# 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-remote-login): `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.

    ```bash
    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
    ```

## Notes

* Read the `motd` helper at `ssh` login for server status
* To change your user password: `passwd`
* To change your samba password: `smbpasswd`

## `ssh` remote login

Connect to the server remotely using the command line.

* Linux/OSX
  * `ssh username@hartmanlab.genetics.uab.edu`
* Windows
  * [PuTTY](http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html)
* Android
  * [JuiceSSH](https://juicessh.com/)
  * [Termux](https://termux.dev/)

### X forwarding

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

![x_forwarding](docs/imgs/x_forwarding.png)

* Linux/OSX
  * Enable X forwarding during ssh login: `ssh -X username@hartmanlab.genetics.uab.edu`
* Windows
  * Install [Xming](http://www.straightrunning.com/XmingNotes/) and enable X11 forwarding in the [PuTTY](http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html) options.

## `sftp` remote filesharing

Browse and manage files stored on the server.

* Access sftp via most file managers using a `sftp://` address.

  Example: `sftp://username@hartmanlab.genetics.uab.edu/home/username`

  ![sftp](docs/imgs/sftp.png)
* [Filezilla](https://filezilla-project.org/download.php?type=client) (Linux/OSX/Windows)

  ![Filezilla](docs/imgs/filezilla.png)
* [sshfs](https://www.digitalocean.com/community/tutorials/how-to-use-sshfs-to-mount-remote-file-systems-over-ssh) (Linux/OSX/Windows)
* [WinSCP](https://winscp.net/eng/index.php) (Windows)

## `samba` remote filesharing

Another method to browse and manage files stored on the server.

The server provides two `samba` shares:

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

The default `samba` credentials are the same as your server username and password until changed with `smbpasswd`.

![samba](docs/imgs/samba.png)

## `x2goclient` remote desktop

Launch a graphical remote desktop session using the X2Go `x2goclient` available for Linux/OSX/Windows from the [X2Go website](http://wiki.x2go.org/doku.php) or by installing the `x2goclient` package.

![x2go_desktop](docs/imgs/x2go_desktop.png)

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.

![x2go_server](docs/imgs/x2go_server.png)

* 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>`.
    ![x2go_server](docs/imgs/x2go_automount.png)

**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`](https://en.wikipedia.org/wiki/Tmux) or [`screen`](https://www.gnu.org/software/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`](vnc://192.168.16.101)

![remote_viewer](docs/imgs/remote_viewer.png)

## Webcam robot monitoring

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

![robot_camera](docs/imgs/robot_camera.png)

## RStudio Server

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

![rstudio_server](docs/imgs/rstudio_server.png)
![rstudio_server2](docs/imgs/rstudio_server2.png)

## Other available software

* [VSCode](https://code.visualstudio.com/)
* [MATLAB](https://www.mathworks.com/help/matlab/index.html)
* [Jupyter Notebook](https://jupyter.org/)
* [`qhtcp-workflow`](https://github.com/UAB-Hartman-Lab/qhtcp)
* [`podman`](https://podman.io/) for containers
* [`toolbox`](https://docs.fedoraproject.org/en-US/fedora-silverblue/toolbox/) for custom software
* [`distrobox`](https://github.com/89luca89/distrobox) for custom environments
* ...and much more ([open an issue](https://github.com/UAB-Hartman-Lab/server/issues) for software requests)

## Backing up your data

`/mnt/data` is snapshotted daily to `/mnt/backup/data-backup`. In case of inadvertent data loss, users can recover lost files from a previous snapshot.

[`rsync`](https://linux.die.net/man/1/rsync) is highly 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 .`

Other popular backup tools are also installed on the server, including `rsnapshot` and `borgbackup`.

## Troubleshooting

Read the `motd` for service statuses and updates: `cat /etc/motd`

* Can't login via `ssh`
  * Make sure that you are using the correct username and caps lock is off.
  * Three consecutive failed logins from an off-campus computer will ban the IP for one hour.
  * Request an administrator to run: `sudo script-user-unban <ip_address>` to unban your IP address
  * Request an administrator to run: `sudo script-user-reset-password <username>` to reset your login password
* 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](#x2goclient-remote-desktop))
  * Login via ssh and reset your desktop: `script-user-reset-desktop`
* Permissions issues
  * Use `ls -al` or add permissions columns to your file manager to double-check the file permissions.
  * `/mnt/data` uses shared group permissions, usually:
    * Group: `smbgrp`
    * User: user that created/owns the file or `smbgrp`
    * Permissions: `2775`
  * To change: `chown -R username:smbgrp <dir> && chmod 2775 <dir>`
  * If your user does not have sufficient access to alter file permissions, either have admin fix, or make a new copy.

## Resources

* [RHEL documentation](https://access.redhat.com/documentation/en/red-hat-enterprise-linux/)
* [Navigating the Linux CLI](https://www.digitalocean.com/community/tutorials/basic-linux-navigation-and-file-management)
* [Explainshell](https://explainshell.com/)
* [UAB Cheaha](https://docs.uabgrid.uab.edu/wiki/Cheaha_GettingStarted)

## 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`](docs/README.md).