HOWTO: Add python packages using the conda package manager

While our python installations come with many popular packages installed, you may come upon a case where you need an addiditonal package that is not installed.  If the specific package you are looking for is available from Anaconda.org (formerlly binstar.org) you can easily install it and required dependencies by using the Conda package manager.

To be able to install a package using the conda package manager:

  • You must use a Anaconda distribution of python:
    • On Oakley the following modules:
      • python/2.7.latest*, python/2.7.8, python/3.4.2
    • On Ruby:
      • python/2.7.latest*, python/2.7.8, python/3.4.2
    • On Owens:
      • python/2.7, python/3.5
  • * = latest suffix refers to a distribution that will be electively updated
  • Package should be available through Anaconda.org and/or using pip (see next section).

If you would like to freeze a distribution so that you can control how often you update Anaconda, please send us a help request at oschelp@osc.edu.

But I use virtualenv and/or pip!

See the comparison to these package management tools here:

http://conda.pydata.org/docs/_downloads/conda-pip-virtualenv-translator.html

Pip installations are supported:

module load python
module list # check which python you just loaded
pip install --upgrade --user PACKAGE # where PACKAGE is a valid package name

If binaries exist in a pip installation they are usually installed in:

$HOME/.local/bin

The one issue with this approach is portability with multiple Python modules.  If you plan to stick with a single Python module, then this should not be an issue.  However, if you commonly switch between Python 2 and Python 3, then be aware of the potential trouble in using the same installation location for all Python versions.

Virtualenv may also work, but is not under active testing at OSC.

Procedure

We will install the yt package to a local directory in this example.

Load proper python module

module load python/2.7.8

Clone python installation to local directory

conda create -n local --clone="$PYTHON_HOME"

This will clone the entire python installation to ~/envs/local directory. The process will take serveral minutes.

conda create -n local

This will create a local python installation without any packages. If you need a small number of packages, you may choose this option.

conda create -n local python={version} anaconda

If you like to install a specific version of python, you can specify it with "python" option. For example, you can use "python=2.4" for version 2.4.

Activate clone environment

source activate local

On newer versions of Anaconda on the Owens cluster you may also need to perform the removal of the following packages before trying to install your specific packages:

conda remove conda-build
conda remove conda-env

Install package

conda install yt
  • Replace yt with the name of the package you want to install, as listed by anaconda.org.
If there are errors on this step you will need to resolve them before continuing.

Test python package

Now we will test our installed python package by loading it in python and checking its location to ensure we are using the correct version.

python -c "import yt;print yt.__file__"

Output:

$HOME/.conda/envs/local/lib/python2.7/site-packages/yt/__init__.py
  • Replace both instances of yt  with the name of the package you installed.
Remember, you will need to load the proper version of python before you go to use your newlly installed package.  Packages are only installed to one version of python.

Install your own python modules

If the method using conda above is not working or if you prefer, you can consider installing python modules from the source. Please read HOWTO: install your own python modules.