Introduction
Our course intension is to run the computer simulations just locally on your individual machines. You have to understand that were then confronted with different operation systems and system setups. Hence software container offer a solution to install and run scientific programs and software independent from the operation system or computer architecture. Furthermore, we have the ambition to run the software in a notebook, where we can add freely formatted text around input files, where output are pushed to a seperate box, and where you can immediately make your graphics running. Similar to a style of what Matlab is offering.
Nevertheless, this employes some (maybe uncomfortable) steps in basic terminal commands and installation of software by it.
Software
The following software (beside what the container includes) need to be installed in your computer. Make sure that you have it ready before the course starts.
Powershell/ Terminal
In order to install required provided software, we need to run initially a powershell (in Windows) or terminal (Linux/Mac).
Linux (Ubuntu, Suse, Debian)
Search in your list of software for terminal (see Figure).
Click in the software (icon) that your search provides. Congratulations, you opened a terminal!
Mac OS X
Search in your list of software for terminal (see Figure).
Click in the software (icon) that your search provides. Congratulations, you opened a terminal!
Windows (via PS and MSL)
Powershell (PS) is a Windows-based command-line interface. You can open Powershell for the start menu in Windows (use maybe the search functionalities)
In the power shell, you can run command like
ls [which shows content of current directory]
cd C:/Users/ [change directory to C:/Users]
cd .. [change directory to parent directory]
More commands will be shown in the section “Basic Terminal commands”
To have further full Linux support under Windows, we need to install “windows subsystem for linux” (WSL). There is a detailed instruction available here .
Run in your powershell
wsl --install
Docker
Docker is a set of coupled software-as-a-service and platform-as-a-service products that use operating-system-level virtualization to develop and deliver software in packages called containers. Containers are an encapsulation of an application with its dependencies. At first glance, they appear to be just a lightweight form of virtual machines (VMs)-like a VM, a container holds an isolated instance of an operating system (OS), which we can use to run applications. The software that hosts the containers is called Docker Engine. It was first started in 2013 and is developed by Docker, Inc. Read more on the docker website.
Linux (Ubuntu, Suse, Debian)
sudo apt-get install docker
Mac OS X (via homebrew)
A good tutorial how to install docker via homebrew can be found at this link. It recommends the following installation
brew update # Fetch latest version of homebrew and formula.
brew tap caskroom/cask # Tap the Caskroom/Cask repository from Github using HTTPS.
brew search docker # Searches all known Casks for a partial or exact match.
brew cask info docker # Displays information about the given Cask
brew cask install docker # Install the given cask.
brew cleanup # Remove any older versions from the cellar.
If possible, we recommend to outsource the images to an external hard drive, when a small internal drive is used.
Windows (via PS and MSL)
To install docker and turn on WSL, check this website.
Note: on the General tab, select Use WSL 2 based engine
You can set the location where docker stores its things via Settings -> Resources -> Advanced, which is useful if your machine has several hard drives.
Git
We intent to provide this software as packed zip file to the audiance. However, it is recommended for easier software handel to use version control via git. Usually, git is installed by default. If not, please run
Linux (Ubuntu, Suse, Debian)
sudo apt-get install git
Mac OS X (via homebrew)
brew install git
The installation guide are provided by click on the individual software headers.