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909 lines
35 KiB
C++
909 lines
35 KiB
C++
//============================================================================
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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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// 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 2014 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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// Copyright 2014 UT-Battelle, LLC.
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// Copyright 2014 Los Alamos National Security.
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//
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// Under the terms of Contract DE-NA0003525 with NTESS,
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// the U.S. Government retains certain rights in this software.
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//
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// Under the terms of Contract DE-AC52-06NA25396 with Los Alamos National
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// Laboratory (LANL), the U.S. Government retains certain rights in
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// this software.
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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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#include <vtkm/Types.h>
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#include <vtkm/cont/ArrayHandle.h>
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#include <vtkm/cont/DataSet.h>
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#include <vtkm/cont/DataSetBuilderUniform.h>
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#include <vtkm/cont/DeviceAdapterTag.h>
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#include <vtkm/cont/Initialize.h>
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#include <vtkm/cont/RuntimeDeviceTracker.h>
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#include <vtkm/cont/Timer.h>
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#include <vtkm/io/BOVDataSetReader.h>
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#include <vtkm/filter/MapFieldPermutation.h>
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#include <vtkm/filter/scalar_topology/ContourTreeUniformAugmented.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/ProcessContourTree.h>
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#include <vtkm/filter/scalar_topology/worklet/contourtree_augmented/Types.h>
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#include <vtkm/filter/scalar_topology/worklet/contourtree_augmented/processcontourtree/Branch.h>
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// clang-format off
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VTKM_THIRDPARTY_PRE_INCLUDE
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#include <vtkm/thirdparty/diy/Configure.h>
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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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#ifdef WITH_MPI
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#include <mpi.h>
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#endif
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#include <fstream>
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#include <iomanip>
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#include <iostream>
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#include <sstream>
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#include <stdio.h>
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#include <string>
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#include <utility>
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#include <vector>
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using ValueType = vtkm::Float32;
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using BranchType = vtkm::worklet::contourtree_augmented::process_contourtree_inc::Branch<ValueType>;
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namespace ctaug_ns = vtkm::worklet::contourtree_augmented;
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// Simple helper class for parsing the command line options
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class ParseCL
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{
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public:
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ParseCL() {}
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void parse(int& argc, char** argv)
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{
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mCLOptions.resize(static_cast<std::size_t>(argc));
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for (std::size_t i = 1; i < static_cast<std::size_t>(argc); ++i)
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{
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this->mCLOptions[i] = std::string(argv[i]);
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}
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}
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vtkm::Id findOption(const std::string& option) const
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{
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auto it =
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std::find_if(this->mCLOptions.begin(),
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this->mCLOptions.end(),
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[option](const std::string& val) -> bool { return val.find(option) == 0; });
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if (it == this->mCLOptions.end())
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{
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return -1;
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}
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else
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{
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return static_cast<vtkm::Id>(it - this->mCLOptions.begin());
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}
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}
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bool hasOption(const std::string& option) const { return this->findOption(option) >= 0; }
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std::string getOption(const std::string& option) const
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{
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std::size_t index = static_cast<std::size_t>(this->findOption(option));
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std::string val = this->mCLOptions[index];
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auto valPos = val.find("=");
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if (valPos)
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{
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return val.substr(valPos + 1);
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}
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return std::string("");
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}
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const std::vector<std::string>& getOptions() const { return this->mCLOptions; }
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private:
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std::vector<std::string> mCLOptions;
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};
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inline vtkm::Id3 ComputeNumberOfBlocksPerAxis(vtkm::Id3 globalSize, vtkm::Id numberOfBlocks)
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{
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vtkm::Id currNumberOfBlocks = numberOfBlocks;
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vtkm::Id3 blocksPerAxis{ 1, 1, 1 };
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while (currNumberOfBlocks > 1)
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{
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vtkm::IdComponent splitAxis = 0;
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for (vtkm::IdComponent d = 1; d < 3; ++d)
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{
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if (globalSize[d] > globalSize[splitAxis])
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{
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splitAxis = d;
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}
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}
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if (currNumberOfBlocks % 2 == 0)
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{
