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Commit 0457f2ee authored by Kenneth Leiter's avatar Kenneth Leiter
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ENH: Split XdmfAttributes in XdmfPartitioner.

parent dbee693a
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Showing with 81 additions and 177 deletions
XdmfArray.cpp
View file @ 0457f2ee
......@@ -5,7 +5,6 @@
* Author: kleiter
*/
#include <boost/foreach.hpp>
#include <boost/tokenizer.hpp>
#include <sstream>
#include "XdmfArray.hpp"
......@@ -629,12 +628,12 @@ void XdmfArray::populateItem(const std::map<std::string, std::string> & itemProp
{
this->initialize(typeVal, precisionVal);
this->reserve(sizeVal);
boost::char_separator<char> sep(" ");
boost::char_separator<char> sep(" \t\n");
boost::tokenizer<boost::char_separator<char> > tokens(contentVal, sep);
BOOST_FOREACH(std::string t, tokens)
for(boost::tokenizer<boost::char_separator<char> >::const_iterator iter = tokens.begin(); iter != tokens.end(); ++iter)
{
double val = atof(t.c_str());
this->pushBack(val);
this->pushBack(atof((*iter).c_str()));
}
}
else
......
XdmfArray.hpp
View file @ 0457f2ee
......@@ -196,7 +196,7 @@ public:
* Copy a value to the back of this array
*/
template <typename T>
void pushBack(T & value);
void pushBack(const T & value);
/**
* Read data from disk into memory.
......
XdmfArray.tpp
View file @ 0457f2ee
......@@ -217,12 +217,16 @@ boost::shared_ptr<std::vector<T> > XdmfArray::initialize()
}
template <typename T>
void XdmfArray::pushBack(T & value)
void XdmfArray::pushBack(const T & value)
{
if(mHaveArrayPointer)
{
internalizeArrayPointer();
}
if(!mHaveArray)
{
initialize<T>();
}
return boost::apply_visitor(PushBack<T>(value), mArray);
}
......
tests/Cxx/TestXdmfArray.cpp
View file @ 0457f2ee
......@@ -96,6 +96,14 @@ int main(int argc, char* argv[])
assert(array5->getSize() == 3);
assert(array->getSize() == 4);
//
// PUSHBACK
//
boost::shared_ptr<XdmfArray> pushBackArray = XdmfArray::New();
assert(pushBackArray->getSize() == 0);
pushBackArray->pushBack(10);
assert(pushBackArray->getSize() == 1);
//
// SETS
//
......
utils/XdmfPartitioner.cpp
View file @ 0457f2ee
......@@ -40,6 +40,7 @@ extern "C"
#include "XdmfGrid.hpp"
#include "XdmfGridCollection.hpp"
#include "XdmfHDF5Writer.hpp"
#include "XdmfSet.hpp"
#include "XdmfTopology.hpp"
XdmfPartitioner::XdmfPartitioner()
......@@ -178,6 +179,7 @@ boost::shared_ptr<XdmfGridCollection> XdmfPartitioner::partition(boost::shared_p
gridToPartition->getGeometry()->getArray()->read();
}
// Split geometry and topology into proper partitions
for(unsigned int i=0; i<numberOfPartitions; ++i)
{
std::map<unsigned int, unsigned int> & currNodeMap = globalToLocalNodeIdMap[i];
......@@ -259,6 +261,7 @@ boost::shared_ptr<XdmfGridCollection> XdmfPartitioner::partition(boost::shared_p
gridToPartition->getGeometry()->getArray()->release();
gridToPartition->getTopology()->getArray()->release();
// Split attributes into proper partitions
for(unsigned int i=0; i<gridToPartition->getNumberOfAttributes(); ++i)
{
boost::shared_ptr<XdmfAttribute> currAttribute = gridToPartition->getAttribute(i);
......@@ -326,99 +329,65 @@ boost::shared_ptr<XdmfGridCollection> XdmfPartitioner::partition(boost::shared_p
currAttribute->getArray()->release();
}
// Split sets into proper partitions
for(unsigned int i=0; i<gridToPartition->getNumberOfSets(); ++i)
{
boost::shared_ptr<XdmfSet> currSet = gridToPartition->getSet(i);
if(!currSet->getArray()->isInitialized())
{
currSet->getArray()->read();
