Instructions, tutorials, FAQs and settings files for Linux

Last updated 2020-10-06 by Adam Lu

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Where do I start?

• Connect to the server via these instructions (also contains instructions on opening applications such as MATLAB, ImageJ, RStudio, Jupyter Notebook or Spyder).
• Go through the first two of these Tutorials to learn how to use the command line and the vim or the nano editor.
• Check out other common built-in commands in the file Common Unix Commands (use CTRL + F to search for a keyword).
• Check out the custom aliases and the custom commands and scripts that already available.
• To add an alias: See these instructions
• To change file permissions: See these instructions
• To write commands (functions): Edit from the template provided at the end of the file adams_commands.sh, using Shell Script Syntax Notes as a reference.
• To write scripts: Use the custom script create_new_script.sh to create a new script from the Shell Script Template, using Shell Script Syntax Notes as a reference.
• To run code on Rivanna: Go through the resources in /media/adamX/Rivanna on fishfish. Then create your own SLURM script from the SLURM Script Template, using SLURM Script Syntax Notes as a reference.
• To add a new user to the server: See these instructions.
• If the server IP is changed: Apply these instructions to update the server IP in the cron job bash scripts.

What do I have to do after the server is rebooted?

• (For fishfish only) Please open a terminal on the server via these instructions, then type in the following two commands:

  # Custom script for mounting all drives
  mount_all_disks.sh
    
  # Custom script for setting up inotifywaits
  watch_all_readmes.sh
  

Useful links

• See instructions here for how to access these links on the server.
• Tutorials
• Frequently Asked Questions
• Troubleshooting

Useful notes and templates

• Common Unix Commands: Contains common Unix commands used in the command line
• Linux notes: Contains terminology and acronyms for the Linux system
• Shell Script Syntax: Contains syntax, usage and common variables for shell scripting
• SLURM Script Syntax: Contains syntax and system variables for SLURM scripting
• Shell Script Template: A template for a shell script (see create_new_script.sh for how to use this on the servers)
• SLURM Script Template: A template for a SLURM script
• Note: I’ve created aliases that everyone can use on the command line to quickly access or edit the above files:
  • To access the files with less: less_commands, less_Linux_notes, less_sh_syntax, less_SLURM_syntax
  • To edit the files with vim: vi_commands, vi_Linux_notes, vi_sh_syntax, vi_SLURM_syntax
• A helpful vi/vim cheat sheet:
• Upgrade/Installation notes

Custom Bash Scripts

• Active scripts available for all
• Scripts still under development
• Older versions of scripts

User accounts

• User accounts on fishfish
• User accounts on chalkboard

Firewalls

• Allowed IPs on fishfish
• Allowed IPs on chalkboard

States and Settings

• backup_states: Outputs and Errors of cron jobs
• backup_settings: Backed up copies of /etc and /proc files on the servers
  • backup_settings/backup_var_spool_cron_fishfish: Backed up user-defined cron jobs on fishfish
  • backup_settings/backup_var_spool_cron_chalkboard: Backed up user-defined cron jobs on chalkboard

Sample folders

• sample_desktopfiles: Useful .desktop files. These are copied to /usr/share/applications.
• sample_icons: Icons used in the .desktop files. These are copied to /usr/share/icons.
• sample_dotfiles: Stored versions of user configuration files such as ~/.bashrc, ~/.bash_aliases, ~/.vimrc, ~/.profile etc.

How can I update these files on the server?

• Method 1: Update them directly from the locations:

  • /media/adamX/Settings_Linux or ~/Settings_Linux (fishfish)
  • /home/adam/Settings_Linux (chalkboard)

• Method 2: Edit them here on GitHub then apply the following commands on the server:

cd ~/Settings_Linux
git_update
bash scripts/setup_binfiles.sh