Shuenhoy/vtk-m
1
0
Fork 0
mirror of https://gitlab.kitware.com/vtk/vtk-m synced 2024-09-16 17:22:55 +00:00
Code Issues 2 Actions Packages Projects Releases Wiki Activity

Started adding DIY code for HierarchicalAugmenter

Browse Source
This commit is contained in:
Gunther H. Weber 2021-05-13 13:53:42 -07:00
parent 1128786951
commit e2fe35e129
7 changed files with 122 additions and 32 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
examples/contour_tree_distributed/ContourTreeApp.cxx
View File

@ -840,6 +840,7 @@ int main(int argc, char* argv[])
localBlockSizes,
useBoundaryExtremaOnly,
useMarchingCubes,
false,
saveDotFiles,
timingsLogLevel,
treeLogLevel);

4
vtkm/filter/ContourTreeUniformDistributed.h
View File

@ -118,6 +118,7 @@ public:
const vtkm::cont::ArrayHandle<vtkm::Id3>& localBlockSizes,
bool useBoundaryExtremaOnly = true,
bool useMarchingCubes = false,
bool augmentHierarchicalTree = false,
bool saveDotFiles = false,
vtkm::cont::LogLevel timingsLogLevel = vtkm::cont::LogLevel::Perf,
vtkm::cont::LogLevel treeLogLevel = vtkm::cont::LogLevel::Info);
@ -183,6 +184,9 @@ private:
/// Use marching cubes connectivity for computing the contour tree
bool UseMarchingCubes;
/// Augment hierarchical tree
bool AugmentHierarchicalTree;
/// Save dot files for all tree computations
bool SaveDotFiles;