}
unsigned int partitionId = 0;
for(unsigned int j=0; j<numberOfPartitions; ++j)
{
std::map<unsigned int, unsigned int> & currNodeMap = globalToLocalNodeIdMap[j];
std::vector<unsigned int> & currElemIds = globalElementIds[j];
if(currElemIds.size() > 0)
{
boost::shared_ptr<XdmfGrid> partitioned = partitionedGrids->getGrid(partitionId);
partitionId++;
boost::shared_ptr<XdmfArray> setVals = XdmfArray::New();
if(currSet->getSetType() == XdmfSetType::Cell() || currSet->getSetType() == XdmfSetType::Face() || currSet->getSetType() == XdmfSetType::Edge())
{
for(unsigned int k=0; k<currSet->getArray()->getSize(); ++k)
{
std::vector<unsigned int>::const_iterator val = std::find(currElemIds.begin(), currElemIds.end(), currSet->getArray()->getValueCopy<unsigned int>(k));
if(val != currElemIds.end())
{
unsigned int valToPush = val - currElemIds.begin();
setVals->pushBack(valToPush);
}
}
}
else if(currSet->getSetType() == XdmfSetType::Node())
{
for(unsigned int k=0; k<currSet->getArray()->getSize(); ++k)
{
std::map<unsigned int, unsigned int>::const_iterator val = currNodeMap.find(currSet->getArray()->getValueCopy<unsigned int>(k));
if(val != currNodeMap.end())
{
setVals->pushBack(val->second);
}
}
}
if(setVals->getSize() > 0)
{
boost::shared_ptr<XdmfSet> createdSet = XdmfSet::New();
createdSet->setName(currSet->getName());
createdSet->setSetType(currSet->getSetType());
createdSet->setArray(setVals);
partitioned->insert(createdSet);
if(heavyDataWriter)
{
createdSet->getArray()->accept(heavyDataWriter);
createdSet->getArray()->release();
}
}
}
}
currSet->getArray()->release();
}
return partitionedGrids;
/*
// Split sets and add to grid
for(int j=0; j<grid->GetNumberOfSets(); ++j)
{
XdmfSet * currSet = grid->GetSets(j);
// If data wasn't read in before, make sure it's released after processing
bool releaseData = 0;
if(currSet->GetIds()->GetNumberOfElements() == 0)
{
currSet->Update();
releaseData = 1;
}
int partitionId = 0;
for(int i=0; i<numPartitions; ++i)
{
std::map<XdmfInt32, XdmfInt32> currNodeMap = globalToLocalNodeIdMap[i];
std::vector<XdmfInt32> currElemIds = globalElementIds[i];
if(currElemIds.size() > 0)
{
XdmfGrid * partition = partitions[partitionId];
partitionId++;
switch(currSet->GetSetType())
{
case(XDMF_SET_TYPE_CELL):
case(XDMF_SET_TYPE_FACE):
case(XDMF_SET_TYPE_EDGE):
{
std::vector<XdmfInt32> myIds;
for(int j=0; j<currSet->GetIds()->GetNumberOfElements(); ++j)
{
std::vector<XdmfInt32>::const_iterator val = std::find(currElemIds.begin(), currElemIds.end(), currSet->GetIds()->GetValueAsInt32(j));
if(val != currElemIds.end())
{
myIds.push_back(val - currElemIds.begin());
}
}
if(myIds.size() != 0)
{
XdmfSet * set = new XdmfSet();
set->SetName(currSet->GetName());
set->SetSetType(currSet->GetSetType());
set->SetSize(myIds.size());
set->SetDeleteOnGridDelete(true);
XdmfArray * ids = set->GetIds();
ids->SetNumberType(XDMF_INT32_TYPE);
ids->SetNumberOfElements(myIds.size());
ids->SetValues(0, &myIds[0], myIds.size());
partition->Insert(set);
}
break;
}
case(XDMF_SET_TYPE_NODE):
{
std::vector<XdmfInt32> myIds;
for(int j=0; j<currSet->GetIds()->GetNumberOfElements(); j++)
{
std::map<XdmfInt32, XdmfInt32>::const_iterator val = currNodeMap.find(currSet->GetIds()->GetValueAsInt32(j));
if(val != currNodeMap.end())
{
myIds.push_back(val->second);
}
}
if(myIds.size() != 0)
{
XdmfSet * set = new XdmfSet();
set->SetName(currSet->GetName());
set->SetSetType(currSet->GetSetType());
set->SetSize(myIds.size());
set->SetDeleteOnGridDelete(true);
XdmfArray * ids = set->GetIds();
