( targetNodes[i][j] )
tgts.push_back( Eref( this, i, j ) );
// This is a hack. I encode the target node # in the FieldIndex
// and the originating Eref in the remainder of the Eref.
// The HopFunc has to extract both these things to push into
// the correct SendBuffer.
}
if ( tgts.size() > 0 ) {
vector< MsgDigest >& md =
msgDigest_[ msgBinding_.size() * i + srcNum ];
md.push_back( MsgDigest( hop, tgts ) );
}
}
}
void OneToAllMsg::sources( vector< vector < Eref > >& v ) const
{
// Same single source for all targets.
v.clear();
vector< Eref > temp( 1, Eref( e1_, i1_ ) );
v.assign( e2_->numData(), temp );
}
Eref SparseMsg::firstTgt( const Eref& src ) const
{
if ( matrix_.nEntries() == 0 )
return Eref( 0, 0 );
if ( src.element() == e1_ ) {
const unsigned int* fieldIndex;
const unsigned int* colIndex;
unsigned int n = matrix_.getRow( src.dataIndex(),
&fieldIndex, &colIndex );
if ( n != 0 ) {
return Eref( e2_, colIndex[0], fieldIndex[0] );
}
} else if ( src.element() == e2_ ) {
return Eref( e1_, 0 );
}
return Eref( 0, 0 );
}
void OneToOneDataIndexMsg::targets( vector< vector< Eref > > & v) const
{
unsigned int n = e1_->numData();
v.resize( e1_->numData() );
if ( n > e2_->numData() )
n = e2_->numData();
for ( unsigned int i = 0; i < n; ++i ) {
v[i].resize( 1, Eref( e2_, i ) );
}
}
void ZombieFunction::zombify( Element* orig, const Cinfo* zClass,
Id ksolve, Id dsolve )
{
//cout << "ZombieFunction::zombify: " << orig->id().path() << endl;
if ( orig->cinfo() == zClass )
return;
// unsigned int start = orig->localDataStart();
unsigned int num = orig->numLocalData();
if ( num == 0 )
return;
if ( num > 1 )
cout << "ZombieFunction::zombify: Warning: ZombieFunction doesn't\n"
"handle volumes yet. Proceeding without this.\n";
Function* f = reinterpret_cast< Function *>( Eref( orig, 0 ).data() );
Function temp = *f;
orig->zombieSwap( zClass );
if ( zClass == ZombieFunction::initCinfo() ) { // call SetSolver
ZombieFunction* zf = reinterpret_cast< ZombieFunction *>(
Eref( orig, 0 ).data() );
*zf = *static_cast< ZombieFunction* >(&temp);
zf->setSolver( ksolve, dsolve );
} else {
Function* nf =
reinterpret_cast< Function *>(Eref( orig, 0 ).data());
*nf = temp;
}
/*
// We can swap the class because the class data is identical, just
// the moose expr and process handlers are different.
if ( orig->cinfo() == ZombieFunction::initCinfo() ) { // unzombify
orig->replaceCinfo( Function::initCinfo() );
} else { // zombify
orig->replaceCinfo( ZombieFunction::initCinfo() );
ZombieFunction* zf = reinterpret_cast< ZombieFunction *>(
Eref( orig, 0 ).data() );
zf->setSolver( ksolve, dsolve );
}
*/
}
Msg* OneToAllMsg::copy( Id origSrc, Id newSrc, Id newTgt,
FuncId fid, unsigned int b, unsigned int n ) const
{
const Element* orig = origSrc();
if ( n <= 1 ) {
OneToAllMsg* ret = 0;
if ( orig == e1() ) {
ret = new OneToAllMsg( Msg::nextMsgId(), Eref( newSrc(), i1_ ), newTgt() );
ret->e1()->addMsgAndFunc( ret->mid(), fid, b );
} else if ( orig == e2() ) {
ret = new OneToAllMsg( Msg::nextMsgId(), Eref( newTgt(), i1_ ), newSrc() );
ret->e2()->addMsgAndFunc( ret->mid(), fid, b );
} else {
assert( 0 );
}
return ret;
} else {
// Here we need a SliceMsg which goes from one 2-d array to another.
cout << "Error: OneToAllMsg::copy: SliceToSliceMsg not yet implemented\n";
return 0;
}
}
// We don't permit e1 to have fields at this point.
