mirror of
https://gitlab.kitware.com/vtk/vtk-m
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812 lines
30 KiB
C++
812 lines
30 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 "ContourTreeAppDataIO.h"
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#include <vtkm/filter/scalar_topology/ContourTreeUniformDistributed.h>
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#include <vtkm/filter/scalar_topology/DistributedBranchDecompositionFilter.h>
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#include <vtkm/filter/scalar_topology/worklet/branch_decomposition/HierarchicalVolumetricBranchDecomposer.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_distributed/HierarchicalContourTree.h>
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#include <vtkm/filter/scalar_topology/worklet/contourtree_distributed/TreeCompiler.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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#include <mpi.h>
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#include <cstdio>
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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 <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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#define SINGLE_FILE_STDOUT_STDERR
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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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// 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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// Set the logging levels we want to use. These could be made command line options as well
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// Log level to be used for outputting timing information.
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vtkm::cont::LogLevel timingsLogLevel = vtkm::cont::LogLevel::Info;
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// Log level to be used for outputting metadata about the trees.
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vtkm::cont::LogLevel treeLogLevel = vtkm::cont::LogLevel::Info;
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// Log level for outputs specific to the example
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vtkm::cont::LogLevel exampleLogLevel = vtkm::cont::LogLevel::Info;
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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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// 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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VTKM_LOG_IF_S(exampleLogLevel, rank == 0, "Running with MPI. #ranks=" << size);
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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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bool augmentHierarchicalTree = false;
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if (parser.hasOption("--augmentHierarchicalTree"))
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{
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augmentHierarchicalTree = true;
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}
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bool computeHierarchicalVolumetricBranchDecomposition = false;
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if (parser.hasOption("--computeVolumeBranchDecomposition"))
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{
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computeHierarchicalVolumetricBranchDecomposition = true;
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if (!augmentHierarchicalTree)
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{
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VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
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"Warning: --computeVolumeBranchDecomposition only "
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"allowed augmentation. Enabling --augmentHierarchicalTree option.");
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augmentHierarchicalTree = true;
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}
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}
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bool useBoundaryExtremaOnly = true;
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if (parser.hasOption("--useFullBoundary"))
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{
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useBoundaryExtremaOnly = false;
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}
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bool useMarchingCubes = false;
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if (parser.hasOption("--mc"))
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{
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useMarchingCubes = true;
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if (useBoundaryExtremaOnly)
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{
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VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
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"Warning: Marching cubes connectivity currently only works when "
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"using full boundary. Enabling the --useFullBoundary option "
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"to ensure that the app works.");
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useBoundaryExtremaOnly = false;
