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//============================================================================
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// Copyright (c) Kitware, Inc.
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// All rights reserved.
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// See LICENSE.txt for details.
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//
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// This software is distributed WITHOUT ANY WARRANTY; without even
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// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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// PURPOSE. See the above copyright notice for more information.
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//============================================================================
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// Copyright (c) 2018, The Regents of the University of California, through
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// Lawrence Berkeley National Laboratory (subject to receipt of any required approvals
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// from the U.S. Dept. of Energy). All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without modification,
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// are permitted provided that the following conditions are met:
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//
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// (1) Redistributions of source code must retain the above copyright notice, this
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// list of conditions and the following disclaimer.
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//
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// (2) Redistributions in binary form must reproduce the above copyright notice,
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// this list of conditions and the following disclaimer in the documentation
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// and/or other materials provided with the distribution.
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//
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// (3) Neither the name of the University of California, Lawrence Berkeley National
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// Laboratory, U.S. Dept. of Energy nor the names of its contributors may be
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// used to endorse or promote products derived from this software without
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// specific prior written permission.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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// ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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// WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
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// IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
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// INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
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// BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
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// OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
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// OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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//=============================================================================
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//
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// This code is an extension of the algorithm presented in the paper:
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// Parallel Peak Pruning for Scalable SMP Contour Tree Computation.
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// Hamish Carr, Gunther Weber, Christopher Sewell, and James Ahrens.
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// Proceedings of the IEEE Symposium on Large Data Analysis and Visualization
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// (LDAV), October 2016, Baltimore, Maryland.
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//
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// The PPP2 algorithm and software were jointly developed by
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// Hamish Carr (University of Leeds), Gunther H. Weber (LBNL), and
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// Oliver Ruebel (LBNL)
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//==============================================================================
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// #define DEBUG_PRINT
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// #define PRINT_RESULT
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#include <vtkm/cont/testing/MakeTestDataSet.h>
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#include <vtkm/cont/testing/Testing.h>
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#include <vtkm/filter/scalar_topology/worklet/contourtree_augmented/DataSetMesh.h>
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#include <vtkm/filter/scalar_topology/worklet/contourtree_augmented/PrintVectors.h>
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#include <vtkm/filter/scalar_topology/worklet/contourtree_augmented/meshtypes/ContourTreeMesh.h>
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#include <vtkm/filter/scalar_topology/worklet/contourtree_distributed/CombineHyperSweepBlockFunctor.h>
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#include <vtkm/filter/scalar_topology/worklet/contourtree_distributed/HierarchicalContourTree.h>
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#include <vtkm/filter/scalar_topology/worklet/contourtree_distributed/HierarchicalHyperSweeper.h>
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#include <vtkm/filter/scalar_topology/worklet/contourtree_distributed/HyperSweepBlock.h>
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#include <vtkm/worklet/testing/TestingContourTreeUniformDistributedLoadArrays.h>
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// clang-format off
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VTKM_THIRDPARTY_PRE_INCLUDE
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#include <vtkm/thirdparty/diy/diy.h>
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VTKM_THIRDPARTY_POST_INCLUDE
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// clang-format on
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namespace
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{
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template <typename FieldType>