void OneToOneMsg::sources( vector< vector< Eref > > & v) const
{
v.resize( 0 );
unsigned int n = e1_->numData();
if ( e2_->hasFields() ) {
if ( Eref( e2_, i2_ ).isDataHere() ) {
assert( i2_ > e2_->localDataStart() );
unsigned int nf = e2_->numField( i2_ - e2_->localDataStart() );
if ( n > nf )
n = nf;
v.resize( n );
for ( unsigned int i = 0; i < n; ++i ) {
v[i].resize( 1, Eref( e1_, i ) );
}
}
} else {
if ( n > e2_->numData() )
n = e2_->numData();
v.resize( e2_->numData() );
for ( unsigned int i = 0; i < n; ++i ) {
v[i].resize( 1, Eref( e1_, i ) );
}
}
}
/**
* Need to revisit to handle nodes
*/
void OneToAllMsg::exec( const Qinfo* q, const double* arg, FuncId fid )
const
{
if ( q->src().element() == e1_ ) {
if ( q->src().dataId == i1_ ) {
const OpFunc* f = e2_->cinfo()->getOpFunc( fid );
e2_->dataHandler()->forall( f, e2_, q, arg, 1, 0 );
}
} else {
if ( e1_->dataHandler()->execThread( q->threadNum(), i1_ ) )
{
const OpFunc* f = e1_->cinfo()->getOpFunc( fid );
f->op( Eref( e1_, i1_ ), q, arg );
}
}
}
void fillErefsFromMatrix(
const SparseMatrix< unsigned int >& matrix,
vector< vector < Eref > >& v, Element* e1, Element* e2 )
{
v.clear();
v.resize( e1->numData() );
assert( e1->numData() == matrix.nRows() );
assert( e2->numData() == matrix.nColumns() );
for ( unsigned int i = 0; i < e1->numData(); ++i ) {
const unsigned int* entry;
const unsigned int* colIndex;
unsigned int num = matrix.getRow( i, &entry, &colIndex );
v[i].resize( num );
for ( unsigned int j = 0; j < num; ++j ) {
v[i][j] = Eref( e2, colIndex[j], entry[j] );
}
}
}
void HSolveHub::manageCompartments()
{
const vector< Id >& idlist = integ_->getCompartments();
vector< Element* > elist;
idlist2elist( idlist, elist );
const vector< vector< Id > >& externalChannelIds =
integ_->getExternalChannels();
vector< Element* > extChanList;
const Finfo* initFinfo = initCompartmentCinfo()->findFinfo( "init" );
vector< Element* >::const_iterator i;
for ( i = elist.begin(); i != elist.end(); i++ ) {
zombify( hub_, *i, compartmentSolveFinfo, compartmentZombieFinfo );
// Compartment receives 2 shared messages from Tick's "process"
Eref( *i ).dropAll( initFinfo->msg() );
redirectDynamicMessages( *i );
}
/*
* Redirecting dest/shared messages
*/
for ( unsigned int ic = 0; ic < elist.size(); ic++ ) {
// The 'retain' flag at the end is 1: we do not delete the original
// message to the compartment.
redirectDestMessages(
hub_, elist[ ic ],
hubCompartmentInjectFinfo, compartmentInjectFinfo,
ic, compartmentInjectMap_,
&elist, 0,
1 );
extChanList.clear();
idlist2elist( externalChannelIds[ ic ], extChanList );
redirectDestMessages(
hub_, elist[ ic ],
hubCompartmentChannelFinfo, compartmentChannelFinfo,
ic, compartmentChannelMap_,
&elist, &extChanList,
1 );
}
}
void OneToAllMsg::targets( vector< vector< Eref > >& v ) const
{
v.clear();
v.resize( e1_->numData() );
v[i1_].resize( 1, Eref( e2_, ALLDATA ) );
}
void SingleMsg::sources( vector< vector< Eref > >& v ) const
{
v.clear();
v.resize( e2_->numData() );
v[i2_].resize( 1, Eref( e1_, i1_ ) );
}
void SingleMsg::targets( vector< vector< Eref > >& v ) const
{
v.clear();
v.resize( e1_->numData() );
v[i1_].resize( 1, Eref( e2_, i2_, f2_ ) );
}
void testBioScan( )
{
cout << "\nTesting Bioscan" << flush;
bool success;
Element* n =
Neutral::create( "Neutral", "n", Element::root()->id(), Id::scratchId() );
/**
* First we test the functions which return the compartments linked to a
* given compartment: adjacent(), and children().
*
* A small tree is created for this:
*
* c0
* L c1
* L c2
* L c3
* L c4
* L c5
*
* (c0 is the parent of c1. c1 is the parent of c2, c3, c4, c5.)
*/
Element* c[ 6 ];
c[ 0 ] = Neutral::create( "Compartment", "c0", n->id(), Id::scratchId() );
c[ 1 ] = Neutral::create( "Compartment", "c1", n->id(), Id::scratchId() );
c[ 2 ] = Neutral::create( "Compartment", "c2", n->id(), Id::scratchId() );
c[ 3 ] = Neutral::create( "Compartment", "c3", n->id(), Id::scratchId() );
c[ 4 ] = Neutral::create( "Compartment", "c4", n->id(), Id::scratchId() );
c[ 5 ] = Neutral::create( "Compartment", "c5", n->id(), Id::scratchId() );
success = Eref( c[ 0 ] ).add( "axial", c[ 1 ], "raxial" );
ASSERT( success, "Linking compartments" );
success = Eref( c[ 1 ] ).add( "axial", c[ 2 ], "raxial" );
ASSERT( success, "Linking compartments" );
success = Eref( c[ 1 ] ).add( "axial", c[ 3 ], "raxial" );
ASSERT( success, "Linking compartments" );
success = Eref( c[ 1 ] ).add( "axial", c[ 4 ], "raxial" );
ASSERT( success, "Linking compartments" );
success = Eref( c[ 1 ] ).add( "axial", c[ 5 ], "raxial" );
ASSERT( success, "Linking compartments" );
vector< Id > found;
unsigned int nFound;
/** Testing version 1 of BioScan::adjacent.