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}
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}
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bool preSplitFiles = false;
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if (parser.hasOption("--preSplitFiles"))
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{
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preSplitFiles = true;
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}
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bool saveDotFiles = false;
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if (parser.hasOption("--saveDot"))
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{
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saveDotFiles = true;
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}
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bool saveOutputData = false;
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if (parser.hasOption("--saveOutputData"))
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{
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saveOutputData = true;
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}
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bool forwardSummary = false;
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if (parser.hasOption("--forwardSummary"))
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{
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forwardSummary = true;
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}
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int numBlocks = size;
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int blocksPerRank = 1;
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if (parser.hasOption("--numBlocks"))
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{
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numBlocks = std::stoi(parser.getOption("--numBlocks"));
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if (numBlocks % size == 0)
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blocksPerRank = numBlocks / size;
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else
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{
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std::cerr << "Error: Number of blocks must be divisible by number of ranks." << std::endl;
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MPI_Finalize();
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return EXIT_FAILURE;
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}
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}
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#ifdef ENABLE_HDFIO
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std::string dataset_name = "data";
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if (parser.hasOption("--dataset"))
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{
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dataset_name = parser.getOption("--dataset");
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}
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vtkm::Id3 blocksPerDimIn(1, 1, size);
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if (parser.hasOption("--blocksPerDim"))
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{
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std::string temp = parser.getOption("--blocksPerDim");
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if (std::count(temp.begin(), temp.end(), ',') != 2)
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{
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std::cerr << "Invalid --blocksPerDim option. Expected string of the form 'x,y,z' got" << temp
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<< std::endl;
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MPI_Finalize();
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return EXIT_FAILURE;
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}
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char* tempC = (char*)temp.c_str();
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blocksPerDimIn[0] = std::stoi(std::strtok(tempC, ","));
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blocksPerDimIn[1] = std::stoi(std::strtok(nullptr, ","));
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blocksPerDimIn[2] = std::stoi(std::strtok(nullptr, ","));
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}
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vtkm::Id3 selectSize(-1, -1, -1);
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if (parser.hasOption("--selectSize"))
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{
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std::string temp = parser.getOption("--selectSize");
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if (std::count(temp.begin(), temp.end(), ',') != 2)
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{
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std::cerr << "Invalid --selectSize option. Expected string of the form 'x,y,z' got" << temp
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<< std::endl;
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MPI_Finalize();
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return EXIT_FAILURE;
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}
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char* tempC = (char*)temp.c_str();
