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vtk-m/examples/contour_tree_distributed/ContourTreeApp.cxx
Kenneth Moreland 1faed3712e Remove the use of ResetTypes for ArrayCopy 
It used to be the case where you needed to call `ResetTypes` on a
`VariantArrayHandle` before using `ArrayCopy` to limit the types it gets
compiled for. However, there is now a general form for
`UnknownArrayHandle`, so `ResetTypes` no longer does anything useful in
this case. Remove the use of that.
2021-02-02 17:34:08 -07:00

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//============================================================================
// Copyright (c) Kitware, Inc.
// All rights reserved.
// See LICENSE.txt for details.
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notice for more information.
//
// Copyright 2014 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
// Copyright 2014 UT-Battelle, LLC.
// Copyright 2014 Los Alamos National Security.
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Under the terms of Contract DE-AC52-06NA25396 with Los Alamos National
// Laboratory (LANL), the U.S. Government retains certain rights in
// this software.
//============================================================================
// Copyright (c) 2018, The Regents of the University of California, through
// Lawrence Berkeley National Laboratory (subject to receipt of any required approvals
// from the U.S. Dept. of Energy). All rights reserved.
//
// Redistribution and use in source and binary forms, with or without modification,
// are permitted provided that the following conditions are met:
//
// (1) Redistributions of source code must retain the above copyright notice, this
// list of conditions and the following disclaimer.
//
// (2) Redistributions in binary form must reproduce the above copyright notice,
// this list of conditions and the following disclaimer in the documentation
// and/or other materials provided with the distribution.
//
// (3) Neither the name of the University of California, Lawrence Berkeley National
// Laboratory, U.S. Dept. of Energy nor the names of its contributors may be
// used to endorse or promote products derived from this software without
// specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
// ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
// WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
// IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
// INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
// BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
// OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
// OF THE POSSIBILITY OF SUCH DAMAGE.
//
//=============================================================================
//
// This code is an extension of the algorithm presented in the paper:
// Parallel Peak Pruning for Scalable SMP Contour Tree Computation.
// Hamish Carr, Gunther Weber, Christopher Sewell, and James Ahrens.
// Proceedings of the IEEE Symposium on Large Data Analysis and Visualization
// (LDAV), October 2016, Baltimore, Maryland.
//
// The PPP2 algorithm and software were jointly developed by
// Hamish Carr (University of Leeds), Gunther H. Weber (LBNL), and
// Oliver Ruebel (LBNL)
//==============================================================================
#include <vtkm/Types.h>
#include <vtkm/cont/ArrayHandle.h>
#include <vtkm/cont/DataSet.h>
#include <vtkm/cont/DataSetBuilderUniform.h>
#include <vtkm/cont/DataSetFieldAdd.h>
#include <vtkm/cont/DeviceAdapterTag.h>
#include <vtkm/cont/Initialize.h>
#include <vtkm/cont/RuntimeDeviceTracker.h>
#include <vtkm/cont/Timer.h>
#include <vtkm/io/BOVDataSetReader.h>
#include <vtkm/filter/ContourTreeUniformDistributed.h>
#include <vtkm/worklet/contourtree_augmented/PrintVectors.h>
#include <vtkm/worklet/contourtree_augmented/ProcessContourTree.h>
#include <vtkm/worklet/contourtree_augmented/Types.h>
#include <vtkm/worklet/contourtree_distributed/TreeCompiler.h>
#ifdef ENABLE_SET_NUM_THREADS
#include "tbb/task_scheduler_init.h"
#endif
// clang-format off
VTKM_THIRDPARTY_PRE_INCLUDE
#include <vtkm/thirdparty/diy/Configure.h>
#include <vtkm/thirdparty/diy/diy.h>
VTKM_THIRDPARTY_POST_INCLUDE
// clang-format on
#include <mpi.h>
#include <fstream>
#include <iomanip>
#include <iostream>
#include <sstream>
#include <cstdio>
#include <string>
#include <utility>
#include <vector>
#define SINGLE_FILE_STDOUT_STDERR
// Simple helper class for parsing the command line options
class ParseCL
{
public:
ParseCL() {}
void parse(int& argc, char** argv)
{
mCLOptions.resize(static_cast<std::size_t>(argc));
for (std::size_t i = 1; i < static_cast<std::size_t>(argc); ++i)
{
this->mCLOptions[i] = std::string(argv[i]);
}
}
vtkm::Id findOption(const std::string& option) const
{
auto it =
std::find_if(this->mCLOptions.begin(),
this->mCLOptions.end(),
[option](const std::string& val) -> bool { return val.find(option) == 0; });
if (it == this->mCLOptions.end())
{
return -1;
}
else
{
return static_cast<vtkm::Id>(it - this->mCLOptions.begin());
}
}
bool hasOption(const std::string& option) const { return this->findOption(option) >= 0; }
std::string getOption(const std::string& option) const
{
std::size_t index = static_cast<std::size_t>(this->findOption(option));
std::string val = this->mCLOptions[index];
auto valPos = val.find("=");
if (valPos)
{
return val.substr(valPos + 1);
}
return std::string("");
}
const std::vector<std::string>& getOptions() const { return this->mCLOptions; }
private:
std::vector<std::string> mCLOptions;
};
// Compute and render an isosurface for a uniform grid example
int main(int argc, char* argv[])
{
// Set the logging levels we want to use. These could be made command line options as well
// Log level to be used for outputting timing information.
