Installing Python Packages

Owned by Cristian Di Pietrantonio
Last updated: Jul 02, 2024 by Alexis Espinosa
4 min read

Pip and Setuptools (setup.py) are the most popular tools for installing Python packages, and also the easiest ways to benefit from the Python performance libraries that come preinstalled on Pawsey systems.

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Versions installed in Pawsey systems

To check the current installed versions, use the module avail command (current versions may be different from content shown here):

Terminal 1. Checking for installed versions
$ module avail python
--------------------- /software/setonix/2024.05/modules/zen3/gcc/12.2.0/programming-languages ---------------------
   python/3.9.15    python/3.11.6 (D)

--------------------------------------- /opt/cray/pe/lmod/modulefiles/core ----------------------------------------
   cray-python/3.9.13.1    cray-python/3.10.10 (D)

We recommend the use of python installed by Pawsey instead of cray-python.

Many scientific and managing tools have been also installed in our software stack. These are named with the prefix py-, and sometimes their flavour is also identified by a suffix -py<VERSION> after the version corresponding to the tool itself (current versions may be different from content shown here):

Terminal 1. Checking for installed versions
$ module avail py-
---------------------- /software/setonix/2024.05/modules/zen3/gcc/12.2.0/astro-applications -----------------------
   py-astropy/4.2.1    py-astropy/5.1 (D)    py-emcee/3.1.1    py-funcsigs/1.0.2

--------------------------- /software/setonix/2024.05/modules/zen3/gcc/12.2.0/utilities ---------------------------
   py-boto3/1.26.26              py-setuptools/59.4.0-py3.9.15    py-setuptools/68.0.0-py3.11.6 (D)
   py-pip/23.1.2-py3.9.15        py-setuptools/59.4.0-py3.11.6
   py-pip/23.1.2-py3.11.6 (D)    py-setuptools/68.0.0-py3.9.15

------------------------ /software/setonix/2024.05/modules/zen3/gcc/12.2.0/python-packages ------------------------
   py-cython/0.29.36         py-ipython/8.14.0           py-numpy/1.24.4         py-scikit-learn/1.3.2
   py-cython/3.0.4    (D)    py-matplotlib/3.8.1         py-numpy/1.26.1  (D)    py-scipy/1.11.3
   py-dask/2023.4.1          py-mpi4py/3.1.5-py3.11.6    py-pandas/1.5.3
   py-h5netcdf/0.10.0        py-netcdf4/1.6.2            py-pandas/2.1.2  (D)
   py-h5py/3.8.0             py-numba/0.57.0             py-plotly/5.14.1

------------------------ /software/setonix/2024.05/modules/zen3/gcc/12.2.0/developer-tools ------------------------
   py-hatchet/1.3.1

Before you begin

Basic information on these installation tools can be found in their websites (external links):

To install Python packages on top of the bare Python interpreter, pip and setuptools are available on Pawsey systems as modules (note the py- prefix for Python packages):

$ module load python/3.11.6 py-pip/23.1.2-py3.11.6

$ module load python/3.11.6 py-setuptools/68.0.0-py3.11.6


Once you choose one of these two options to install Python packages, you should keep using it, to avoid conflicts and errors arising from packages installed in different locations.

Pawsey Python modules also preconfigure the shell environment by default to provide a meaningful location for user-specific package installations:

export PYTHONUSERBASE=/software/projects/<project-id>/<user-name>/setonix/python

export PATH=$PATH:$PYTHONUSERBASE/bin

Install a package using pip

Let's assume you've found a pip-installable package, for instance by browsing the Python Package Index (external link). In this example, we're installing astropy, a popular package for astronomy.

First, we need to load the relevant system modules, including python, py-pip and any required dependency packages (in this case, py-numpy):

Terminal 1: Set up environment for pip
$ module load python/<VERSION_OF_PYTHON>
$ module load py-pip/<VERSION>-py<VERSION_OF_PYTHON>

$ module load py-numpy/<VERSION>

Now let's proceed with the installation. We're going to use pip with the --user  flag to install in the Python user directory. (Users cannot install software in system directories on shared Pawsey supercomputer systems.)

