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854 lines
33 KiB
C++
854 lines
33 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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// I/O functions used by the ContourTreeApp for data read.
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//==============================================================================
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#ifndef vtk_m_examples_ContourTreeAppDataIO_hxx
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#define vtk_m_examples_ContourTreeAppDataIO_hxx
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#include <vtkm/Types.h>
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#include <vtkm/cont/ArrayCopy.h>
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#include <vtkm/cont/ArrayHandle.h>
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#include <vtkm/cont/CellSetStructured.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/PartitionedDataSet.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/scalar_topology/worklet/contourtree_augmented/Types.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 <numeric>
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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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#ifdef ENABLE_HDFIO
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// #include "H5Cpp.h"
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#include "hdf5.h"
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//using namespace H5;
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#include <mpi.h>
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/// Convert a 3D index of a cube to rank index
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vtkm::Id to1DIndex(vtkm::Id3 idx, vtkm::Id3 dims)
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{
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// return (idx[2] * dims[0] * dims[1]) + (idx[1] * dims[0]) + idx[0];
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// Swap first and second dimension
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return (idx[2] * dims[0] * dims[1]) + (idx[0] * dims[1]) + idx[1];
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}
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/// Convert the rank index to the index of the cube
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vtkm::Id3 to3DIndex(vtkm::Id idx, vtkm::Id3 dims)
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{
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vtkm::Id3 res;
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res[2] = idx / (dims[0] * dims[1]);
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idx -= (res[2] * dims[0] * dims[1]);
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// Swap index 0 and 1
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// res[0] = idx / dims[0];
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// res[1] = idx % dims[0];
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// Don't swap index here, because this function is used with the original
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// HDF5 layout and the 3D index is swapped later on
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res[1] = idx / dims[0];
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res[0] = idx % dims[0];
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return res;
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}
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/// Read data from pre-split ASCII files
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/// @param[in] rank The current MPI rank the function is called from
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/// @param[in] filename Name of the file with %d as placeholder for the integer index of the block
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/// @param[in] dataset_name Name of the dataset in the HDF5 file to read
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/// @param[in] blocksPerRank Number of data blocks to process on each rank
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/// @param[in] blocksPerDim Number of data blocks to use per dimension
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/// @param[in] selectSize Select subset of this size from the dataset. Set to (-1,-1,-1) to select the full size
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/// @param[out] nDims Number of data dimensions (i.e, 2 or 3)
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/// @param[out] useDataSet VTKm partioned dataset to be used with the distributed contour tree filter
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/// @param[out] globalSize Global extends of the input mesh (i.e., number of mesh points in each dimension)
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/// @param[out] localBlockIndices Array with the (x,y,z) index of each local data block with
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/// with respect to blocksPerDim
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/// @param[out] dataReadTime Time to read the data
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/// @param[out] buildDatasetTime Time to construct the VTKm datasets
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/// @returns bool indicating whether the read was successful or not
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template <typename ValueType>
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bool read3DHDF5File(const int& mpi_rank,
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const std::string& filename,
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const std::string& dataset_name,
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const int& blocksPerRank,
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vtkm::Id3& blocksPerDim,
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const vtkm::Id3& selectSize,
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std::vector<vtkm::Float32>::size_type& nDims,
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vtkm::cont::PartitionedDataSet& useDataSet,
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vtkm::Id3& globalSize,
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vtkm::cont::ArrayHandle<vtkm::Id3>& localBlockIndices,
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vtkm::Float64& dataReadTime,
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vtkm::Float64& buildDatasetTime)
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{
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vtkm::cont::Timer totalTime;
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totalTime.Start();
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vtkm::Float64 prevTime = 0;
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vtkm::Float64 currTime = 0;
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// TODO not supported yet
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if (blocksPerRank > 1)
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{
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VTKM_LOG_S(
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vtkm::cont::LogLevel::Error,
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"HDF5 reader for ContourTreeDistributed does not support multiple blocks per rank yet");
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return false;
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}
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vtkm::Id blockNo = 0; // TODO: Update this if we have multiple blocks per rank
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localBlockIndices.Allocate(blocksPerRank);
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auto localBlockIndicesPortal = localBlockIndices.WritePortal();
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herr_t status;
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//Set up file access property list with parallel I/O access
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hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
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MPI_Comm comm = MPI_COMM_WORLD;
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MPI_Info info = MPI_INFO_NULL;
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H5Pset_fapl_mpio(plist_id, comm, info);
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// Open the file and the dataset
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//hid_t file = H5Fopen(filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT); // plist_id);//
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hid_t file = H5Fopen(filename.c_str(), H5F_ACC_RDONLY, plist_id); //
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hid_t dataset = H5Dopen(file, dataset_name.c_str(), H5P_DEFAULT);
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// Get filespace for rank and dimension
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hid_t filespace = H5Dget_space(dataset);
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// Get number of dimensions in the file dataspace
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nDims = H5Sget_simple_extent_ndims(filespace);
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if (nDims != 3)
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{
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VTKM_LOG_S(vtkm::cont::LogLevel::Error,
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"HDF5 reader for ContourTreeDistributed requires 3D dataset");
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return false;
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}
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hsize_t dims[nDims]; // dataset dimensions
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status = H5Sget_simple_extent_dims(filespace, dims, NULL);
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globalSize[0] = selectSize[0] < 0 ? dims[0] : selectSize[0];
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globalSize[1] = selectSize[1] < 0 ? dims[1] : selectSize[1];
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globalSize[2] = selectSize[2] < 0 ? dims[2] : selectSize[2];
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// Define the memory space to read dataset.