92
vtkm/filter/ContourTreeUniformDistributed.hxx
View File

@ -68,7 +68,6 @@
#include <vtkm/worklet/contourtree_distributed/BoundaryTreeMaker.h>
#include <vtkm/worklet/contourtree_distributed/ComputeDistributedContourTreeFunctor.h>
#include <vtkm/worklet/contourtree_distributed/DistributedContourTreeBlockData.h>
#include <vtkm/worklet/contourtree_distributed/HierarchicalContourTree.h>
#include <vtkm/worklet/contourtree_distributed/InteriorForest.h>
#include <vtkm/worklet/contourtree_distributed/PrintGraph.h>
#include <vtkm/worklet/contourtree_distributed/SpatialDecomposition.h>
@ -169,8 +168,8 @@ void SaveAfterFanInResults(
template <typename FieldType>
void SaveHierarchicalTreeDot(
vtkm::worklet::contourtree_distributed::DistributedContourTreeBlockData<FieldType>* blockData,
vtkm::worklet::contourtree_distributed::HierarchicalContourTree<FieldType>& hierarchicalTree,
const vtkm::worklet::contourtree_distributed::DistributedContourTreeBlockData<FieldType>*
blockData,
vtkm::Id rank,
vtkm::Id nRounds)
{
@ -190,7 +189,7 @@ void SaveHierarchicalTreeDot(
std::ofstream hierarchicalTreeFile(hierarchicalTreeFileName);
hierarchicalTreeFile
<< vtkm::worklet::contourtree_distributed::HierarchicalContourTreeDotGraphPrint<FieldType>(
hierarchicalTreeLabel, hierarchicalTree, hierarchicalTreeDotSettings);
hierarchicalTreeLabel, blockData->HierarchicalTree, hierarchicalTreeDotSettings);
}
} // end namespace contourtree_distributed_detail
@ -207,12 +206,14 @@ ContourTreeUniformDistributed::ContourTreeUniformDistributed(
const vtkm::cont::ArrayHandle<vtkm::Id3>& localBlockSizes,
bool useBoundaryExtremaOnly,
bool useMarchingCubes,
bool augmentHierarchicalTree,
bool saveDotFiles,
vtkm::cont::LogLevel timingsLogLevel,
vtkm::cont::LogLevel treeLogLevel)
: vtkm::filter::FilterField<ContourTreeUniformDistributed>()
, UseBoundaryExtremaOnly(useBoundaryExtremaOnly)
, UseMarchingCubes(useMarchingCubes)
, AugmentHierarchicalTree(augmentHierarchicalTree)
, SaveDotFiles(saveDotFiles)
, TimingsLogLevel(timingsLogLevel)
, TreeLogLevel(treeLogLevel)
@ -863,9 +864,6 @@ VTKM_CONT void ContourTreeUniformDistributed::DoPostExecute(
timer.Start();
// 2. Fan out to update all the tree
// 2.1 DataSets for creating output data
std::vector<vtkm::cont::DataSet> hierarchicalTreeOutputDataSet(localDataBlocks.size());
// 2.2. Use foreach to compute the fan-out
master.foreach (
[&](
vtkm::worklet::contourtree_distributed::DistributedContourTreeBlockData<FieldType>* blockData,
@ -882,16 +880,15 @@ VTKM_CONT void ContourTreeUniformDistributed::DoPostExecute(
// Fan out
auto nRounds = blockData->ContourTrees.size() - 1;
vtkm::worklet::contourtree_distributed::HierarchicalContourTree<FieldType> hierarchicalTree;
hierarchicalTree.Initialize(static_cast<vtkm::Id>(nRounds),
blockData->ContourTrees[nRounds],
blockData->ContourTreeMeshes[nRounds - 1]);
blockData->HierarchicalTree.Initialize(static_cast<vtkm::Id>(nRounds),
blockData->ContourTrees[nRounds],
blockData->ContourTreeMeshes[nRounds - 1]);
// save the corresponding .gv file
if (this->SaveDotFiles)
{
vtkm::filter::contourtree_distributed_detail::SaveHierarchicalTreeDot(
blockData, hierarchicalTree, rank, nRounds);
blockData, rank, nRounds);
} // if(this->SaveDotFiles)
fanoutTimingsStream << " Fan Out Init Hierarchical Tree (block=" << blockData->BlockIndex
@ -907,13 +904,13 @@ VTKM_CONT void ContourTreeUniformDistributed::DoPostExecute(
blockData->ContourTrees[round],
&(blockData->InteriorForests[round]));
grafter.GraftInteriorForests(static_cast<vtkm::Id>(round),
hierarchicalTree,
blockData->HierarchicalTree,
blockData->ContourTreeMeshes[round - 1].SortedValues);
// save the corresponding .gv file
if (this->SaveDotFiles)
{
vtkm::filter::contourtree_distributed_detail::SaveHierarchicalTreeDot(
blockData, hierarchicalTree, rank, nRounds);
blockData, rank, nRounds);
} // if(this->SaveDotFiles)
// Log the time for each of the iterations of the fan out loop
fanoutTimingsStream << " Fan Out Time (block=" << blockData->BlockIndex
@ -939,29 +936,71 @@ VTKM_CONT void ContourTreeUniformDistributed::DoPostExecute(
this->MultiBlockSpatialDecomposition.LocalBlockSizes.ReadPortal().Get(
blockData->BlockIndex),
