Welcome on-site!
Course punchline
Move from being a Linux novice to an UPPMAX expert.
Learning outcomes
Get overview of UPPMAX and NAISS
Work with your files in a LINUX environment
Learn to use the UPPMAX resources in a good way
Learn the basics in the Python programming language
Lesson material
First day will be on this github website
All other days can be reached at the main course page
Questions
Questions very much related to the present talk during the lessons
best posed directly by voice
Questions requiring more effort to explain or answer
Use the HackMD session: https://hackmd.io/@dianai/uppmax-intro/both
Type along
You will be able to follow along using the built-in terminals in all OS:s.
Linux/Mac Terminal
Windows: Powershell or command prompt
For your day-to-day work you may benefit from other applications, see the Login session
Exercises
Exercises may be solved individually or in small groups in classroom
Example of arrangement on your screen
HackMD
lesson material
your own terminal
Lesson Modules
Linux I at 9-12 Monday
Links in the left menu
Overview
Logging in to UPPMAX
Linux basics
Using the command line
Intro to UPPMAX 13-16 Monday
Links in the left menu
Organisation
HPC computing
NAISS
Using software and tools
Submitting jobs to calculation nodes (intro)
Working on UPPMAX
Courses and workshops
Short intro to Bianca and NAISS-SENS for the interested
Linux II 9-12 Tuesday
Using the command line level 2
Input, output and pipes
Wildcards
The find command
Links
Linux III 13-16 Tuesday
The grep command
Using the command line level 3
Variables, parameters and $(…)
Filenames
Bash Scripts 9-12 Wednesday
Bash scripting, why’s and basics
Parameters
The IF statement
File tests
FOR and WHILE loops
Background processes and job control
Slurm at UPPMAX 13-16 Wednesday
The workload manager
Quick testing and debugging as interactive jobs
Monitoring and modifying jobs
Priority
Efficiency
Script and workflow examples
Parallel computing and GPU
Snakemake and nextflow
Python I 9-12 Thursday
Introduction
Getting started
Data types
Control flow statements
Python II 13-16 Thursday
Functions
Modules
Command line arguments and IO
Object-oriented Python (bonus)