libhdf5 installation problem

Question

I've installed libhdf5-dev with apt-get but gcc cannot find it:

~$ locate libhdf5.so
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so
~$ gcc -lhdf5
/usr/bin/ld: cannot find -lhdf5
collect2: error: ld returned 1 exit status

I'm on Ubuntu 17.10.

Solution

In order to help ld to find your hdf5 library you can add the following flag:

-L /usr/lib/x86_64-linux-gnu/hdf5/serial

i.e.

~$ gcc -lhdf5 -L/usr/lib/x86_64-linux-gnu/hdf5/serial

man gcc

-Ldir
   Add directory dir to the list of directories to be searched for -l.

---

Official install instructions

Configure the HDF5 version

Note: this is a quick fix for a minor bug / issue with the version of libhdf5. If you know a better / proper way to solve it, let me know. If this section doesn't apply to you, omit it.

1. Go to the libraries directory:

   cd /usr/lib/x86_64-linux-gnu
   

2. Set LD_LIBRARY_PATH for libraries in Anacoda, such as libhdf5.so.10, libhdf5_hl.so.10:

   export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/ubuntu/anaconda/lib" >> ~/.bashrc
   

3. Update the "Dynamic Linker":

   sudo ldconfig
   

Comments

[Victor Poughon]

duplicate of: askubuntu.com/questions/870237/…

[Victor Poughon]

Obviously I'm not using ld or gcc directly but a more complex build system

[Victor Poughon]

Adding this path to the build library dir worked. But why doesn't ubuntu install this package in the correct location?

[Yaron]

seems like a known issue. I've added to my answer the official install instructions

[Victor Poughon]

Thanks, I've fixed it by adding the search path to my build system config, which is a bit cleaner solution.