Using the Compute Canada HPC

by David Bujold, M.Sc.

This document provides information on how to get started with the Compute Canada HPC setup prepared for this workshop.

Connecting to the Mammouth HPC workshop node:

Host: workshop103.ccs.usherbrooke.ca

Login / Password: Provided to you on a separate piece of paper at the beginning of the workshop.

Linux/Mac

Use the following line from the command line, replacing username with your assigned username.

ssh username@workshop103.ccs.usherbrooke.ca

Windows

Connect to the workshop103.ccs.usherbrooke.ca server using the Putty tool that you installed for this workshop.

The first time you log in

As the $MUGQIC_INSTALL_HOME environment variable is required by some CVMFS modules, you should set an environment variable to define it. To do so, we’ll add a command to the ~/.bashrc file. which is executed automatically every time you start an interactive session.

[lect99@workshop103 ~]$ echo 'export MUGQIC_INSTALL_HOME=/cvmfs/soft.mugqic/CentOS6' >> ~/.bashrc
[lect99@workshop103 ~]$ source ~/.bashrc

You can see that the environment variable has been properly set by running the following command:

[lect99@workshop103 ~]$ echo $MUGQIC_INSTALL_HOME
/cvmfs/soft.mugqic/CentOS6

Loading a module

All available software are organized as modules that you can load. For example, to start using Java 7, you need to load the Java 7 module.

1- Get the list of available modules

[lect99@workshop103 ~]$ module avail

2- Load your module of choice

[lect99@workshop103 ~]$ module load mugqic/java/openjdk-jdk1.7.0_60

3- You can now run the module you loaded directly The following command will display on screen the current version of Java that’s been loaded:

[lect99@workshop103 ~]$ javac -version
javac 1.7.0_60-ea

Using a bash script

You can specify a bash script to launch multiple compute jobs directly from the command line, like the testjob.sh script in this example :

#!/bin/bash

module load mugqic/bowtie2/2.2.4 mugqic/bismark/0.17.0
bismark_genome_preparation --bowtie2 --verbose .

Here, we load the bowtie2 and bismark modules, and then launch the bismark_genome_preparation command.

Downloading a file from the workshop server to your computer

Note that these are example commands and shouldn’t be run

Linux/Mac

Use the following from a local command line session:

cd /path/to/local/destination/folder
scp lect99@workshop103.ccs.usherbrooke.ca:/home/lect99/myfile.txt .

To download a full directory (with all sub-directories), add the -R option

cd /path/to/destination/folder
scp -r lect99@workshop103.ccs.usherbrooke.ca:/home/lect99/myfiles/ .

Windows

Use the WinSCP software that you installed for this workshop, connecting to workshop103.ccs.usherbrooke.ca with your login and password.