Anaconda

Description

Anaconda is an open source distribution of Python and R which aims to simplify the management and deployment of modules.

Installation

Python distributions installed on Compute Canada servers are compiled from the source available at the python.org site. Users are however free to install Anaconda in their own directory. The following instructions should simplify this job and thus avoid compatibility errors.

In order to limit the installation time and the amount of storage needed, we encourage the installation of Miniconda instead of Anaconda. Miniconda includes the conda package manager and Python. You can then use the conda command to install the software you need.

Home directory (user-based installation)

By default the installation is performed in your home directory to which only you have access. If you want to share your installation with other members of your group, use the instructions in the following section.

To install Miniconda with Python 2, execute the following command:

[name@server ~]$ eb Miniconda2-4.3.27.eb

For Miniconda with Python 3, execute the following command:

[name@server ~]$ eb Miniconda3-4.3.27.eb

Be patient, the installation of Miniconda can take several minutes.

Project directory (group-based installation)

To install Anaconda with Python 2, use the following commands, replacing the field <project> by your project identifier:

[name@server ~]$ eb --sticky-bit --set-gid-bit --prefix=$(readlink ~/projects/<project>) Miniconda2-4.3.27.eb

For Anaconda with Python 3, execute the following command, replacing the field <project> by your group identifier:

[name@server ~]$ eb --sticky-bit --set-gid-bit --prefix=$(readlink ~/projects/<project>) Miniconda3-4.3.27.eb

Be patient, the installation of Miniconda can take several minutes.

The installation of Miniconda automatically creates a module file that you can load with the command of the same name. For the module command to find this file, you need to tell it where to look with the following command, replacing the field <project> by your project identifier:

[name@server ~]$ module use ~/projects/<project>/modules/*/Core

If you want this module to be available every time you connect to the cluster, you can add the preceding command to the end of your .bashrc file.

Other versions

To install any other version of Anaconda, we recommend that you contact the Compute Canada support staff by e-mail at support@calculcanada.ca.

Usage

Load the Miniconda 2 module

[name@server ~]$ module load miniconda2

or the Miniconda 3 module

[name@server ~]$ module load miniconda3

conda

You can install Python modules in your Miniconda installation by using the command conda directly. For example, to install the theano module:

[name@server ~]$ conda install theano