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blocksPerAxis[splitAxis] *= 2;
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globalSize[splitAxis] /= 2;
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currNumberOfBlocks /= 2;
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}
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else
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{
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blocksPerAxis[splitAxis] *= currNumberOfBlocks;
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break;
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}
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}
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return blocksPerAxis;
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}
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inline std::tuple<vtkm::Id3, vtkm::Id3, vtkm::Id3> ComputeBlockExtents(vtkm::Id3 globalSize,
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vtkm::Id3 blocksPerAxis,
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vtkm::Id blockNo)
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{
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// DEBUG: std::cout << "ComputeBlockExtents("<<globalSize <<", " << blocksPerAxis << ", " << blockNo << ")" << std::endl;
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// DEBUG: std::cout << "Block " << blockNo;
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vtkm::Id3 blockIndex, blockOrigin, blockSize;
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for (vtkm::IdComponent d = 0; d < 3; ++d)
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{
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blockIndex[d] = blockNo % blocksPerAxis[d];
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blockNo /= blocksPerAxis[d];
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float dx = float(globalSize[d] - 1) / float(blocksPerAxis[d]);
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blockOrigin[d] = vtkm::Id(blockIndex[d] * dx);
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vtkm::Id maxIdx =
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blockIndex[d] < blocksPerAxis[d] - 1 ? vtkm::Id((blockIndex[d] + 1) * dx) : globalSize[d] - 1;
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blockSize[d] = maxIdx - blockOrigin[d] + 1;
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// DEBUG: std::cout << " " << blockIndex[d] << dx << " " << blockOrigin[d] << " " << maxIdx << " " << blockSize[d] << "; ";
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}
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// DEBUG: std::cout << " -> " << blockIndex << " " << blockOrigin << " " << blockSize << std::endl;
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return std::make_tuple(blockIndex, blockOrigin, blockSize);
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}
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inline vtkm::cont::DataSet CreateSubDataSet(const vtkm::cont::DataSet& ds,
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vtkm::Id3 blockOrigin,
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vtkm::Id3 blockSize,
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const std::string& fieldName)
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{
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vtkm::Id3 globalSize;
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ds.GetCellSet().CastAndCallForTypes<VTKM_DEFAULT_CELL_SET_LIST_STRUCTURED>(
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vtkm::worklet::contourtree_augmented::GetPointDimensions(), globalSize);
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const vtkm::Id nOutValues = blockSize[0] * blockSize[1] * blockSize[2];
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const auto inDataArrayHandle = ds.GetPointField(fieldName).GetData();
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vtkm::cont::ArrayHandle<vtkm::Id> copyIdsArray;
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copyIdsArray.Allocate(nOutValues);
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auto copyIdsPortal = copyIdsArray.WritePortal();
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vtkm::Id3 outArrIdx;
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for (outArrIdx[2] = 0; outArrIdx[2] < blockSize[2]; ++outArrIdx[2])
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for (outArrIdx[1] = 0; outArrIdx[1] < blockSize[1]; ++outArrIdx[1])
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for (outArrIdx[0] = 0; outArrIdx[0] < blockSize[0]; ++outArrIdx[0])
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{
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vtkm::Id3 inArrIdx = outArrIdx + blockOrigin;
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vtkm::Id inIdx = (inArrIdx[2] * globalSize[1] + inArrIdx[1]) * globalSize[0] + inArrIdx[0];
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vtkm::Id outIdx =
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(outArrIdx[2] * blockSize[1] + outArrIdx[1]) * blockSize[0] + outArrIdx[0];
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VTKM_ASSERT(inIdx >= 0 && inIdx < inDataArrayHandle.GetNumberOfValues());
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VTKM_ASSERT(outIdx >= 0 && outIdx < nOutValues);
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copyIdsPortal.Set(outIdx, inIdx);
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}
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// DEBUG: std::cout << copyIdsPortal.GetNumberOfValues() << std::endl;
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vtkm::cont::Field permutedField;
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bool success =
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vtkm::filter::MapFieldPermutation(ds.GetPointField(fieldName), copyIdsArray, permutedField);
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if (!success)
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throw vtkm::cont::ErrorBadType("Field copy failed (probably due to invalid type)");
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vtkm::cont::DataSetBuilderUniform dsb;
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if (globalSize[2] <= 1) // 2D Data Set
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{
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vtkm::Id2 dimensions{ blockSize[0], blockSize[1] };
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vtkm::cont::DataSet dataSet = dsb.Create(dimensions);
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vtkm::cont::CellSetStructured<2> cellSet;
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cellSet.SetPointDimensions(dimensions);
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cellSet.SetGlobalPointDimensions(vtkm::Id2{ globalSize[0], globalSize[1] });
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cellSet.SetGlobalPointIndexStart(vtkm::Id2{ blockOrigin[0], blockOrigin[1] });
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dataSet.SetCellSet(cellSet);
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dataSet.AddField(permutedField);
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return dataSet;
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}
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else
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{
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vtkm::cont::DataSet dataSet = dsb.Create(blockSize);
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vtkm::cont::CellSetStructured<3> cellSet;
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cellSet.SetPointDimensions(blockSize);
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cellSet.SetGlobalPointDimensions(globalSize);
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cellSet.SetGlobalPointIndexStart(blockOrigin);
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dataSet.SetCellSet(cellSet);
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dataSet.AddField(permutedField);
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return dataSet;
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}
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}
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// Compute and render an isosurface for a uniform grid example
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int main(int argc, char* argv[])
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{
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#ifdef WITH_MPI
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// Setup the MPI environment.
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MPI_Init(&argc, &argv);
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auto comm = MPI_COMM_WORLD;
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// Tell VTK-m which communicator it should use.
