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Simulation-Software-Engineering · Oct 29, 2024 · c7d45cf · c7d45cf
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diff --git a/02_virtualization_and_containers/containers_slides.md b/02_virtualization_and_containers/containers_slides.md
@@ -33,8 +33,8 @@ slideOptions:
 
 - Container operates in "fenced off" part of the operating system (`namespaces`)
 - Lower overhead than virtual machines
-  - Runs on kernel (and libraries) of the host OS
-  - Cheap to start and stop a container
+    - Runs on kernel (and libraries) of the host OS
+    - Cheap to start and stop a container
 - Available features depend on Host (Linux, Windows)
 - Container can be isolated.
 
@@ -46,23 +46,23 @@ slideOptions:
 - Reproducible environments for developing and testing (DevOps)
 - Container hype strongly driven by [Docker](https://www.docker.com/).
 - More and more in science
-  - High-performance computing, "Bring Your Own Environment"
-  - Reproducible research
+    - High-performance computing, "Bring Your Own Environment"
+    - Reproducible research
 
 ---
 
 ## Container Solutions
 
 - Plenty of different container formats
 
-  - [lxc/lxd](https://linuxcontainers.org/), [Docker](https://www.docker.com/), [Apptainer](https://apptainer.org/) (Singularity), [podman](https://podman.io/), [Sarus](https://user.cscs.ch/tools/containers/sarus/)...
+  * [lxc/lxd](https://linuxcontainers.org/), [Docker](https://www.docker.com/), [Apptainer](https://apptainer.org/), [podman](https://podman.io/), [Sarus](https://user.cscs.ch/tools/containers/sarus/)...
 
 - Different solutions with different strengths due to different use cases
-  - Working on the (Super-)Userspace
-  - Direct access to hardware vs. encapsulation
-  - Generic or with integration in software ecosystem (e.g. job schedulers)
+    - Working on the (Super-)Userspace
+    - Direct access to hardware vs. encapsulation
+    - Generic or with integration in software ecosystem (e.g. job schedulers)
 - Effort to establish certain standards
-  - [Open Container Initiative (OCI)](https://opencontainers.org/)
+    - [Open Container Initiative (OCI)](https://opencontainers.org/)
 
 ---
 
@@ -80,12 +80,12 @@ slideOptions:
 ## Summary
 
 - Shares many similarities with VMs, but
-  - Lightweight alternative to VMs
-  - Stricter limitations than VMs
-  - Often different use cases and working together
+    - Lightweight alternative to VMs
+    - Stricter limitations than VMs
+    - Often different use cases and working together
 - Many different containers solutions
-  - Standardization effort
-  - Choose right solution for your use case
+    - Standardization effort
+    - Choose right solution for your use case
 
 ---
 

diff --git a/02_virtualization_and_containers/singularity_slides.md b/02_virtualization_and_containers/singularity_slides.md
@@ -31,43 +31,43 @@ slideOptions:
 
 - Initiated in 2015 at Lawrence Berkeley National Laboratory
 - Two open source projects, fork in 2021:
-  - [Apptainer](https://apptainer.org/) (The Linux Foundation)
-  - SingularityCE (Sylabs)
+    - [Apptainer](https://apptainer.org/) (The Linux Foundation)
+    - SingularityCE (Sylabs)
 - More [related enterprise products by Sylabs](https://sylabs.io/products/)
 
 ---
 
 ## Image registries
 
 - [Sylabs Cloud](https://cloud.sylabs.io/library)
-  - Image registry and remote builder
+    - Image registry and remote builder
 - [Singularity Hub](https://singularityhub.github.io)
-  - Older open source registry
+   - Older open source registry
 
 ---
 
 ## Goals
 
 - Verifiable reproducibility and security
-  - Immutable images with encryption and verification support
+    - Immutable images with encryption and verification support
 - Integration over isolation by default
-  - Access hardware (GPU, network...) and filesystems
+    - Access hardware (GPU, network...) and filesystems
 - Simple and effective security model
-  - Same user inside and outside container
+    - Same user inside and outside container
 - "Mobility of Compute"
-  - Single file container for easy transport and sharing
+    - Single file container for easy transport and sharing
 