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selectSize[0] = std::stoi(std::strtok(tempC, ","));
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selectSize[1] = std::stoi(std::strtok(nullptr, ","));
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selectSize[2] = std::stoi(std::strtok(nullptr, ","));
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}
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#endif
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if (argc < 2 || parser.hasOption("--help") || parser.hasOption("-h"))
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{
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if (rank == 0)
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{
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std::cout << "ContourTreeDistributed <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 connectivity (Default=False)." << std::endl;
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std::cout << "--useFullBoundary Use the full boundary during. Typically only useful"
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<< std::endl
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<< " to compare the performance between using the full boundary"
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<< std::endl;
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std::cout << " and when using only boundary extrema." << std::endl;
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std::cout << "--augmentHierarchicalTree Augment the hierarchical tree." << std::endl;
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std::cout << "--computeVolumeBranchDecomposition Compute the volume branch decomposition. "
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<< std::endl;
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std::cout << " Requries --augmentHierarchicalTree to be set." << std::endl;
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std::cout << "--preSplitFiles Input data is already pre-split into blocks." << std::endl;
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std::cout << "--saveDot Save DOT files of the distributed contour tree " << std::endl
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<< " computation (Default=False). " << std::endl;
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std::cout << "--saveOutputData Save data files with hierarchical tree or volume data"
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<< std::endl;
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std::cout << "--numBlocks Number of blocks to use during computation. (Sngle block "
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"ASCII/BOV file reader only)"
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<< "(Default=number of MPI ranks.)" << std::endl;
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std::cout << "--forwardSummary Forward the summary timings also to the per-rank " << std::endl
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<< " log files. Default is to round-robin print the " << std::endl
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<< " summary instead" << std::endl;
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#ifdef ENABLE_HDFIO
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std::cout << "--dataset Name of the dataset to load (HDF5 reader only)(Default=data)"
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<< std::endl;
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std::cout << "--blocksPerDim Number of blocks to split the data into. This is a string of "
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"the form 'x,y,z'."
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"(HDF5 reader only)(Default='1,1,#ranks')"
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<< std::endl;
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std::cout
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<< "--selectSize Size of the subblock to read. This is a string of the form 'x,y,z'."
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"(HDF5 reader only)(Default='-1,-1,-1')"
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<< std::endl;
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#endif
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std::cout << std::endl;
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}
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MPI_Finalize();
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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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VTKM_LOG_S(exampleLogLevel,
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std::endl
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<< " ------------ Settings -----------" << std::endl
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<< " filename=" << filename << std::endl
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<< " preSplitFiles=" << preSplitFiles << std::endl
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<< " device=" << device.GetName() << std::endl
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<< " mc=" << useMarchingCubes << std::endl
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<< " useFullBoundary=" << !useBoundaryExtremaOnly << std::endl
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<< " saveDot=" << saveDotFiles << std::endl
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<< " augmentHierarchicalTree=" << augmentHierarchicalTree << std::endl