ids->SetNumberType(XDMF_INT32_TYPE);
ids->SetNumberOfElements(myIds.size());
ids->SetValues(0, &myIds[0], myIds.size());
partition->Insert(set);
}
break;
}
default:
{
std::cout << "Unknown set type encountered: " << currSet->GetSetTypeAsString() << std::endl;
break;
}
}
}
}
if(releaseData)
{
currSet->Release();
}
}
return collection;*/
}
#else
......@@ -510,84 +479,7 @@ int main(int argc, char* argv[])
boost::shared_ptr<XdmfWriter> writer = XdmfWriter::New(xmlFileName.str(), heavyDataWriter);
newDomain->accept(writer);
/*XdmfDOM dom;
XdmfInt32 error = dom.Parse(argv[1]);
std::string fileName = argv[1];
size_t fileNameFound = fileName.find_last_of("/\\");
if (fileNameFound != std::string::npos)
{
dom.SetWorkingDirectory(fileName.substr(0, fileNameFound).substr().c_str());
}
if(error == XDMF_FAIL)
{
std::cout << "File does not appear to be a valid Xdmf file" << std::endl;
return 1;
}
XdmfXmlNode gridElement = dom.FindElementByPath("/Xdmf/Domain/Grid");
if(gridElement == NULL)
{
std::cout << "Cannot parse Xdmf file!" << std::endl;
return 1;
}
XdmfGrid * grid = new XdmfGrid();
grid->SetDOM(&dom);
grid->SetElement(gridElement);
grid->Update();
XdmfDOM newDOM;
XdmfRoot newRoot;
XdmfDomain newDomain;
newRoot.SetDOM(&newDOM);
newRoot.Build();
newRoot.Insert(&newDomain);
XdmfPartitioner partitioner;
XdmfGrid * partitionedGrid = partitioner.Partition(grid, numPartitions, &newDomain);
delete grid;
for(int i=0; i<partitionedGrid->GetNumberOfChildren(); ++i)
{
XdmfGrid * child = partitionedGrid->GetChild(i);
// Set heavy data set names for geometry and topology
std::stringstream heavyPointName;
heavyPointName << meshName << ".h5:/" << child->GetName() << "/XYZ";
child->GetGeometry()->GetPoints()->SetHeavyDataSetName(heavyPointName.str().c_str());
std::stringstream heavyConnName;
heavyConnName << meshName << ".h5:/" << child->GetName() << "/Connections";
child->GetTopology()->GetConnectivity()->SetHeavyDataSetName(heavyConnName.str().c_str());
// Set heavy data set names for mesh attributes and sets
for(int i=0; i<child->GetNumberOfAttributes(); i++)
{
std::stringstream heavyAttrName;
heavyAttrName << meshName << ".h5:/" << child->GetName() << "/Attribute/" << child->GetAttribute(i)->GetAttributeCenterAsString() << "/" << child->GetAttribute(i)->GetName();
child->GetAttribute(i)->GetValues()->SetHeavyDataSetName(heavyAttrName.str().c_str());
}
for(int i=0; i<child->GetNumberOfSets(); i++)
{
std::stringstream heavySetName;
heavySetName << meshName << ".h5:/" << child->GetName() << "/Set/" << child->GetSets(i)->GetSetTypeAsString() << "/" << child->GetSets(i)->GetName();
child->GetSets(i)->GetIds()->SetHeavyDataSetName(heavySetName.str().c_str());
}
}
partitionedGrid->Build();
std::stringstream outputFileName;
outputFileName << meshName << ".xmf";
newDOM.Write(outputFileName.str().c_str());
delete partitionedGrid;
std::cout << "Wrote: " << outputFileName.str().c_str() << std::endl;*/
std::cout << "Wrote: " << xmlFileName.str() << std::endl;
}
#endif //BUILD_EXE
utils/XdmfPartitioner.hpp
View file @ 0457f2ee
......@@ -33,6 +33,7 @@ public:
* XdmfTopologyType::Hexahedron_20
* XdmfTopologyType::Hexahedron_24
* XdmfTopologyType::Hexahedron_27
* XdmfTopologyType::Hexahedron_64
*
* The partitioner splits the XdmfGrid and all attached XdmfAttributes and XdmfSets into their proper partition.
* An XdmfAttribute named "GlobalNodeId" is added to each partitioned grid to map partitioned node ids to their
......
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