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hid_t dataspace = H5Dget_space(dataset);
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// Read a hyperslap
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// define the hyperslap
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hsize_t count[3]; // size of the hyperslab in the file
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hsize_t offset[3]; // hyperslab offset in the file
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// Compute the origin and count
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vtkm::Id3 blockSize(std::floor(vtkm::Id(globalSize[0] / blocksPerDim[0])),
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std::floor(vtkm::Id(globalSize[1] / blocksPerDim[1])),
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std::floor(vtkm::Id(globalSize[2] / blocksPerDim[2])));
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vtkm::Id3 blockIndex = to3DIndex(mpi_rank, blocksPerDim);
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// compute the offset and count for the block for this rank
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offset[0] = blockSize[0] * blockIndex[0];
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offset[1] = blockSize[1] * blockIndex[1];
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offset[2] = blockSize[2] * blockIndex[2];
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count[0] = blockSize[0];
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count[1] = blockSize[1];
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count[2] = blockSize[2];
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// add ghost zone on the left
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if (blockIndex[0] > 0)
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{
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offset[0] = offset[0] - 1;
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count[0] = count[0] + 1;
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}
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if (blockIndex[1] > 0)
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{
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offset[1] = offset[1] - 1;
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count[1] = count[1] + 1;
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}
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if (blockIndex[2] > 0)
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{
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offset[2] = offset[2] - 1;
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count[2] = count[2] + 1;
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}
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// Check that we are not running over the end of the dataset
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if (vtkm::Id(offset[0] + count[0]) > globalSize[0])
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{
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count[0] = globalSize[0] - offset[0];
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}
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if (vtkm::Id(offset[1] + count[1]) > globalSize[1])
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{
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count[1] = globalSize[1] - offset[1];
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}
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if (vtkm::Id(offset[2] + count[2]) > globalSize[2])
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{
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count[2] = globalSize[2] - offset[2];
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}
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blockSize = vtkm::Id3{ static_cast<vtkm::Id>(count[0]),
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static_cast<vtkm::Id>(count[1]),
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static_cast<vtkm::Id>(count[2]) };
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/*vtkm::Id3 blockOrigin = vtkm::Id3{ static_cast<vtkm::Id>(offset[0]),
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static_cast<vtkm::Id>(offset[1]),
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static_cast<vtkm::Id>(offset[2]) };*/
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// Define the hyperslap to read the data into memory
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status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, NULL, count, NULL);
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// Define the memory space for reading
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hid_t memspace = H5Screate_simple(nDims, count, NULL);
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// Read data from hyperslab in the file into the hyperslab in
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std::size_t numVertices = count[0] * count[1] * count[2];
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std::vector<ValueType> values(numVertices);
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{
