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Commit ae42e9d5 authored by Kenneth Leiter's avatar Kenneth Leiter
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ENH: Add ability to unpartition partitioned meshes from command line. 

Use -u flag to unpartition a previously partitioned mesh.
parent 0dee6275
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Inline Side-by-side
utils/XdmfPartitioner.cpp
View file @ ae42e9d5
......@@ -81,7 +81,7 @@ XdmfPartitioner::partition(const shared_ptr<XdmfUnstructuredGrid> gridToPartitio
// Make sure geometry and topology are non null
if(!(gridToPartition->getGeometry() && gridToPartition->getTopology()))
XdmfError::message(XdmfError::FATAL,
XdmfError::message(XdmfError::FATAL,
"Current grid's geometry or topology is null in "
"XdmfPartitioner::partition");
......@@ -104,11 +104,11 @@ XdmfPartitioner::partition(const shared_ptr<XdmfUnstructuredGrid> gridToPartitio
int numElements = topology->getNumberElements();
int numNodes = geometry->getNumberPoints();
// allocate metisConnectivity arrays
idx_t * metisConnectivityEptr = new idx_t[numElements + 1];
idx_t * metisConnectivityEind = new idx_t[nodesPerElement * numElements];
metisConnectivityEptr[0] = 0;
unsigned int metisConnectivityEptrValue = 0;
......@@ -134,7 +134,7 @@ XdmfPartitioner::partition(const shared_ptr<XdmfUnstructuredGrid> gridToPartitio
idx_t * elementsPartition = new idx_t[numElements];
idx_t * nodesPartition = new idx_t[numNodes];
if(metisScheme == DUAL_GRAPH) {
METIS_PartMeshDual(&numElements,
&numNodes,
......@@ -165,7 +165,7 @@ XdmfPartitioner::partition(const shared_ptr<XdmfUnstructuredGrid> gridToPartitio
nodesPartition);
}
else {
XdmfError::message(XdmfError::FATAL,
XdmfError::message(XdmfError::FATAL,
"Invalid metis partitioning scheme selected in "
"XdmfPartitioner::partition");
......@@ -305,7 +305,7 @@ XdmfPartitioner::partition(const shared_ptr<XdmfUnstructuredGrid> gridToPartitio
// Split attributes into proper partitions
for(unsigned int i=0; i<gridToPartition->getNumberAttributes(); ++i) {
const shared_ptr<XdmfAttribute> currAttribute =
const shared_ptr<XdmfAttribute> currAttribute =
gridToPartition->getAttribute(i);
bool releaseAttribute = false;
if(!currAttribute->isInitialized()) {
......@@ -321,7 +321,7 @@ XdmfPartitioner::partition(const shared_ptr<XdmfUnstructuredGrid> gridToPartitio
const shared_ptr<XdmfUnstructuredGrid> partitioned =
partitionedGrids->getUnstructuredGrid(partitionId);
partitionId++;
shared_ptr<XdmfAttribute> createdAttribute =
shared_ptr<XdmfAttribute> createdAttribute =
shared_ptr<XdmfAttribute>();
if(currAttribute->getCenter() == XdmfAttributeCenter::Grid()) {
// Insert into each partition
......@@ -333,7 +333,7 @@ XdmfPartitioner::partition(const shared_ptr<XdmfUnstructuredGrid> gridToPartitio
createdAttribute->setCenter(currAttribute->getCenter());
createdAttribute->setType(currAttribute->getType());
unsigned int index = 0;
const unsigned int numberComponents =
const unsigned int numberComponents =
currAttribute->getSize() / topology->getNumberElements();
createdAttribute->initialize(currAttribute->getArrayType(),
currElemIds.size() * numberComponents);
......@@ -353,9 +353,9 @@ XdmfPartitioner::partition(const shared_ptr<XdmfUnstructuredGrid> gridToPartitio
createdAttribute->setName(currAttribute->getName());
createdAttribute->setCenter(currAttribute->getCenter());
createdAttribute->setType(currAttribute->getType());
createdAttribute->initialize(currAttribute->getArrayType(),
createdAttribute->initialize(currAttribute->getArrayType(),
