hartman-server/README.md

Hartman Lab Server Manual

First-time login

1. Obtain your username and temporary password from an admin.

2. Change your temporary password.

   • Login via ssh: ssh username@hartmanlab.genetics.uab.edu
   • Set a new password when prompted — you will be logged out automatically.

3. Change your temporary samba password.

   • Login via ssh: ssh username@hartmanlab.genetics.uab.edu
   • Change your samba password (default: same temporary password): smbpasswd

4. Optional: Set up key-based authentication for faster, more secure logins:

   ssh-keygen -t rsa -b 4096 -f ~/.ssh/id_rsa_4096
   ssh-copy-id -i ~/.ssh/id_rsa_4096.pub username@hartmanlab.genetics.uab.edu
   

5. Read the ssh login message for server status updates. See Troubleshooting and GitHub Resources for help.

x2goclient remote desktop

Connect to a persistent remote desktop using x2goclient (Linux/Windows/OSX).

Sessions can be paused or suspended from the client window. Create multiple sessions with different quality settings for different network conditions.

x2goclient configuration

• Session tab

  • Session name: Hartman Lab Server
  • Host: hartmanlab.genetics.uab.edu
  • Login: username
  • SSH port: 22
  • Session type: MATE (provides the best experience with X2Go)

• Connection tab

  • Set connection speed to LAN (on-campus) or WAN (off-campus); leave compression as adaptive.

• Input/output tab

  • If automatic resizing fails (common on HiDPI), set a manual startup resolution. For scaling issues, try DPI 96.
  • For keyboard mapping issues (e.g., broken arrow keys), select Configure Keyboard and keep the defaults.

• Media tab

  • Disable sound support to prevent pulseaudio log spam.

• Shared folders tab

  • Browse to a folder, add it to the share, and select automount. Shared folders appear at /media/disk/<share_name>.

ssh remote login

• Linux/OSX: ssh username@hartmanlab.genetics.uab.edu
• Windows: PuTTY
• Android: JuiceSSH or Termux

ssh X forwarding

Run graphical programs on the server with local display output.

• Linux/OSX: ssh -X username@hartmanlab.genetics.uab.edu
• Windows: Install Xming and enable X11 forwarding in PuTTY options.

sftp remote filesharing

• File manager (Caja): enter sftp://username@hartmanlab.genetics.uab.edu/home/username in the URL bar

  

• Filezilla (Linux/OSX/Windows)

  

• sshfs (Linux/OSX/Windows)

• WinSCP (Windows)

samba remote filesharing

The server provides two samba shares (credentials: server username/password):

1. Shared data array (/mnt/data): \\username\\data
2. User home directory (/home/username): \\username\\username

Note: Samba shares are only available on-campus. For off-campus access, use SSH tunneling: ssh -L 1445:localhost:445 user@remote-server

Robot computer remote desktop

• In X2Go, open Applications > Internet > Remote Viewer, enter vnc://robot:5900 in Connection Address, and click Connect.

  

Robot computer remote filesharing

• In X2Go, open Applications > System Tools > Caja, enter ftp://robot in the Location bar. Open a second Caja window to drag and drop projects to /mnt/data.

  

Robot webcam

• In an X2Go session, via a web browser at http://localhost:9999
• Locally via a web browser via an SSH tunnel: ssh -f username@hartmanlab.genetics.uab.edu -L 9999:localhost:9999 -N

RStudio Server

• In an X2Go session, via a web browser at http://localhost:8787
• Locally via a web browser via an SSH tunnel: ssh -f username@hartmanlab.genetics.uab.edu -L 8787:localhost:8787 -N

Other available software

• VSCode
• MATLAB
• Jupyter Notebook
• qhtcp-workflow
• podman for containers
• toolbox for custom software
• distrobox for custom environments
• ...and much more (see dnf list --installed for installed packages). Open an issue for missing or out-of-date software.

Backing up data

/mnt/data is snapshotted daily to /mnt/backup/data-backup and rolling backups are retained for six months.

rsync is recommended for periodically backing up user files to a local client.

• Copy a user's $HOME directory locally to /home-backup from a client: rsync -azH --delete username@hartmanlab.genetics.uab.edu:/home/username/ home-backup/
• Copy a shared directory locally to the current directory from a client: rsync -azh username@hartmanlab.genetics.uab.edu:/mnt/data/scans/20250723_roessler_project .

Backups can also be run from the server using pre-installed tools (rsnapshot, borgbackup, ...).

Troubleshooting

Read the ssh login message (cat /etc/motd) for server status and updates. Open an issue if there is one.

• Can't login via ssh
  • Verify your username and that caps lock is off.
  • Three consecutive failed logins from off-campus will ban the IP for one hour.
  • Have an admin run: sudo script-user-unban <ip_address>
  • Have an admin run: sudo script-user-reset-password <username>
• Can't login via X2Go
  • Login via ssh and reset corrupt X2Go sessions: script-user-reset-x2go
• X2Go desktop is corrupted (desktop not similar to screenshot)
  • Login via ssh and reset your desktop: script-user-reset-desktop
• File permissions issues
  • Check permissions with ls -al or your file manager.
  • /mnt/data uses shared group permissions, usually:
    • Group: smbgrp
    • User: username that created/owns the file (or smbgrp)
    • Permissions: 2775
  • To change: chown -R username:smbgrp <dir> && chmod 2775 <dir>
  • If you lack the necessary privileges, ask an admin to fix permissions or make a copy.
• Program runs slowly in paused X2Go session
  • Run program via ssh in a tmux or screen session instead.

GitHub Resources

• Issues
• Wiki
• Chat

External Resources

• RHEL documentation
• Navigating the Linux CLI
• Explainshell
• UAB Cheaha

Platform

• AlmaLinux 9.6 w/ Linux 6.1 LTS Hyperscale SIG kernel
• Intel Xeon X99 E5-2650v4 12-core CPU
• 96GB DDR4 RAM
• 4TB PCIe 3.0 NVMe SSD: /, /home
• 20TB btrfs raid1 array: /mnt/data
• 20TB btrfs raid1 backup array: /mnt/backup

Administrators

For additional documentation see docs/README.md.