How to include hdf5 header files in a C program on Mac OS X?

Question

I am trying to learn how to program in C, and I want to be able to import data into my C program from a .hdf file.

I am using a mid 2009 MacBook Pro with Mac OS X lion.

I think I am having problems, because I didn't know where on my system to put all the header files associated with hdd (remember, I'm a bit of a noob). So I just downloaded the hdf5-1.8.9-freebsd-shared folder from the hdd website, and manually dragged all the .h files from the /include subdirectory into the /usr/include directory onto my computer.

When I try to compile my .c program using the normal gcc terminal command, I get an error which is along the lines of (sorry about the formatting but I think the exact error doesn't matter too much anyway):

Undefined symbols for architecture x86_64:
  "_H5check_version", referenced from:
      _main in cc9FVO6S.o
  "_H5Fcreate", referenced from:
      _main in cc9FVO6S.o
  "_H5Screate_simple", referenced from:
      _main in cc9FVO6S.o
  "_H5open", referenced from:
      _main in cc9FVO6S.o
  "_H5T_STD_I32LE_g", referenced from:
      _main in cc9FVO6S.o
  "_H5Dcreate2", referenced from:
      _main in cc9FVO6S.o
  "_H5T_NATIVE_INT_g", referenced from:
      _main in cc9FVO6S.o
  "_H5Dwrite", referenced from:
      _main in cc9FVO6S.o
  "_H5Dclose", referenced from:
      _main in cc9FVO6S.o
  "_H5Sclose", referenced from:
      _main in cc9FVO6S.o
  "_H5Fclose", referenced from:
      _main in cc9FVO6S.o
  "_H5Fopen", referenced from:
      _main in cc9FVO6S.o
  "_H5Dopen2", referenced from:
      _main in cc9FVO6S.o
  "_H5Dread", referenced from:
      _main in cc9FVO6S.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status

Though the exact error varies depending on exactly what code I am trying to compile. This was generated when I tried to compile a sample program.

Does anybody have any experience with getting hdf5 to work in C in Mac OS X? I have found it all very confusing.

By the way, I normally use python, and frequently use h5py without trouble.

Answer 1

You have to tell your linker when you are using a library using -l<library-name> and -L<library-dir> for non-standard locations.

If you installed hdf5 in /usr/local/hdf5, you need something like:

gcc -o h5ex_d_rdwr h5ex_d_rdwr.c -I/usr/local/hdf5/include -L/usr/local/hdf5/lib -lhdf5

If you are using the High-Level API, also add -lhdf5_hl.

---

If you have pkg-config installed and it is aware of your hdf5 installation, you can let it do it for you:

gcc -o h5ex_d_rdwr h5ex_d_rdwr.c `pkg-config hdf5 --cflags --libs`