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void LoadHierarchicalContourTree(
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const char* filename,
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vtkm::worklet::contourtree_distributed::HierarchicalContourTree<FieldType>& ht)
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{
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using vtkm::worklet::testing::contourtree_distributed::ReadIndexArray;
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using vtkm::worklet::testing::contourtree_distributed::ReadIndexArrayVector;
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//template <typename FieldType>
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using vtkm::worklet::testing::contourtree_distributed::ReadDataArray; //<FieldType>;
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std::ifstream is(filename, std::ios_base::binary);
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ReadIndexArray(is, ht.RegularNodeGlobalIds);
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ReadDataArray<FieldType>(is, ht.DataValues);
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ReadIndexArray(is, ht.RegularNodeSortOrder);
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ReadIndexArray(is, ht.Regular2Supernode);
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ReadIndexArray(is, ht.Superparents);
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ReadIndexArray(is, ht.Supernodes);
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ReadIndexArray(is, ht.Superarcs);
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ReadIndexArray(is, ht.Hyperparents);
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ReadIndexArray(is, ht.Super2Hypernode);
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ReadIndexArray(is, ht.WhichRound);
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ReadIndexArray(is, ht.WhichIteration);
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ReadIndexArray(is, ht.Hypernodes);
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ReadIndexArray(is, ht.Hyperarcs);
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ReadIndexArray(is, ht.Superchildren);
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int nRounds;
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is.read(reinterpret_cast<char*>(&nRounds), sizeof(nRounds));
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//std::cout << "nRounds = " << nRounds << std::endl;
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ht.NumRounds = nRounds;
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//ht.NumOwnedRegularVertices = 0;
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ReadIndexArray(is, ht.NumRegularNodesInRound);
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ReadIndexArray(is, ht.NumSupernodesInRound);
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ReadIndexArray(is, ht.NumHypernodesInRound);
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ReadIndexArray(is, ht.NumIterations);
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ReadIndexArrayVector(is, ht.FirstSupernodePerIteration);
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ReadIndexArrayVector(is, ht.FirstHypernodePerIteration);
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}
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template <typename FieldType>
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void TestContourTreeMeshCombine(const std::string& mesh1_filename,
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const std::string& mesh2_filename,
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const std::string& combined_filename)
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{
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std::cout << "Testing combining meshes " << mesh1_filename << " " << mesh2_filename
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<< " with expected result " << combined_filename << std::endl;
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vtkm::worklet::contourtree_augmented::ContourTreeMesh<FieldType> contourTreeMesh1;
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contourTreeMesh1.Load(mesh1_filename.c_str());
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vtkm::worklet::contourtree_augmented::ContourTreeMesh<FieldType> contourTreeMesh2;
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contourTreeMesh2.Load(mesh2_filename.c_str());
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contourTreeMesh2.MergeWith(contourTreeMesh1);
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// Result is written to contourTreeMesh2
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vtkm::worklet::contourtree_augmented::ContourTreeMesh<FieldType> combinedContourTreeMesh;
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combinedContourTreeMesh.Load(combined_filename.c_str());
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VTKM_TEST_ASSERT(
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test_equal_ArrayHandles(contourTreeMesh2.SortedValues, combinedContourTreeMesh.SortedValues));
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VTKM_TEST_ASSERT(test_equal_ArrayHandles(contourTreeMesh2.GlobalMeshIndex,
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combinedContourTreeMesh.GlobalMeshIndex));
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VTKM_TEST_ASSERT(test_equal_ArrayHandles(contourTreeMesh2.GlobalMeshIndex,
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combinedContourTreeMesh.GlobalMeshIndex));
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VTKM_TEST_ASSERT(test_equal_ArrayHandles(contourTreeMesh2.NeighborConnectivity,
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combinedContourTreeMesh.NeighborConnectivity));
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VTKM_TEST_ASSERT(test_equal_ArrayHandles(contourTreeMesh2.NeighborOffsets,
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combinedContourTreeMesh.NeighborOffsets));
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VTKM_TEST_ASSERT(contourTreeMesh2.NumVertices == combinedContourTreeMesh.NumVertices);
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VTKM_TEST_ASSERT(contourTreeMesh2.MaxNeighbors == combinedContourTreeMesh.MaxNeighbors);
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}
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void TestHierarchicalHyperSweeper()
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{
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std::cout << "Testing HierarchicalHyperSweeper" << std::endl;
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using vtkm::cont::testing::Testing;
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using ContourTreeDataFieldType = vtkm::FloatDefault;
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// Test input