currNodeMap.size());
const unsigned int numberComponents =
const unsigned int numberComponents =
currAttribute->getSize() / geometry->getNumberPoints();
for(std::map<unsigned int, unsigned int>::const_iterator iter =
currNodeMap.begin();
......@@ -443,9 +443,9 @@ XdmfPartitioner::partition(const shared_ptr<XdmfUnstructuredGrid> gridToPartitio
}
if(currAttribute->getCenter() == XdmfAttributeCenter::Node() ||
currAttribute->getCenter() == XdmfAttributeCenter::Cell()) {
const unsigned int numberComponents =
const unsigned int numberComponents =
currAttribute->getSize() / currSet->getSize();
const shared_ptr<XdmfAttribute> partitionedAttribute =
XdmfAttribute::New();
partitionedAttribute->setCenter(currAttribute->getCenter());
......@@ -516,28 +516,28 @@ shared_ptr<XdmfUnstructuredGrid>
XdmfPartitioner::unpartition(const shared_ptr<XdmfGridCollection> gridToUnPartition) const
{
const shared_ptr<XdmfUnstructuredGrid> returnValue =
const shared_ptr<XdmfUnstructuredGrid> returnValue =
XdmfUnstructuredGrid::New();
const shared_ptr<XdmfTopology> returnValueTopology =
const shared_ptr<XdmfTopology> returnValueTopology =
returnValue->getTopology();
const shared_ptr<XdmfGeometry> returnValueGeometry =
returnValue->getGeometry();
const unsigned int numberUnstructuredGrids =
const unsigned int numberUnstructuredGrids =
gridToUnPartition->getNumberUnstructuredGrids();
unsigned int elementOffset = 0;
for(unsigned int i=0; i<numberUnstructuredGrids; ++i) {
const shared_ptr<XdmfUnstructuredGrid> grid =
const shared_ptr<XdmfUnstructuredGrid> grid =
gridToUnPartition->getUnstructuredGrid(i);
const shared_ptr<XdmfAttribute> globalNodeIds =
const shared_ptr<XdmfAttribute> globalNodeIds =
grid->getAttribute("GlobalNodeId");
if(!globalNodeIds) {
XdmfError::message(XdmfError::FATAL,
XdmfError::message(XdmfError::FATAL,
"Cannot find GlobalNodeId attribute in "
"XdmfPartitioner::unpartition");
}
......@@ -550,13 +550,13 @@ XdmfPartitioner::unpartition(const shared_ptr<XdmfGridCollection> gridToUnPartit
// handle topology
const shared_ptr<XdmfTopology> topology = grid->getTopology();
if(i==0) {
returnValueTopology->setType(topology->getType());
returnValueTopology->initialize(topology->getArrayType());
}
returnValueTopology->reserve(returnValueTopology->getSize() +
returnValueTopology->reserve(returnValueTopology->getSize() +
topology->getSize());
bool releaseTopology = false;
......@@ -567,7 +567,7 @@ XdmfPartitioner::unpartition(const shared_ptr<XdmfGridCollection> gridToUnPartit
for(unsigned int j=0; j<topology->getSize(); ++j) {
const unsigned int localNodeId = topology->getValue<unsigned int>(j);
const unsigned int globalNodeId =
const unsigned int globalNodeId =
globalNodeIds->getValue<unsigned int>(localNodeId);
returnValueTopology->pushBack(globalNodeId);
}
......@@ -575,13 +575,13 @@ XdmfPartitioner::unpartition(const shared_ptr<XdmfGridCollection> gridToUnPartit
if(releaseTopology) {
topology->release();
}
// handle geometry
const shared_ptr<XdmfGeometry> geometry = grid->getGeometry();
const shared_ptr<const XdmfGeometryType> geometryType =
const shared_ptr<const XdmfGeometryType> geometryType =
geometry->getType();
const unsigned int geometryDimension = geometryType->getDimensions();
if(i==0) {
returnValueGeometry->setType(geometryType);
returnValueGeometry->initialize(geometry->getArrayType());
......@@ -594,7 +594,7 @@ XdmfPartitioner::unpartition(const shared_ptr<XdmfGridCollection> gridToUnPartit
}
for(unsigned int j=0; j<globalNodeIds->getSize(); ++j) {
const unsigned int globalNodeId =
const unsigned int globalNodeId =