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if (H5Tequal(H5Dget_type(dataset), H5T_NATIVE_DOUBLE))
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{
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double data_out[count[0]][count[1]][count[2]]; // output buffer
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status = H5Dread(dataset, H5T_NATIVE_DOUBLE, memspace, dataspace, H5P_DEFAULT, data_out);
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// Copy data to 1D array of the expected ValueType
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for (hsize_t k = 0; k < count[0]; k++)
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{
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for (hsize_t j = 0; j < count[1]; j++)
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{
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for (hsize_t i = 0; i < count[2]; i++)
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{
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values[to1DIndex(vtkm::Id3(k, j, i), blockSize)] = ValueType(data_out[k][j][i]);
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}
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}
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}
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}
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else if (H5Tequal(H5Dget_type(dataset), H5T_NATIVE_FLOAT))
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{
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float data_out[count[0]][count[1]][count[2]]; // output buffer
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status = H5Dread(dataset, H5T_NATIVE_FLOAT, memspace, dataspace, H5P_DEFAULT, data_out);
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// Copy data to 1D array of the expected ValueType
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for (hsize_t k = 0; k < count[0]; k++)
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{
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for (hsize_t j = 0; j < count[1]; j++)
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{
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for (hsize_t i = 0; i < count[2]; i++)
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{
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values[to1DIndex(vtkm::Id3(k, j, i), blockSize)] = ValueType(data_out[k][j][i]);
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}
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}
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}
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}
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else if (H5Tequal(H5Dget_type(dataset), H5T_NATIVE_INT))
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{
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int data_out[count[0]][count[1]][count[2]]; // output buffer
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status = H5Dread(dataset, H5T_NATIVE_INT, memspace, dataspace, H5P_DEFAULT, data_out);
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// Copy data to 1D array of the expected ValueType
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for (hsize_t k = 0; k < count[0]; k++)
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{
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for (hsize_t j = 0; j < count[1]; j++)
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{
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for (hsize_t i = 0; i < count[2]; i++)
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{
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values[to1DIndex(vtkm::Id3(k, j, i), blockSize)] = ValueType(data_out[k][j][i]);
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}
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}
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}
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}
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else if (H5Tequal(H5Dget_type(dataset), H5T_NATIVE_UCHAR))
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{
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unsigned char data_out[count[0]][count[1]][count[2]]; // output buffer
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status = H5Dread(dataset, H5T_NATIVE_UCHAR, memspace, dataspace, H5P_DEFAULT, data_out);
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// Copy data to 1D array of the expected ValueType
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for (hsize_t k = 0; k < count[0]; k++)
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{
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for (hsize_t j = 0; j < count[1]; j++)
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{
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for (hsize_t i = 0; i < count[2]; i++)
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{
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values[to1DIndex(vtkm::Id3(k, j, i), blockSize)] = ValueType(data_out[k][j][i]);
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}
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}
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}
