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vtk-m/vtkm/worklet/contourtree_distributed/ComputeDistributedContourTreeFunctor.h
Kenneth Moreland c55d15f397 Deprecate ArrayHandle::ExecutionTypes 
The newer version of `ArrayHandle` no longer supports different types of
portals for different devices. Thus, the `ReadPortalType` and
`WritePortalType` are sufficient for all types of portals across all
devices.

This significantly simplifies supporting execution objects on devices,
and thus this change also includes many changes to various execution
objects to remove their dependence on the device adapter tag.
2021-02-08 12:17:37 -07:00

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//============================================================================
// Copyright (c) Kitware, Inc.
// All rights reserved.
// See LICENSE.txt for details.
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notice for more information.
//============================================================================
// Copyright (c) 2018, The Regents of the University of California, through
// Lawrence Berkeley National Laboratory (subject to receipt of any required approvals
// from the U.S. Dept. of Energy). All rights reserved.
//
// Redistribution and use in source and binary forms, with or without modification,
// are permitted provided that the following conditions are met:
//
// (1) Redistributions of source code must retain the above copyright notice, this
// list of conditions and the following disclaimer.
//
// (2) Redistributions in binary form must reproduce the above copyright notice,
// this list of conditions and the following disclaimer in the documentation
// and/or other materials provided with the distribution.
//
// (3) Neither the name of the University of California, Lawrence Berkeley National
// Laboratory, U.S. Dept. of Energy nor the names of its contributors may be
// used to endorse or promote products derived from this software without
// specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
// ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
// WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
// IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
// INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
// BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
// OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
// OF THE POSSIBILITY OF SUCH DAMAGE.
//
//=============================================================================
//
// This code is an extension of the algorithm presented in the paper:
// Parallel Peak Pruning for Scalable SMP Contour Tree Computation.
// Hamish Carr, Gunther Weber, Christopher Sewell, and James Ahrens.
// Proceedings of the IEEE Symposium on Large Data Analysis and Visualization
// (LDAV), October 2016, Baltimore, Maryland.
//
// The PPP2 algorithm and software were jointly developed by
// Hamish Carr (University of Leeds), Gunther H. Weber (LBNL), and
// Oliver Ruebel (LBNL)
//==============================================================================
#ifndef vtk_m_worklet_contourtree_distributed_computedistributedcontourtreefunctor_h
#define vtk_m_worklet_contourtree_distributed_computedistributedcontourtreefunctor_h
#include <vtkm/Types.h>
#include <vtkm/worklet/contourtree_augmented/Types.h>
#include <vtkm/worklet/contourtree_distributed/DistributedContourTreeBlockData.h>
#include <vtkm/worklet/contourtree_distributed/PrintGraph.h>
// clang-format off
VTKM_THIRDPARTY_PRE_INCLUDE
#include <vtkm/thirdparty/diy/diy.h>
VTKM_THIRDPARTY_POST_INCLUDE
// clang-format on
namespace vtkm
{
namespace worklet
{
namespace contourtree_distributed
{
/// Functor used by DIY reduce the merge data blocks in parallel
template <typename FieldType>
class ComputeDistributedContourTreeFunctor
{
public:
/// Create the functor
/// @param[in] globalSize Global extends of the input mesh (i.e., number of mesh points in each dimension)
/// @param[in] timingsLogLevel Set the vtkm::cont:LogLevel to be used to record timings information
/// specific to the computation of the hierachical contour tree
/// @param[in] treeLogLevel Set the vtkm::cont:LogLevel to be used to record metadata information
/// about the various trees computed as part of the hierarchical contour tree compute
ComputeDistributedContourTreeFunctor(
vtkm::Id3 globalSize,
bool useBoundaryExtremaOnly,
vtkm::cont::LogLevel timingsLogLevel = vtkm::cont::LogLevel::Perf,
vtkm::cont::LogLevel treeLogLevel = vtkm::cont::LogLevel::Info)
: GlobalSize(globalSize)
, UseBoundaryExtremaOnly(useBoundaryExtremaOnly)
, TimingsLogLevel(timingsLogLevel)
, TreeLogLevel(treeLogLevel)
{
}
void operator()(
vtkm::worklet::contourtree_distributed::DistributedContourTreeBlockData<FieldType>*
block, // local Block.
const vtkmdiy::ReduceProxy& rp, // communication proxy
const vtkmdiy::RegularSwapPartners& // partners of the current block (unused)
) const
{
// Track timing of main steps
vtkm::cont::Timer totalTimer; // Total time for each call
totalTimer.Start();
vtkm::cont::Timer timer; // Time individual steps
timer.Start();
std::stringstream timingsStream;
// Get our rank and DIY id
const vtkm::Id rank = vtkm::cont::EnvironmentTracker::GetCommunicator().rank();
const auto selfid = rp.gid();
// Here we do the deque first before the send due to the way the iteration is handled in DIY, i.e., in each iteration
// A block needs to first collect the data from its neighours and then send the combined block to its neighbours
// for the next iteration.
