Getting Started on the SAIAB HPC Server
SOP ID: HPC-GS-001 Version: 1.0 Date: 2026-02-23 Author: AGRP
Overview
This guide will help you log in to the SAIAB HPC server (lab417.saiab.ac.za) for the first time and run your first SLURM jobs. No prior HPC experience is needed.
Recommended Training
Before diving in, we strongly recommend working through the full course:
Introduction to the Unix Shell and High Performance Computing
It covers everything from basic shell commands to SLURM job scheduling on this very server — and will make everything below much easier.
1. Logging In
You connect to the server using SSH from a terminal.
Mac / Linux
Open the Terminal app and run:
Windows
Use MobaXterm or PuTTY. Set the hostname to lab417.saiab.ac.za and your username.
First Login — Change Your Password
On your very first login you will be prompted to change your temporary password:
Changing password for your_username.
Current password: (enter the temporary password sent to you)
New password: (choose a strong password)
Retype new password:
Choose a password that is at least 8 characters and includes uppercase, lowercase, numbers, and a special character.
2. Understanding the Server Layout
The server has two types of nodes:
| Node | Purpose |
|---|---|
Login node (lab417) |
Where you land after SSH. Use for file management, editing scripts, and submitting jobs. Do not run heavy computations here. |
| Compute nodes | Where your actual analyses run, via SLURM. |
3. Useful Shortcuts
Your account comes pre-configured with the following shortcuts:
| Alias | What it does |
|---|---|
sq |
Show the current SLURM job queue |
si |
Show available compute node resources |
slogin |
Start an interactive session on a compute node |
ll |
List files in detail (ls -la) |
4. Running Jobs with SLURM
SLURM is the job scheduler — it manages who gets to use the compute nodes and when.
Interactive Session
Use slogin when you want to run commands interactively on a compute node (e.g., for testing):
Your prompt will change to show the SLURM job ID, confirming you are now on a compute node:
Type exit to leave the interactive session and return to the login node.
Batch Job
For longer analyses, write a SLURM script and submit it so it runs in the background:
Example script (my_job.sh):
#!/bin/bash
#SBATCH --job-name=my_analysis
#SBATCH --partition=agrp
#SBATCH --cpus-per-task=4
#SBATCH --mem=8G
#SBATCH --time=02:00:00
#SBATCH --output=logs/my_job_%j.out
echo "Job started on: $(date)"
# Your commands go here
# e.g. python my_script.py
echo "Job finished on: $(date)"
Submit the job:
Check its status:
Cancel a job (if needed):
5. Transferring Files
Copy a file from your computer to the server
Copy a file from the server to your computer
6. Next Steps
Once you are comfortable with the basics:
- Conda Environments — Set up and manage software environments
- SLURM Basics (advanced) — More detailed SLURM options and best practices
- Storage Management — Understand disk quotas and where to store data
Need Help?
Contact the HPC administrator at evilliers@saiab.ac.za