Python on Pegasus

Users are free to compile and install Python modules in their own home directories on Pegasus. Most Python modules can be installed with the --user flag using PIP, easy_install, or the setup.py file provided by the package. If you need a specific version of a Python module, we suggest using PIP with a direct link or downloading, extracting, and installing using setup.py. If you need to maintain multiple versions, see Python Virtual Environments (below).

The --user flag will install Python 2.7 modules here: ~/.local/lib/python2.7/site-packages Note the default location ~/.local is a hidden directory. If the Python module includes executable programs, they will usually be installed into ~/.local/bin.

To specify a different location, use --prefix=$HOME/local/python2mods (or another path). The above prefix flag example will install Python 2.7 modules here: ~/local/python2mods/lib/python2.7/site-packages

Loading and Switching Python Modules

Confirm Python is loaded:

[username@pegasus ~]$ module list
Currently Loaded Modulefiles:
  1) perl/5.18.1             3) gcc/4.4.7(default)
  2) python/2.7.3(default)   4) share-rpms65

Switch Python modules:

[username@pegasus ~]$ module switch python/3.3.1
$ module list
Currently Loaded Modulefiles:
  1) perl/5.18.1          3) share-rpms65
  2) gcc/4.4.7(default)   4) python/3.3.1

Installing Python Modules with Package Managers

Install using PIP with --user:

[username@pegasus ~]$ pip install --user munkres
or install a specific version:
[username@pegasus ~]$ pip install --user munkres==1.0.7

Install using easy_install with --user:

[username@pegasus ~]$ easy_install --user munkres

Installing Downloaded Python Modules

Install using PIP with --user:

[username@pegasus ~]$ pip install --user https://pypi.python.org/packages/source/m/munkres/munkres-1.0.7.tar.gz
Downloading/unpacking https://pypi.python.org/packages/source/m/munkres/munkres-1.0.7.tar.gz
  Downloading munkres-1.0.7.tar.gz
  Running setup.py egg_info for package from https://pypi.python.org/packages/source/m/munkres/munkres-1.0.7.tar.gz

Cleaning up...

Install using setup.py with --user:

[username@pegasus ~]$ wget https://pypi.python.org/packages/source/m/munkres/munkres-1.0.7.tar.gz --no-check-certificate
[username@pegasus ~]$ tar xvzf munkres-1.0.7.tar.gz
[username@pegasus ~]$ cd munkres-1.0.7
[username@pegasus munkres-1.0.7]$ python setup.py --user install

Checking Module Versions

Launch Python and confirm module installation:

[username@pegasus ~]$ python
...
>>> import munkres
>>> print munkres.__version__
1.0.7
>>> CTRL-D (to exit Python)