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const int numBlocks = 4;
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const char* filenames[numBlocks] = { "misc/8x9test_HierarchicalAugmentedTree_Block0.dat",
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"misc/8x9test_HierarchicalAugmentedTree_Block1.dat",
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"misc/8x9test_HierarchicalAugmentedTree_Block2.dat",
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"misc/8x9test_HierarchicalAugmentedTree_Block3.dat" };
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vtkm::Id3 globalSize{ 9, 8, 1 };
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vtkm::Id3 sizes[numBlocks] = { { 5, 4, 1 }, { 5, 5, 1 }, { 5, 4, 1 }, { 5, 5, 1 } };
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vtkm::Id3 origins[numBlocks] = { { 0, 0, 0 }, { 0, 3, 0 }, { 4, 0, 0 }, { 4, 3, 0 } };
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vtkm::Id3 blockIndices[numBlocks] = { { 0, 0, 0 }, { 0, 1, 0 }, { 1, 0, 0 }, { 1, 1, 0 } };
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// Expected output
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vtkm::cont::ArrayHandle<vtkm::Id> expectedIntrinsicVolume[numBlocks] = {
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vtkm::cont::make_ArrayHandle<vtkm::Id>({ 6, 9, 8, 24, 20, 1, 1 }),
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vtkm::cont::make_ArrayHandle<vtkm::Id>({ 6, 9, 8, 24, 20, 1, 1 }),
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vtkm::cont::make_ArrayHandle<vtkm::Id>({ 6, 9, 8, 24, 20, 1 }),
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vtkm::cont::make_ArrayHandle<vtkm::Id>({ 6, 9, 8, 24, 20, 1, 2 })
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};
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vtkm::cont::ArrayHandle<vtkm::Id> expectedDependentVolume[numBlocks] = {
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vtkm::cont::make_ArrayHandle<vtkm::Id>({ 6, 9, 18, 24, 46, 72, 1 }),
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vtkm::cont::make_ArrayHandle<vtkm::Id>({ 6, 9, 18, 24, 46, 72, 1 }),
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vtkm::cont::make_ArrayHandle<vtkm::Id>({ 6, 9, 18, 24, 46, 72 }),
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vtkm::cont::make_ArrayHandle<vtkm::Id>({ 6, 9, 18, 24, 46, 72, 2 })
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};
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// Load trees
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vtkm::worklet::contourtree_distributed::HierarchicalContourTree<vtkm::FloatDefault>
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hct[numBlocks];
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for (vtkm::Id blockNo = 0; blockNo < numBlocks; ++blockNo)
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{
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LoadHierarchicalContourTree(Testing::DataPath(filenames[blockNo]).c_str(), hct[blockNo]);
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#ifdef DEBUG_PRINT
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std::cout << hct[blockNo].DebugPrint("AfterLoad", __FILE__, __LINE__);
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#endif
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}
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// Create and add DIY blocks
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auto comm = vtkm::cont::EnvironmentTracker::GetCommunicator();
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vtkm::Id rank = comm.rank();
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vtkmdiy::Master master(comm,
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1, // Use 1 thread, VTK-M will do the treading
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-1 // All block in memory
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);
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// Set up connectivity
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using RegularDecomposer = vtkmdiy::RegularDecomposer<vtkmdiy::DiscreteBounds>;
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RegularDecomposer::BoolVector shareFace(3, true);
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RegularDecomposer::BoolVector wrap(3, false);
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RegularDecomposer::CoordinateVector ghosts(3, 1);
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RegularDecomposer::DivisionsVector diyDivisions{ 2, 2, 1 }; // HARDCODED FOR TEST
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int numDims = 2;
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vtkmdiy::DiscreteBounds diyBounds(2);
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diyBounds.min[0] = diyBounds.min[1] = 0;
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diyBounds.max[0] = static_cast<int>(globalSize[0]);
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diyBounds.max[1] = static_cast<int>(globalSize[1]);
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RegularDecomposer decomposer(
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numDims, diyBounds, numBlocks, shareFace, wrap, ghosts, diyDivisions);
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// ... coordinates of local blocks
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std::vector<int> vtkmdiyLocalBlockGids(numBlocks);
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for (vtkm::Id bi = 0; bi < numBlocks; bi++)
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{
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RegularDecomposer::DivisionsVector diyCoords(static_cast<size_t>(numDims));
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auto currentCoords = blockIndices[bi];
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for (vtkm::IdComponent d = 0; d < numDims; ++d)
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{
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diyCoords[d] = static_cast<int>(currentCoords[d]);
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}
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vtkmdiyLocalBlockGids[static_cast<size_t>(bi)] =
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RegularDecomposer::coords_to_gid(diyCoords, diyDivisions);
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}
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// Define which blocks live on which rank so that vtkmdiy can manage them
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vtkmdiy::DynamicAssigner assigner(comm, comm.size(), numBlocks);
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for (vtkm::Id bi = 0; bi < numBlocks; bi++)
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{
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assigner.set_rank(static_cast<int>(rank),