 ---
 
 ## Differences to Docker
 
 - User rights enough for running container
 - Automatically mounts [common directories](https://apptainer.org/docs/user/latest/bind_paths_and_mounts.html#system-defined-bind-paths)
-  - `${HOME}`, `${PWD}`, network etc.
+    - `${HOME}`, `${PWD}`, network etc.
 - Allows "untrusted user to run untrusted containers"
-  - Important for shared facilities (computing centers etc.)
+    - Important for shared facilities (computing centers etc.)
 - (Normally) Immutable containers
-  - Set up environment and immutable data in container
+    - Set up environment and immutable data in container
 - Support for typical HPC environments (schedulers, MPI, GPU...)
 
 ---
@@ -77,7 +77,7 @@ slideOptions:
 - Bring Your Own Environment
 - Reproducible research
 - Software needs specific environment
-  - Legacy code, commercial software, unmaintained research software
+    - Legacy code, commercial software, unmaintained research software
 - "Hiding" complicated software stack
 - Conservation of (complicated) workflows
 
@@ -86,16 +86,16 @@ slideOptions:
 ## Useful Commands
 
 - `singularity exec`
-  - Execute a command within container
+    - Execute a command within container
 - `singularity run`
-  - Launch a runscript within container
+    - Launch a runscript within container
 - `singularity shell`
-  - Run a Bourne shell within container
+    - Run a Bourne shell within container
 - `singularity build`
-  - Build a new Singularity container
-  - Use `--sandbox` for mutable container
+    - Build a new Singularity container
+    - Use `--sandbox` for mutable container
 - `singularity pull`
-  - Pull a Singularity image (`.sif` file)
+    - Pull a Singularity image (`.sif` file)
 
 ---
 
@@ -108,16 +108,16 @@ Details available in [`singularity_demo.md`](https://github.com/Simulation-Softw
 ## Defining and Building own Images
 
 - Build instructions in text file
-  - Git friendly
+    - Git friendly
 - Start from base images
-  - Several bootstrap strategies (container sources)
-  - Images can be based on Docker images
+    - Several bootstrap strategies (container sources)
+    - Images can be based on Docker images
 - Extra steps
-  - `%post`: Steps after OS installation
-  - `%environment`: Set environment variables (`PATH` etc.)
-  - `%runscript`: Container behavior under `singularity run`
-  - `%labels`: Extra information
-  - `%pre`, `%setup`... (see [Documentation](https://apptainer.org/docs/user/latest/definition_files.html))
+    - `%post`: Steps after OS installation
+    - `%environment`: Set environment variables (`PATH` etc.)
+    - `%runscript`: Container behavior under `singularity run`
+    - `%labels`: Extra information
+    - `%pre`, `%setup`... (see [Documentation](https://apptainer.org/docs/user/latest/definition_files.html))
 
 ---
 
@@ -153,12 +153,12 @@ Details available in [`singularity_demo.md`](https://github.com/Simulation-Softw
 
 - Run container as service (called `instance`)
 - Parallel computing
-  - Using correct MPI, network drivers
-  - MPI: hybrid model, bind model
+    - Using correct MPI, network drivers
+    - MPI: hybrid model, bind model
 - Mounting additional directories
 - Signing, sharing and sandbox containers
 - Performance vs. Portability
-  - Compile content with `arch=generic` or `arch=TARGET`?
+    - Compile content with `arch=generic` or `arch=TARGET`?
 
