Remote Computing with SSH & Rsync¶
Complex multi-dimensional electrochemical models, parameter fits, and large batch scans frequently run on remote lab workstations, university computing clusters, or cloud virtual machines.
In this tutorial, you will learn:
1. Connecting securely to remote computers with ssh.
2. Setting up passwordless authentication using SSH key pairs.
3. Synchronizing code and simulation datasets with rsync.
4. Using terminal multiplexers (tmux) to keep long sessions persistent.
1. Connecting via SSH¶
SSH (Secure Shell) provides an encrypted terminal connection to a remote machine:
# Connect to a remote machine with username and hostname or IP
ssh oliver@lab-cluster.university.edu
# If the server uses a non-standard port (e.g. 2222)
ssh -p 2222 oliver@192.168.1.50
Once connected, your terminal prompt changes to reflect the remote machine. Any command you type runs on the remote server's CPU!
2. Passwordless Authentication with SSH Keys¶
Instead of typing your password every time, generate an SSH cryptographic key pair:
# 1. Generate an modern Ed25519 key pair on your local computer
ssh-keygen -t ed25519 -C "your_email@example.com"
# Press Enter to accept default location ~/.ssh/id_ed25519
# 2. Copy your public key to the remote server
ssh-copy-id oliver@lab-cluster.university.edu
Now you can log in instantly without entering a password, and automated scripts can securely connect.
3. Transferring Simulation Data with rsync¶
While scp copies entire files, rsync (remote sync) compares local and remote folders and only transfers the modified blocks, saving gigabytes of bandwidth.
# Push local code and scripts to remote server
# -a: archive mode (preserves permissions, times, symlinks)
# -v: verbose output
# -z: compress data during transfer
# -P: show progress bar and allow resume
rsync -avzP ./my_simulation_code/ oliver@lab-cluster:~/simulations/
# Pull simulation results and figures back to your local computer
rsync -avzP oliver@lab-cluster:~/simulations/results/ ./local_results/
The Trailing Slash in rsync
In rsync, a trailing slash on the source folder (./data/) means "copy the contents of this folder". Omitting the trailing slash (./data) means "copy the folder itself into the destination".
4. Persistent Sessions with tmux¶
If your connection drops, an SSH session will terminate and kill any foreground processes. Use tmux to keep your environment running on the server indefinitely:
# 1. Start a new named tmux session on the remote server
tmux new -s electrochem
# 2. Run your simulation inside tmux
python run_heavy_simulation.py
# 3. Detach from tmux and safely disconnect your SSH connection:
# Press Ctrl+B, release, then press D
When you log back into the server tomorrow from anywhere:
Your session, terminals, and outputs will be right where you left them!