SSH login
This section will show you how to access our temporary remote cluster through SSH.
Why not use RStudio server?
In our introduction to R, we used an RStudio server running on a remote cluster. In this course, we will log in a similar remote supercomputer using Secure Shell, then run R scripts from the command line.
Why are we not making use of the interactivity of R which is an interpreted language and why are we not using the added comfort of an IDE? The short answer is: resource efficiency.
Once you have developed your code in an interactive fashion in the IDE of your choice using small hardware resources on a sample of your data, running scripts allows you to only request large resources when you need them (i.e. when your code is running). This prevents heavy resources from sitting idle when not in use, as would happen in an interactive session while you type, think, etc. It will save you money on commercial clusters and waiting time on the Alliance clusters.
This course being about high-performance R, let’s learn to use it through scripts.
Logging in the temporary cluster through SSH
You do not need to install anything on your machine for this course as we will provide access to a temporary remote cluster.
A username, hostname, and password will be given to you during the workshop.
Note that this temporary cluster will only be available for the duration of this course.
Open a terminal emulator
Windows users: Install the free version of MobaXTerm and launch it.
MacOS users: Launch Terminal.
Linux users: Open the terminal emulator of your choice.
Access the cluster through secure shell
Windows users
Follow the first 18% of this demo.
For “Remote host”, use the hostname we gave you.
Select the box “Specify username” and provide your username.
Note that the password is entered through blind typing, meaning that you will not see anything happening as you type it. This is a Linux feature. While it is a little disturbing at first, do know that it is working. Make sure to type it slowly to avoid typos, then press the “enter” key on your keyboard.
MacOS and Linux users
In the terminal, run:
ssh <username>@<hostname>Replace the username and hostname by their values.
For instance:
ssh user021@somecluster.c3.caYou will be asked a question, answer “Yes”.
When prompted, type the password.
Note that the password is entered through blind typing, meaning that you will not see anything happening as you type it. This is a Linux feature. While it is a little disturbing at first, do know that it is working. Make sure to type it slowly to avoid typos, then press the “enter” key on your keyboard.
Troubleshooting
Problems logging in are almost always due to typos. If you cannot log in, retry slowly, entering your password carefully.