globalNodeIds->getValue<unsigned int>(j);
returnValueGeometry->insert(globalNodeId * geometryDimension,
geometry,
......@@ -610,9 +610,9 @@ XdmfPartitioner::unpartition(const shared_ptr<XdmfGridCollection> gridToUnPartit
for(unsigned int j=0; j<grid->getNumberAttributes(); ++j) {
const shared_ptr<XdmfAttribute> attribute = grid->getAttribute(j);
const shared_ptr<const XdmfAttributeCenter> attributeCenter =
const shared_ptr<const XdmfAttributeCenter> attributeCenter =
attribute->getCenter();
bool releaseAttribute = false;
if(!attribute->isInitialized()) {
attribute->read();
......@@ -620,7 +620,7 @@ XdmfPartitioner::unpartition(const shared_ptr<XdmfGridCollection> gridToUnPartit
}
shared_ptr<XdmfAttribute> returnValueAttribute;
if(i==0) {
returnValueAttribute = XdmfAttribute::New();
returnValueAttribute->setName(attribute->getName());
......@@ -638,7 +638,7 @@ XdmfPartitioner::unpartition(const shared_ptr<XdmfGridCollection> gridToUnPartit
returnValueAttribute->insert(0,
attribute,
0,
attribute->getSize());
attribute->getSize());
}
else if(attributeCenter == XdmfAttributeCenter::Cell()) {
returnValueAttribute->insert(returnValueAttribute->getSize(),
......@@ -647,21 +647,21 @@ XdmfPartitioner::unpartition(const shared_ptr<XdmfGridCollection> gridToUnPartit
attribute->getSize());
}
else if(attributeCenter == XdmfAttributeCenter::Node()) {
const unsigned int numberComponents =
const unsigned int numberComponents =
attribute->getSize() / geometry->getNumberPoints();
for(unsigned int k=0; k<globalNodeIds->getSize(); ++k) {
const unsigned int globalNodeId =
const unsigned int globalNodeId =
globalNodeIds->getValue<unsigned int>(k);
returnValueAttribute->insert(globalNodeId * numberComponents,
attribute,
k * numberComponents,
numberComponents);
}
}
if(releaseAttribute) {
attribute->release();
}
......@@ -673,7 +673,7 @@ XdmfPartitioner::unpartition(const shared_ptr<XdmfGridCollection> gridToUnPartit
const shared_ptr<XdmfSet> set = grid->getSet(j);
const shared_ptr<const XdmfSetType> setType = set->getType();
bool releaseSet = false;
if(!set->isInitialized()) {
set->read();
......@@ -687,7 +687,7 @@ XdmfPartitioner::unpartition(const shared_ptr<XdmfGridCollection> gridToUnPartit
returnValueSet->setType(setType);
returnValue->insert(returnValueSet);
}
if(setType == XdmfSetType::Cell()) {
for(unsigned int k=0; k<set->getSize(); ++k) {
const unsigned int localCellId = set->getValue<unsigned int>(k);
......@@ -697,7 +697,7 @@ XdmfPartitioner::unpartition(const shared_ptr<XdmfGridCollection> gridToUnPartit
else if(setType == XdmfSetType::Node()) {
for(unsigned int k=0; k<set->getSize(); ++k){
const unsigned int localNodeId = set->getValue<unsigned int>(k);
const unsigned int globalNodeId =
const unsigned int globalNodeId =
globalNodeIds->getValue<unsigned int>(localNodeId);
returnValueSet->pushBack(globalNodeId);
}
......@@ -705,7 +705,7 @@ XdmfPartitioner::unpartition(const shared_ptr<XdmfGridCollection> gridToUnPartit
for(unsigned int k=0; k<set->getNumberAttributes(); ++k) {
const shared_ptr<XdmfAttribute> attribute = set->getAttribute(k);
const shared_ptr<const XdmfAttributeCenter> attributeCenter =
const shared_ptr<const XdmfAttributeCenter> attributeCenter =
attribute->getCenter();
const shared_ptr<const XdmfAttributeType> attributeType =
attribute->getType();
......@@ -727,17 +727,17 @@ XdmfPartitioner::unpartition(const shared_ptr<XdmfGridCollection> gridToUnPartit
0,
attribute->getSize());
}
}
}
elementOffset += topology->getNumberElements();
if(releaseGlobalNodeIds) {
globalNodeIds->release();
}
}
