# Welcome on-site!

```{admonition} Course punchline
- Move from being a Linux novice to an UPPMAX expert. 
```

```{admonition} 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](https://uppmax.github.io/uppmax_intro/overview.html) 
- All other days can be reached at the [main course page](https://www.uppmax.uu.se/support/courses-and-workshops/introductory-course-summer-2023/)

## 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](https://uppmax.github.io/uppmax_intro/login2.html)

## 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
[Linux II pdf](https://www.uppmax.uu.se/digitalAssets/560/c_560271-l_1-k_uppmax-linux-ii.pptx.pdf)
- Using the command line level 2
- Input, output and pipes
- Wildcards
- The find command
- Links
### Linux III 13-16 Tuesday
[Linux III pdf](https://www.uppmax.uu.se/digitalAssets/560/c_560271-l_1-k_uppmax-linux-iii.pptx.pdf)
- The grep command
- Using the command line level 3
- Variables, parameters and $(...)
- Filenames
### Bash Scripts 9-12 Wednesday
[BASH scripts pdf](https://www.uppmax.uu.se/digitalAssets/560/c_560271-l_1-k_uppmax-bash-scripts.pptx.pdf)
- 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
[Slurm pdf](https://www.uppmax.uu.se/digitalAssets/560/c_560271-l_1-k_uppmax-slurm-2022.pdf)
- 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
[Python material](https://uppmax.github.io/uppmax_intro_python/)
- Introduction
- Getting started
- Data types
- Control flow statements
### Python II 13-16 Thursday
[Python material](https://uppmax.github.io/uppmax_intro_python/)
- Functions
- Modules
- Command line arguments and IO
- Object-oriented Python (bonus)


## Icebreaker in HackMD
- <https://hackmd.io/@dianai/uppmax-intro/both>