Terminal 2: Install with pip
$ pip install --user astropy==4.1

Collecting astropy==4.1
  Downloading https://files.pythonhosted.org/packages/74/9c/a1e51955d4a2af497a507c323409ebe55c122a91c438d2884d918360efc1/astropy-4.1-cp36-cp36m-manylinux1_x86_64.whl (10.3MB)
     |████████████████████████████████| 10.3MB 14.7MB/s 
Requirement already satisfied: numpy>=1.16 in /pawsey/sles12sp3/python/3.6.3/numpy/1.19.0/lib/python3.6/site-packages/numpy-1.19.0-py3.6-linux-x86_64.egg (from astropy==4.1) (1.19.0)
Installing collected packages: astropy
Successfully installed astropy-4.1

Reproducible installations with pip

Let's go through a simple way of making the installation above more reproducible.

After the installation, we can use pip freeze to save the list of installed packages and their versions:

Terminal 3: Pip freeze
$ pip freeze >requirements.txt

$ cat requirements.txt
astropy==4.1
numpy==1.19.0

If we need to reinstall exactly the same Python environment later on, we can make use of the list we have just created:

Terminal 4: Pip install from requirements
$ module load python/<VERSION_OF_PYTHON>
$ module load py-pip/<VERSION>-py<VERSION_OF_PYTHON>

$ module load py-numpy/<VERSION>

$ sg <projectcode> -c 'pip install --user --no-deps -r requirements.txt'
Collecting astropy==4.1 (from -r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/74/9c/a1e51955d4a2af497a507c323409ebe55c122a91c438d2884d918360efc1/astropy-4.1-cp36-cp36m-manylinux1_x86_64.whl (10.3MB)
     |████████████████████████████████| 10.3MB 16.0MB/s 
Requirement already satisfied: numpy==1.19.0 in /pawsey/sles12sp3/python/3.6.3/numpy/1.19.0/lib/python3.6/site-packages/numpy-1.19.0-py3.6-linux-x86_64.egg (from -r requirements.txt (line 2)) (1.19.0)
Installing collected packages: astropy
Successfully installed astropy-4.1

Note how we use the flag --no-deps to make sure that pip only installs the packages that are listed in the requirements. This is a fully functional list of packages, as we got it from a previous installation.

Installing a package with setuptools

Sometimes you need to install a package without the support of pip, for example, installing the development branch to obtain a bug fix that has not been published yet. In this case, you can still rely on a software-aided procedure.

For example, to install the development branch of the Python package tqdm, first download the source code:

$ git clone https://github.com/tqdm/tqdm

Change to the tqdm source code directory and then load the required modules, namely python and py-setuptools:

$ module load python/<VERSION_OF_PYTHON> py-setuptools/<VERSION>-py<VERSION_OF_PYTHON>

Finally, execute the build and installation process:

Terminal 5. Using setuptools to install a Python package.
$ sg <projectcode> -c 'python setup.py build'
running build
running build_py
creating build
[...]
$ sg <projectcode> -c 'python setup.py install --user'
running install
running bdist_egg
running egg_info
[...]
Finished processing dependencies for tqdm==4.61.1

Using virtual environments

Python packages can also be installed in a virtual environment, where all packages will be stored in the virtual environment directory. This virtual environment is a local copy of the installation of Python that can be modified without affecting the original one, which can be a very useful feature. This approach is similar to installing packages locally with --usr  or by using the Conda package manager. 

Terminal 6: Create and then activate a virtual environment
$ python -m venv $MYSOFTWARE/manual/pythonEnvironments/python-venv # create a virtual environment 
$ source $MYSOFTWARE/manual/pythonEnvironments/python-venv/bin/activate # activate the environment, updating python paths 
$ sg <projectcode> -c 'pip install astropy==4.1' # install astropy in the environment 
$ deactivate # deactivate the environment, now cannot load packages installed in venv.

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