// 1. dequeue the block and compute the new contour tree and contour tree mesh for the block if we have the hight GID
std::vector<int> incoming;
rp.incoming(incoming);
// log the time for getting the data from DIY
timingsStream << " " << std::setw(38) << std::left << "DIY Incoming Data"
<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
timer.Start();
// Compute the joint contour tree
for (const int ingid : incoming)
{
// NOTE/IMPORTANT: In each round we should have only one swap partner (despite for-loop here).
// If that assumption does not hold, it will break things.
// NOTE/IMPORTANT: This assumption only holds if the number of blocks is a power of two.
// Otherwise, we may need to process more than one incoming block
if (ingid != selfid)
{
vtkm::cont::Timer loopTimer; // time the steps of this loop
loopTimer.Start();
vtkm::Id3 otherBlockOrigin;
rp.dequeue(ingid, otherBlockOrigin);
vtkm::Id3 otherBlockSize;
rp.dequeue(ingid, otherBlockSize);
vtkm::worklet::contourtree_augmented::ContourTreeMesh<FieldType> otherContourTreeMesh;
rp.dequeue(ingid, otherContourTreeMesh);
timingsStream << " Subphase of Merge Block" << std::endl;
timingsStream << " |-->" << std::setw(38) << std::left << "DIY Deque Data"
<< ": " << loopTimer.GetElapsedTime() << " seconds" << std::endl;
loopTimer.Start();
#ifdef DEBUG_PRINT_CTUD
VTKM_LOG_S(vtkm::cont::LogLevel::Info,
"Local block has extents: " << block->BlockOrigin << " " << block->BlockSize
<< std::endl
<< "Combining with block received from ID " << ingid
<< " with extents: " << otherBlockOrigin << " "
<< otherBlockSize << std::endl);
#endif
// Merge the two contour tree meshes
block->ContourTreeMeshes.back().MergeWith(otherContourTreeMesh);
timingsStream << " |-->" << std::setw(38) << std::left << "Merge Contour Tree Mesh"
<< ": " << loopTimer.GetElapsedTime() << " seconds" << std::endl;
loopTimer.Start();
#ifdef DEBUG_PRINT_CTUD
// save the corresponding .gv file for the contour tree mesh
std::string contourTreeMeshFileName = std::string("Rank_") +
std::to_string(static_cast<int>(rank)) + std::string("_Block_") +
std::to_string(static_cast<int>(block->BlockIndex)) + "_Round_" +
std::to_string(rp.round()) + "_Partner_" + std::to_string(ingid) +
std::string("_Step_0_Combined_Mesh.gv");
std::string contourTreeMeshLabel = std::string("Block ") +
std::to_string(static_cast<int>(block->BlockIndex)) + " Round " +
std::to_string(rp.round()) + " Partner " + std::to_string(ingid) +
std::string(" Step 0 Combined Mesh");
std::string contourTreeMeshString =
vtkm::worklet::contourtree_distributed::ContourTreeMeshDotGraphPrint<FieldType>(
contourTreeMeshLabel,
block->ContourTreeMeshes.back(),
worklet::contourtree_distributed::SHOW_CONTOUR_TREE_MESH_ALL);
std::ofstream contourTreeMeshFile(contourTreeMeshFileName);
contourTreeMeshFile << contourTreeMeshString;
timingsStream << " |-->" << std::setw(38) << std::left
<< "Save Contour Tree Mesh Dot"
<< ": " << loopTimer.GetElapsedTime() << " seconds" << std::endl;
loopTimer.Start();
#endif
// Compute the origin and size of the new block
vtkm::Id3 currBlockOrigin{
std::min(otherBlockOrigin[0], block->BlockOrigin[0]),
std::min(otherBlockOrigin[1], block->BlockOrigin[1]),
std::min(otherBlockOrigin[2], block->BlockOrigin[2]),
};
vtkm::Id3 currBlockMaxIndex{ // Needed only to compute the block size
std::max(otherBlockOrigin[0] + otherBlockSize[0],
block->BlockOrigin[0] + block->BlockSize[0]),
std::max(otherBlockOrigin[1] + otherBlockSize[1],
block->BlockOrigin[1] + block->BlockSize[1]),
std::max(otherBlockOrigin[2] + otherBlockSize[2],
block->BlockOrigin[2] + block->BlockSize[2])
};
vtkm::Id3 currBlockSize{ currBlockMaxIndex[0] - currBlockOrigin[0],
currBlockMaxIndex[1] - currBlockOrigin[1],
currBlockMaxIndex[2] - currBlockOrigin[2] };