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vtkm::cont::EnvironmentTracker::SetCommunicator(vtkmdiy::mpi::communicator());
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// get the rank and size
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int rank, size;
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MPI_Comm_rank(comm, &rank);
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MPI_Comm_size(comm, &size);
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int numBlocks = size;
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#endif
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// initialize vtkm-m (e.g., logging via -v and device via the -d option)
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vtkm::cont::InitializeOptions vtkm_initialize_options =
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vtkm::cont::InitializeOptions::RequireDevice;
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vtkm::cont::InitializeResult vtkm_config =
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vtkm::cont::Initialize(argc, argv, vtkm_initialize_options);
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auto device = vtkm_config.Device;
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#ifdef WITH_MPI
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VTKM_LOG_IF_S(vtkm::cont::LogLevel::Info, rank == 0, "Running with MPI. #ranks=" << size);
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#else
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VTKM_LOG_S(vtkm::cont::LogLevel::Info, "Single node run");
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int rank = 0;
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#endif
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// Setup timing
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vtkm::Float64 prevTime = 0;
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vtkm::Float64 currTime = 0;
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vtkm::cont::Timer totalTime;
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totalTime.Start();
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////////////////////////////////////////////
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// Parse the command line options
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////////////////////////////////////////////
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ParseCL parser;
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parser.parse(argc, argv);
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std::string filename = parser.getOptions().back();
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unsigned int computeRegularStructure = 1; // 1=fully augmented
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bool useMarchingCubes = false;
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bool computeBranchDecomposition = true;
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bool printContourTree = false;
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if (parser.hasOption("--augmentTree"))
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computeRegularStructure =
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static_cast<unsigned int>(std::stoi(parser.getOption("--augmentTree")));
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if (parser.hasOption("--mc"))
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useMarchingCubes = true;
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if (parser.hasOption("--printCT"))
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printContourTree = true;
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if (parser.hasOption("--branchDecomp"))
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computeBranchDecomposition = std::stoi(parser.getOption("--branchDecomp"));
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// We need the fully augmented tree to compute the branch decomposition
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if (computeBranchDecomposition && (computeRegularStructure != 1))
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{
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VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
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"Regular structure is required for branch decomposition."
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" Disabling branch decomposition");
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computeBranchDecomposition = false;
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}
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// Iso value selection parameters
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// Approach to be used to select contours based on the tree
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vtkm::Id contourType = 0;
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// Error away from critical point
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ValueType eps = 0.00001f;