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}
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else
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{
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VTKM_LOG_S(vtkm::cont::LogLevel::Error, "Data type not supported by the example HDF5 reader");
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throw "Data type not supported by the example HDF5 reader";
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}
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}
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// Release HDF5 resources
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H5Sclose(dataspace);
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H5Dclose(dataset);
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H5Fclose(file);
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// Create vtk-m data set
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vtkm::cont::DataSetBuilderUniform dsb;
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vtkm::cont::DataSet ds;
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VTKM_ASSERT(nDims == 3);
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// Swap dimensions so that they are from fastest to slowest growing
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// dims[0] -> col; dims[1] -> row, dims[2] ->slice
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// Swap the dimensions to match the pre-split file reader
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globalSize = vtkm::Id3(globalSize[1], globalSize[0], globalSize[2]);
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// Swap also the blocks per dimension accordingly
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blocksPerDim = vtkm::Id3(blocksPerDim[1], blocksPerDim[0], blocksPerDim[2]);
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// Swap first and second dimenion here as well for consistency
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const vtkm::Vec<ValueType, 3> v_origin{ static_cast<ValueType>(offset[1]),
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static_cast<ValueType>(offset[0]),
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static_cast<ValueType>(offset[2]) };
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const vtkm::Id3 v_dims{ static_cast<vtkm::Id>(blockSize[1]),
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static_cast<vtkm::Id>(blockSize[0]),
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static_cast<vtkm::Id>(blockSize[2]) };
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vtkm::Vec<ValueType, 3> v_spacing(1, 1, 1);
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ds = dsb.Create(v_dims, v_origin, v_spacing);
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vtkm::cont::CellSetStructured<3> cs;
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cs.SetPointDimensions(v_dims);
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cs.SetGlobalPointDimensions(globalSize);
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cs.SetGlobalPointIndexStart(vtkm::Id3{ v_origin[0], v_origin[1], v_origin[2] });
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ds.SetCellSet(cs);
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ds.AddPointField("values", values);
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// and add to partition
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useDataSet.AppendPartition(ds);
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// Swap order to match pre-splot
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localBlockIndicesPortal.Set(blockNo, vtkm::Id3(blockIndex[1], blockIndex[0], blockIndex[2]));
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// Log information of the (first) local data block
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VTKM_LOG_S(vtkm::cont::LogLevel::Info,
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"" << std::setw(42) << std::left << "blockSize"
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<< ":" << v_dims << std::endl
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<< std::setw(42) << std::left << "blockOrigin=" << v_origin << std::endl
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<< std::setw(42) << std::left << "blockIndices=" << localBlockIndicesPortal.Get(0)
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<< std::endl
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<< std::setw(42) << std::left << "globalSize=" << globalSize << std::endl);
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// Finished data read
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currTime = totalTime.GetElapsedTime();
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dataReadTime = currTime - prevTime;
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prevTime = currTime;
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currTime = totalTime.GetElapsedTime();
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buildDatasetTime = currTime - prevTime;
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return true;
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}
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#endif