// Compute the contour tree from our merged mesh
vtkm::Id currNumIterations;
block->ContourTrees.emplace_back(); // Create new empty contour tree object
vtkm::worklet::contourtree_augmented::IdArrayType currSortOrder;
vtkm::worklet::ContourTreeAugmented worklet;
worklet.TimingsLogLevel =
vtkm::cont::LogLevel::Off; // disable the print logging, we'll print this later
vtkm::Id3 maxIdx{ currBlockOrigin[0] + currBlockSize[0] - 1,
currBlockOrigin[1] + currBlockSize[1] - 1,
currBlockOrigin[2] + currBlockSize[2] - 1 };
auto meshBoundaryExecObj = block->ContourTreeMeshes.back().GetMeshBoundaryExecutionObject(
this->GlobalSize, currBlockOrigin, maxIdx);
worklet.Run(block->ContourTreeMeshes.back()
.SortedValues, // Unused param. Provide something to keep the API happy
block->ContourTreeMeshes.back(),
block->ContourTrees.back(),
currSortOrder,
currNumIterations,
1, // Fully augmented
meshBoundaryExecObj);
// Update block extents
block->BlockOrigin = currBlockOrigin;
block->BlockSize = currBlockSize;
timingsStream << " |-->" << std::setw(38) << std::left
<< "Compute Joint Contour Tree"
<< ": " << loopTimer.GetElapsedTime() << " seconds" << std::endl;
loopTimer.Start();
#ifdef DEBUG_PRINT_CTUD
/*
// TODO: GET THIS COMPILING. NEED TO LIKELY PUT THIS IN A SEPARATE FUNCTION TO GET THE STORAGE TYPE TEMPLATE PARAMETER
// TODO/FIXME: At this time we should only be dealing with contour tree meshes and not possibly other mesh types,
// and block does not have a Meshes member. Shouldn't this all be ContourTreeMesh instead?
// and the ones for the contour tree regular and superstructures
std::string regularStructureFileName = std::string("Rank_") +
std::to_string(static_cast<int>(rank)) + std::string("_Block_") +
std::to_string(static_cast<int>(block->BlockIndex)) + "_Round_" +
std::to_string(rp.round()) + " Partner " + std::to_string(ingid) +
std::string("_Step_1_Contour_Tree_Regular_Structure.gv");
std::string regularStructureLabel = std::string("Block ") +
std::to_string(static_cast<int>(block->BlockIndex)) + " Round " +
std::to_string(rp.round()) + " Partner " + std::to_string(ingid) +
std::string(" Step 1 Contour Tree Regular Structure");
std::string regularStructureString =
worklet::contourtree_distributed::ContourTreeDotGraphPrint < FieldType,
MeshType,
vtkm::worklet::contourtree_augmented::IdArrayType()(
regularStructureLabel,
block->Meshes.back(),
block->ContourTrees.back(),
worklet::contourtree_distributed::SHOW_REGULAR_STRUCTURE |
worklet::contourtree_distributed::SHOW_ALL_IDS);
std::ofstream regularStructureFile(regularStructureFileName);
regularStructureFile << regularStructureString;
std::string superStructureFileName = std::string("Rank_") +
std::to_string(static_cast<int>(rank)) + std::string("_Block_") +
std::to_string(static_cast<int>(block->BlockIndex)) + "_Round_" +
std::to_string(rp.round()) + " Partner " + std::to_string(ingid) +
std::string("_Step_2_Contour_Tree_Super_Structure.gv");
std::ofstream superStructureFile(superStructureFileName);
superStructureFile << worklet::contourtree_distributed::ContourTreeDotGraphPrint < T,
MeshType,
vtkm::worklet::contourtree_augmented::IdArrayType()(
std::string("Block ") + std::to_string(static_cast<int>(block->BlockIndex)) +
" Round " + std::to_string(rp.round()) + " Partner " + std::to_string(ingid) +
std::string(" Step 2 Contour Tree Super Structure"),
block->Meshes.back(),
block->ContourTrees.back(),
worklet::contourtree_distributed::SHOW_SUPER_STRUCTURE |
worklet::contourtree_distributed::SHOW_HYPER_STRUCTURE |
worklet::contourtree_distributed::SHOW_ALL_IDS |
worklet::contourtree_distributed::SHOW_ALL_SUPERIDS |
worklet::contourtree_distributed::SHOW_ALL_HYPERIDS);
*/
#endif
// Log the contour tree timiing stats
(void)rank; // Suppress unused variable warning if logging is disabled.