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// Number of iso levels to be selected. By default we disable the isovalue selection.
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vtkm::Id numLevels = 0;
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// Number of components the tree should be simplified to
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vtkm::Id numComp = numLevels + 1;
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// Method to be used to compute the relevant iso values
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vtkm::Id contourSelectMethod = 0;
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bool usePersistenceSorter = true;
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if (parser.hasOption("--levels"))
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numLevels = std::stoi(parser.getOption("--levels"));
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if (parser.hasOption("--type"))
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contourType = std::stoi(parser.getOption("--type"));
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if (parser.hasOption("--eps"))
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eps = std::stof(parser.getOption("--eps"));
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if (parser.hasOption("--method"))
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contourSelectMethod = std::stoi(parser.getOption("--method"));
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if (parser.hasOption("--comp"))
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numComp = std::stoi(parser.getOption("--comp"));
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if (contourSelectMethod == 0)
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numComp = numLevels + 1;
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if (parser.hasOption("--useVolumeSorter"))
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usePersistenceSorter = false;
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if ((numLevels > 0) && (!computeBranchDecomposition))
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{
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VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
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"Iso level selection only available when branch decomposition is enabled. "
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"Disabling iso value selection");
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numLevels = 0;
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}
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if (rank == 0 && (argc < 2 || parser.hasOption("--help") || parser.hasOption("-h")))
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{
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std::cout << "ContourTreeAugmented <options> <fileName>" << std::endl;
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std::cout << std::endl;
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std::cout << "<fileName> Name of the input data file." << std::endl;
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std::cout << "The file is expected to be ASCII with either: " << std::endl;
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std::cout << " - xdim ydim integers for 2D or" << std::endl;
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std::cout << " - xdim ydim zdim integers for 3D" << std::endl;
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std::cout << "followed by vector data last dimension varying fastest" << std::endl;
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std::cout << std::endl;
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std::cout << "----------------------------- VTKM Options -----------------------------"
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<< std::endl;
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std::cout << vtkm_config.Usage << std::endl;
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std::cout << std::endl;
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std::cout << "------------------------- Contour Tree Options -------------------------"
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<< std::endl;
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std::cout << "Options: (Bool options are give via int, i.e. =0 for False and =1 for True)"
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<< std::endl;
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std::cout << "--mc Use marching cubes interpolation for contour tree calculation. "
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"(Default=False)"
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<< std::endl;
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std::cout << "--augmentTree 1 = compute the fully augmented contour tree (Default)"
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<< std::endl;
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std::cout << " 2 = compute the boundary augmented contour tree " << std::endl;