vtkm::cont::LogLevel timingsLogLevel = vtkm::cont::LogLevel::Info;
// Log level to be used for outputting metadata about the trees.
vtkm::cont::LogLevel treeLogLevel = vtkm::cont::LogLevel::Info;
// Log level for outputs specific to the example
vtkm::cont::LogLevel exampleLogLevel = vtkm::cont::LogLevel::Info;
// Setup the MPI environment.
MPI_Init(&argc, &argv);
auto comm = MPI_COMM_WORLD;
// Tell VTK-m which communicator it should use.
vtkm::cont::EnvironmentTracker::SetCommunicator(vtkmdiy::mpi::communicator());
// get the rank and size
int rank, size;
MPI_Comm_rank(comm, &rank);
MPI_Comm_size(comm, &size);
// initialize vtkm-m (e.g., logging via -v and device via the -d option)
vtkm::cont::InitializeOptions vtkm_initialize_options =
vtkm::cont::InitializeOptions::RequireDevice;
vtkm::cont::InitializeResult vtkm_config =
vtkm::cont::Initialize(argc, argv, vtkm_initialize_options);
auto device = vtkm_config.Device;
VTKM_LOG_IF_S(exampleLogLevel, rank == 0, "Running with MPI. #ranks=" << size);
// Setup timing
vtkm::Float64 prevTime = 0;
vtkm::Float64 currTime = 0;
vtkm::cont::Timer totalTime;
totalTime.Start();
////////////////////////////////////////////
// Parse the command line options
////////////////////////////////////////////
ParseCL parser;
parser.parse(argc, argv);
std::string filename = parser.getOptions().back();
bool useBoundaryExtremaOnly = true;
if (parser.hasOption("--useFullBoundary"))
{
useBoundaryExtremaOnly = false;
}
bool useMarchingCubes = false;
if (parser.hasOption("--mc"))
{
useMarchingCubes = true;
if (useBoundaryExtremaOnly)
{
VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
"Warning: Marching cubes connectivity currently only works when "
"using full boundary. Enabling the --useFullBoundary option "
"to ensure that the app works.");
useBoundaryExtremaOnly = false;
}
}
bool preSplitFiles = false;
if (parser.hasOption("--preSplitFiles"))
{
preSplitFiles = true;
}
bool saveDotFiles = false;
if (parser.hasOption("--saveDot"))
{
saveDotFiles = true;
}
bool saveTreeCompilerData = false;
if (parser.hasOption("--saveTreeCompilerData"))
{
saveTreeCompilerData = true;
}
bool forwardSummary = false;
if (parser.hasOption("--forwardSummary"))
{
forwardSummary = true;
}
#ifdef ENABLE_SET_NUM_THREADS
int numThreads = tbb::task_scheduler_init::default_num_threads();
if (parser.hasOption("--numThreads"))
{
bool deviceIsTBB = (device.GetName() == "TBB");
// Set the number of threads to be used for TBB
if (deviceIsTBB)
{
numThreads = std::stoi(parser.getOption("--numThreads"));
tbb::task_scheduler_init schedulerInit(numThreads);
}
// Print warning about mismatch between the --numThreads and -d/--device option
else
{
VTKM_LOG_S(vtkm::cont::LogLevel::Warn,
"WARNING: Mismatch between --numThreads and -d/--device option."