VTKM_LOG_S(this->TimingsLogLevel,
std::endl
<< " ---------------- Contour Tree Worklet Timings ------------------"
<< std::endl
<< " Rank : " << rank << std::endl
<< " DIY Id : " << selfid << std::endl
<< " Round : " << rp.round() << std::endl
<< worklet.TimingsLogString);
// Log the contour tree size stats
VTKM_LOG_S(this->TreeLogLevel,
std::endl
<< " ---------------- Contour Tree Array Sizes ---------------------"
<< std::endl
<< " Rank : " << rank << std::endl
<< " DIY Id : " << selfid << std::endl
<< " Round : " << rp.round() << std::endl
<< block->ContourTrees.back().PrintArraySizes());
} // end if (ingid != selfid)
} // end for
// log the time needed to compute the local contour tree
timingsStream << " " << std::setw(38) << std::left << "Merge Block (Compute Joint Tree)"
<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
timer.Start();
// If we are not in the first round (contour tree mesh for that round was pre-computed
// in filter outside functor) and if we are sending to someone else (i.e., not in
// last round) then compute contour tree mesh to send and save it.
if (rp.round() != 0 && rp.out_link().size() != 0)
{
vtkm::Id3 maxIdx{ block->BlockOrigin[0] + block->BlockSize[0] - 1,
block->BlockOrigin[1] + block->BlockSize[1] - 1,
block->BlockOrigin[2] + block->BlockSize[2] - 1 };
// Compute BRACT
vtkm::worklet::contourtree_distributed::BoundaryTree boundaryTree;
// ... Get the mesh boundary object
auto meshBoundaryExecObj = block->ContourTreeMeshes.back().GetMeshBoundaryExecutionObject(
this->GlobalSize, block->BlockOrigin, maxIdx);
// Make the BRACT and InteriorForest (i.e., residue)
block->InteriorForests.emplace_back();
auto boundaryTreeMaker = vtkm::worklet::contourtree_distributed::BoundaryTreeMaker<
vtkm::worklet::contourtree_augmented::ContourTreeMesh<FieldType>,
vtkm::worklet::contourtree_augmented::MeshBoundaryContourTreeMeshExec>(
&(block->ContourTreeMeshes.back()),
meshBoundaryExecObj,
block->ContourTrees.back(),
&boundaryTree,
&(block->InteriorForests.back()));
// Construct the BRACT and InteriorForest. Since we are working on a ContourTreeMesh we do
// not need to provide and IdRelabeler here in order to compute the InteriorForest
boundaryTreeMaker.Construct(nullptr, this->UseBoundaryExtremaOnly);
// Construct contour tree mesh from BRACT
block->ContourTreeMeshes.emplace_back(
boundaryTree.VertexIndex, boundaryTree.Superarcs, block->ContourTreeMeshes.back());
#ifdef DEBUG_PRINT_CTUD
/*
// TODO: GET THIS COMPILING.
