Linking HDF5 with CMake for C, C++ and Fortran

CMake links HDF5 into the C, C++, or Fortran program with just two lines in CMakeLists.txt. In most cases, CMake’s built-in FindHDF5 works well with current HDF5 releases. If experiencing trouble finding HDF5 with CMake, try an alternate FindHDF5.cmake as a fallback. An example CMake for writing network data to HDF5 in C: CMakeLists.txt.

We show an example for C and another example for Fortran. “HL” refers to the high-level HDF5 interface that is more convenient and thus commonly used.

Note: if terminal has the Conda environment loaded and you keep getting the Conda HDF5 library, do first:

conda deactivate

before running the CMake configure command.

project(myproj LANGUAGES C)

find_package(HDF5 REQUIRED COMPONENTS C HL)

add_executable(myprog myprog.c)
target_link_libraries(myprog PRIVATE HDF5::HDF5)
project(myproj LANGUAGES Fortran)

find_package(HDF5 REQUIRED COMPONENTS Fortran HL)

add_executable(myprog myprog.f90)
target_link_libraries(myprog PRIVATE HDF5::HDF5)

HDF5 C example

The Fortran HDF5 syntax is quite similar.

#include "hdf5.h"

int main(void) {

   hid_t       file_id, dataset_id,dataspace_id; /* identifiers */
   herr_t      status;
   int         i, j, dset_data[4][6], read_data[4][6];
  hsize_t     dims[2];

   /* Initialize the dataset. */
   for (i = 0; i < 4; i++)
      for (j = 0; j < 6; j++)
         dset_data[i][j] = i * 6 + j + 1;

   /* Create a new file using default properties. */
   file_id = H5Fcreate("test.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

   /* Create the data space for the dataset. */
   dims[0] = 4;
   dims[1] = 6;
   dataspace_id = H5Screate_simple(2, dims, NULL);

   /* Create the dataset. */
   dataset_id = H5Dcreate2(file_id, "/dset", H5T_STD_I32BE, dataspace_id,
                          H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

   /* Write the dataset. */
   status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
                     dset_data);

   /* End access to the dataset and release resources used by it. */
   status = H5Dclose(dataset_id);

//------------------------------------------------------

   /* Open an existing dataset. */
   dataset_id = H5Dopen2(file_id, "/dset", H5P_DEFAULT);


   status = H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
                    read_data);

   for (i = 0; i < 4; i++)
      for (j = 0; j < 6; j++)
        printf("%d ",read_data[i][j]); // 1-24

   /* Close the dataset. */
   status = H5Dclose(dataset_id);

   /* Close the file. */
   status = H5Fclose(file_id);

   return 0;
}

HDF5 compiler script

As an alternative to CMake, HDF5 compiler script h5cc links HDF5 and necessary libraries:

h5cc myprog.c func.c -lm
  • h5cc: C
  • h5c++: C++
  • h5fc: Fortran