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Install updates/upgrades

sudo apt update
sudo apt upgrade
sudo apt autoremove

Upgrade release

sudo do-release-upgrade

Wireless network (Eduroam)

./eduroam-linux-UoG.py
  • Now edit the wife connection settings, e.g. by running the following and selecting the wireless connection:
nm-connection-editor

The below shows the correct settings: Eduroam setting

Note how the username is set and how the certificate is selected.

Wired internet connection

Install "Carbon Black"

  • Extract the archive e.g. the tar file cb-psc-sensor-ubuntu-2.14.0.1321525 or an equivalent provided by ISS.
  • Right click the install.sh file, Properties, Permissions, tick Allow Execution as Program
  • Run the installation using
sudo ./install.sh

Edit wired connection settings

  • Now edit the wired connection settings, e.g. by running the following and selecting the wired connection:
nm-connection-editor
  • Go to the IPv4 Settings, and set the DHCP Client id to CARBON.

The below shows the correct settings:

Wired connection settings

Check of "Additional drivers" e.g. for NVIDIA

Some devices, e.g. the NVIDIA graphics card, might require a proprietary driver, or an alternative driver. The below images shows how one can pick one.

Note some graphics drivers may not be compatible with all software (e.g. MATLAB).

Install usefull packages

  • git (and a GUI called git Cola if you like)
  • GIMP
  • Inkscape
  • Ghostwriter
  • Xournal++
  • Meld
  • Telegram
  • Slack
  • MS Teams
  • VLC media player
  • Catfish File Search
  • PDF Chain
  • FreeCAD
  • Meshlab
  • view3Dscene
  • blender
  • Shotcut
  • Peek

Configure Git + GitHub SSH

ssh-keygen -t ed25519 -C "[email protected]"

and press Enter to accept the default file location (or alter the file location if desired). Next type a secure passphrase.

  • To add your SSH key to the ssh-agent, first start the ssh-agent in the background using
eval "$(ssh-agent -s)"

Next add the ssh key using:

ssh-add ~/.ssh/id_ed25519
  • Follow these instructions to add an SSH key to your GitHub account.
  • Use these instructions to connect to GitHub with SSH.
  • You may need to use the following to avoid what might be firewall issues, (see also this link), i.e. open a terminal and make the following ssh configuration steps:
sudo nano ~/.ssh/config

Next add the following lines:

Host github.com
 Hostname ssh.github.com
 Port 443

Download + install packages

VS code

Add Julia

  • Download: https://julialang.org/downloads/, e.g. the latest 64-bit glibc version

  • Extract.

  • Then browse into the extracted folder to find the folder containing the content like the bin folder etc. Copy/cut all content and move to a local folder where you want julia to exist e.g. /home/kevin/julia/. It is recommended to not have the version tag in this folder name, since using just julia rather than julia-1.8.5 means the symbolic links can stay constant when you upgrade julia in the future.

  • Setup julia symbolic links

sudo ln -s /home/kevin/julia/bin/julia /usr/bin/julia
  • Add the julia path to PATH
export PATH="$PATH:/home/kevin/julia/bin"

Julia packages to add:

  • IJulia for jupyter notebook functionality
]add IJulia
  • Gridap for julia based finite element analysis
]add Gridap
  • Makie for advanced visualisation
]add GLMakie

Git

  • Install
sudo apt install git
  • Configure git with the correct user name and user email (see also this link)
    • Set user name:
git config --global user.name "Kevin-Mattheus-Moerman"

* Set user email: 

git config --global user.email [email protected]

Install Conda

  • Download the installation .sh file here.
  • Right click, Properties, Permissions, tick Allow Execution as Program
  • Open a terminal in that folder run equivalent of:
./Anaconda3-2023.03-Linux-x86_64.sh

Conda packages to add:

  • Jupyter notebooks
conda install jupyter
  • The RISE Jupyter notebook add on, allowing Jupyter based presentations.
conda install -c conda-forge rise

conda config --add channels conda-forge
conda install octave_kernel
conda install texinfo # For the inline documentation (shift-tab) to appear

GNU Octave

Octave, an open source AMTLAB alternative (which is easier to set-up for Jupyter notebooks) can be installed as below or via snap or via conda.

sudo apt install octave

Conda might provide the latest version whereas the above might install a rather old version.

Tex / LATeX (SLOW/LONG!)

sudo apt install texlive-full

TexMaker

sudo apt install texmaker

Grsync

grsync is a GUI for the rsync system for backing up/synchronising between two folders. You can install grsync using:

sudo apt-get -y install grsync

Zotero

Download and setup automated updating, see also instructions on this GitHub page:

wget -qO- https://raw.githubusercontent.com/retorquere/zotero-deb/master/install.sh | sudo bash
sudo apt update
sudo apt install zotero

After installation opening Zotero will help you to install the LibreOffice plug-in, as well as the browset (e.g. Firefox) extension.

Get LibreOffice plugins

MATLAB

  • Download installer
  • Right click, Properties, Permissions, tick Allow Execution as Program
  • Extract
  • Browse to folder containing install, open a terminal and run:
./install

Do not run the install as administrator. You can create symbolic links later *

-Djogl.disable.openglarbcontext=1
  • Create the symbolic links
sudo ln -s /home/kevin/matlab/bin/matlab /usr/bin/matlab

Export path

export PATH="$PATH:/home/kevin/matlab/bin"
  • Install the MATLAB support package
sudo apt install matlab-support

cd /home/kevin/matlab/sys/os/glnxa64/
$ sudo mv libstdc++.so.6 libstdc++.so.6.bak

Jekyll (GitHub based website making)

https://jekyllrb.com/docs/installation/ubuntu/

sudo apt-get install ruby-full build-essential zlib1g-dev

echo '# Install Ruby Gems to ~/gems' >> ~/.bashrc
echo 'export GEM_HOME="$HOME/gems"' >> ~/.bashrc
echo 'export PATH="$HOME/gems/bin:$PATH"' >> ~/.bashrc
source ~/.bashrc

Add/install Jekyll:

gem install jekyll bundler

You can test the building of a website locally using:

bundle exec jekyll serve

Remove the website / clean up using:

bundle exec jekyll clean

To update ruby gems, go to the website folder where the gemlock file is and use:

bundler update

Ubuntu things

  • Enable add new empty file on right click e.g.
touch ~/Templates/newTextFile.txt

Tweaks

For easy custom appearance/behaviour setting changes

sudo apt install gnome-tweak-tool

Minimize on click

Clicking on icon minimises open window

sudo apt install dconf-editor

dconf-editor

Navigate to /org/gnome/shell/extensions/dash-to-dock.

Scroll down to the "click-action" tab

At the bottom of the click-action panel is an option for ‘default value’. Slide this to the off position. Then click the “custom value” button to access a list of options.

Select 'minimize'

Add "restricted extras"

The restricted extras consists of proprietary fonts and codecs

sudo apt install ubuntu-restricted-extras

Set tray icon click to show preview of application windows for an application

gsettings set org.gnome.shell.extensions.dash-to-dock click-action 'previews'