HOWTO: Install Python packages from source

While we provide a number of Python packages, you may need a package we do not provide. If it is a commonly used package or one that is particularly difficult to compile, you can contact OSC Help for assistance. We also have provided an example below showing how to build and install your own Python packages and make them available inside of Python. These instructions use "bash" shell syntax, which is our default shell. If you are using something else (csh, tcsh, etc), some of the syntax may be different.

Please consider using conda Python package manager before you try to build Python using the method explained here. We have instructions on conda here.

Gather your materials

First, you need to collect what you need in order to perform the installation. We will do all of our work in $HOME/local/src. You should make this directory now.

mkdir -p $HOME/local/src

Next, we will need to download the source code for the package we want to install. In our example, we will use NumExpr. (NumExpr is already available through conda, so it is recommended you use conda to install it: tutorial here. The following steps are simply an example of the procedure you would follow to perform an installation of software unavailable in conda or pip). You can either download the file to your desktop and then upload it to OSC, or directly download it using the wget utility (if you know the URL for the file).

cd ~/local/src

Next, extract the downloaded file. In this case, since it's a "tar.gz" format, we can use tar to decompress and extract the contents.

tar xvfz numexpr-2.8.4.tar.gz

You can delete the downloaded archive now or keep it should you want to start the installation from scratch.

Build it!


To build the package, we will want to first create a temporary environment variable to aid in installation. We'll call INSTALL_DIR.

export INSTALL_DIR=${HOME}/local/numexpr/2.8.4

We are roughly following the convention we use at the system level. This allows us to easily install new versions of software without risking breaking anything that uses older versions. We have specified a folder for the program (numexpr), and for the version (2.8.4). To be consistent with Python installations, we will create a second temporary environment variable that will contain the actual installation location.

export TREE=${INSTALL_DIR}/lib/python3.6/site-packages

Next, make the directory tree.

mkdir -p $TREE


To compile the package, we should switch to the GNU compilers. The system installation of Python was compiled with the GNU compilers, and this will help avoid any unnecessary complications. We will also load the Python package, if it hasn't already been loaded.

module swap intel gnu
module load python/3.6-conda5.2

Next, build it. This step may vary a bit, depending on the package you are compiling. You can execute python --help to see what options are available. Since we are overriding the install path to one that we can write to and that fits our management plan, we need to use the --prefix option.

NumExpr build also requires us to set the PYTHONPATH variable before building:

export PYTHONPATH=$PYTHONPATH:~/local/numexpr/2.8.4/lib/python3.6/site-packages

Find the file:

cd numexpr-2.8.4

Now to build:

python install --prefix=$INSTALL_DIR

Make it usable

At this point, the package is compiled and installed in ~/local/numexpr/2.8.4/lib/python3.6/site-packages. Occasionally, some files will be installed in ~/local/numexpr/2.8.4/bin as well. To ensure Python can locate these files, we need to modify our environment.


The most immediate way -- but the one that must be repeated every time you wish to use the package -- is to manually modify your environment. If files are installed in the "bin" directory, you'll need to add it to your path. As before, these examples are for bash, and may have to be modified for other shells. Also, you will have to modify the directories to match your install location.

export PATH=$PATH:~/local/numexpr/2.8.4/bin

And for the Python libraries:

export PYTHONPATH=$PYTHONPATH:~/local/numexpr/2.8.4/lib/python3.6/site-packages

Hardcode it

We don't recommend this option, as it is less flexible and can cause conflicts with system software. But if you want, you can modify your .bashrc (or similar file, depending on your shell) to set these environment variables automatically. Be extra careful; making a mistake in .bashrc (or similar) can destroy your login environment in a way that will require a system administrator to fix. To do this, you can copy the lines above modifying $PATH and $PYTHONPATH into .bashrc. Remember to test them interactively first. If you destroy your shell interactively, the fix is as simple as logging out and then logging back in. If you break your login environment, you'll have to get our help to fix it.

Make a module (recommended!)

This is the most complicated option, but it is also the most flexible, as you can have multiple versions of this particular software installed and specify at run-time which one to use. This is incredibly useful if a major feature changes that would break old code, for example. You can see our tutorial on writing modules here, but the important variables to modify are, again, $PATH and $PYTHONPATH. You should specify the complete path to your home directory here and not rely on any shortcuts like ~ or $HOME.  Below is a modulefile written in Lua:

If you are following the tutorial on writing modules, you will want to place this file in $HOME/local/share/lmodfiles/numexpr/2.8.4.lua:

-- This is a Lua modulefile, this file 2.8.4.lua can be located anywhere
-- But if you are following a local modulefile location convention, we place them in
-- $HOME/local/share/lmodfiles/
-- For numexpr we place it in $HOME/local/share/lmodfiles/numexpr/2.8.4.lua
-- This finds your home directory
local homedir = os.getenv("HOME")
pathJoin(homedir, "/local/numexpr/2.8.4/lib/python3.6/site-packages"))
prepend_path(homedir, "local/numexpr/2.8.4/bin")

Once your module is created (again, see the guide), you can use your Python package simply by loading the software module you created.

module use $HOME/local/share/lmodfiles/
module load numexpr/2.8.4