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static_cast<int>(vtkmdiyLocalBlockGids[static_cast<size_t>(bi)]));
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}
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vtkmdiy::fix_links(master, assigner);
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vtkm::worklet::contourtree_distributed::HyperSweepBlock<ContourTreeDataFieldType>*
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localHyperSweeperBlocks[numBlocks];
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for (vtkm::Id blockNo = 0; blockNo < numBlocks; ++blockNo)
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{
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localHyperSweeperBlocks[blockNo] =
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new vtkm::worklet::contourtree_distributed::HyperSweepBlock<ContourTreeDataFieldType>(
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blockNo,
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vtkmdiyLocalBlockGids[blockNo],
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origins[blockNo],
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sizes[blockNo],
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globalSize,
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hct[blockNo]);
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master.add(
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vtkmdiyLocalBlockGids[blockNo], localHyperSweeperBlocks[blockNo], new vtkmdiy::Link());
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}
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master.foreach (
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[](vtkm::worklet::contourtree_distributed::HyperSweepBlock<ContourTreeDataFieldType>* b,
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const vtkmdiy::Master::ProxyWithLink&) {
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#ifdef DEBUG_PRINT
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std::cout << "Block " << b->GlobalBlockId << std::endl;
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std::cout << b->HierarchicalContourTree.DebugPrint(
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"Before initializing HyperSweeper", __FILE__, __LINE__);
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#endif
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// Create HyperSweeper
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vtkm::worklet::contourtree_distributed::HierarchicalHyperSweeper<vtkm::Id,
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ContourTreeDataFieldType>
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hyperSweeper(
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b->GlobalBlockId, b->HierarchicalContourTree, b->IntrinsicVolume, b->DependentVolume);
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#ifdef DEBUG_PRINT
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std::cout << "Block " << b->GlobalBlockId << std::endl;
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std::cout << b->HierarchicalContourTree.DebugPrint(
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"After initializing HyperSweeper", __FILE__, __LINE__);
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#endif
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// Create mesh and initialize vertex counts
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vtkm::worklet::contourtree_augmented::mesh_dem::IdRelabeler idRelabeler{ b->Origin,
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b->Size,
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b->GlobalSize };
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if (b->GlobalSize[2] <= 1)
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{
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vtkm::worklet::contourtree_augmented::DataSetMeshTriangulation2DFreudenthal mesh(
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|
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vtkm::Id2{ b->Size[0], b->Size[1] });
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hyperSweeper.InitializeIntrinsicVertexCount(
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b->HierarchicalContourTree, mesh, idRelabeler, b->IntrinsicVolume);
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}
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else
|
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|
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{
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// TODO/FIXME: For getting owned vertices, it should not make a difference if marching
|
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// cubes or not. Verify.
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vtkm::worklet::contourtree_augmented::DataSetMeshTriangulation3DFreudenthal mesh(b->Size);
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hyperSweeper.InitializeIntrinsicVertexCount(
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b->HierarchicalContourTree, mesh, idRelabeler, b->IntrinsicVolume);
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}
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#ifdef DEBUG_PRINT
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std::cout << "Block " << b->GlobalBlockId << std::endl;
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std::cout << b->HierarchicalContourTree.DebugPrint(
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|
|
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|
"After initializing intrinsic vertex count", __FILE__, __LINE__);
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#endif
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|
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// Initialize dependentVolume by copy from intrinsicVolume
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|
vtkm::cont::Algorithm::Copy(b->IntrinsicVolume, b->DependentVolume);
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|
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|
// Perform the local hypersweep
|
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|
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|
hyperSweeper.LocalHyperSweep();
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|
|
|
#ifdef DEBUG_PRINT
|
|
|
|
|
std::cout << "Block " << b->GlobalBlockId << std::endl;
|
|
|
|
|
std::cout << b->HierarchicalContourTree.DebugPrint(
|
|
|
|
|
"After local hypersweep", __FILE__, __LINE__);
|
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|
|
|
#endif
|
|
|
|
|
});
|
|
|
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|
|
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|
|
// Reduce
|
|
|
|
|
// partners for merge over regular block grid
|
|
|
|
|
vtkmdiy::RegularSwapPartners partners(
|
|
|
|
|
decomposer, // domain decomposition
|
|
|
|
|
2, // radix of k-ary reduction.