 ---
 
@@ -176,3 +176,4 @@ Details available in [`singularity_demo.md`](https://github.com/Simulation-Softw
 - [Apptainer user guide](https://apptainer.org/docs/user/latest/index.html)
 - [Singularity User Guide](https://docs.sylabs.io/guides/main/user-guide/)
 - [Singularity Cloud](https://cloud.sylabs.io/library)
+- [Sarus](https://user.cscs.ch/tools/containers/sarus/)
diff --git a/02_virtualization_and_containers/vagrant_slides.md b/02_virtualization_and_containers/vagrant_slides.md
@@ -44,24 +44,24 @@ slideOptions:
 ## Building Blocks
 
 - Provisioners
-  - Tool for configuring the boxes (install software on machine)
-  - Examples: shell scripts, Ansible, Chef, Puppet..
+    - Tool for configuring the boxes (install software on machine)
+    - Examples: shell scripts, Ansible, Chef, Puppet..
 - Providers
-  - "Backend" on which the box is based
-  - Examples: VirtualBox, Hyper-V, libvirt, AWS, Docker...
+    - "Backend" on which the box is based
+    - Examples: VirtualBox, Hyper-V, libvirt, AWS, Docker...
 
 ---
 
 ## What for?
 
 - Developing software
-  - Set up consistent development environment
-  - Share environment with others
+    - Set up consistent development environment
+    - Share environment with others
 - Testing software, workflows...
-  - Disposable environments
-  - Consistent workflows
+    - Disposable environments
+    - Consistent workflows
 - More general
-  - Simple way to setup virtual machine
+    - Simple way to setup virtual machine
 - Reproducible environment
 
 ---
@@ -71,41 +71,41 @@ slideOptions:
 - Strong focus on workflow consistency
 - (Re)use existing images
 - Automatize VM creation and configuration
-  - Easier than with VirtualBox CLI and shell scripts
+    - Easier than with VirtualBox CLI and shell scripts
 - Store in Git-friendly format
 - For us:
-  - Management of VirtualBox VMs (testing, developing...)
-  - Sharing of VMs (debugging, workshops...)
+    - Management of VirtualBox VMs (testing, developing...)
+    - Sharing of VMs (debugging, workshops...)
 
 ---
 
 ## Some Useful Commands 1/2
 
 - `vagrant init USERNAME/BOXNAME or URL`
-  - Initializes repository in current directory
-  - Creates `Vagrantfile` -> Text file (Git friendly)
+    - Initializes repository in current directory
+    - Creates `Vagrantfile` -> Text file (Git friendly)
 - `vagrant up`
-  - Create VM and start it
-  - VM is stored in `${HOME}/.vagrant.d/boxes` (overruled by `VAGRANT_HOME`)
+    - Create VM and start it
+    - VM is stored in `${HOME}/.vagrant.d/boxes` (overruled by `VAGRANT_HOME`)
 - `vagrant ssh`
-  - Connect to VM via ssh
+    - Connect to VM via ssh
 - `vagrant destroy`
-  - Stops the virtual machine and removes its disk
+    - Stops the virtual machine and removes its disk
 
 ---
 
 ## Some Useful Commands 2/2
 
 - `vagrant box list`
-  - Show available boxes
+    - Show available boxes
 - `vagrant box remove NAMEOFBOX`
-  - Remove a box completely
+    - Remove a box completely
 - `vagrant suspend`
-  - Suspends machine (sleep)
+    - Suspends machine (sleep)
 - `vagrant halt`
-  - Shuts down machine keeping changes
+    - Shuts down machine keeping changes
 - `vagrant reload --provision` or `vagrant provision`
-  - Rebuild (partially) built image
+    - Rebuild (partially) built image
 
 ---
 
@@ -118,9 +118,9 @@ Details available in [`vagrant_demo.md`](https://github.com/Simulation-Software-
 ## Structure of Vagrant Box
 
 - File `Vagrantfile`
-  - Contains configuration of VM
+    - Contains configuration of VM
 - Supplementary files, scripts etc. for configuring VM
-  - Example: `bootstrap.sh`
+    - Example: `bootstrap.sh`
 - Files are usually text files (Git friendly)
 
 ---
@@ -150,16 +150,16 @@ Details available in [`vagrant_demo.md`](https://github.com/Simulation-Software-
 ## Exchanging Files
 
 - Vagrant mounts shared folders
-  - Check output when VM starts
+    - Check output when VM starts
 
-  ```bash
-  default: Mounting shared folders...
-  ```
+    ```bash
+    default: Mounting shared folders...
+    ```
 
