hartman-server

Hartman Lab Server Manual

First-time login

1. Ensure an admin has enabled your user account and provided you a username.
2. Login via ssh: ssh username@hartmanlab.genetics.uab.edu (default password is your username)
3. You will be prompted to create a new password and then logged out.
4. Login again using your new password: ssh username@hartmanlab.genetics.uab.edu
5. Change the default samba password (default password is also your username): smbpasswd

6. Optional: Generate a public-private keypair on your client and copy it to the server for faster and 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
   

   ssh

   Connect to the server remotely using the command line.

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

   X forwarding

   Launch graphical server programs locally on a client that execute on the server.

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

   sftp

   Browse and manage files stored on the server. Best for Linux.

   • Access the server sftp via most file managers using a sftp:// address.

   

   • Filezilla (Linux/OSX/Windows)
   • sshfs (Linux/OSX/Windows)
   • WinSCP (Windows)

   samba

   Another method to browse and manage files stored on the server. Best for OSX/Windows.

   The server provides two samba shares:

   1. Shared data array (/mnt/data): \\username\\data
   2. User's $HOME directory: \\username\\username

   The default samba credentials are the same as your server username and password. Users can change their samba password using smbpasswd.

   

   x2goclient

   

   Access an X2Go remote desktop session using the X2Go x2goclient available for Linux/OSX/Windows from the X2Go website or by installing the x2goclient package.

   X2Go sessions can be paused or suspended from the X2Go client window. Multiple sessions can be created on the client, making it possible to select alternate quality settings based on location and bandwidth.

   

   • Session tab
   • Session name: Hartman Lab Server
   • Host: hartmanlab.genetics.uab.edu
   • Login: username
   • SSH port: 22
   • Session type: MATE (MATE provides the best experience with X2Go)
   • Connection tab
   • Set the connection speed to LAN when connecting from within the UAB network and WAN when outside of the UAB network
   • Compression settings should be left unchanged or set to adaptive.
   • Input/output tab
   • If automatic window resizing is not working properly (common on HiDPI monitors), set the desired startup window resolution size manually. For full screen sessions, this should match your client display. In case of scaling issues, play with the DPI setting, 96 is a sane starting value.
   • If there are any issues with keyboard mapping (ex. the arrow keys are not working), select Configure Keyboard and leave the default selected settings.
   • Media tab
   • Disable sound support. This will prevent pulseaudio from spamming the server logs.
   • Shared folders tab
   • Select folders on the client to be shared with the server during a session. Browse to the chosen folder, add it to the share, and select automount.
   • These folders will then appear on the server under /media/disk/<share_name>.

   Note: Some programs do not continue to run at full speed when an X2Go session is paused. In these cases, the program should be run via ssh in a tmux or screen session.

   Robot computer remote desktop access (currently unavailable)

   In an X2Go session, go to *Applications>Internet>Remote Viewer>Connection Address and enter vnc://192.168.16.101

   

   Webcam robot monitoring

   • 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 (containers)
   • toolbox for custom software
   • distrobox for custom environments
   • ...and much more (open an issue for software requests)

   Data backups

   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 .

   There are other tools installed for initiating backups from the server, such as rsnapshot and borgbackup.

   Troubleshooting

   • Reset your X2Go sessions: script-user-reset-x2go
   • Reset your X2Go desktop: script-user-reset-desktop
   • Change your user login password: passwd
   • Change your samba password: smbpasswd
   • Read the motd for service statuses and updates: cat /etc/motd

   Resources

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

   Hardware 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

   See additional documentation in docs/README.md.