Initializing and activating your conda environment

Conda is a command line software installation tool based on python. It will allow us to install and run various useful applications inside our home directory that we would otherwise have to hassle the HPC admins to install for us. Conda provides an isolated environment for each user, allowing us all to manage our own independent suites of applications, based on our own computing needs.

Run this command inside an ssh window on the cluster:

$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

Note: wget is a command line utility for fetching content from the internet. You use it when you want to get stuff from the web, so that’s why it’s called wget.

After the download finishes you can execute the conda installer using bash. bash is the name of the terminal program that runs on the cluster, and .sh files are scripts that bash knows how to run. The extra argument -b at the end is specific to this .sh script, and tells it to automatically run the entire script (in batch mode) instead of stopping to ask us questions as it goes.

$ bash Miniconda3-latest-Linux-x86_64.sh -b

This will create a new directory where the conda program will be located, and also where all of the software that we will eventually install with conda will be stored. By default the new directory will be placed in your home directory and will be called miniconda3.

$ ./miniconda3/bin/conda init
$ bash
$ which python
/usit/abel/u1/iovercast/miniconda3/bin/python

The first line here initializes our conda install, something that the -b flag above does not do. Now we need to log out and log back in to start working in the conda environment. An easy way to do this is just to run bash again by hand. This will give us a new terminal where you can ask which python version is preferred, and it will show you the conda version installed inside your home directory.

NB: Conda has a notion of ‘environments’ which are isolated containers for installing suites of programs and their dependencies. The ‘base’ environment is the default and you’ll see when conda is active that (base) is prepended to your terminal prompt. Mine looks like this:

(base) bash-4.1$

Install workshop software and dependencies

Turns out 95% of all the software we need for the whole workshop is included as a dependency of MESS, so here we’ll just install MESS through conda.

## Install MESS using conda
$ conda install -c conda-forge -c mess mess -y

This often takes a while (~5 minutes), and produces a bunch of pretty arcane output. After it finishes you can test it by running MESS. If this works then you are good to go:

$ MESS -h

usage: MESS [-h] [-n new] [-p params] [-s sims] [-c cores] [-r] [-e empirical]
            [-f] [-q] [-Q] [-d] [-l] [--ipcluster [ipcluster]] [--fancy-plots]