====== New Member Onboarding ======

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

===== Overview =====

^ Step ^ What ^ Time ^
| 1 | Set up SSH | 10 minutes |
| 2 | Request an account | 10 minutes with 1 business day response time |
| 3 | Connect via SSH | 5 minutes |
| 4 | Explore the cluster | 15 minutes |
| 5 | Run your first job | 10 minutes |

----

===== Step 1: Set Up SSH =====

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

=== If you already have an SSH key ===

Check if you already have one:

<code bash>
ls ~/.ssh/id_ed25519.pub
# or
ls ~/.ssh/id_rsa.pub
</code>

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

=== Generate a new SSH key ===

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

<code bash>
ssh-keygen -t ed25519 -C "your_email@abi.am"
</code>

  * 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)

=== Windows users ===

If you are on Windows, we recommend using one of:
  * **MobaXterm** -- includes a built-in SSH client and terminal ([[https://mobaxterm.mobatek.net/|download]])
  * **Windows Terminal + OpenSSH** -- built into Windows 10/11
  * **PuTTY** -- classic SSH client ([[https://www.putty.org/|download]])

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

----

===== Step 2: Request an Account =====

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

**How to request:**

  - Contact **[[mailto:it-support@abi.am|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

----

===== Step 3: Connect via SSH =====

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

<code bash>
ssh your_username@ssh.abi.am
</code>

=== First login ===

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

You should see a command prompt like:

<code>
your_username@ssh-01.abi.am:~$
</code>

=== SSH config (optional but recommended) ===

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

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

Then you can connect simply with:

<code bash>
ssh abi
</code>

----

===== Step 4: Explore the Cluster =====

Once logged in, familiarize yourself with the environment.

=== Important directories ===

^ Path ^ Purpose ^
| ''/mnt/home/your_username'' | Your home directory |
| ''/mnt/nas0/user/your_username'' | Your personal storage directory |
| ''/mnt/nas<X>/proj/'' | Project directories (shared per project) |
| ''/mnt/nas1/db/'' | Shared databases and reference genomes |

=== Check your groups and projects ===

<code bash>
# See which groups you belong to
groups

# See available disk space
df -h /mnt/home/your_username
</code>

=== Software ===

See the [[software:start|Software]] section for available tools, or [[software:conda|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.

----

===== Step 5: Run Your First Job =====

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

Create a file called ''hello.sh'':

<code bash>
#!/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!"
</code>

Submit it:

<code bash>
sbatch hello.sh
</code>

Check the status:

<code bash>
squeue --me
</code>

View the output after completion:

<code bash>
cat hello_*.log
</code>

For a comprehensive Slurm guide, see **[[software:slurm|Using Slurm]]**.

----

===== Next Steps =====

  * **[[getting_started:cluster_basics|Cluster Basics]]** -- Deeper understanding of partitions, storage, and resource limits.
  * **[[software:slurm|Slurm Guide]]** -- Full job submission reference.
  * **[[software:conda|Conda Guide]]** -- Install and manage your own software.
  * **[[pipelines:start|Pipelines]]** -- Run bioinformatics workflows.
  * **[[databases:start|Databases & Reference Data]]** -- Find reference genomes and shared datasets.

===== Need Help? =====

  * Contact IT at **[[mailto:it-support@abi.am|it-support@abi.am]]**
  * See the [[support:|Support]] page for more options.