-  - Files can be exchanged between Guest and Host (bidirectional)
+    - Files can be exchanged between Guest and Host (bidirectional)
 - Default:
-  - Directory containing `Vagrantfile` mounted to `/vagrant`
-  - Natural use case: Build your code in a VM
+    - Directory containing `Vagrantfile` mounted to `/vagrant`
+    - Natural use case: Build your code in a VM
 
 ---
 
@@ -172,21 +172,21 @@ Details available in [`vagrant_demo.md`](https://github.com/Simulation-Software-
     vagrant package --base "NAMEOFVM" --output BOXNAME.box
     ```
 
-  - `NAMEOFVM` is name as shown in VirtualBox
-  - `BOXNAME` name to store box to
+    - `NAMEOFVM` is name as shown in VirtualBox
+    - `BOXNAME` name to store box to
 - [Publish own boxes](https://developer.hashicorp.com/vagrant/docs/providers/virtualbox/boxes)
 
 ---
 
 ## Demo: Own box
 
 - `bento/ubuntu-24.04`:
-  - [HashiCorp Cloud](https://portal.cloud.hashicorp.com/vagrant/discover/bento/ubuntu-24.04)
-  - [GitHub](https://github.com/chef/bento)
+    - [HashiCorp Cloud](https://portal.cloud.hashicorp.com/vagrant/discover/bento/ubuntu-24.04)
+    - [GitHub](https://github.com/chef/bento)
 - `precice/precice-vm`:
-  - [HashiCorp Cloud](https://portal.cloud.hashicorp.com/vagrant/discover/precice/precice-vm)
-  - [GitHub](https://github.com/precice/vm)
-  - [User Documentation](https://precice.org/installation-vm.html)
+    - [HashiCorp Cloud](https://portal.cloud.hashicorp.com/vagrant/discover/precice/precice-vm)
+    - [GitHub](https://github.com/precice/vm)
+    - [User Documentation](https://precice.org/installation-vm.html)
 
 ---
 

diff --git a/02_virtualization_and_containers/virtualbox_slides.md b/02_virtualization_and_containers/virtualbox_slides.md
@@ -42,9 +42,9 @@ slideOptions:
 
 - Linux, macOS, Windows
 - Reasonably new hardware with virtualization support
-  - Check virtualization settings in your BIOS/UEFI
+    - Check virtualization settings in your BIOS/UEFI
 - Sufficient space on hard drive
-  - VM uses a virtual hard drive, i.e., a file on your drive
+    - VM uses a virtual hard drive, i.e., a file on your drive
 - Some video memory
 - Exact requirements depend on VM: CPU cores, RAM, ...
 
@@ -54,10 +54,10 @@ slideOptions:
 
 - Virtual hard drive as a file
 - Multiple formats, for example:
-  - **VDI**: "Virtual Disk Image", VirtualBox' native format
-  - **VHD**: Format used by Microsoft
-  - **VMDK**: VMWare's virtual disk format
-  - Support for dynamic allocation
+    - **VDI**: "Virtual Disk Image", VirtualBox' native format
+    - **VHD**: Format used by Microsoft
+    - **VMDK**: VMWare's virtual disk format
+    - Support for dynamic allocation
 
 ---
 
@@ -74,9 +74,8 @@ slideOptions:
 ## Guest Additions
 
 - Software and drivers to improves Guest's performance
-  - Better video support, shared clipboard, ...
+    - Better video support, shared clipboard, ...
 - Might need additional packages. On Ubuntu 24.04 (guest):
-
     ```bash
     sudo apt install virtualbox-guest-utils virtualbox-guest-x11
     ```
@@ -95,10 +94,10 @@ Details available in [`virtualbox_demo.md`](https://github.com/Simulation-Softwa
 - Simple to set up and run
 - Manual setup, but command-line interface exists
 - Next step: Infrastructure as code
-  - Consistency of the environment?
-  - How to share a VM image with others?
+    - Consistency of the environment?
+    - How to share a VM image with others?
 
-  > "If you can't git diff a file format, it's broken."
+    > "If you can't git diff a file format, it's broken."
 
 ---