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/// Read data from pre-split ASCII files
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/// @param[in] rank The current MPI rank the function is called from
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/// @param[in] filename Name of the file with %d as placeholder for the integer index of the block
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/// @param[in] blocksPerRank Number of data blocks to process on each rank
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/// @param[out] nDims Number of data dimensions (i.e, 2 or 3)
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/// @param[out] useDataSet VTKm partioned dataset to be used with the distributed contour tree filter
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/// @param[out] globalSize Global extends of the input mesh (i.e., number of mesh points in each dimension)
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/// @param[in] blocksPerDim Number of data blocks used in each data dimension
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/// @param[in] localBlockIndices Array with the (x,y,z) index of each local data block with
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/// with respect to blocksPerDim
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/// @param[in] dataReadTime Time to read the data
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/// @param[in] buildDatasetTime Time to construct the VTKm datasets
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/// @returns bool indicating whether the read was successful or not
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template <typename ValueType>
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bool readPreSplitFiles(const int& rank,
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const std::string& filename,
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const int& blocksPerRank,
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std::vector<vtkm::Float32>::size_type& nDims,
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vtkm::cont::PartitionedDataSet& useDataSet,
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vtkm::Id3& globalSize,
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vtkm::Id3& blocksPerDim,
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vtkm::cont::ArrayHandle<vtkm::Id3>& localBlockIndices,
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vtkm::Float64& dataReadTime,
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vtkm::Float64& buildDatasetTime)
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{
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vtkm::cont::Timer totalTime;
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totalTime.Start();
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vtkm::Float64 prevTime = 0;
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vtkm::Float64 currTime = 0;
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localBlockIndices.Allocate(blocksPerRank);
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auto localBlockIndicesPortal = localBlockIndices.WritePortal();
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for (int blockNo = 0; blockNo < blocksPerRank; ++blockNo)
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{
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// Translate pattern into filename for this block
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char block_filename[256];
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snprintf(block_filename,
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sizeof(block_filename),
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filename.c_str(),
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|
static_cast<int>(rank * blocksPerRank + blockNo));
|
|
std::cout << "Reading file " << block_filename << std::endl;
|
|
|
|
// Open file
|
|
std::ifstream inFile(block_filename);
|
|
if (!inFile.is_open() || inFile.bad())
|
|
{
|
|
std::cerr << "Error: Couldn't open file " << block_filename << std::endl;
|
|
return false;
|
|
}
|
|
|
|
// Read header with dimensions
|
|
std::string line;
|
|
std::string tag;
|
|
vtkm::Id dimVertices;
|
|
|
|
getline(inFile, line);
|
|
std::istringstream global_extents_stream(line);
|
|
global_extents_stream >> tag;
|
|
if (tag != "#GLOBAL_EXTENTS")
|
|
{
|
|
std::cerr << "Error: Expected #GLOBAL_EXTENTS, got " << tag << std::endl;
|
|
return false;
|
|
}
|
|
|
|
std::vector<vtkm::Id> global_extents;
|
|
while (global_extents_stream >> dimVertices)
|
|
global_extents.push_back(dimVertices);
|
|
|
|
// Swap dimensions so that they are from fastest to slowest growing
|
|
// dims[0] -> col; dims[1] -> row, dims[2] ->slice
|
|
std::swap(global_extents[0], global_extents[1]);
|
|
|
|
if (blockNo == 0)
|
|
{ // First block: Set globalSize
|
|
globalSize =
|
|
vtkm::Id3{ static_cast<vtkm::Id>(global_extents[0]),
|
|
static_cast<vtkm::Id>(global_extents[1]),
|
|
static_cast<vtkm::Id>(global_extents.size() > 2 ? global_extents[2] : 1) };
|
|
}
|
|
else
|
|
{ // All other blocks: Consistency check of globalSize
|
|
if (globalSize !=
|
|
