Experiment adding libhdf5

.github/workflows/linux_tests.yml

@@ -44,7 +44,7 @@ jobs:
       - name: Install dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install libfftw3-dev libgomp1 python3
+          sudo apt-get install libfftw3-dev libhdf5-dev libgomp1 python3
 
       - name: Install Python dependencies
         shell: bash

.github/workflows/macos_tests.yml

@@ -44,7 +44,7 @@ jobs:
 
       - name: Install dependencies
         run: |
-          brew install fftw
+          brew install fftw hdf5
       - name: Hack to fix omp headers not linked
         run: |
           brew unlink libomp

.github/workflows/windows_tests.yml

@@ -51,6 +51,8 @@ jobs:
         run: |
           conda install fftw --yes
           echo "FFTWDIR=C:\Miniconda\envs\test\Library" | Out-File -FilePath $Env:GITHUB_ENV -Encoding utf8 -Append
+          conda install hdf5
+          echo "HDF5_DIR=C:\Miniconda\envs\test\Library" | Out-File -FilePath $Env:GITHUB_ENV -Encoding utf8 -Append
 
       - name: Install Python dependencies
         shell: bash

README.md

@@ -48,13 +48,14 @@ where lines need to be commented in and the paths modified if cmake cannot
     -DCMAKE_CXX_COMPILER=/Users/username/.local/homebrew/opt/llvm/bin/clang++
     -DOMP_ROOT=/Users/username/.local/homebrew/opt/llvm/
     -DCXX_ROOT=/Users/username/.local/homebrew/opt/llvm
+    -DHDF5_ROOT=/Users/username/.local/homebrew/opt/hdf5
     ```
 
     On an ARM Mac install the x86 version of brew with
     ```bash
     arch -x86_64 zsh
     arch -x86_64 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
-    arch -x86_64 /usr/local/bin/brew install llvm
+    arch -x86_64 /usr/local/bin/brew install llvm hdf5
     ```
 </details>
 

tdms/CMakeLists.txt

@@ -1,7 +1,7 @@
 # General setup ---------------------------------------------------------------
 cmake_minimum_required(VERSION 3.21)
 
-project(tdms LANGUAGES CXX)
+project(tdms LANGUAGES CXX C)
 set(CMAKE_CXX_STANDARD 17)
 
 # Allow building with testing, and default to off
@@ -57,6 +57,9 @@ else()
     find_package(OpenMP REQUIRED)
 endif()
 
+# hdf5 ------------------------------------------------------------------------
+find_package(HDF5 REQUIRED COMPONENTS CXX)
+include_directories(${HDF5_INCLUDE_DIR})
 
 # spdlog ----------------------------------------------------------------------
 find_package(spdlog NO_CMAKE_PACKAGE_REGISTRY QUIET)

tdms/cmake/targets.cmake

@@ -9,6 +9,7 @@ function(release_target)
             ${Matlab_MX_LIBRARY}
             ${Matlab_MAT_LIBRARY}
             ${LIBCXX_LIBRARY}
+            ${HDF5_CXX_LIBRARIES}
             OpenMP::OpenMP_CXX
             spdlog::spdlog
             )
@@ -44,6 +45,7 @@ function(test_target)
             ${Matlab_MX_LIBRARY}
             ${Matlab_MAT_LIBRARY}
             ${LIBCXX_LIBRARY}
+            ${HDF5_CXX_LIBRARIES}
             OpenMP::OpenMP_CXX
             spdlog::spdlog
             )

tdms/include/openandorder.h

@@ -50,3 +50,8 @@ void check_files_can_be_accessed(ArgumentNamespace &args);
  * @param pointers Pointers to the matrices.
  */
 void assign_matrix_pointers(MatrixCollection &expected, MatFileMatrixCollection &actual, const mxArray **pointers);
+
+/**
+ * @brief Test of HDF5 I/O
+ */
+void test_hdf5();

tdms/src/openandorder.cpp

@@ -8,10 +8,13 @@
  */
 #include "openandorder.h"
 
+#include <string>
+#include <iostream>
 #include <cstdio>
 #include <stdexcept>
 
 #include <spdlog/spdlog.h>
+#include <H5Cpp.h>
 
 #include "utils.h"
 #include "fdtd_grid_initialiser.h"
@@ -161,3 +164,56 @@ void assign_matrix_pointers(MatrixCollection &expected, MatFileMatrixCollection
     }// j
   }// i
 }
+
+/********************/
+#define MAX_NAME_LENGTH 32
+const std::string FileName("SimpleCompound.h5");
+const std::string DatasetName("PersonalInformation");
+const std::string member_age("Age");
+const std::string member_sex("Sex");
+const std::string member_name("Name");
+const std::string member_height("Height");
+
+typedef struct {
+    int age;
+    char sex;
+    char name[MAX_NAME_LENGTH];
+    float height;
+} PersonalInformation;
+
+void test_hdf5() {
+
+    // Data to write
+    PersonalInformation person_list[] = {
+        { 18, 'M', "Mary",  152.0   },
+        { 32, 'F', "Tom",   178.6   },
+        { 29, 'M', "Tarou", 166.6   }
+    };
+    // the length of the data
+    //int length = sizeof(person_list) / sizeof(PersonalInformation);
+    // the array of each length of multidimentional data.
+    hsize_t dim[1];
+    dim[0] = sizeof(person_list) / sizeof(PersonalInformation);
+
+    // the length of dim
+    int rank = sizeof(dim) / sizeof(hsize_t);
+
+    // defining the datatype to pass HDF55
+    H5::CompType mtype(sizeof(PersonalInformation));
+    mtype.insertMember(member_age, HOFFSET(PersonalInformation, age), H5::PredType::NATIVE_INT);
+    mtype.insertMember(member_sex, HOFFSET(PersonalInformation, sex), H5::PredType::C_S1);
+    mtype.insertMember(member_name, HOFFSET(PersonalInformation, name), H5::StrType(H5::PredType::C_S1, MAX_NAME_LENGTH));
+    mtype.insertMember(member_height, HOFFSET(PersonalInformation, height), H5::PredType::NATIVE_FLOAT);
+
+    // preparation of a dataset and a file.
+    H5::DataSpace space(rank, dim);
+    H5::H5File *file = new H5::H5File(FileName, H5F_ACC_TRUNC);
+    H5::DataSet *dataset = new H5::DataSet(file->createDataSet(DatasetName, mtype, space));
+    // Write
+    dataset->write(person_list, mtype);
+
+    delete dataset;
+    delete file;
+    return;
+
+}