hartman-server/README.md

Hartman Lab Server Manual

First-time login

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

7. 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
   

   Users may need to add their keypair to PuTTy/Filezilla/WinSCP manually.

   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 run 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.

   • Native access to sftp shares using client file manager (sftp://username@hartmanlab.genetics.uab.edu:/home/username):
   • Linux/OSX/Windows
   • Filezilla

   

   • sshfs
   • Windows
   • WinSCP

   samba

   Samba file shares can be mounted cross-platform as if th server data existed locally. The server provides two 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

   Users can access an X2Go remote desktop session using x2goclient from a client. x2goclient is 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.

   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.

   • 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>.
   • Shared folder permissions can be modified by admin for multi-user access.

   Robot computer remote desktop access

   In an X2Go session, go to Applications>Internet>Remote Viewer>Connection>New and enter vnc://192.168.16.101:5900

   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

   JupyterLab (Python) IDE

   • In an X2Go session, via a web browser at http://localhost:8888
   • Locally via a web browser via an SSH tunnel: ssh -f username@hartmanlab.genetics.uab.edu -L 8888:localhost:8888 -N

   Data backup

   rsync is recommended for users that would just like to periodically backup their $HOME directory to a local machine.

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

   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 CPU
   • 96GB RAM
   • 4TB PCIE3 NVMe SSD: /, /home
   • 20TB btrfs raid1 array: /mnt/data
   • 20TB btrfs raid1 backup array: /mnt/backup

   Administrators

   See additional documentation in docs/README.md