Fixing H5py Wheel Build Failures In GitHub Actions

Nov 7, 2025 by SLV Team 51 views

Hey guys, have you ever run into a head-scratcher while building wheels with h5py in your GitHub Actions workflow? It's like, everything was working swimmingly, and then bam, out of the blue, you're staring at an error message that just doesn't make sense. I've been there, and I know how frustrating it can be. Let's dive into how to tackle this issue, specifically when dealing with h5py and its dependency on HDF5 within a GitHub Actions environment. This guide is tailored to help you troubleshoot and get your wheel-building process back on track. We'll explore the common causes, the specific error you might encounter, and, most importantly, the solutions to get you rolling again. Ready? Let's get started!

The Problem: `h5py` Wheel Build Failure

So, what's the deal? You're building a wheel, likely for a Python package that relies on h5py to interact with HDF5 files. Everything was sunshine and rainbows, but suddenly, the build fails. The error message you get is something along the lines of: "Unable to load dependency HDF5, make sure HDF5 is installed properly." It then goes on to specify that it's having trouble finding the necessary HDF5 libraries. This means that during the wheel build process, the system can't locate the HDF5 library that h5py needs to function. It's like the program is missing a vital ingredient, and it can't complete the recipe. The root cause usually boils down to the environment in which your GitHub Actions workflow is running. Specifically, it often involves how the HDF5 library is installed and made available to the build process. Let's get into the nitty-gritty of why this happens and, of course, how to fix it.

Understanding the Error in Detail

When you see an error like "error: Unable to load dependency HDF5, make sure HDF5 is installed properly", what's really happening? This error, h5py can't find the necessary HDF5 libraries during the build. h5py is a Python package that provides an interface to the HDF5 library, a file format designed for storing and organizing large amounts of data. During the wheel build, the build system (usually setuptools or wheel) needs to compile the h5py extension modules, which are written in C and require the HDF5 library. The error message indicates the build process can't locate the HDF5 library on your system. It is missing the necessary files or the system can't find the necessary files. This happens because the build environment is missing the HDF5 library, or the system doesn't know where to find it. This can be due to a variety of reasons, including:

Missing HDF5 Installation: The HDF5 library isn't installed in the GitHub Actions runner environment. This is the most common reason. The runner image might not include HDF5 or, if it does, it might not be in a standard location where the build process can find it.
Incorrect Library Paths: The build process isn't configured to look in the correct directories for the HDF5 libraries. Even if HDF5 is installed, the build might be searching in the wrong places.
Environment Variables: Environment variables that the build process uses to locate the HDF5 libraries (like HDF5_DIR or LD_LIBRARY_PATH) might not be set correctly. This leads to the build failing to find the necessary files.
Dependencies: Conflicts or incorrect versions of dependencies can prevent h5py from linking correctly to the HDF5 library. This can be complex, and you can solve it by specifying the exact version of the dependency library.

The Specific Error Message Decoded

The specific error messages, like the one you provided:

error: Unable to load dependency HDF5, make sure HDF5 is installed properly
on sys.platform='linux' with platform.machine()='x86_64'
Library dirs checked: []
error: libhdf5.so: cannot open shared object file: No such file or directory

This breakdown tells us a few key things:

sys.platform='linux' and platform.machine()='x86_64': Confirms that the build is happening on a Linux system with a 64-bit architecture. This is important because it dictates which pre-built HDF5 libraries you might be able to use and how to install them.
Library dirs checked: []: This is a crucial clue. It shows that the build process hasn't checked any directories for the HDF5 libraries. This usually means that the build system isn't aware of where to look for the library. This is a telltale sign that the environment isn't set up to find HDF5.
error: libhdf5.so: cannot open shared object file: No such file or directory: This is the final nail in the coffin. It's telling you that the build process can't find the libhdf5.so file, which is the shared library file for HDF5 on Linux. This means the HDF5 library isn't accessible to the build process, and the wheel build will fail. This is the common failure you are looking for. You are in the right spot to learn how to fix it.

Fixing the `h5py` Wheel Build in GitHub Actions

Alright, now that we've diagnosed the issue, let's get down to the solutions. The main goal is to ensure that the HDF5 library is installed and accessible in your GitHub Actions workflow. Here's a step-by-step guide to get you back on track. We'll cover some common approaches.

Installing HDF5 in Your GitHub Actions Workflow

The most straightforward approach is to install the HDF5 library within your GitHub Actions workflow. Here’s how you can do it, incorporating a few different methods to cover various scenarios.

Using apt-get (for Linux): If your workflow runs on a Linux runner (which is common), you can use apt-get to install the HDF5 library. Add a step to your *.yml file to run apt-get update and then install the necessary packages. This will install the HDF5 library and its development files, ensuring that h5py can find what it needs. A good practice is to update the package list before installing:
```
- name: Install HDF5
  run: |
    sudo apt-get update
    sudo apt-get install -y libhdf5-dev
```

Using conda (if you're using Conda): If your project uses Conda for environment management, installing HDF5 through Conda is a good idea. This ensures that the HDF5 library is correctly managed within your Conda environment. Add a step to your workflow to create and activate your Conda environment and then install HDF5 using Conda. This ensures the correct environment for h5py.

- name: Set up Python
  uses: actions/setup-python@v4
  with:
    python-version: '3.x'
- name: Install Conda
  uses: conda-incubator/setup-conda@v2
  with:
    conda-version: latest
    python-version: '3.x'
- name: Create and activate conda environment
  run: |
    conda create --name myenv python=3.x -y
    conda activate myenv
    conda install -c conda-forge h5py hdf5 -y
- name: Build wheel
  run: python -m build

Using pip with pre-built wheels: Another strategy is to ensure that the pre-built wheels are available. This will require you to specify where to locate the libraries during the build. This can involve setting environment variables or passing specific flags to the build command to tell it where to search for the HDF5 library. The main strategy is to make sure your pip can correctly identify the correct library.
```
- name: Install HDF5
  run: |
    sudo apt-get update
    sudo apt-get install -y libhdf5-dev
- name: Build wheel
  run: | 
    python -m pip install --upgrade pip setuptools wheel
    python -m build --wheel --no-isolation
```

Setting Environment Variables

Sometimes, even after installing HDF5, the build process still can't find the libraries. This is where environment variables come into play. You might need to set environment variables to help the build system locate the HDF5 libraries. The key variables to consider include:

HDF5_DIR: This variable should point to the directory where the HDF5 installation resides. For example, if you installed HDF5 using apt-get, the include files might be in /usr/include/hdf5 and the libraries in /usr/lib/x86_64-linux-gnu/. You might need to set HDF5_DIR to /usr or /usr/include/hdf5 depending on your setup.
LD_LIBRARY_PATH: This variable tells the dynamic linker where to search for shared libraries at runtime. You might need to add the directory containing libhdf5.so to this variable. For example, if the library is in /usr/lib/x86_64-linux-gnu/, you would add that to your LD_LIBRARY_PATH.

To set these environment variables in your GitHub Actions workflow, you can use the env section in your step. Here's an example:

    - name: Set environment variables
      run: |
        echo