return returnValue;
......@@ -766,12 +766,13 @@ namespace {
{
std::cerr << "usage: " << programName << " "
<< "[-s metis_scheme] "
<< "[-s metis_scheme] [-u]"
<< "<input file> <number of partitions> [output file]"
<< std::endl;
std::cerr << "metis_scheme: 1 - Dual Graph" << std::endl;
std::cerr << "metis_scheme: 2 - Node Graph" << std::endl;
std::cerr << "\t-s metis_scheme: 1 - Dual Graph" << std::endl;
std::cerr << "\t-s metis_scheme: 2 - Node Graph" << std::endl;
std::cerr << "\t-u unpartition file" << std::endl;
//
//
//
......@@ -787,14 +788,15 @@ namespace {
std::string & outputFileName,
unsigned int & numPartitions,
XdmfPartitioner::MetisScheme & metisScheme,
bool & unpartition,
int ac,
char * av[])
{
int c;
bool errorFlag = false;
while( (c=getopt(ac, av, "s:")) != -1 )
while( (c=getopt(ac, av, "s:u")) != -1 )
switch(c){
case 's': {
......@@ -810,6 +812,9 @@ namespace {
}
break;
}
case 'u':
unpartition = true;
break;
case '?':
errorFlag = true;
break;
......@@ -822,18 +827,20 @@ namespace {
++optind;
}
if (optind >= ac)
errorFlag = true;
else {
numPartitions = atoi(av[optind]);
++optind;
if(!unpartition) {
if (optind >= ac)
errorFlag = true;
else {
numPartitions = atoi(av[optind]);
++optind;
}
}
if (optind < ac) {
outputFileName = av[optind];
++optind;
}
//
// check errorFlag
//
......@@ -863,11 +870,13 @@ int main(int argc, char* argv[])
std::string outputFileName = "";
unsigned int numPartitions;
XdmfPartitioner::MetisScheme metisScheme = XdmfPartitioner::DUAL_GRAPH;
bool unpartition = false;
processCommandLine(inputFileName,
outputFileName,
numPartitions,
metisScheme,
unpartition,
argc,
argv);
......@@ -901,18 +910,31 @@ int main(int argc, char* argv[])
}
if(outputFileName.compare("") == 0) {
std::stringstream partitionedMeshName;
partitionedMeshName << meshName << "_p" << numPartitions;
meshName = partitionedMeshName.str();
std::stringstream newMeshName;
if(unpartition) {
newMeshName << meshName << "_unpartitioned";
}
else {
newMeshName << meshName << "_p" << numPartitions;
}
meshName = newMeshName.str();
}
shared_ptr<XdmfReader> reader = XdmfReader::New();
shared_ptr<XdmfDomain> domain =
shared_dynamic_cast<XdmfDomain>(reader->read(inputFileName));
if(domain->getNumberUnstructuredGrids() <= 0) {
std::cout << "No grids to partition" << std::endl;
return 1;
if(unpartition) {
if(domain->getNumberGridCollections() == 0) {
std::cout << "No grid collections to unpartition" << std::endl;
return 1;
}
}
else {
if(domain->getNumberUnstructuredGrids() <= 0) {
std::cout << "No grids to partition" << std::endl;
return 1;
}
}
std::stringstream heavyFileName;
......@@ -920,15 +942,25 @@ int main(int argc, char* argv[])
shared_ptr<XdmfHDF5Writer> heavyDataWriter =
XdmfHDF5Writer::New(heavyFileName.str());
shared_ptr<XdmfDomain> newDomain = XdmfDomain::New();
shared_ptr<XdmfPartitioner> partitioner = XdmfPartitioner::New();
shared_ptr<XdmfGridCollection> toWrite =
partitioner->partition(domain->getUnstructuredGrid(0),
numPartitions,
metisScheme,
heavyDataWriter);
shared_ptr<XdmfDomain> newDomain = XdmfDomain::New();
newDomain->insert(toWrite);
shared_ptr<XdmfGrid> toWrite;
if(unpartition) {
shared_ptr<XdmfUnstructuredGrid> toWrite =
partitioner->unpartition(domain->getGridCollection(0));
newDomain->insert(toWrite);
}
else {
shared_ptr<XdmfGridCollection> toWrite =
partitioner->partition(domain->getUnstructuredGrid(0),
numPartitions,
metisScheme,
heavyDataWriter);
newDomain->insert(toWrite);
}
std::stringstream xmlFileName;
xmlFileName << meshName << ".xmf";
......
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