"numThreads option requires the use of TBB as device. "
"Ignoring the numThread option.");
}
}
#endif
int numBlocks = size;
int blocksPerRank = 1;
if (parser.hasOption("--numBlocks"))
{
numBlocks = std::stoi(parser.getOption("--numBlocks"));
if (numBlocks % size == 0)
blocksPerRank = numBlocks / size;
else
{
std::cerr << "Error: Number of blocks must be divisible by number of ranks." << std::endl;
MPI_Finalize();
return EXIT_FAILURE;
}
}
if (argc < 2 || parser.hasOption("--help") || parser.hasOption("-h"))
{
if (rank == 0)
{
std::cout << "ContourTreeAugmented <options> <fileName>" << std::endl;
std::cout << std::endl;
std::cout << "<fileName> Name of the input data file." << std::endl;
std::cout << "The file is expected to be ASCII with either: " << std::endl;
std::cout << " - xdim ydim integers for 2D or" << std::endl;
std::cout << " - xdim ydim zdim integers for 3D" << std::endl;
std::cout << "followed by vector data last dimension varying fastest" << std::endl;
std::cout << std::endl;
std::cout << "----------------------------- VTKM Options -----------------------------"
<< std::endl;
std::cout << vtkm_config.Usage << std::endl;
std::cout << std::endl;
std::cout << "------------------------- Contour Tree Options -------------------------"
<< std::endl;
std::cout << "Options: (Bool options are give via int, i.e. =0 for False and =1 for True)"
<< std::endl;
std::cout << "--mc Use marching cubes connectivity (Default=False)." << std::endl;
std::cout << "--useFullBoundary Use the full boundary during. Typically only useful"
<< std::endl;
std::cout << " to compare the performance between using the full boundary"
<< std::endl;
std::cout << " and when using only boundary extrema." << std::endl;
std::cout << "--preSplitFiles Input data is already pre-split into blocks." << std::endl;
std::cout << "--saveDot Save DOT files of the distributed contour tree "
<< "computation (Default=False). " << std::endl;
std::cout << "--saveTreeCompilerData Save data files needed for the tree compiler"
<< std::endl;
#ifdef ENABLE_SET_NUM_THREADS
std::cout << "--numThreads Specifiy the number of threads to use. "
<< "Available only with TBB." << std::endl;
#endif
std::cout << "--numBlocks Number of blocks to use during computation "
<< "(Default=number of MPI ranks.)" << std::endl;
std::cout << "--forwardSummary Forward the summary timings also to the per-rank "
<< "log files. Default is to round-robin print the summary instead" << std::endl;
std::cout << std::endl;
}
MPI_Finalize();
return EXIT_SUCCESS;
}
if (rank == 0)
{
VTKM_LOG_S(exampleLogLevel,
std::endl
<< " ------------ Settings -----------" << std::endl
<< " filename=" << filename << std::endl
<< " preSplitFiles=" << preSplitFiles << std::endl
<< " device=" << device.GetName() << std::endl
<< " mc=" << useMarchingCubes << std::endl
<< " useFullBoundary=" << !useBoundaryExtremaOnly << std::endl
<< " saveDot=" << saveDotFiles << std::endl
<< " saveTreeCompilerData=" << saveTreeCompilerData << std::endl
<< " forwardSummary=" << forwardSummary << std::endl
#ifdef ENABLE_SET_NUM_THREADS
<< " numThreads=" << numThreads << std::endl
#endif
<< " nblocks=" << numBlocks << std::endl);
}
// Redirect stdout to file if we are using MPI with Debugging
// From https://www.unix.com/302983597-post2.html
char cstr_filename[255];
std::snprintf(cstr_filename, sizeof(cstr_filename), "cout_%d.log", rank);
int out = open(cstr_filename, O_RDWR | O_CREAT | O_TRUNC, 0600);
if (-1 == out)
{
perror("opening cout.log");
return 255;
}
#ifndef SINGLE_FILE_STDOUT_STDERR
std::snprintf(cstr_filename, sizeof(cstr_filename), "cerr_%d.log", rank);
int err = open(cstr_filename, O_RDWR | O_CREAT | O_TRUNC, 0600);
if (-1 == err)
{
perror("opening cerr.log");
return 255;
}
#endif
int save_out = dup(fileno(stdout));