|
|
|
|
|
true // contiguous: true=distance doubling, false=distance halving
|
|
|
|
|
);
|
|
|
|
|
vtkmdiy::reduce(master,
|
|
|
|
|
assigner,
|
|
|
|
|
partners,
|
|
|
|
|
vtkm::worklet::contourtree_distributed::CobmineHyperSweepBlockFunctor<
|
|
|
|
|
ContourTreeDataFieldType>{});
|
|
|
|
|
|
|
|
|
|
#ifdef PRINT_RESULT
|
|
|
|
|
// Print
|
|
|
|
|
vtkm::Id totalVolume = globalSize[0] * globalSize[1] * globalSize[2];
|
|
|
|
|
master.foreach (
|
|
|
|
|
[&totalVolume](
|
|
|
|
|
vtkm::worklet::contourtree_distributed::HyperSweepBlock<ContourTreeDataFieldType>* b,
|
|
|
|
|
const vtkmdiy::Master::ProxyWithLink&) {
|
|
|
|
|
std::cout << "Block " << b->GlobalBlockId << std::endl;
|
|
|
|
|
std::cout << "=========" << std::endl;
|
|
|
|
|
vtkm::worklet::contourtree_augmented::PrintHeader(b->IntrinsicVolume.GetNumberOfValues(),
|
|
|
|
|
std::cout);
|
|
|
|
|
vtkm::worklet::contourtree_augmented::PrintIndices(
|
|
|
|
|
"Intrinsic Volume", b->IntrinsicVolume, -1, std::cout);
|
|
|
|
|
vtkm::worklet::contourtree_augmented::PrintIndices(
|
|
|
|
|
"Dependent Volume", b->DependentVolume, -1, std::cout);
|
|
|
|
|
|
|
|
|
|
std::cout << b->HierarchicalContourTree.DebugPrint(
|
|
|
|
|
"Called from DumpVolumes", __FILE__, __LINE__);
|
|
|
|
|
std::cout << vtkm::worklet::contourtree_distributed::HierarchicalContourTree<
|
|
|
|
|
ContourTreeDataFieldType>::DumpVolumes(b->HierarchicalContourTree.Supernodes,
|
|
|
|
|
b->HierarchicalContourTree.Superarcs,
|
|
|
|
|
b->HierarchicalContourTree.RegularNodeGlobalIds,
|
|
|
|
|
totalVolume,
|
|
|
|
|
b->IntrinsicVolume,
|
|
|
|
|
b->DependentVolume);
|
|
|
|
|
});
|
|
|
|
|
#endif
|
|
|
|
|
|
|
|
|
|
// Compare to expected results
|
|
|
|
|
master.foreach (
|
|
|
|
|
[&expectedIntrinsicVolume, &expectedDependentVolume](
|
|
|
|
|
vtkm::worklet::contourtree_distributed::HyperSweepBlock<ContourTreeDataFieldType>* b,
|
|
|
|
|
const vtkmdiy::Master::ProxyWithLink&) {
|
|
|
|
|
#ifdef DEBUG_PRINT
|
|
|
|
|
vtkm::worklet::contourtree_augmented::PrintIndices(
|
|
|
|
|
"Intrinsic Volume", b->IntrinsicVolume, -1, std::cout);
|
|
|
|
|
vtkm::worklet::contourtree_augmented::PrintIndices(
|
|
|
|
|
"Expected Intrinsic Volume", expectedIntrinsicVolume[b->GlobalBlockId], -1, std::cout);
|
|
|
|
|
vtkm::worklet::contourtree_augmented::PrintIndices(
|
|
|
|
|
"Dependent Volume", b->DependentVolume, -1, std::cout);
|
|
|
|
|
vtkm::worklet::contourtree_augmented::PrintIndices(
|
|
|
|
|
"Expected Dependent Volume", expectedDependentVolume[b->GlobalBlockId], -1, std::cout);
|
|
|
|
|
#endif
|
|
|
|
|
VTKM_TEST_ASSERT(test_equal_portals(expectedIntrinsicVolume[b->GlobalBlockId].ReadPortal(),
|
|
|
|
|
b->IntrinsicVolume.ReadPortal()));
|
|
|
|
|
VTKM_TEST_ASSERT(test_equal_portals(expectedDependentVolume[b->GlobalBlockId].ReadPortal(),
|
|
|
|
|
b->DependentVolume.ReadPortal()));
|
|
|
|
|
});
|
|
|
|
|
|
|
|
|
|
// Clean-up
|
|
|
|
|
for (auto b : localHyperSweeperBlocks)
|
|
|
|
|
{
|
|
|
|
|
delete b;
|
|
|
|
|
}
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
void TestContourTreeUniformDistributed()
|
|
|
|
|
{
|
|
|
|
|
using vtkm::cont::testing::Testing;
|
|
|
|
|
TestContourTreeMeshCombine<vtkm::FloatDefault>(
|
|
|
|
|
Testing::DataPath("misc/5x6_7_MC_Rank0_Block0_Round1_BeforeCombineMesh1.ctm"),
|
|
|
|
|
Testing::DataPath("misc/5x6_7_MC_Rank0_Block0_Round1_BeforeCombineMesh2.ctm"),
|
|
|
|
|
Testing::RegressionImagePath("5x6_7_MC_Rank0_Block0_Round1_CombinedMesh.ctm"));
|
|
|
|
|
|
|
|
|
|
TestHierarchicalHyperSweeper();
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
} // anonymous namespace
|
|
|
|
|
|
|
|
|
|
int UnitTestContourTreeUniformDistributed(int argc, char* argv[])
|
|
|
|
|
{
|
|
|
|
|
return vtkm::cont::testing::Testing::Run(TestContourTreeUniformDistributed, argc, argv);
|
|
|
|
|
}
|
Gunther Weber