this->MultiBlockSpatialDecomposition.GlobalSize);
grafter.GraftInteriorForests(0, hierarchicalTree, fieldData, &localToGlobalIdRelabeler);
grafter.GraftInteriorForests(
0, blockData->HierarchicalTree, fieldData, &localToGlobalIdRelabeler);
// Log the time for each of the iterations of the fan out loop
fanoutTimingsStream << " Fan Out Time (block=" << blockData->BlockIndex << " , round=" << 0
<< ") : " << iterationTimer.GetElapsedTime() << " seconds" << std::endl;
// Log the timing stats we collected
VTKM_LOG_S(this->TimingsLogLevel,
std::endl
<< " ------------ Fan Out (block=" << blockData->BlockIndex
<< ") ------------" << std::endl
<< fanoutTimingsStream.str());
});
if (this->AugmentHierarchicalTree)
{
master.foreach (
[&](vtkm::worklet::contourtree_distributed::DistributedContourTreeBlockData<FieldType>*
blockData,
const vtkmdiy::Master::ProxyWithLink&) {
blockData->HierarchicalAugmenter.Initialize(
blockData->BlockIndex, &blockData->HierarchicalTree, &blockData->AugmentedTree);
});
// TODO/FIXME: Exchange
master.foreach (
[&](vtkm::worklet::contourtree_distributed::DistributedContourTreeBlockData<FieldType>*
blockData,
const vtkmdiy::Master::ProxyWithLink&) {
blockData->HierarchicalAugmenter.BuildAugmentedTree();
});
}
// Create output data set
std::vector<vtkm::cont::DataSet> hierarchicalTreeOutputDataSet(localDataBlocks.size());
master.foreach (
[&](
vtkm::worklet::contourtree_distributed::DistributedContourTreeBlockData<FieldType>* blockData,
const vtkmdiy::Master::ProxyWithLink&) {
std::stringstream fanoutTimingsStream;
vtkm::cont::Timer iterationTimer;
iterationTimer.Start();
// Create data set from output
vtkm::cont::Field dataValuesField(
"DataValues", vtkm::cont::Field::Association::WHOLE_MESH, hierarchicalTree.DataValues);
vtkm::cont::Field dataValuesField("DataValues",
vtkm::cont::Field::Association::WHOLE_MESH,
blockData->HierarchicalTree.DataValues);
hierarchicalTreeOutputDataSet[blockData->BlockIndex].AddField(dataValuesField);
vtkm::cont::Field regularNodeGlobalIdsField("RegularNodeGlobalIds",
vtkm::cont::Field::Association::WHOLE_MESH,
hierarchicalTree.RegularNodeGlobalIds);
blockData->HierarchicalTree.RegularNodeGlobalIds);
hierarchicalTreeOutputDataSet[blockData->BlockIndex].AddField(regularNodeGlobalIdsField);
vtkm::cont::Field superarcsField(
"Superarcs", vtkm::cont::Field::Association::WHOLE_MESH, hierarchicalTree.Superarcs);
vtkm::cont::Field superarcsField("Superarcs",
vtkm::cont::Field::Association::WHOLE_MESH,
blockData->HierarchicalTree.Superarcs);
hierarchicalTreeOutputDataSet[blockData->BlockIndex].AddField(superarcsField);
vtkm::cont::Field supernodesField(
"Supernodes", vtkm::cont::Field::Association::WHOLE_MESH, hierarchicalTree.Supernodes);
vtkm::cont::Field supernodesField("Supernodes",
vtkm::cont::Field::Association::WHOLE_MESH,
blockData->HierarchicalTree.Supernodes);
hierarchicalTreeOutputDataSet[blockData->BlockIndex].AddField(supernodesField);
vtkm::cont::Field superparentsField(
"Superparents", vtkm::cont::Field::Association::WHOLE_MESH, hierarchicalTree.Superparents);
vtkm::cont::Field superparentsField("Superparents",
vtkm::cont::Field::Association::WHOLE_MESH,
blockData->HierarchicalTree.Superparents);
hierarchicalTreeOutputDataSet[blockData->BlockIndex].AddField(superparentsField);
// Copy cell set from input data set. This is mainly to ensure that the output data set
@ -978,8 +1017,9 @@ VTKM_CONT void ContourTreeUniformDistributed::DoPostExecute(
// save the corresponding .gv file
if (this->SaveDotFiles)
{
auto nRounds = blockData->ContourTrees.size() - 1;
vtkm::filter::contourtree_distributed_detail::SaveHierarchicalTreeDot(
blockData, hierarchicalTree, rank, nRounds);
blockData, rank, nRounds);
fanoutTimingsStream << " Fan Out Save Dot (block=" << blockData->BlockIndex
<< ") : " << iterationTimer.GetElapsedTime() << " seconds" << std::endl;
@ -1000,7 +1040,7 @@ VTKM_CONT void ContourTreeUniformDistributed::DoPostExecute(
<< std::endl
<< std::setw(42) << std::left << " BlockIndex"
<< ": " << blockData->BlockIndex << std::endl
<< hierarchicalTree.PrintTreeStats() << std::endl);
<< blockData->HierarchicalTree.PrintTreeStats() << std::endl);
}); // master.foreach
// Clean-up

