How to compile c program with HDF5 source code?

I have the specific requirement where I want to compile and execute some code which has HDF5 dependencies. I don't want to use the hdf5 compiler, but I want to compile the HDF5 Source code.

I am very new on how to link the HDF5 to my C program. Please can you explain in detail how to do so, such that I can execute this program using c compiler and linking the source files which is downloaded from here.

Sample C program -

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Copyright by The HDF Group.                                               *
 * Copyright by the Board of Trustees of the University of Illinois.         *
 * All rights reserved.                                                      *
 *                                                                           *
 * This file is part of HDF5.  The full HDF5 copyright notice, including     *
 * terms governing use, modification, and redistribution, is contained in    *
 * the files COPYING and Copyright.html.  COPYING can be found at the root   *
 * of the source code distribution tree; Copyright.html can be found at the  *
 * root level of an installed copy of the electronic HDF5 document set and   *
 * is linked from the top-level documents page.  It can also be found at     *
 * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
 * access to either file, you may request a copy from [email protected].     *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

/*
 *  This example illustrates how to create a dataset that is a 4 x 6 
 *  array.  It is used in the HDF5 Tutorial.
 */

#include "hdf5.h"
#define FILE "dset.h5"

int main() {

   hid_t       file_id, dataset_id, dataspace_id;  /* identifiers */
   hsize_t     dims[2];
   herr_t      status;

   /* Create a new file using default properties. */
   file_id = H5Fcreate(FILE, 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);

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

   /* Terminate access to the data space. */ 
   status = H5Sclose(dataspace_id);

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

Solution

For compiling, it is necessary to have the -I flag point to the include directory of HDF5. For a system install, it will typically be /usr/include but there are many variations depending on whether HDF5 is installed in serial or parallel, 32/64-bit, etc. For linking the -L and -l flags are the ones that matter. -L should point to the directory holding the .so,.dll or .dylib files of the HDF5 libraries (again, there can be variations) and -l simply gives the library names, -lhdf5 and others (I believe that -lz and -lm are almost always used). If you use the high-level library, -lhdf5_hl is needed.

The simplest way to check those flags is to call

h5cc -show

that will list them all.

PS: you can compile and link in a single step (from .c to executable file) or first compile (.c to .o) then link (.o to executable file). In the first case all -I, -L and -l flags are needed.