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std::cout << " 0 = no augmentation. NOTE: When using MPI, local ranks use"
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<< std::endl;
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std::cout << " boundary augmentation to support parallel merge of blocks"
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<< std::endl;
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std::cout << "--branchDecomp Compute the volume branch decomposition for the contour tree. "
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"Requires --augmentTree (Default=True)"
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<< std::endl;
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std::cout << "--printCT Print the contour tree. (Default=False)" << std::endl;
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std::cout << std::endl;
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std::cout << "---------------------- Isovalue Selection Options ----------------------"
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<< std::endl;
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std::cout << "Isovalue selection options: (require --branchDecomp=1 and augmentTree=1)"
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<< std::endl;
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std::cout << "--levels=<int> Number of iso-contour levels to be used (default=0, i.e., "
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"disable isovalue computation)"
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<< std::endl;
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std::cout << "--comp=<int> Number of components the contour tree should be simplified to. "
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"Only used if method==1. (default=0)"
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<< std::endl;
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std::cout
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<< "--eps=<float> Floating point offset awary from the critical point. (default=0.00001)"
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<< std::endl;
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std::cout << "--type=<int> Approach to be used for selection of iso-values. 0=saddle+-eps; "
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"1=mid point between saddle and extremum, 2=extremum+-eps. (default=0)"
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<< std::endl;
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std::cout << "--method=<int> Method used for selecting relevant iso-values. (default=0)"
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<< std::endl;
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std::cout << std::endl;
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#ifdef WITH_MPI
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MPI_Finalize();
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#endif
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return EXIT_SUCCESS;
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}
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if (rank == 0)
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{
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std::stringstream logmessage;
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logmessage << " ------------ Settings -----------" << std::endl
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<< " filename=" << filename << std::endl
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<< " device=" << device.GetName() << std::endl
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<< " mc=" << useMarchingCubes << std::endl
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<< " augmentTree=" << computeRegularStructure << std::endl
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<< " branchDecomp=" << computeBranchDecomposition << std::endl
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<<
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#ifdef WITH_MPI
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" nblocks=" << numBlocks << std::endl
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<<
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|
#endif
|
|
" computeIsovalues=" << (numLevels > 0);
|
|
VTKM_LOG_S(vtkm::cont::LogLevel::Info, std::endl << logmessage.str());
|
|
VTKM_LOG_IF_S(vtkm::cont::LogLevel::Info,
|
|
numLevels > 0,
|
|
std::endl
|
|
<< " ------------ Settings Isolevel Selection -----------" << std::endl
|
|
<< " levels=" << numLevels << std::endl
|
|
<< " eps=" << eps << std::endl
|
|
<< " comp" << numComp << std::endl
|
|
<< " type=" << contourType << std::endl
|
|
<< " method=" << contourSelectMethod << std::endl
|
|
<< " mc=" << useMarchingCubes << std::endl
|
|
<< " use" << (usePersistenceSorter ? "PersistenceSorter" : "VolumeSorter"));
|
|
}
|
|
currTime = totalTime.GetElapsedTime();
|
|
vtkm::Float64 startUpTime = currTime - prevTime;
|
|
prevTime = currTime;
|
|
|
|
// Redirect stdout to file if we are using MPI with Debugging
|
|