int save_err = dup(fileno(stderr));
if (-1 == dup2(out, fileno(stdout)))
{
perror("cannot redirect stdout");
return 255;
}
#ifdef SINGLE_FILE_STDOUT_STDERR
if (-1 == dup2(out, fileno(stderr)))
#else
if (-1 == dup2(err, fileno(stderr)))
#endif
{
perror("cannot redirect stderr");
return 255;
}
// 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;
vtkm::cont::ArrayHandle<vtkm::Id3> localBlockOrigins;
vtkm::cont::ArrayHandle<vtkm::Id3> localBlockSizes;
localBlockIndices.Allocate(blocksPerRank);
localBlockOrigins.Allocate(blocksPerRank);
localBlockSizes.Allocate(blocksPerRank);
auto localBlockIndicesPortal = localBlockIndices.WritePortal();
auto localBlockOriginsPortal = localBlockOrigins.WritePortal();
auto localBlockSizesPortal = localBlockSizes.WritePortal();
// Read the pre-split data files
if (preSplitFiles)
{
for (int blockNo = 0; blockNo < blocksPerRank; ++blockNo)
{
// Translate pattern into filename for this block
char block_filename[256];
snprintf(block_filename,
sizeof(block_filename),
filename.c_str(),
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;
MPI_Finalize();
return EXIT_FAILURE;
}
// 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;
MPI_Finalize();
return EXIT_FAILURE;
}
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;
MPI_Finalize();
return EXIT_FAILURE;
}
}
getline(inFile, line);
std::istringstream offset_stream(line);
offset_stream >> tag;
if (tag != "#OFFSET")
{
std::cerr << "Error: Expected #OFFSET, got " << tag << std::endl;
MPI_Finalize();
return EXIT_FAILURE;
}
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;
MPI_Finalize();
return EXIT_FAILURE;
}
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;
MPI_Finalize();
return EXIT_FAILURE;
}
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;
MPI_Finalize();
return EXIT_FAILURE;
}
// 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)
{
MPI_Finalize();
return EXIT_FAILURE;
}
// Read data
using ValueType = vtkm::Float64;
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);
}
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);
}
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) });
localBlockOriginsPortal.Set(blockNo,
vtkm::Id3{ static_cast<vtkm::Id>(offset[0]),
static_cast<vtkm::Id>(offset[1]),
static_cast<vtkm::Id>(nDims == 3 ? offset[2] : 0) });
localBlockSizesPortal.Set(blockNo,
vtkm::Id3{ static_cast<vtkm::Id>(dims[0]),
static_cast<vtkm::Id>(dims[1]),
static_cast<vtkm::Id>(nDims == 3 ? dims[2] : 0) });
#ifdef DEBUG_PRINT_CTUD
std::cout << "blockIndex: "
<< vtkm::Id3{ static_cast<vtkm::Id>(std::ceil(static_cast<float>(offset[0]) /
static_cast<float>(dims[0]))),
static_cast<vtkm::Id>(std::ceil(static_cast<float>(offset[1]) /
static_cast<float>(dims[1]))),
static_cast<vtkm::Id>(nDims == 3
? std::ceil(static_cast<float>(offset[2]) /
static_cast<float>(dims[2]))
: 0) }
<< std::endl;
std::cout << "blockOrigin: "
<< vtkm::Id3{ static_cast<vtkm::Id>(offset[0]),
static_cast<vtkm::Id>(offset[1]),
static_cast<vtkm::Id>(nDims == 3 ? offset[2] : 0) }
<< std::endl;
std::cout << "blockSize: "
<< vtkm::Id3{ static_cast<vtkm::Id>(dims[0]),
static_cast<vtkm::Id>(dims[1]),
static_cast<vtkm::Id>(nDims == 3 ? dims[2] : 0) };
#endif
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) };
#ifdef DEBUG_PRINT_CTUD
std::cout << "blocksPerDim: " << blocksPerDim << std::endl;
#endif
}
}
// Print the mesh metadata
if (rank == 0)
{
VTKM_LOG_S(exampleLogLevel,
std::endl
<< " ---------------- Input Mesh Properties --------------" << std::endl
<< " Number of dimensions: " << nDims << std::endl);
}
}
// Read single-block data and split it for the ranks
else
{
vtkm::cont::DataSet inDataSet;
// Currently FloatDefualt would be fine, but it could cause problems if we ever
// read binary files here.