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<< " computeVolumetricBranchDecomposition="
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<< computeHierarchicalVolumetricBranchDecomposition << std::endl
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<< " saveOutputData=" << saveOutputData << std::endl
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<< " forwardSummary=" << forwardSummary << std::endl
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<< " nblocks=" << numBlocks << std::endl
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#ifdef ENABLE_HDFIO
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<< " dataset=" << dataset_name << " (HDF5 only)" << std::endl
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<< " blocksPerDim=" << blocksPerDimIn[0] << "," << blocksPerDimIn[1] << ","
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<< blocksPerDimIn[2] << " (HDF5 only)" << std::endl
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<< " selectSize=" << selectSize[0] << "," << selectSize[1] << ","
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<< selectSize[2] << " (HDF5 only)" << std::endl
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#endif
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);
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}
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// Redirect stdout to file if we are using MPI with Debugging
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// From https://www.unix.com/302983597-post2.html
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char cstr_filename[255];
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std::snprintf(cstr_filename, sizeof(cstr_filename), "cout_%d.log", rank);
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int out = open(cstr_filename, O_RDWR | O_CREAT | O_TRUNC, 0600);
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if (-1 == out)
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{
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perror("opening cout.log");
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return 255;
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}
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#ifndef SINGLE_FILE_STDOUT_STDERR
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std::snprintf(cstr_filename, sizeof(cstr_filename), "cerr_%d.log", rank);
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int err = open(cstr_filename, O_RDWR | O_CREAT | O_TRUNC, 0600);
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if (-1 == err)
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{
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perror("opening cerr.log");
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return 255;
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}
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#endif
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int save_out = dup(fileno(stdout));
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int save_err = dup(fileno(stderr));
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if (-1 == dup2(out, fileno(stdout)))
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{
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perror("cannot redirect stdout");
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return 255;
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}
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#ifdef SINGLE_FILE_STDOUT_STDERR
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if (-1 == dup2(out, fileno(stderr)))
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#else
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if (-1 == dup2(err, fileno(stderr)))
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#endif
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{
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perror("cannot redirect stderr");
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return 255;
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}
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VTKM_LOG_S(exampleLogLevel,
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std::endl
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<< " ------------ Settings -----------" << std::endl
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<< " filename=" << filename << std::endl
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<< " preSplitFiles=" << preSplitFiles << std::endl
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<< " device=" << device.GetName() << std::endl
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<< " mc=" << useMarchingCubes << std::endl
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<< " useFullBoundary=" << !useBoundaryExtremaOnly << std::endl
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<< " saveDot=" << saveDotFiles << std::endl
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<< " saveOutputData=" << saveOutputData << std::endl
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<< " forwardSummary=" << forwardSummary << std::endl
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<< " numBlocks=" << numBlocks << std::endl
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<< " augmentHierarchicalTree=" << augmentHierarchicalTree << std::endl
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<< " numRanks=" << size << std::endl
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<< " rank=" << rank << std::endl