#ifdef WITH_MPI
|
|
#ifdef DEBUG_PRINT
|
|
// From https://www.unix.com/302983597-post2.html
|
|
char cstr_filename[32];
|
|
snprintf(cstr_filename, sizeof(cstr_filename), "cout_%d.log", rank);
|
|
int out = open(cstr_filename, O_RDWR | O_CREAT | O_TRUNC | O_APPEND, 0600);
|
|
if (-1 == out)
|
|
{
|
|
perror("opening cout.log");
|
|
return 255;
|
|
}
|
|
|
|
snprintf(cstr_filename, sizeof(cstr_filename), "cerr_%d.log", rank);
|
|
int err = open(cstr_filename, O_RDWR | O_CREAT | O_TRUNC | O_APPEND, 0600);
|
|
if (-1 == err)
|
|
{
|
|
perror("opening cerr.log");
|
|
return 255;
|
|
}
|
|
|
|
int save_out = dup(fileno(stdout));
|
|
int save_err = dup(fileno(stderr));
|
|
|
|
if (-1 == dup2(out, fileno(stdout)))
|
|
{
|
|
perror("cannot redirect stdout");
|
|
return 255;
|
|
}
|
|
if (-1 == dup2(err, fileno(stderr)))
|
|
{
|
|
perror("cannot redirect stderr");
|
|
return 255;
|
|
}
|
|
#endif
|
|
#endif
|
|
|
|
///////////////////////////////////////////////
|
|
// Read the input data
|
|
///////////////////////////////////////////////
|
|
vtkm::Float64 dataReadTime = 0;
|
|
vtkm::Float64 buildDatasetTime = 0;
|
|
std::vector<vtkm::Float32>::size_type nDims = 0;
|
|
vtkm::cont::DataSet inDataSet;
|
|
std::vector<ValueType> values;
|
|
std::vector<vtkm::Id> dims;
|
|
if (filename.compare(filename.length() - 3, 3, "bov") == 0)
|
|
{
|
|
vtkm::io::BOVDataSetReader reader(filename);
|
|
inDataSet = reader.ReadDataSet();
|
|
nDims = 3;
|
|
currTime = totalTime.GetElapsedTime();
|
|
dataReadTime = currTime - prevTime;
|
|
prevTime = currTime;
|
|
}
|
|
else // Read ASCII data input
|
|
{
|
|
std::ifstream inFile(filename);
|
|
if (inFile.bad())
|
|
return 0;
|
|
|
|
// Read the dimensions of the mesh, i.e,. number of elementes in x, y, and z
|
|
std::string line;
|
|
getline(inFile, line);
|
|
std::istringstream linestream(line);
|
|
vtkm::Id dimVertices;
|
|
while (linestream >> dimVertices)
|
|
{
|
|
dims.push_back(dimVertices);
|
|
}
|
|
|
|
// Compute the number of vertices, i.e., xdim * ydim * zdim
|
|
nDims = static_cast<unsigned short>(dims.size());
|
|
std::size_t numVertices = static_cast<std::size_t>(
|
|
std::accumulate(dims.begin(), dims.end(), std::size_t(1), std::multiplies<std::size_t>()));
|
|
|
|
// Check for fatal input errors
|
|
// Check the the number of dimensiosn is either 2D or 3D
|
|
bool invalidNumDimensions = (nDims < 2 || nDims > 3);
|
|
// Log any errors if found on rank 0
|
|
VTKM_LOG_IF_S(vtkm::cont::LogLevel::Error,
|
|
invalidNumDimensions && (rank == 0),
|
|
"The input mesh is " << nDims << "D. The input data must be either 2D or 3D.");
|
|
// If we found any errors in the setttings than finalize MPI and exit the execution
|
|
if (invalidNumDimensions)
|
|
{
|
|
#ifdef WITH_MPI
|
|
MPI_Finalize();
|
|
#endif
|
|
return EXIT_SUCCESS;
|
|
}
|
|
|
|
// Read data
|
|
values.resize(numVertices);
|
|
for (std::size_t vertex = 0; vertex < numVertices; ++vertex)
|
|
{
|
|
inFile >> values[vertex];
|
|
}
|
|
|
|
// finish reading the data
|
|
inFile.close();
|
|
|
|
currTime = totalTime.GetElapsedTime();
|
|
dataReadTime = currTime - prevTime;
|
|
prevTime = currTime;
|
|
|
|
// swap dims order
|
|
std::swap(dims[0], dims[1]);
|
|
|
|
// build the input dataset
|
|
vtkm::cont::DataSetBuilderUniform dsb;
|
|
// 2D data
|
|
if (nDims == 2)
|
|
{
|
|
vtkm::Id2 vdims;
|
|
vdims[0] = static_cast<vtkm::Id>(dims[0]);
|
|
vdims[1] = static_cast<vtkm::Id>(dims[1]);
|
|
inDataSet = dsb.Create(vdims);
|
|
}
|
|
// 3D data
|
|
else
|
|
{
|
|
vtkm::Id3 vdims;
|
|
vdims[0] = static_cast<vtkm::Id>(dims[0]);
|
|
vdims[1] = static_cast<vtkm::Id>(dims[1]);
|
|
vdims[2] = static_cast<vtkm::Id>(dims[2]);
|
|
inDataSet = dsb.Create(vdims);
|
|
}
|
|
inDataSet.AddPointField("values", values);
|
|
} // END ASCII Read
|
|
|
|
// Print the mesh metadata
|
|
if (rank == 0)
|
|
{
|
|
VTKM_LOG_S(vtkm::cont::LogLevel::Info,
|
|
std::endl
|
|
<< " ---------------- Input Mesh Properties --------------" << std::endl
|
|
<< " Number of dimensions: " << nDims);
|
|
}
|
|
|
|
// Check if marching cubes is enabled for non 3D data
|
|
bool invalidMCOption = (useMarchingCubes && nDims != 3);
|
|
VTKM_LOG_IF_S(vtkm::cont::LogLevel::Error,
|
|
invalidMCOption && (rank == 0),
|
|
"The input mesh is "
|
|
<< nDims << "D. "
|
|
<< "Contour tree using marching cubes is only supported for 3D data.");
|
|
|
|
// If we found any errors in the setttings than finalize MPI and exit the execution
|
|
if (invalidMCOption)
|
|
{
|
|
#ifdef WITH_MPI
|
|
MPI_Finalize();
|
|
#endif
|
|
return EXIT_SUCCESS;
|
|
}
|
|
|
|
#ifndef WITH_MPI // construct regular, single-block VTK-M input dataset
|
|
vtkm::cont::DataSet useDataSet = inDataSet; // Single block dataset
|
|
#else // Create a multi-block dataset for multi-block DIY-paralle processing
|
|
// Determine split
|
|
vtkm::Id3 globalSize = nDims == 3 ? vtkm::Id3(static_cast<vtkm::Id>(dims[0]),
|
|
static_cast<vtkm::Id>(dims[1]),
|
|
static_cast<vtkm::Id>(dims[2]))
|
|
: vtkm::Id3(static_cast<vtkm::Id>(dims[0]),
|
|
static_cast<vtkm::Id>(dims[1]),
|
|
static_cast<vtkm::Id>(1));
|
|