vtkm::Id3{ static_cast<vtkm::Id>(global_extents[0]),
|
|
static_cast<vtkm::Id>(global_extents[1]),
|
|
static_cast<vtkm::Id>(global_extents.size() > 2 ? global_extents[2] : 1) })
|
|
{
|
|
std::cerr << "Error: Global extents mismatch between blocks!" << std::endl;
|
|
return false;
|
|
}
|
|
}
|
|
|
|
getline(inFile, line);
|
|
std::istringstream offset_stream(line);
|
|
offset_stream >> tag;
|
|
if (tag != "#OFFSET")
|
|
{
|
|
std::cerr << "Error: Expected #OFFSET, got " << tag << std::endl;
|
|
return false;
|
|
}
|
|
std::vector<vtkm::Id> offset;
|
|
while (offset_stream >> dimVertices)
|
|
offset.push_back(dimVertices);
|
|
// Swap dimensions so that they are from fastest to slowest growing
|
|
// dims[0] -> col; dims[1] -> row, dims[2] ->slice
|
|
std::swap(offset[0], offset[1]);
|
|
|
|
getline(inFile, line);
|
|
std::istringstream bpd_stream(line);
|
|
bpd_stream >> tag;
|
|
if (tag != "#BLOCKS_PER_DIM")
|
|
{
|
|
std::cerr << "Error: Expected #BLOCKS_PER_DIM, got " << tag << std::endl;
|
|
return false;
|
|
}
|
|
std::vector<vtkm::Id> bpd;
|
|
while (bpd_stream >> dimVertices)
|
|
bpd.push_back(dimVertices);
|
|
// Swap dimensions so that they are from fastest to slowest growing
|
|
// dims[0] -> col; dims[1] -> row, dims[2] ->slice
|
|
std::swap(bpd[0], bpd[1]);
|
|
|
|
getline(inFile, line);
|
|
std::istringstream blockIndex_stream(line);
|
|
blockIndex_stream >> tag;
|
|
if (tag != "#BLOCK_INDEX")
|
|
{
|
|
std::cerr << "Error: Expected #BLOCK_INDEX, got " << tag << std::endl;
|
|
return false;
|
|
}
|
|
std::vector<vtkm::Id> blockIndex;
|
|
while (blockIndex_stream >> dimVertices)
|
|
blockIndex.push_back(dimVertices);
|
|
// Swap dimensions so that they are from fastest to slowest growing
|
|
// dims[0] -> col; dims[1] -> row, dims[2] ->slice
|
|
std::swap(blockIndex[0], blockIndex[1]);
|
|
|
|
getline(inFile, line);
|
|
std::istringstream linestream(line);
|
|
std::vector<vtkm::Id> dims;
|
|
while (linestream >> dimVertices)
|
|
{
|
|
dims.push_back(dimVertices);
|
|
}
|
|
|
|
if (dims.size() != global_extents.size() || dims.size() != offset.size())
|
|
{
|
|
std::cerr << "Error: Dimension mismatch" << std::endl;
|
|
return false;
|
|
}
|
|
// Swap dimensions so that they are from fastest to slowest growing
|
|
// dims[0] -> col; dims[1] -> row, dims[2] ->slice
|
|
std::swap(dims[0], dims[1]);
|
|
|
|
// 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 that 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)
|
|
{
|
|
return false;
|
|
}
|
|
|
|
// Read data
|
|
std::vector<ValueType> values(numVertices);
|
|
if (filename.compare(filename.length() - 5, 5, ".bdem") == 0)
|
|
{
|
|
inFile.read(reinterpret_cast<char*>(values.data()),
|
|
static_cast<std::streamsize>(numVertices * sizeof(ValueType)));
|
|
}
|
|
else
|
|
{
|
|
for (std::size_t vertex = 0; vertex < numVertices; ++vertex)
|
|
{
|
|
inFile >> values[vertex];
|
|
}
|
|
}
|
|
|
|
currTime = totalTime.GetElapsedTime();
|
|
dataReadTime = currTime - prevTime;
|
|
prevTime = currTime;
|
|
|
|
// Create vtk-m data set
|
|
vtkm::cont::DataSetBuilderUniform dsb;
|
|
vtkm::cont::DataSet ds;
|
|
if (nDims == 2)
|
|
{
|
|
const vtkm::Id2 v_dims{
|
|
static_cast<vtkm::Id>(dims[0]),
|
|
static_cast<vtkm::Id>(dims[1]),
|
|
};
|
|
const vtkm::Vec<ValueType, 2> v_origin{ static_cast<ValueType>(offset[0]),
|
|
static_cast<ValueType>(offset[1]) };
|
|
const vtkm::Vec<ValueType, 2> v_spacing{ 1, 1 };
|
|
ds = dsb.Create(v_dims, v_origin, v_spacing);
|
|
vtkm::cont::CellSetStructured<2> cs;
|
|
cs.SetPointDimensions(v_dims);
|
|
cs.SetGlobalPointDimensions(vtkm::Id2{ globalSize[0], globalSize[1] });
|
|
cs.SetGlobalPointIndexStart(vtkm::Id2{ offset[0], offset[1] });
|
|
ds.SetCellSet(cs);
|
|
}
|
|
else
|
|
{
|
|
VTKM_ASSERT(nDims == 3);
|
|
const vtkm::Id3 v_dims{ static_cast<vtkm::Id>(dims[0]),
|
|
static_cast<vtkm::Id>(dims[1]),
|
|
static_cast<vtkm::Id>(dims[2]) };
|
|
const vtkm::Vec<ValueType, 3> v_origin{ static_cast<ValueType>(offset[0]),
|
|
static_cast<ValueType>(offset[1]),
|
|
static_cast<ValueType>(offset[2]) };
|
|
vtkm::Vec<ValueType, 3> v_spacing(1, 1, 1);
|
|
ds = dsb.Create(v_dims, v_origin, v_spacing);
|
|
vtkm::cont::CellSetStructured<3> cs;
|
|
cs.SetPointDimensions(v_dims);
|
|
cs.SetGlobalPointDimensions(globalSize);
|
|
cs.SetGlobalPointIndexStart(vtkm::Id3{ offset[0], offset[1], offset[2] });
|
|
ds.SetCellSet(cs);
|
|
}
|
|
|
|
ds.AddPointField("values", values);
|
|
// and add to partition
|
|
useDataSet.AppendPartition(ds);
|
|
|
|
localBlockIndicesPortal.Set(blockNo,
|
|
vtkm::Id3{ static_cast<vtkm::Id>(blockIndex[0]),
|
|
static_cast<vtkm::Id>(blockIndex[1]),
|
|
static_cast<vtkm::Id>(nDims == 3 ? blockIndex[2] : 0) });
|
|
|
|
if (blockNo == 0)
|
|
{
|
|
blocksPerDim = vtkm::Id3{ static_cast<vtkm::Id>(bpd[0]),
|
|
static_cast<vtkm::Id>(bpd[1]),
|
|
static_cast<vtkm::Id>(nDims == 3 ? bpd[2] : 1) };
|
|
}
|
|
}
|
|
currTime = totalTime.GetElapsedTime();
|
|
buildDatasetTime = currTime - prevTime;
|
|
return true;
|
|
}
|
|
|
|
|
|
/// Read data from a single file and split the data into blocks across ranks
|
|
/// This is a simple implementation that will read the full data on all ranks
|
|
/// and then extract only the relevant subblock for that rank.