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#ifdef ENABLE_HDFIO
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<< " dataset=" << dataset_name << " (HDF5 only)" << std::endl
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<< " blocksPerDim=" << blocksPerDimIn[0] << "," << blocksPerDimIn[1] << ","
|
|
<< blocksPerDimIn[2] << " (HDF5 only)" << std::endl
|
|
<< " selectSize=" << selectSize[0] << "," << selectSize[1] << "," << selectSize[2]
|
|
<< " (HDF5 only)" << std::endl
|
|
#endif
|
|
);
|
|
|
|
// Measure our time for startup
|
|
currTime = totalTime.GetElapsedTime();
|
|
vtkm::Float64 startUpTime = currTime - prevTime;
|
|
prevTime = currTime;
|
|
|
|
// Make sure that all ranks have started up before we start the data read
|
|
MPI_Barrier(comm);
|
|
currTime = totalTime.GetElapsedTime();
|
|
vtkm::Float64 startUpSyncTime = currTime - prevTime;
|
|
prevTime = currTime;
|
|
|
|
///////////////////////////////////////////////
|
|
// Read the input data
|
|
///////////////////////////////////////////////
|
|
vtkm::Float64 dataReadTime = 0;
|
|
vtkm::Float64 buildDatasetTime = 0;
|
|
std::vector<vtkm::Float32>::size_type nDims = 0;
|
|
|
|
// Multi-block dataset for multi-block DIY-paralle processing
|
|
vtkm::cont::PartitionedDataSet useDataSet;
|
|
|
|
// Domain decomposition information for DIY/contour tree
|
|
vtkm::Id3 globalSize;
|
|
vtkm::Id3 blocksPerDim;
|
|
vtkm::cont::ArrayHandle<vtkm::Id3> localBlockIndices;
|
|
localBlockIndices.Allocate(blocksPerRank);
|
|
auto localBlockIndicesPortal = localBlockIndices.WritePortal();
|
|
|
|
// Read the pre-split data files
|
|
bool readOk = true;
|
|
if (preSplitFiles)
|
|
{
|
|
readOk = readPreSplitFiles<ValueType>(
|
|
// inputs
|
|
rank,
|
|
filename,
|
|
blocksPerRank,
|
|
// outputs
|
|
nDims,
|
|
useDataSet,
|
|
globalSize,
|
|
blocksPerDim,
|
|
localBlockIndices,
|
|
// output timers
|
|
dataReadTime,
|
|
buildDatasetTime);
|
|
}
|
|
// Read single-block data and split it for the ranks
|
|
else
|
|
{
|
|
bool isHDF5 = (0 == filename.compare(filename.length() - 3, 3, ".h5"));
|
|
if (isHDF5)
|
|
{
|
|
#ifdef ENABLE_HDFIO
|
|
blocksPerDim = blocksPerDimIn;
|
|
readOk = read3DHDF5File<ValueType>(
|
|
// inputs (blocksPerDim is being modified to swap dimension to fit we re-ordering of dimension)
|
|
rank,
|
|
filename,
|
|
dataset_name,
|
|
blocksPerRank,
|
|
blocksPerDim,
|
|
selectSize,
|
|
// outputs
|
|
nDims,
|
|
useDataSet,
|
|
globalSize,
|
|
localBlockIndices,
|
|
// output timers
|
|
dataReadTime,
|
|
buildDatasetTime);
|
|
#else
|
|
VTKM_LOG_S(vtkm::cont::LogLevel::Error,
|
|
"Can't read HDF5 file. HDF5 reader disabled for this build.");
|
|
readOk = false;
|
|
#endif
|
|
}
|
|
else
|
|
{
|
|
readOk = readSingleBlockFile<ValueType>(
|
|
// inputs
|
|
rank,
|
|
size,
|
|
filename,
|
|
numBlocks,
|
|
blocksPerRank,
|
|
// outputs
|
|
nDims,
|
|
useDataSet,
|
|
globalSize,
|
|
blocksPerDim,
|
|
localBlockIndices,
|
|
// output timers
|
|
dataReadTime,
|
|
buildDatasetTime);
|
|
}
|
|
}
|
|
if (!readOk)
|
|
{
|
|
VTKM_LOG_S(vtkm::cont::LogLevel::Error, "Data read failed.");
|
|
MPI_Finalize();
|
|
return EXIT_FAILURE;
|
|
}
|
|
|
|
// Print the mesh metadata
|
|
if (rank == 0)
|
|
{
|
|
VTKM_LOG_S(exampleLogLevel,
|
|
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 settings than finalize MPI and exit the execution
|
|
if (invalidMCOption)
|
|
{
|
|
MPI_Finalize();
|
|
return EXIT_FAILURE;
|
|
}
|
|
|
|
// reset timer after read. the dataReadTime and buildDatasetTime are measured by the read functions
|
|
prevTime = totalTime.GetElapsedTime();
|
|
|
|
// Make sure that all ranks have started up before we start the data read
|
|
MPI_Barrier(comm);
|
|
currTime = totalTime.GetElapsedTime();
|
|
vtkm::Float64 dataReadSyncTime = currTime - prevTime;
|
|
prevTime = currTime;
|
|
|
|
// Log information of the (first) local data block
|
|
// TODO: Get localBlockSize and localBlockOrigins from the cell set to log results
|
|
VTKM_LOG_S(vtkm::cont::LogLevel::Info,
|
|
"" //<< std::setw(42) << std::left << "blockSize"
|
|
//<< ":" << localBlockSizesPortal.Get(0) << std::endl
|
|
//<< std::setw(42) << std::left << "blockOrigin=" << localBlockOriginsPortal.Get(0)
|
|
//<< std::endl
|
|
<< std::setw(42) << std::left << "blockIndices=" << localBlockIndicesPortal.Get(0)
|
|
<< std::endl
|
|
<< std::setw(42) << std::left << "blocksPerDim=" << blocksPerDim << std::endl
|
|
<< std::setw(42) << std::left << "globalSize=" << globalSize << std::endl
|
|
|
|
);
|
|
|
|
// Convert the mesh of values into contour tree, pairs of vertex ids
|
|
vtkm::filter::scalar_topology::ContourTreeUniformDistributed filter(timingsLogLevel,
|
|
treeLogLevel);
|
|
filter.SetBlockIndices(blocksPerDim, localBlockIndices);
|
|
filter.SetUseBoundaryExtremaOnly(useBoundaryExtremaOnly);
|
|
filter.SetUseMarchingCubes(useMarchingCubes);
|
|
filter.SetAugmentHierarchicalTree(augmentHierarchicalTree);
|
|
filter.SetSaveDotFiles(saveDotFiles);
|
|
filter.SetActiveField("values");
|
|
|
|
// Execute the contour tree analysis
|
|
auto result = filter.Execute(useDataSet);
|
|
|
|
currTime = totalTime.GetElapsedTime();
|
|
vtkm::Float64 computeContourTreeTime = currTime - prevTime;
|
|
prevTime = currTime;
|
|
|
|
// Record the time to synchronize after the filter has finished
|
|
MPI_Barrier(comm);
|
|
currTime = totalTime.GetElapsedTime();
|
|
vtkm::Float64 postFilterSyncTime = currTime - prevTime;
|
|
prevTime = currTime;
|
|
|
|
// Compute branch decomposition if requested
|
|
vtkm::cont::PartitionedDataSet bd_result;