1
vtkm/filter/testing/TestingContourTreeUniformDistributedFilter.h
View File

@ -293,6 +293,7 @@ inline vtkm::cont::PartitionedDataSet RunContourTreeDUniformDistributed(
!useMarchingCubes,
useMarchingCubes,
false,
false,
vtkm::cont::LogLevel::UserVerboseLast,
vtkm::cont::LogLevel::UserVerboseLast);
filter.SetActiveField(fieldName);

17
vtkm/worklet/contourtree_distributed/DistributedContourTreeBlockData.h
View File

@ -56,6 +56,8 @@
#include <vtkm/Types.h>
#include <vtkm/worklet/contourtree_augmented/Types.h>
#include <vtkm/worklet/contourtree_augmented/meshtypes/ContourTreeMesh.h>
#include <vtkm/worklet/contourtree_distributed/HierarchicalAugmenter.h>
#include <vtkm/worklet/contourtree_distributed/HierarchicalContourTree.h>
// clang-format off
VTKM_THIRDPARTY_PRE_INCLUDE
@ -82,15 +84,22 @@ struct DistributedContourTreeBlockData
delete static_cast<DistributedContourTreeBlockData<FieldType>*>(b);
}
// Block data
// Block metadata
vtkm::Id BlockIndex;
vtkm::Id3 BlockOrigin; // Origin of the data block
vtkm::Id3 BlockSize; // Extends of the data block
// Fan in data
std::vector<vtkm::worklet::contourtree_augmented::ContourTree> ContourTrees;
std::vector<vtkm::worklet::contourtree_augmented::ContourTreeMesh<FieldType>> ContourTreeMeshes;
std::vector<vtkm::worklet::contourtree_distributed::InteriorForest> InteriorForests;
// Block metadata
vtkm::Id3 BlockOrigin; // Origin of the data block
vtkm::Id3 BlockSize; // Extends of the data block
// Fan out data
vtkm::worklet::contourtree_distributed::HierarchicalContourTree<FieldType> HierarchicalTree;
// Augmentation phase
vtkm::worklet::contourtree_distributed::HierarchicalAugmenter<FieldType> HierarchicalAugmenter;
vtkm::worklet::contourtree_distributed::HierarchicalContourTree<FieldType> AugmentedTree;
};
} // namespace contourtree_distributed
} // namespace worklet

37
vtkm/worklet/contourtree_distributed/HierarchicalAugmenter.h
View File

@ -259,7 +259,7 @@ void HierarchicalAugmenter<FieldType>::Initialize(
{
vtkm::worklet::contourtree_distributed::hierarchical_augmenter::IsAttachementPointPredicate
isAttachementPointPredicate(
this->BaseTree->Superarcs, this->BaseTree->whichRound, this->BaseTree->NumRounds);
this->BaseTree->Superarcs, this->BaseTree->WhichRound, this->BaseTree->NumRounds);
vtkm::cont::Algorithm::CopyIf(
// first we generate a list of all of the supernodes
vtkm::cont::ArrayHandleIndex(this->BaseTree->Supernodes.GetNumberOfValues()),
@ -1311,4 +1311,39 @@ std::string HierarchicalAugmenter<FieldType>::DebugPrint(std::string message,
} // namespace worklet
} // namespace vtkm
namespace vtkmdiy
{
// Struct to serialize ContourTreeMesh objects (i.e., load/save) needed in parralle for DIY
template <typename FieldType>
struct Serialization<vtkm::worklet::contourtree_distributed::HierarchicalAugmenter<FieldType>>
{
static void save(
vtkmdiy::BinaryBuffer& bb,
const vtkm::worklet::contourtree_distributed::HierarchicalAugmenter<FieldType>& ha)
{
vtkmdiy::save(bb, ha.OutGlobalRegularIds);
vtkmdiy::save(bb, ha.OutDataValues);
vtkmdiy::save(bb, ha.OutSupernodeIds);
vtkmdiy::save(bb, ha.OutSuperparents);
vtkmdiy::save(bb, ha.OutSuperparentRounds);
vtkmdiy::save(bb, ha.OutWhichRounds);
}
static void load(vtkmdiy::BinaryBuffer& bb,
vtkm::worklet::contourtree_distributed::HierarchicalAugmenter<FieldType>& ha)
{
// TODO/FIXME: Save to Out or some other array?
vtkmdiy::load(bb, ha.OutGlobalRegularIds);
vtkmdiy::load(bb, ha.OutDataValues);
vtkmdiy::load(bb, ha.OutSupernodeIds);
vtkmdiy::load(bb, ha.OutSuperparents);
vtkmdiy::load(bb, ha.OutSuperparentRounds);
vtkmdiy::load(bb, ha.OutWhichRounds);
}
};
} // namespace mangled_vtkmdiy_namespace
#endif

2
vtkm/worklet/contourtree_distributed/PrintGraph.h
View File

@ -1013,7 +1013,7 @@ template <typename FieldType>
// template <typename FieldType, typename VectorType>
std::string HierarchicalContourTreeDotGraphPrint(
const std::string& label, // the label to use as title for the graph
vtkm::worklet::contourtree_distributed::HierarchicalContourTree<FieldType>&
const vtkm::worklet::contourtree_distributed::HierarchicalContourTree<FieldType>&
hierarchicalTree, // the hierarchical contour tree itself
const vtkm::Id showMask = vtkm::worklet::contourtree_distributed::
SHOW_HIERARCHICAL_STANDARD) // mask with flags for what elements to show