Introduction

Scientific Software Tools and Parallel Algorithms¶

PhD in High Performance Scientific Computing (HPSC)

Luca Heltai (luca.heltai@unipi.it)

Academic Year: 2025–2026

Why SSPA?¶

Lessons learned from 25 years of development of the deal.II library¶

• Modern, collaborative, workflows – Git, CI, containers, docs.

• Reproducible research – code that runs everywhere.

• Scalable simulations – get speed‑ups from 1 CPU → 1 k CPUs.

5‑Weeks¶

What You’ll Build¶

Hands‑On Labs¶

• Bash scripts that launch jobs on a mini‑cluster.

• Git PRs – merge‑conflict playground.

• Docker build → run on an HPC node.

• Parallel programming crash course – 1→8 cores for π Monte‑Carlo.

Preliminary steps¶

Tools to install¶

Quick start list – these are the essential tools you’ll need before the labs begin.

Visual Studio Code¶

• Lightweight, highly extensible IDE

• Install on Ubuntu: sudo snap install --classic code

• Or download from https://code.visualstudio.com/

OpenSSH¶

• Secure remote login to the cluster (and to Docker containers)

• Install:

sudo apt install openssh-client openssh-server

Git¶

• Version control, branch/PR workflow

• Install:

sudo apt install git

Docker¶

• Build & run containers locally and on the cluster

• Install: sudo apt install docker.io

• Or follow the official guide: https://docs.docker.com/engine/install/

Tip – Add your user to the docker group so you can run containers without sudo:

sudo usermod -aG docker $USER

and then log‑out / back‑in.

Set Up a GitHub Account¶

Configure SSH‑Key Auth¶

No passwords, just key‑based login

1. Create a GitHub account – https://github.com/join

2. Generate a new SSH key (leave the passphrase empty for painless CI)

ssh-keygen -t ed25519 -C "your_email@example.com"
# default: ~/.ssh/id_ed25519
eval "$(ssh-agent -s)"
ssh-add ~/.ssh/id_ed25519

Add Your SSH Key to GitHub¶

1. Copy your public key

cat ~/.ssh/id_ed25519.pub

Copy the whole output to your clipboard.

2. Log in to GitHub
   Open https://github.com and go to Settings → SSH and GPG keys.

3. Create a new key

• Click New SSH key

• Give it a descriptive title (e.g., Laptop – 2025)

• Paste the key you copied into the Key field.

4. Save

• Click Add SSH key – you may be asked to re‑enter your GitHub password.

5. Verify

ssh -T git@github.com

You should see:

Hi your‑username! You’ve successfully authenticated, but GitHub does not provide shell access.

6. Optional – Force SSH for Git

git config --global url."git@github.com:".insteadOf "https://github.com/"

Configure git¶

1. Set your user identity

git config --global user.name "Your Full Name"
git config --global user.email "you@example.com"

2. Choose a default editor (optional)

git config --global core.editor "code --wait"

3. Enable color output

git config --global color.ui auto

4. Show a friendly status prompt

git config --global status.showUntrackedFiles all

6. Verify the config

git config --list --show-origin

Tip:
• Use git config --global --edit to manually tweak the ~/.gitconfig.
• If you work on multiple accounts, set a local config per repository (git config user.name … inside that repo).

With these settings, your Git history will always show the correct author, and the command line will feel a lot friendlier.

Check docker installation¶

docker --version
docker run hello-world

Next Steps¶

1. Clone the course repo: git clone git@github.com:luca-heltai/sspa.git

2. Explore around