|
|
/// The function support reading from BOV as well from ASCII files
|
|
///
|
|
/// @param[in] rank The current MPI rank the function is called from
|
|
/// @param[in] size The number of MPI ranks
|
|
/// @param[in] filename Name of the file with %d as placeholder for the integer index of the block
|
|
/// @param[in] numBlocks Number of blocks to use during computation
|
|
/// @param[in] blocksPerRank Number of data blocks to process on each rank
|
|
/// @param[out] nDims Number of data dimensions (i.e, 2 or 3)
|
|
/// @param[out] useDataSet VTKm partioned dataset to be used with the distributed contour tree filter
|
|
/// @param[out] globalSize Global extends of the input mesh (i.e., number of mesh points in each dimension)
|
|
/// @param[in] blocksPerDim Number of data blocks used in each data dimension
|
|
/// @param[in] localBlockIndices Array with the (x,y,z) index of each local data block with
|
|
/// with respect to blocksPerDim
|
|
/// @param[in] dataReadTime Time to read the data
|
|
/// @param[in] buildDatasetTime Time to construct the VTKm datasets
|
|
/// @returns bool indicating whether the read was successful or not
|
|
template <typename ValueType>
|
|
bool readSingleBlockFile(const int& rank,
|
|
const int& size,
|
|
const std::string& filename,
|
|
const int& numBlocks,
|
|
const int& blocksPerRank,
|
|
std::vector<vtkm::Float32>::size_type& nDims,
|
|
vtkm::cont::PartitionedDataSet& useDataSet,
|
|
vtkm::Id3& globalSize,
|
|
vtkm::Id3& blocksPerDim,
|
|
vtkm::cont::ArrayHandle<vtkm::Id3>& localBlockIndices,
|
|
vtkm::Float64& dataReadTime,
|
|
vtkm::Float64& buildDatasetTime)
|
|
{
|
|
vtkm::cont::Timer totalTime;
|
|
totalTime.Start();
|
|
vtkm::Float64 prevTime = 0;
|
|
vtkm::Float64 currTime = 0;
|
|
|
|
localBlockIndices.Allocate(blocksPerRank);
|
|
auto localBlockIndicesPortal = localBlockIndices.WritePortal();
|
|
|
|
vtkm::cont::DataSet inDataSet;
|
|
// TODO: Currently FloatDefault would be fine, but it could cause problems if we ever read binary files here.
|
|
std::vector<ValueType> values;
|
|
std::vector<vtkm::Id> dims;
|
|
|
|
// Read BOV data file
|
|
if (filename.compare(filename.length() - 3, 3, "bov") == 0)
|
|
{
|
|
std::cout << "Reading BOV file" << std::endl;
|
|
vtkm::io::BOVDataSetReader reader(filename);
|
|
inDataSet = reader.ReadDataSet();
|
|
nDims = 3;
|
|
currTime = totalTime.GetElapsedTime();
|
|
dataReadTime = currTime - prevTime;
|
|
prevTime = currTime;
|
|
// Copy the data into the values array so we can construct a multiblock dataset
|
|
vtkm::Id3 pointDimensions;
|
|
auto cellSet = inDataSet.GetCellSet();
|
|
vtkm::cont::CastAndCall(
|
|
cellSet, vtkm::worklet::contourtree_augmented::GetPointDimensions(), pointDimensions);
|
|
std::cout << "Point dimensions are " << pointDimensions << std::endl;
|
|
dims.resize(3);
|
|
dims[0] = pointDimensions[0];
|
|
dims[1] = pointDimensions[1];
|
|
dims[2] = pointDimensions[2];
|
|
auto tempFieldData = inDataSet.GetField(0).GetData();
|
|
values.resize(static_cast<std::size_t>(tempFieldData.GetNumberOfValues()));
|
|
auto valuesHandle = vtkm::cont::make_ArrayHandle(values, vtkm::CopyFlag::Off);
|
|
vtkm::cont::ArrayCopy(tempFieldData, valuesHandle);
|
|
valuesHandle.SyncControlArray(); //Forces values to get updated if copy happened on GPU
|
|
}
|
|
// Read ASCII data input
|
|
else
|
|
{
|
|
std::cout << "Reading ASCII file" << std::endl;
|
|
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);
|
|
}
|
|
// Swap dimensions so that they are from fastest to slowest growing
|
|
// dims[0] -> col; dims[1] -> row, dims[2] ->slice
|
|
std::swap(dims[0], dims[1]);
|
|
|
|
// 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 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)
|
|
{
|
|
return false;
|
|
}
|
|
|
|
// 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;
|
|
|
|
} // END ASCII Read
|
|
|
|
// Create a multi-block dataset for multi-block DIY-paralle processing
|
|
blocksPerDim =
|
|
nDims == 3 ? vtkm::Id3(1, 1, numBlocks) : vtkm::Id3(1, numBlocks, 1); // Decompose the data into
|
|
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));
|
|
std::cout << blocksPerDim << " " << globalSize << std::endl;
|
|
{
|
|
vtkm::Id lastDimSize =
|
|
(nDims == 2) ? static_cast<vtkm::Id>(dims[1]) : static_cast<vtkm::Id>(dims[2]);
|
|
if (size > (lastDimSize / 2.))
