Installing PyTables when you’re not root

By Koen van de Sande.

Warning

contents of this recipe may be outdated.

This guide describes how to install PyTables and its dependencies on Linux or other *nix systems when your user account is not root. Installing the HDF5 1 shared libraries and Python extension NumPy requires some non-trivial steps to work. We describe all steps needed. They only assumption is that you have Python 3.6 or higher and a C/C++ compiler (gcc) installed.

Installing HDF5

  • First go to or make a temporary folder where we can download and compile software. We’ll assume you’re in this temporary folder in the rest of this section.

  • Download hdf5-1.12.1.tar.gz from https://www.hdfgroup.org/downloads/hdf5

  • Extract the archive to the current folder:

    tar xzvf hdf5-1.12.1.tar.gz
    
  • Go to the extracted HDF5 folder:

    cd hdf5-1.12.1
    
  • Run the configure script:

    ./configure
    
  • Run make:

    make install
    
  • We’ve now compiled HDF5 1 into the hdf5 folder inside the source tree. We’ll need to move this to its final location. For this guide, we’ll make a software folder inside your home directory to store installed libraries:

    mkdir ~/software
    
  • Move the files to the right location:

    mv hdf5 ~/software/
    

Installing NumPy

  • From the NumPy page on PyPI download NumPy 1.21.5 (at time of writing) to our temporary folder.

  • Extract the archive:

    tar xzvf numpy-1.21.5.tar.gz
    
  • Go to the NumPy folder:

    cd numpy-1.21.5
    
  • Build and install the Python module into our software folder:

    python3 setup.py install --home=~/software
    

Python wrapper script

We’ve installed all dependencies of PyTables. We need to create a wrapper script for Python to let PyTables actually find all these dependencies. Had we installed them as root, they’d be trivial to find, but now we need to help a bit.

  • Create a script with the following contents (I’ve called this script p on my machine):

    #!/bin/bash
    export PYTHONPATH=~/software/lib/python
    export HDF5_DIR=~/software/hdf5
    export LD_LIBRARY_PATH=~/software/lib/python/tables:~/software/hdf5/lib
    python3 $*
    
  • Make the script executable:

    chmod 755 p
    
  • Place the script somewhere on your path (for example, inside a folder called bin inside your home dir, which is normally added to the path automatically). If you do not add this script to your path, you’ll have to replace p in scripts below by the full path (and name of) your script, e.g. ~/pytablespython.sh if you called it pytablespython.sh and put it in your home dir.

  • Test your Python wrapper script:

    p
    
  • It should now start Python. And you should be able to import numpy without errors:

    >>> import numpy
    

Note

you could do this differently by defining these environment settings somewhere in your startup scripts, but this wrapper script approach is cleaner.

Installing PyTables

  • From the PyPI page download PyTables 3.7.0 (at time of writing) to our temporary folder.

  • Extract the archive:

    tar xzvf pytables-3.7.0.tar.gz
    
  • Go to the PyTables folder:

    cd pytables-3.7.0
    
  • Install PyTables using our wrapper script:

    p setup.py install --home=~/software
    

Running Python with PyTables support

  • Use your Python wrapper script to start Python:

    p
    
  • You can now import tables without errors:

    >>> import tables
    >>> tables.__version__
    '3.7.0'
    

Concluding remarks

  • It is safe to remove the temporary folder we have used in this guide, there are no dependencies on it.

  • This guide was written for and tested with HDF5 1.12.1, PyTables 3.7.6 and Numpy 1.21.5.

Enjoy working with PyTables!

Koen


1(1,2)

http://www.hdfgroup.org/HDF5