New Member Onboarding

Welcome to ABI! This guide walks you through everything you need to do to get started as a new member.

ABI's servers are accessed exclusively via SSH (Secure Shell). You need an SSH key pair.

Check if you already have one:

ls ~/.ssh/id_ed25519.pub
# or
ls ~/.ssh/id_rsa.pub

If either file exists, you can send the .pub file (the public key) to IT. Never share your private key.

If you do not have one, generate a new key:

ssh-keygen -t ed25519 -C "your_email@abi.am"

• Press Enter to accept the default file location.
• Enter a passphrase when prompted (recommended for security).

This creates two files:

• ~/.ssh/id_ed25519 – your private key (keep this secret)
• ~/.ssh/id_ed25519.pub – your public key (send this to IT)

If you are on Windows, we recommend using one of:

• MobaXterm – includes a built-in SSH client and terminal (download)
• Windows Terminal + OpenSSH – built into Windows 10/11
• PuTTY – classic SSH client (download)

To generate keys on Windows with MobaXterm, use the built-in terminal which supports the same ssh-keygen command.

To get access to ABI's computing resources, you need an account managed through our LDAP directory.

How to request:

1. Contact it-support@abi.am with the following information:
   • Your full name
   • Your email address (preferably @abi.am)
   • Your SSH public key (from Step 1)
   • The project you are joining (e.g., cfDNA, microbiome, vine)

NOTICE: IT also has a self-service portal, which will be available in the future.

The IT team will create your account and notify you when it is ready. You will receive:

• A username
• Confirmation that your SSH key has been added

Once your account is confirmed, connect to the ABI server:

ssh your_username@ssh.abi.am

On your first login, you may be asked to verify the server fingerprint. Type yes to continue.

You should see a command prompt like:

your_username@ssh-01.abi.am:~$

To simplify future connections, add this to ~/.ssh/config:

Host abi
    HostName ssh.abi.am
    User your_username
    IdentityFile ~/.ssh/id_ed25519

Then you can connect simply with:

ssh abi

Once logged in, familiarize yourself with the environment.

# See which groups you belong to
groups
 
# See available disk space
df -h /mnt/home/your_username

See the Software section for available tools, or install your own with Conda.

NOTICE: most software should be available on the server. If you end up using Conda, make sure you don't load it in your startup script to avoid long login times.

ABI uses Slurm to schedule compute jobs. Here is a minimal example:

Create a file called hello.sh:

#!/bin/bash
#SBATCH --mem=1gb
#SBATCH --cpus-per-task=1
#SBATCH --output=hello_%j.log
 
echo "Hello from $(hostname) at $(date)"
echo "My username is $(whoami)"
sleep 10
echo "Done!"

Submit it:

sbatch hello.sh

Check the status:

squeue --me

View the output after completion:

cat hello_*.log

For a comprehensive Slurm guide, see Using Slurm.

• Cluster Basics – Deeper understanding of partitions, storage, and resource limits.
• Slurm Guide – Full job submission reference.
• Conda Guide – Install and manage your own software.
• Pipelines – Run bioinformatics workflows.
• Databases & Reference Data – Find reference genomes and shared datasets.

• Contact IT at it-support@abi.am
• See the Support page for more options.