|
|
{
|
|
VTKM_LOG_IF_S(vtkm::cont::LogLevel::Error,
|
|
rank == 0,
|
|
"Number of ranks too large for data. Use " << lastDimSize / 2
|
|
<< "or fewer ranks");
|
|
return false;
|
|
}
|
|
vtkm::Id standardBlockSize = (vtkm::Id)(lastDimSize / numBlocks);
|
|
vtkm::Id blockSize = standardBlockSize;
|
|
vtkm::Id blockSliceSize =
|
|
nDims == 2 ? static_cast<vtkm::Id>(dims[0]) : static_cast<vtkm::Id>((dims[0] * dims[1]));
|
|
vtkm::Id blockNumValues = blockSize * blockSliceSize;
|
|
|
|
vtkm::Id startBlock = blocksPerRank * rank;
|
|
vtkm::Id endBlock = startBlock + blocksPerRank;
|
|
for (vtkm::Id blockIndex = startBlock; blockIndex < endBlock; ++blockIndex)
|
|
{
|
|
vtkm::Id localBlockIndex = blockIndex - startBlock;
|
|
vtkm::Id blockStart = blockIndex * blockNumValues;
|
|
vtkm::Id blockEnd = blockStart + blockNumValues;
|
|
if (blockIndex < (numBlocks - 1)) // add overlap between regions
|
|
{
|
|
blockEnd += blockSliceSize;
|
|
}
|
|
else
|
|
{
|
|
blockEnd = lastDimSize * blockSliceSize;
|
|
}
|
|
vtkm::Id currBlockSize = (vtkm::Id)((blockEnd - blockStart) / blockSliceSize);
|
|
|
|
vtkm::cont::DataSetBuilderUniform dsb;
|
|
vtkm::cont::DataSet ds;
|
|
|
|
// 2D data
|
|
if (nDims == 2)
|
|
{
|
|
vtkm::Id2 vdims;
|
|
vdims[0] = static_cast<vtkm::Id>(dims[0]);
|
|
vdims[1] = static_cast<vtkm::Id>(currBlockSize);
|
|
vtkm::Vec<ValueType, 2> origin(0, blockIndex * blockSize);
|
|
vtkm::Vec<ValueType, 2> spacing(1, 1);
|
|
ds = dsb.Create(vdims, origin, spacing);
|
|
vtkm::cont::CellSetStructured<2> cs;
|
|
cs.SetPointDimensions(vdims);
|
|
cs.SetGlobalPointDimensions(vtkm::Id2{ globalSize[0], globalSize[1] });
|
|
cs.SetGlobalPointIndexStart(vtkm::Id2{ 0, (blockStart / blockSliceSize) });
|
|
ds.SetCellSet(cs);
|
|
localBlockIndicesPortal.Set(localBlockIndex, vtkm::Id3(0, blockIndex, 0));
|
|
}
|
|
// 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>(currBlockSize);
|
|
vtkm::Vec<ValueType, 3> origin(0, 0, (blockIndex * blockSize));
|
|
vtkm::Vec<ValueType, 3> spacing(1, 1, 1);
|
|
ds = dsb.Create(vdims, origin, spacing);
|
|
vtkm::cont::CellSetStructured<3> cs;
|
|
cs.SetPointDimensions(vdims);
|
|
cs.SetGlobalPointDimensions(globalSize);
|
|
cs.SetGlobalPointIndexStart(vtkm::Id3(0, 0, blockStart / blockSliceSize));
|
|
ds.SetCellSet(cs);
|
|
localBlockIndicesPortal.Set(localBlockIndex, vtkm::Id3(0, 0, blockIndex));
|
|
}
|
|
|
|
std::vector<vtkm::Float32> subValues((values.begin() + blockStart),
|
|
(values.begin() + blockEnd));
|
|
|
|
ds.AddPointField("values", subValues);
|
|
useDataSet.AppendPartition(ds);
|
|
}
|
|
}
|
|
currTime = totalTime.GetElapsedTime();
|
|
buildDatasetTime = currTime - prevTime;
|
|
return true;
|
|
}
|
|
|
|
#endif
|