|
|
if (computeHierarchicalVolumetricBranchDecomposition)
|
|
{
|
|
vtkm::filter::scalar_topology::DistributedBranchDecompositionFilter bd_filter;
|
|
bd_result = bd_filter.Execute(result);
|
|
}
|
|
currTime = totalTime.GetElapsedTime();
|
|
vtkm::Float64 branchDecompTime = currTime - prevTime;
|
|
prevTime = currTime;
|
|
|
|
// Save output
|
|
if (saveOutputData)
|
|
{
|
|
if (augmentHierarchicalTree)
|
|
{
|
|
if (computeHierarchicalVolumetricBranchDecomposition)
|
|
{
|
|
for (vtkm::Id ds_no = 0; ds_no < result.GetNumberOfPartitions(); ++ds_no)
|
|
{
|
|
auto ds = bd_result.GetPartition(ds_no);
|
|
std::string branchDecompositionFileName = std::string("BranchDecomposition_Rank_") +
|
|
std::to_string(static_cast<int>(rank)) + std::string("_Block_") +
|
|
std::to_string(static_cast<int>(ds_no)) + std::string(".txt");
|
|
|
|
std::ofstream treeStream(branchDecompositionFileName.c_str());
|
|
treeStream
|
|
<< vtkm::filter::scalar_topology::HierarchicalVolumetricBranchDecomposer::PrintBranches(
|
|
ds);
|
|
}
|
|
}
|
|
else
|
|
{
|
|
for (vtkm::Id ds_no = 0; ds_no < result.GetNumberOfPartitions(); ++ds_no)
|
|
{
|
|
auto ds = result.GetPartition(ds_no);
|
|
vtkm::worklet::contourtree_augmented::IdArrayType supernodes;
|
|
ds.GetField("Supernodes").GetData().AsArrayHandle(supernodes);
|
|
vtkm::worklet::contourtree_augmented::IdArrayType superarcs;
|
|
ds.GetField("Superarcs").GetData().AsArrayHandle(superarcs);
|
|
vtkm::worklet::contourtree_augmented::IdArrayType regularNodeGlobalIds;
|
|
ds.GetField("RegularNodeGlobalIds").GetData().AsArrayHandle(regularNodeGlobalIds);
|
|
vtkm::Id totalVolume = globalSize[0] * globalSize[1] * globalSize[2];
|
|
vtkm::worklet::contourtree_augmented::IdArrayType intrinsicVolume;
|
|
ds.GetField("IntrinsicVolume").GetData().AsArrayHandle(intrinsicVolume);
|
|
vtkm::worklet::contourtree_augmented::IdArrayType dependentVolume;
|
|
ds.GetField("DependentVolume").GetData().AsArrayHandle(dependentVolume);
|
|
|
|
std::string dumpVolumesString =
|
|
vtkm::worklet::contourtree_distributed::HierarchicalContourTree<ValueType>::DumpVolumes(
|
|
supernodes,
|
|
superarcs,
|
|
regularNodeGlobalIds,
|
|
totalVolume,
|
|
intrinsicVolume,
|
|
dependentVolume);
|
|
|
|
std::string volumesFileName = std::string("TreeWithVolumes_Rank_") +
|
|
std::to_string(static_cast<int>(rank)) + std::string("_Block_") +
|
|
std::to_string(static_cast<int>(ds_no)) + std::string(".txt");
|
|
std::ofstream treeStream(volumesFileName.c_str());
|
|
treeStream << dumpVolumesString;
|
|
}
|
|
}
|
|
}
|
|
else
|
|
{
|
|
for (vtkm::Id ds_no = 0; ds_no < result.GetNumberOfPartitions(); ++ds_no)
|
|
{
|
|
vtkm::worklet::contourtree_distributed::TreeCompiler treeCompiler;
|
|
treeCompiler.AddHierarchicalTree(result.GetPartition(ds_no));
|
|
char fname[256];
|
|
std::snprintf(fname,
|
|
sizeof(fname),
|
|
"TreeCompilerOutput_Rank%d_Block%d.dat",
|
|
rank,
|
|
static_cast<int>(ds_no));
|
|
FILE* out_file = std::fopen(fname, "wb");
|
|
treeCompiler.WriteBinary(out_file);
|
|
std::fclose(out_file);
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
currTime = totalTime.GetElapsedTime();
|
|
vtkm::Float64 saveOutputDataTime = currTime - prevTime;
|
|
prevTime = currTime;
|
|
|
|
std::cout << std::flush;
|
|
std::cerr << std::flush;
|
|
close(out);
|
|
#ifndef SINGLE_FILE_STDOUT_STDERR
|
|
close(err);
|
|
#endif
|
|
|
|
if (!forwardSummary)
|
|
{
|
|
// write our log data now and close the files so that the summary is written round-robin to
|
|
// the normal log output stream
|
|
dup2(save_out, fileno(stdout));
|
|
dup2(save_err, fileno(stderr));
|
|
// close our MPI forward
|
|
close(save_out);
|
|
close(save_err);
|
|
|
|
// 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);
|
|
}
|
|
}
|
|
currTime = totalTime.GetElapsedTime();
|
|
VTKM_LOG_S(timingsLogLevel,
|
|
std::endl
|
|
<< " -------------------------- Totals " << rank
|
|
<< " -----------------------------" << std::endl
|
|
<< std::setw(42) << std::left << " Start-up"
|
|
<< ": " << startUpTime << " seconds" << std::endl
|
|
<< std::setw(42) << std::left << " Start-up Sync"
|
|
<< ": " << startUpSyncTime << " 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 << " Data Read/Build Sync"
|
|
<< ": " << dataReadSyncTime << " seconds" << std::endl
|
|
<< std::setw(42) << std::left << " Compute Contour Tree"
|
|
<< ": " << computeContourTreeTime << " seconds" << std::endl
|
|
<< std::setw(42) << std::left << " Post filter Sync"
|
|
<< ": " << postFilterSyncTime << " seconds" << std::endl
|
|
<< std::setw(42) << std::left << " Branch Decomposition"
|
|
<< ": " << branchDecompTime << " seconds" << std::endl
|
|
<< std::setw(42) << std::left << " Save Tree Compiler Data"
|
|
<< ": " << saveOutputDataTime << " seconds" << std::endl
|
|
<< std::setw(42) << std::left << " Total Time"
|
|
<< ": " << currTime << " seconds");
|
|
|
|
// Flush ouput streams just to make sure everything has been logged (in particular when using MPI)
|
|
std::cout << std::flush;
|
|
std::cerr << std::flush;
|
|
|
|
// Round robin output
|
|
if (!forwardSummary)
|
|
{
|
|
// 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);
|
|
}
|
|
}
|
|
// Finish logging to our per-rank log-files
|
|
else
|
|
{
|
|
// write our log data now
|
|
// the normal log output stream
|
|
dup2(save_out, fileno(stdout));
|
|
dup2(save_err, fileno(stderr));
|
|
// close our MPI forward
|
|
close(save_out);
|
|
close(save_err);
|
|
}
|
|
|
|
// Finalize and finish the execution
|
|
MPI_Finalize();
|
|
return EXIT_SUCCESS;
|
|
}
|