using ValueType = vtkm::Float64;
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
// TODO All we should need to do to implement BOV support is to copy the values
// in the values vector and copy the dimensions in the dims vector
vtkm::Id3 pointDimensions;
auto cellSet = inDataSet.GetCellSet();
cellSet.CastAndCall(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)
{
MPI_Finalize();
return EXIT_FAILURE;
}
// 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
// Print the mesh metadata
if (rank == 0)
{
VTKM_LOG_S(exampleLogLevel,
std::endl
<< " ---------------- Input Mesh Properties --------------" << std::endl
<< " Number of dimensions: " << nDims);
}
// 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");
MPI_Finalize();
return EXIT_FAILURE;
}
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);
localBlockIndicesPortal.Set(localBlockIndex, vtkm::Id3(0, blockIndex, 0));
localBlockOriginsPortal.Set(localBlockIndex,
vtkm::Id3(0, (blockStart / blockSliceSize), 0));
localBlockSizesPortal.Set(localBlockIndex,
vtkm::Id3(static_cast<vtkm::Id>(dims[0]), currBlockSize, 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);
localBlockIndicesPortal.Set(localBlockIndex, vtkm::Id3(0, 0, blockIndex));
localBlockOriginsPortal.Set(localBlockIndex,
vtkm::Id3(0, 0, (blockStart / blockSliceSize)));
localBlockSizesPortal.Set(localBlockIndex,
vtkm::Id3(static_cast<vtkm::Id>(dims[0]),
static_cast<vtkm::Id>(dims[1]),
currBlockSize));
}
std::vector<vtkm::Float32> subValues((values.begin() + blockStart),
(values.begin() + blockEnd));
ds.AddPointField("values", subValues);
useDataSet.AppendPartition(ds);
}
}
}
// Check if marching cubes is enabled for non 3D data
bool invalidMCOption = (useMarchingCubes && nDims != 3);
VTKM_LOG_IF_S(vtkm::cont::LogLevel::Error,
invalidMCOption && (rank == 0),
"The input mesh is "
<< nDims << "D. "
<< "Contour tree using marching cubes is only supported for 3D data.");
// If we found any errors in the setttings than finalize MPI and exit the execution
if (invalidMCOption)
{
MPI_Finalize();
return EXIT_FAILURE;
}
currTime = totalTime.GetElapsedTime();
buildDatasetTime = 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 dataReadSyncTime = currTime - prevTime;
prevTime = currTime;
// Convert the mesh of values into contour tree, pairs of vertex ids
vtkm::filter::ContourTreeUniformDistributed filter(blocksPerDim,
globalSize,
localBlockIndices,
localBlockOrigins,
localBlockSizes,
useBoundaryExtremaOnly,
useMarchingCubes,
saveDotFiles,
timingsLogLevel,
treeLogLevel);
filter.SetActiveField("values");
// Execute the contour tree analysis
auto result = filter.Execute(useDataSet);
currTime = totalTime.GetElapsedTime();
vtkm::Float64 computeContourTreeTime = 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 postFilterSyncTime = currTime - prevTime;
prevTime = currTime;
/*
std::cout << "Result dataset has " << result.GetNumberOfPartitions() << " partitions" << std::endl;
for (vtkm::Id ds_no = 0; ds_no < result.GetNumberOfPartitions(); ++ds_no)
{
auto ds = result.GetPartition(ds_no);
for (vtkm::Id f_no = 0; f_no < ds.GetNumberOfFields(); ++f_no)
{
auto field = ds.GetField(f_no);
std::cout << field.GetName() << ": ";
PrintArrayContents(field.GetData());
std::cout << std::endl;
}
}
*/
if (saveTreeCompilerData)
{
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 saveTreeCompilerDataTime = 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 << " Save Tree Compiler Data"
<< ": " << saveTreeCompilerDataTime << " 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;
}
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