vtkm::Id3 blocksPerDim = ComputeNumberOfBlocksPerAxis(globalSize, numBlocks);
|
|
vtkm::Id blocksPerRank = numBlocks / size;
|
|
vtkm::Id numRanksWithExtraBlock = numBlocks % size;
|
|
vtkm::Id blocksOnThisRank, startBlockNo;
|
|
if (rank < numRanksWithExtraBlock)
|
|
{
|
|
blocksOnThisRank = blocksPerRank + 1;
|
|
startBlockNo = (blocksPerRank + 1) * rank;
|
|
}
|
|
else
|
|
{
|
|
blocksOnThisRank = blocksPerRank;
|
|
startBlockNo = numRanksWithExtraBlock * (blocksPerRank + 1) +
|
|
(rank - numRanksWithExtraBlock) * blocksPerRank;
|
|
}
|
|
|
|
if (blocksOnThisRank != 1)
|
|
{
|
|
std::cerr << "Currently only one block per rank supported!";
|
|
MPI_Finalize();
|
|
return EXIT_FAILURE;
|
|
}
|
|
|
|
// Created partitioned (split) data set
|
|
vtkm::cont::PartitionedDataSet useDataSet;
|
|
vtkm::cont::ArrayHandle<vtkm::Id3> localBlockIndices;
|
|
localBlockIndices.Allocate(blocksPerRank);
|
|
auto localBlockIndicesPortal = localBlockIndices.WritePortal();
|
|
|
|
for (vtkm::Id blockNo = 0; blockNo < blocksOnThisRank; ++blockNo)
|
|
{
|
|
vtkm::Id3 blockOrigin, blockSize, blockIndex;
|
|
std::tie(blockIndex, blockOrigin, blockSize) =
|
|
ComputeBlockExtents(globalSize, blocksPerDim, startBlockNo + blockNo);
|
|
useDataSet.AppendPartition(CreateSubDataSet(inDataSet, blockOrigin, blockSize, "values"));
|
|
localBlockIndicesPortal.Set(blockNo, blockIndex);
|
|
}
|
|
#endif // WITH_MPI construct input dataset
|
|
|
|
currTime = totalTime.GetElapsedTime();
|
|
buildDatasetTime = currTime - prevTime;
|
|
prevTime = currTime;
|
|
|
|
// Convert the mesh of values into contour tree, pairs of vertex ids
|
|
vtkm::filter::scalar_topology::ContourTreeAugmented filter(useMarchingCubes,
|
|
computeRegularStructure);
|
|
|
|
#ifdef WITH_MPI
|
|
filter.SetBlockIndices(blocksPerDim, localBlockIndices);
|
|
#endif
|
|
filter.SetActiveField("values");
|
|
|
|
// Execute the contour tree analysis. NOTE: If MPI is used the result will be
|
|
// a vtkm::cont::PartitionedDataSet instead of a vtkm::cont::DataSet
|
|
auto result = filter.Execute(useDataSet);
|
|
|
|
currTime = totalTime.GetElapsedTime();
|
|
vtkm::Float64 computeContourTreeTime = currTime - prevTime;
|
|
prevTime = currTime;
|
|
|
|
#ifdef WITH_MPI
|
|
#ifdef DEBUG_PRINT
|
|
std::cout << std::flush;
|
|
close(out);
|
|
std::cerr << std::flush;
|
|
close(err);
|
|
|
|
dup2(save_out, fileno(stdout));
|
|
dup2(save_err, fileno(stderr));
|
|
|
|
close(save_out);
|
|
close(save_err);
|
|
#endif
|
|
#endif
|
|
|
|
////////////////////////////////////////////
|
|
// Compute the branch decomposition
|
|
////////////////////////////////////////////
|
|
if (rank == 0 && computeBranchDecomposition && computeRegularStructure)
|
|
{
|
|
// Time branch decompostion
|
|
vtkm::cont::Timer branchDecompTimer;
|
|
branchDecompTimer.Start();
|
|
// compute the volume for each hyperarc and superarc
|
|
ctaug_ns::IdArrayType superarcIntrinsicWeight;
|
|
ctaug_ns::IdArrayType superarcDependentWeight;
|
|
ctaug_ns::IdArrayType supernodeTransferWeight;
|
|
ctaug_ns::IdArrayType hyperarcDependentWeight;
|
|
ctaug_ns::ProcessContourTree::ComputeVolumeWeightsSerial(filter.GetContourTree(),
|
|
filter.GetNumIterations(),
|
|
superarcIntrinsicWeight, // (output)
|
|
superarcDependentWeight, // (output)
|
|
supernodeTransferWeight, // (output)
|
|
hyperarcDependentWeight); // (output)
|
|
// Record the timings for the branch decomposition
|
|
std::stringstream timingsStream; // Use a string stream to log in one message
|
|
timingsStream << std::endl;
|
|
timingsStream << " --------------- Branch Decomposition Timings " << rank
|
|
<< " --------------" << std::endl;
|
|
timingsStream << " " << std::setw(38) << std::left << "Compute Volume Weights"
|
|
<< ": " << branchDecompTimer.GetElapsedTime() << " seconds" << std::endl;
|
|
branchDecompTimer.Start();
|
|
|
|
// compute the branch decomposition by volume
|
|
ctaug_ns::IdArrayType whichBranch;
|
|
ctaug_ns::IdArrayType branchMinimum;
|
|
ctaug_ns::IdArrayType branchMaximum;
|
|
ctaug_ns::IdArrayType branchSaddle;
|
|
ctaug_ns::IdArrayType branchParent;
|
|
ctaug_ns::ProcessContourTree::ComputeVolumeBranchDecompositionSerial(filter.GetContourTree(),
|
|
superarcDependentWeight,
|
|
superarcIntrinsicWeight,
|
|
whichBranch, // (output)
|
|
branchMinimum, // (output)
|
|
branchMaximum, // (output)
|
|
branchSaddle, // (output)
|
|
branchParent); // (output)
|
|
// Record and log the branch decompostion timings
|
|
timingsStream << " " << std::setw(38) << std::left << "Compute Volume Branch Decomposition"
|
|
<< ": " << branchDecompTimer.GetElapsedTime() << " seconds" << std::endl;
|
|
VTKM_LOG_S(vtkm::cont::LogLevel::Info, timingsStream.str());
|
|
|
|
//----main branch decompostion end
|
|
//----Isovalue seleciton start
|
|
if (numLevels > 0) // if compute isovalues
|
|
{
|
|
// Get the data values for computing the explicit branch decomposition
|
|
vtkm::cont::ArrayHandle<ValueType> dataField;
|
|
#ifdef WITH_MPI
|
|
result.GetPartitions()[0].GetField("values").GetData().AsArrayHandle(dataField);
|
|
bool dataFieldIsSorted = true;
|
|
#else
|
|
