Conda on ARC

Background

Conda is a tool for managing and deploying applications, environments and packages.

Brief help message

$ conda --help
usage: conda [-h] [-V] command ...

conda is a tool for managing and deploying applications, environments and packages.

Options:

positional arguments:
  command
    clean        Remove unused packages and caches.
    config       Modify configuration values in .condarc. This is modeled
                 after the git config command. Writes to the user .condarc
                 file (/home/drozmano/.condarc) by default.
    create       Create a new conda environment from a list of specified
                 packages.
    help         Displays a list of available conda commands and their help
                 strings.
    info         Display information about current conda install.
    init         Initialize conda for shell interaction. [Experimental]
    install      Installs a list of packages into a specified conda
                 environment.
    list         List linked packages in a conda environment.
    package      Low-level conda package utility. (EXPERIMENTAL)
    remove       Remove a list of packages from a specified conda environment.
    uninstall    Alias for conda remove.
    run          Run an executable in a conda environment. [Experimental]
    search       Search for packages and display associated information. The
                 input is a MatchSpec, a query language for conda packages.
                 See examples below.
    update       Updates conda packages to the latest compatible version.
    upgrade      Alias for conda update.

optional arguments:
  -h, --help     Show this help message and exit.
  -V, --version  Show the conda version number and exit.

conda commands available from other packages:
  build
  convert
  debug
  develop
  env
  index
  inspect
  metapackage
  render
  server
  skeleton
  verify

Installing Conda in your home directory

Using Miniconda

You can install a local copy of miniconda in your home directory on our clusters. It will give you flexibility to install packages needed for the workflow. Here are the steps to follow:

Once connected to the login node, in your SSH session, make sure you are in your home directory:

$ cd 

Create a "software" subdirectory for all custom software you are going to have:

$ mkdir software; cd software 

Download the software the latest Miniconda distribution file:

$wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

Install the downloaded .sh file:

$ bash Miniconda3-latest-Linux-x86_64.sh

Follow the instructions (choosing ~/software/miniconda3 as the directory to create), agree to the license, decline the offer to initialize.

Every time you launch a new terminal and want to use this version of python, set the path as follows

$ export PATH=/home/<username>/software/miniconda3/bin:$PATH

Ensure it is using the python installed in your home directory

$ which python 
~/software/miniconda3/bin/python

Create a virtual environment for your project

$ conda create -n <yourenvname>

Install additional Python packages to the virtual environment

$ conda install -n <yourenvname> [package]

Activate the virtual environment

$ source activate <yourenvname>

At this point you should be able to use your own python with the modules you added to it.