// TODO/FIXME: Need to get inggid here somehow
// save the Boundary Tree as a dot file
std::string boundaryTreeFileName = std::string("Rank_") +
std::to_string(static_cast<int>(rank)) + std::string("_Block_") +
std::to_string(static_cast<int>(block->BlockIndex)) + "_Round_" +
std::to_string(rp.round()) + "_Partner_" + std::to_string(ingid) +
std::string("_Step_3_Boundary_Tree.gv");
std::ofstream boundaryTreeFile(boundaryTreeFileName);
boundaryTreeFile << vtkm::worklet::contourtree_distributed::BoundaryTreeDotGraphPrint
(std::string("Block ") + std::to_string(static_cast<int>(block->BlockIndex)) + " Round " +
std::to_string(rp.round()) + " Partner " + std::to_string(ingid) +
std::string(" Step 3 Boundary Tree"),
block->Meshes.back()],
block->BoundaryTrees.back());
// and save the Interior Forest as another dot file
std::string interiorForestFileName = std::string("Rank_") +
std::to_string(static_cast<int>(rank)) + std::string("_Block_") +
std::to_string(static_cast<int>(block->BlockIndex)) + "_Round_" +
std::to_string(rp.round()) + "_Partner_" + std::to_string(ingid) +
std::string("_Step_4_Interior_Forest.gv");
std::ofstream interiorForestFile(interiorForestFileName);
interiorForestFileName << InteriorForestDotGraphPrintFile<MeshType>(
std::string("Block ") + std::to_string(static_cast<int>(block->BlockIndex)) + " Round " +
std::to_string(rp.round()) + " Partner " + std::to_string(ingid) +
std::string(" Step 4 Interior Forest"),
block->InteriorForests.back(),
block->ContourTrees.back(),
block->BoundaryTrees.back(),
block->Meshes.back());
// save the corresponding .gv file
std::string boundaryTreeMeshFileName = std::string("Rank_") +
std::to_string(static_cast<int>(rank)) + std::string("_Block_") +
std::to_string(static_cast<int>(block->BlockIndex)) + "_Round_" +
std::to_string(rp.round()) + "_Partner_" + std::to_string(ingid) +
std::string("_Step_5_Boundary_Tree_Mesh.gv");
std::ofstream boundaryTreeMeshFile(boundaryTreeMeshFileName);
boundaryTreeMeshFile
<< vtkm::worklet::contourtree_distributed::ContourTreeMeshDotGraphPrint<FieldType>(
std::string("Block ") + std::to_string(static_cast<int>(block->BlockIndex)) +
" Round " + std::to_string(rp.round()) + " Partner " + std::to_string(ingid) +
std::string(" Step 5 Boundary Tree Mesh"),
block->ContourTreeMeshes.back(),
worklet::contourtree_distributed::SHOW_CONTOUR_TREE_MESH_ALL);
*/
#endif
// Log the boundary tree size statistics
VTKM_LOG_S(this->TreeLogLevel,
std::endl
<< " ---------------- Boundary Tree Array Sizes ---------------------"
<< std::endl
<< " Rank : " << rank << std::endl
<< " DIY Id : " << selfid << std::endl
<< " Round : " << rp.round() << std::endl
<< boundaryTree.PrintArraySizes());
// Log the interior forest statistics
VTKM_LOG_S(this->TreeLogLevel,
std::endl
<< " ---------------- Interior Forest Array Sizes ---------------------"
<< std::endl
<< " Rank : " << rank << std::endl
<< " DIY Id : " << selfid << std::endl
<< " Round : " << rp.round() << std::endl
<< block->InteriorForests.back().PrintArraySizes());
} // end if (rp.round() != 0 && rp.out_link().size() != 0)
// log the time to compute the boundary tree, interior forest, and contour tree mesh, i.e, the data we need to send
timingsStream << " " << std::setw(38) << std::left << "Compute Trees To Send"
<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
timer.Start();
// Send our current block (which is either our original block or the one we just combined from the ones we received) to our next neighbour.
// Once a rank has send his block (either in its orignal or merged form) it is done with the reduce
for (int cc = 0; cc < rp.out_link().size(); ++cc)
{
auto target = rp.out_link().target(cc);
if (target.gid != selfid)
{
rp.enqueue(target, block->BlockOrigin);
rp.enqueue(target, block->BlockSize);
rp.enqueue(target, block->ContourTreeMeshes.back());
}
} // end for
// Log the time for enqueue the data for sending via DIY
timingsStream << " " << std::setw(38) << std::left << "DIY Enqueue Data"
<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
// Log the total this functor call step took
timingsStream << " " << std::setw(38) << std::left << "Total Time Functor Step"
<< ": " << totalTimer.GetElapsedTime() << " seconds" << std::endl;
// Record the times we logged
VTKM_LOG_S(this->TimingsLogLevel,
std::endl
<< " ---------------- Fan In Functor Step ---------------------" << std::endl
<< " Rank : " << rank << std::endl
<< " DIY Id : " << selfid << std::endl
<< " Round : " << rp.round() << std::endl
<< timingsStream.str());
} //end ComputeDistributedContourTreeFunctor
private:
/// Extends of the global mesh
vtkm::Id3 GlobalSize;
/// Use boundary extrema only (instead of the full boundary) during the fan in
bool UseBoundaryExtremaOnly;
/// Log level to be used for outputting timing information. Default is vtkm::cont::LogLevel::Perf
vtkm::cont::LogLevel TimingsLogLevel = vtkm::cont::LogLevel::Perf;
/// Log level to be used for outputting metadata about the trees. Default is vtkm::cont::LogLevel::Info
vtkm::cont::LogLevel TreeLogLevel = vtkm::cont::LogLevel::Info;
};
} // namespace contourtree_distributed
} // namespace worklet
} // namespace vtkm
#endif
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