deleted opening-hdf5
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robin
parent
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commit
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.DS_Store
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src/.DS_Store
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src/.cache
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src/build
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.idea
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src/cmake-build-debug
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## Location of data
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The data path is hardcoded such that the following tree structure is assumed:
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```
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data/
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grid.h5
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hydrodynamic_U.h5
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hydrodynamic_V.h5
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interactive-track-and-trace/
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opening-hdf5/
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...
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```
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## Compiling
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Let the current directory be the `src` directory. Run:
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```shell
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mkdir build
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cd build
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cmake ..
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make
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```
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### Building with Linux
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Makes use of `mdspan` which is not supported by glibc++ at time of writing. See [compiler support](https://en.cppreference.com/w/cpp/compiler_support/23) for `mdspan`. The solution to this is to use Clang and libc++; this is configured in our CMake setup, however the default installation of the `netcdf-cxx` package on at least Arch linux (and suspectedly Debian derivatives as well) specifically builds for the glibc implementation. To get the netcdf C++ bindings functional with the libc++ implementation, one needs to build from source. On Linux, this requires a few changes to the CMake file included with the netcdf-cxx source code, which are detailed below.
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Step-by-step to build the program using clang++ and libc++ on linux:
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1. Download the source code of netcdf-cxx, found at 'https://github.com/Unidata/netcdf-cxx4/releases/tag/v4.3.1' (make sure to download the release source code, as the master branch contains non-compilable code).
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2. Edit the CMakeLists.txt file, by appending '-stdlib=libc++' to the `CMAKE_CXX_FLAGS` variable in line 430. This means line 430 should read:
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```cmake
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SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -Wall -Wno-unused-variable -Wno-unused-parameter -stdlib=libc++")
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```
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2. Build the source code with the following:
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```sh
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mkdir build && cd build
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cmake .. -DCMAKE_CXX_COMPILER=/usr/bin/clang++
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make
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ctest
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sudo make install
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```
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3. Now the code should compile through the standard steps described in the Compiling section.
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cmake_minimum_required (VERSION 3.28)
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project (ReadHDF5)
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set(CMAKE_CXX_STANDARD 23)
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set(CMAKE_CXX_STANDARD_REQUIRED ON)
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# Force use of libc++ for mdspan support
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set(CMAKE_CXX_COMPILER "clang++")
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++ ")
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set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
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find_package(netCDF REQUIRED)
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add_executable(ReadHDF5 main.cpp)
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execute_process(
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COMMAND nc-config --includedir
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OUTPUT_VARIABLE NETCDF_INCLUDE_DIR
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OUTPUT_STRIP_TRAILING_WHITESPACE
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)
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execute_process(
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COMMAND ncxx4-config --libdir
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OUTPUT_VARIABLE NETCDFCXX_LIB_DIR
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OUTPUT_STRIP_TRAILING_WHITESPACE
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)
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target_include_directories(ReadHDF5 PUBLIC ${netCDF_INCLUDE_DIR})
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find_library(NETCDF_LIB NAMES netcdf-cxx4 netcdf_c++4 PATHS ${NETCDFCXX_LIB_DIR} NO_DEFAULT_PATH)
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target_link_libraries(ReadHDF5 ${NETCDF_LIB})
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#include <iostream>
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#include <mdspan>
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#include <print>
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#include <stdexcept>
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#include <netcdf>
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using namespace std;
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using namespace netCDF;
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template <typename T>
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void printContentsOfVec(const std::vector<T>& vec) {
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for (const auto& element : vec) {
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cout << element << " ";
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}
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cout << std::endl;
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}
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template <typename T>
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vector<T> getVarVector(NcVar var) {
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int length = 1;
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for (NcDim dim : var.getDims()) {
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length *= dim.getSize();
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}
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vector<T> vec(length);
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var.getVar(vec.data());
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return vec;
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}
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template <typename T>
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using arr3d = std::mdspan<
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T,
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std::dextents<
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std::size_t,
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3
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>
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>;
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template <typename T>
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void print3DMatrixSlice(arr3d<T> arr, int t) {
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for (int x = 0; x < arr.extent(1); x++) {
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for (int y = 0; y < arr.extent(2); y++) {
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print("{} ", arr[t,x,y]);
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}
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println("");
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}
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}
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void print3DMatrixSlice(arr3d<double> arr, int t) {
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for (int x = 0; x < arr.extent(1); x++) {
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for (int y = 0; y < arr.extent(2); y++) {
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print("{:>10.4f} ", arr[t,x,y]);
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}
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println("");
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}
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}
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/**
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* Read a 3D matrix from a NetCDF variable.
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* Reads data into a contiguous 1D data vector.
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* Returns a pair of the size of the matrix (in the form of an extent) with the data vector.
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*
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* Inteded usage of this function involves using the two returned values
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* to create an mdspan:
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*
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* auto arr = mdspan(vec.data(), size);
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*/
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template <typename T>
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pair<vector<T>, std::dextents<std::size_t, 3>> get3DMat(NcVar var) {
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if(var.getDimCount() != 3) {
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throw invalid_argument("Variable is not 3D");
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}
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int timeLength = var.getDim(0).getSize();
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int latLength = var.getDim(1).getSize();
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int longLength = var.getDim(2).getSize();
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vector<T> vec(timeLength*latLength*longLength);
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var.getVar(vec.data());
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auto arr = std::mdspan(vec.data(), timeLength, latLength, longLength);
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return {vec, arr.extents()};
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}
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int main () {
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netCDF::NcFile data("../../../../data/hydrodynamic_U.h5", netCDF::NcFile::read);
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multimap< string, NcVar > vars = data.getVars();
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auto [vec, size] = get3DMat<double>(vars.find("uo")->second);
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auto arr = std::mdspan(vec.data(), size);
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print3DMatrixSlice(arr, 100);
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return 0;
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}
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