This course is the first one in our series of workshops on scientific computing, programming, data analysis and visualisation. It is intended for beginners with limited computer experience.
The course teaches the utilization of the bash shell, a command line interpreter for the UNIX or Linux operating system. Completing this course will enable you to use the institute's High Performance Computing cluster e.g. to run bioinformatic analysis pipelines or simulations that require lots of compute resources. The course will start with very simple commands to navigate the computer's file system. At the end, the participants will have learned how to write a script to execute complex tasks including launching parallel jobs on the cluster.
The course will be held on-site under "2G-hybrid" regulations (onsite participants must be vaccinated or have recovered from an infection, access via zoom is also possible). The number of participants is limited to 15.
Prerequisites
Participants should have basic understanding of using a computer. At the course, we will provide PCs. Bringing your own laptop is ok, too.
Registration
Registration starts on Oct. 6. Follow this link to the registration form.
Syllabus
Day 1
- Why on earth should I use the command line?
- What's in my computer? Disks, directories, files
- Lifting the confusion: Terminal, console, command line, shell, bash, ...
- Editing the command line
- The two most useful commands: `ls` and `cd`
- Navigating the file system
- Printing on the command line: `echo`
- Printing file content: `cat`, `head`, `tail`, `less`
- Iterations with `for`, `do`, `done`
- Conditions: `if`, `else if`, `else`, `fi`
- Pipes `|` and redirections `>`, `<`
- Tips and tricks for the lazy ones: wildcards, tab completion, history
Day 2
- Scripts
- Connecting to the cluster: `ssh`, `scp`, `rsync`
- login nodes and compute nodes
- Shared directories
- Compute Resources
- Finding available compute nodes
- Batch jobs
- Interactive jobs
- The job scheduler SLURM
- Useful SLURM commands