* It finds all neighbours of given compartment.
*/
// Neighbours of c0
nFound = BioScan::adjacent( c[ 0 ]->id(), found );
ASSERT( nFound == found.size(), "Finding adjacent compartments" );
// c1 is adjacent
ASSERT( nFound == 1, "Finding adjacent compartments" );
ASSERT( found[ 0 ] == c[ 1 ]->id(), "Finding adjacent compartments" );
// Neighbours of c1
found.clear();
nFound = BioScan::adjacent( c[ 1 ]->id(), found );
ASSERT( nFound == 5, "Finding adjacent compartments" );
// c0 is adjacent
success =
find( found.begin(), found.end(), c[ 0 ]->id() ) != found.end();
ASSERT( success, "Finding adjacent compartments" );
// c2 - c5 are adjacent
for ( int i = 2; i < 6; i++ ) {
success =
find( found.begin(), found.end(), c[ i ]->id() ) != found.end();
ASSERT( success, "Finding adjacent compartments" );
}
// Neighbours of c2
found.clear();
nFound = BioScan::adjacent( c[ 2 ]->id(), found );
// c1 is adjacent
ASSERT( nFound == 1, "Finding adjacent compartments" );
ASSERT( found[ 0 ] == c[ 1 ]->id(), "Finding adjacent compartments" );
/** Testing version 2 of BioScan::adjacent.
* It finds all but one neighbours of given compartment.
* The the second argument to 'adjacent' is the one that is excluded.
*/
// Neighbours of c1 (excluding c0)
found.clear();
nFound = BioScan::adjacent( c[ 1 ]->id(), c[ 0 ]->id(), found );
ASSERT( nFound == 4, "Finding adjacent compartments" );
// c2 - c5 are adjacent
for ( int i = 2; i < 6; i++ ) {
success =
find( found.begin(), found.end(), c[ i ]->id() ) != found.end();
ASSERT( success, "Finding adjacent compartments" );
}
// Neighbours of c1 (excluding c2)
found.clear();
nFound = BioScan::adjacent( c[ 1 ]->id(), c[ 2 ]->id(), found );
ASSERT( nFound == 4, "Finding adjacent compartments" );
// c0 is adjacent
success =
find( found.begin(), found.end(), c[ 0 ]->id() ) != found.end();
ASSERT( success, "Finding adjacent compartments" );
// c3 - c5 are adjacent
for ( int i = 3; i < 6; i++ ) {
success =
find( found.begin(), found.end(), c[ i ]->id() ) != found.end();
ASSERT( success, "Finding adjacent compartments" );
}
// Neighbours of c2 (excluding c1)
found.clear();
nFound = BioScan::adjacent( c[ 2 ]->id(), c[ 1 ]->id(), found );
// None adjacent, if c1 is excluded
ASSERT( nFound == 0, "Finding adjacent compartments" );
// Neighbours of c2 (excluding c3)
found.clear();
nFound = BioScan::adjacent( c[ 2 ]->id(), c[ 3 ]->id(), found );
// c1 is adjacent, while c3 is not even connected
ASSERT( nFound == 1, "Finding adjacent compartments" );
ASSERT( found[ 0 ] == c[ 1 ]->id(), "Finding adjacent compartments" );
/** Testing BioScan::children.
* It finds all compartments which are dests for the "axial" message.
*/
// Children of c0
found.clear();
nFound = BioScan::children( c[ 0 ]->id(), found );
ASSERT( nFound == 1, "Finding child compartments" );
// c1 is a child
ASSERT( found[ 0 ] == c[ 1 ]->id(), "Finding child compartments" );
// Children of c1
found.clear();
nFound = BioScan::children( c[ 1 ]->id(), found );
ASSERT( nFound == 4, "Finding child compartments" );
// c2 - c5 are c1's children
for ( int i = 2; i < 6; i++ ) {
success =
find( found.begin(), found.end(), c[ i ]->id() ) != found.end();
ASSERT( success, "Finding child compartments" );
}
// Children of c2
found.clear();
nFound = BioScan::children( c[ 2 ]->id(), found );
// c2 has no children
ASSERT( nFound == 0, "Finding child compartments" );
// Clean up
set( n, "destroy" );
}
Eref Id::eref() const
{
return Eref( elements()[ id_ ], 0 );
// return Eref( elements()[ id_ ], index_ );
}