useDataSet.GetField("values").GetData().AsArrayHandle(dataField);
|
|
bool dataFieldIsSorted = false;
|
|
#endif
|
|
|
|
// create explicit representation of the branch decompostion from the array representation
|
|
BranchType* branchDecompostionRoot =
|
|
ctaug_ns::ProcessContourTree::ComputeBranchDecomposition<ValueType>(
|
|
filter.GetContourTree().Superparents,
|
|
filter.GetContourTree().Supernodes,
|
|
whichBranch,
|
|
branchMinimum,
|
|
branchMaximum,
|
|
branchSaddle,
|
|
branchParent,
|
|
filter.GetSortOrder(),
|
|
dataField,
|
|
dataFieldIsSorted);
|
|
|
|
#ifdef DEBUG_PRINT
|
|
branchDecompostionRoot->PrintBranchDecomposition(std::cout);
|
|
#endif
|
|
|
|
// Simplify the contour tree of the branch decompostion
|
|
branchDecompostionRoot->SimplifyToSize(numComp, usePersistenceSorter);
|
|
|
|
// Compute the relevant iso-values
|
|
std::vector<ValueType> isoValues;
|
|
switch (contourSelectMethod)
|
|
{
|
|
default:
|
|
case 0:
|
|
{
|
|
branchDecompostionRoot->GetRelevantValues(static_cast<int>(contourType), eps, isoValues);
|
|
}
|
|
break;
|
|
case 1:
|
|
{
|
|
vtkm::worklet::contourtree_augmented::process_contourtree_inc::PiecewiseLinearFunction<
|
|
ValueType>
|
|
plf;
|
|
branchDecompostionRoot->AccumulateIntervals(static_cast<int>(contourType), eps, plf);
|
|
isoValues = plf.nLargest(static_cast<unsigned int>(numLevels));
|
|
}
|
|
break;
|
|
}
|
|
|
|
// Print the compute iso values
|
|
std::stringstream isoStream; // Use a string stream to log in one message
|
|
isoStream << std::endl;
|
|
isoStream << " ------------------- Isovalue Suggestions --------------------" << std::endl;
|
|
std::sort(isoValues.begin(), isoValues.end());
|
|
isoStream << " Isovalues: ";
|
|
for (ValueType val : isoValues)
|
|
{
|
|
isoStream << val << " ";
|
|
}
|
|
isoStream << std::endl;
|
|
// Unique isovalues
|
|
std::vector<ValueType>::iterator it = std::unique(isoValues.begin(), isoValues.end());
|
|
isoValues.resize(static_cast<std::size_t>(std::distance(isoValues.begin(), it)));
|
|
isoStream << " Unique Isovalues (" << isoValues.size() << "):";
|
|
for (ValueType val : isoValues)
|
|
{
|
|
isoStream << val << " ";
|
|
}
|
|
VTKM_LOG_S(vtkm::cont::LogLevel::Info, isoStream.str());
|
|
} //end if compute isovalue
|
|
}
|
|
|
|
currTime = totalTime.GetElapsedTime();
|
|
vtkm::Float64 computeBranchDecompTime = currTime - prevTime;
|
|
prevTime = currTime;
|
|
|
|
//vtkm::cont::Field resultField = result.GetField();
|
|
//vtkm::cont::ArrayHandle<vtkm::Pair<vtkm::Id, vtkm::Id> > saddlePeak;
|
|
//resultField.GetData().AsArrayHandle(saddlePeak);
|
|
|
|
// Dump out contour tree for comparison
|
|
if (rank == 0 && printContourTree)
|
|
{
|
|
std::cout << "Contour Tree" << std::endl;
|
|
std::cout << "============" << std::endl;
|
|
ctaug_ns::EdgePairArray saddlePeak;
|
|
ctaug_ns::ProcessContourTree::CollectSortedSuperarcs(
|
|
filter.GetContourTree(), filter.GetSortOrder(), saddlePeak);
|
|
ctaug_ns::PrintEdgePairArrayColumnLayout(saddlePeak, std::cout);
|
|
}
|
|
|
|
#ifdef WITH_MPI
|
|
// Force a simple round-robin on the ranks for the summary prints. Its not perfect for MPI but
|
|
// it works well enough to sort the summaries from the ranks for small-scale debugging.
|
|
if (rank > 0)
|
|
{
|
|
int temp;
|
|
MPI_Status status;
|
|
MPI_Recv(&temp, 1, MPI_INT, (rank - 1), 0, comm, &status);
|
|
}
|
|
#endif
|
|
currTime = totalTime.GetElapsedTime();
|
|
VTKM_LOG_S(vtkm::cont::LogLevel::Info,
|
|
std::endl
|
|
<< " -------------------------- Totals " << rank
|
|
<< " -----------------------------" << std::endl
|
|
<< std::setw(42) << std::left << " Start-up"
|
|
<< ": " << startUpTime << " seconds" << std::endl
|
|
<< std::setw(42) << std::left << " Data Read"
|
|
<< ": " << dataReadTime << " seconds" << std::endl
|
|
<< std::setw(42) << std::left << " Build VTKM Dataset"
|
|
<< ": " << buildDatasetTime << " seconds" << std::endl
|
|
<< std::setw(42) << std::left << " Compute Contour Tree"
|
|
<< ": " << computeContourTreeTime << " seconds" << std::endl
|
|
<< std::setw(42) << std::left << " Compute Branch Decomposition"
|
|
<< ": " << computeBranchDecompTime << " seconds" << std::endl
|
|
<< std::setw(42) << std::left << " Total Time"
|
|
<< ": " << currTime << " seconds");
|
|
|
|
const ctaug_ns::ContourTree& ct = filter.GetContourTree();
|
|
VTKM_LOG_S(vtkm::cont::LogLevel::Info,
|
|
std::endl
|
|
<< " ---------------- Contour Tree Array Sizes ---------------------" << std::endl
|
|
<< ct.PrintArraySizes());
|
|
// Print hyperstructure statistics
|
|
VTKM_LOG_S(vtkm::cont::LogLevel::Info,
|
|
std::endl
|
|
<< ct.PrintHyperStructureStatistics(false) << std::endl);
|
|
|
|
// Flush ouput streams just to make sure everything has been logged (in particular when using MPI)
|
|
std::cout << std::flush;
|
|
std::cerr << std::flush;
|
|
|
|
#ifdef WITH_MPI
|
|
// Let the next rank know that it is time to print their summary.
|
|
if (rank < (size - 1))
|
|
{
|
|
int message = 1;
|
|
MPI_Send(&message, 1, MPI_INT, (rank + 1), 0, comm);
|
|
}
|
|
#endif
|
|
|
|
#ifdef WITH_MPI
|
|
MPI_Finalize();
|
|
#endif
|
|
return EXIT_SUCCESS;
|
|
}
|