# Prepare Ubuntu 24.04 for Spatial Ecology courses


In order to execute the Spatial Ecology exercise we will need first install the Ubuntu 24.04 Linux Virtual Machine and then populate with additional software and data.

[Ubuntu 24.04 Noble Numbat](https://www.osboxes.org/ubuntu/#ubuntu-24-04-vbox) is a Linux Virtual Machine, that allows you to try a wide variety of open source geospatial software previous installation anything. It is composed entirely of free software, allowing it to be freely distributed, duplicated and passed around.

You can follow the below instructions. Moreover the [Ubuntu 24.04 LTS installation YouTube video](https://youtu.be/wnRkkpaxqBU) even if use another VM image can be used to guide along the full procedure. Pay attention that the video is base on the Osgeolive 13 version, so some differences can be present comparing with the current Ubuntu 24.04 version.


## Software requirements

For running a Virtual Machine in your OS we need a virtualization software such as [Virtualbox](https://www.virtualbox.org/) and a vmdk or vdi  file that contains the virtualized OS.

## Hardware requirements
### Hard disk

Be sure to have at least 60 GIGA of free space in your hard disk before to start the VM installation procedure. Avoid the use of USB-external-hard-disk, due that the USB connection will slow down the VM performance.  

### RAM

Be sure that your computer have at lest 16 GIGA ram (more better). Indeed with the VM running and the zoom session open for following the lecture the 16 GIGA will be barely on the limit.  

## Install Virtualbox

Open you browser and go to [https://www.virtualbox.org/wiki/Downloads](https://www.virtualbox.org/wiki/Downloads) and base on your OS download the Virtualbox executable and install it. Be sure you also install the VirtualBox 7.2.0 Extension Pack.

![title](dropbox_download.png)

## Install Ubuntu 24.04 LTS Noble Numbat
### Download Ubuntu 24.04

Open you browser and go to [https://www.osboxes.org](https://www.osboxes.org/ubuntu/#ubuntu-24-04-vbox) and proceed to  download the Ubuntu 24.04 Noble Numbat for VirtualBox. This action will download the 64bit.7z file. The 64bit.7z is a quite large file therefore according to your Internet connection it can take several hours. When the download is finished unzipped using [7zip](https://www.7-zip.org). Mac users can use [The Unarchiver](https://apps.apple.com/in/app/the-unarchiver/id425424353?mt=12) for unzip the 64bit.7z. A this point you are ready to load the Ubuntu 24.04 (64bit).vdi inside Virtualbox.


### Install Ubuntu 24.04 inside Virtualbox

Lunch Virtualbox from OS and follow the below instructions. 

![title](Installation_vm_Ubuntu22.04_p0.png)
![title](Installation_vm_Ubuntu22.04_p1.png)
![title](Installation_vm_Ubuntu22.04_p2.png)
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![title](Installation_vm_Ubuntu22.04_p5.png)
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![title](Installation_vm_Ubuntu22.04_p7.png)
![title](Installation_vm_Ubuntu22.04_p8.png)
![title](Installation_vm_Ubuntu22.04_p9.png)
![title](Installation_vm_Ubuntu22.04_p10.png)
![title](Installation_vm_Ubuntu22.04_p11.png)


### Test your Ubuntu 24.04 LTS Virtual Machine

If you follow all the steps correctly the Ubuntu 24.04 LTS Virtual Machine  should pop-up in the Virtual Box window showing something like this:

![title](Installation_vm_Ubuntu22.04_p12.png)
![title](Installation_vm_Ubuntu22.04_p14.png)
![title](Installation_vm_Ubuntu22.04_p15.png)

If the Ubuntu 24.04 LTS start with a black screen with a "kernel panic message" means that there are still some settings that are not allowing the virtualization. 
This [page](https://techcult.com/enable-virtualization-windows-10/) is a good tutorial for solving the issues in Windows-10 and [this one](https://www.windowscentral.com/software-apps/windows-11/how-to-enable-virtualization-on-windows-11) for Windows-11. 

### Setting you keyboard layout

If are not use the US keyboard you have to add your keyboard layout to the bottom menubar. Therefore click on the spiral on the left bottom corner and write "keyboard" in the search box, and select in settings Keyboard.

![title](keyboard_setting1_ubuntu24.04_1.png)

Then select "Add Input Source" > "Add" and select your keyboard layout in accordance to your country and language.

![title](keyboard_setting1_ubuntu24.04_2.png)

Your keyboard layout will appear as below. Move up to select it as default keyboard layout.

![title](keyboard_setting1_ubuntu24.04_3.png)
![title](keyboard_setting1_ubuntu24.04_4.png)
![title](keyboard_setting1_ubuntu24.04_5.png)

Open the terminal and test if the keyboard layout is correct. 

![title](terminal_ubuntu.png)

### Update the OS

The first operation after the installation is to run un update of the OS. Therefore, open the bash terminal and run line by line the following codes. The sudo password is **"osboxes.org"**. For security what you type is not shown, anyway it is recorded. After typed the password press enter.

Update the OS. This operation can last few minutes. Be patient. If during the installation, some screen pop-up asking some question just accept the default option. 

    sudo apt update      # update the repositories
    sudo apt upgrade -y  # installation of the sw
    sudo apt autoremove -y




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## Troubleshooting screen size/resolution and shared folder of your Ubuntu 24.04 LTS Virtual Machine

Guest Additions in VirtualBox enable better performance and functionality in virtual machines, including shared clipboard/drag and drop, shared folders, improved graphics support, and seamless app windows. **Thus, it is very important that you install it correctly.** 

If the screen is very small try to enlarge clicking ""View -> Auto-resize Guest Display", and if the enlargement is not working properly try to reboot.
 
If you still have issues after the reboot, there are mainly two options:  

1) Install the Virtual Box guest edition
2) Use "arandr" for setting a customized resolution

### Install the Virtual Box guest edition with the GUI

Sometime the Virtual Box guest edition is not installed correctly so you have to follow the procedure described below. 

From the Virtualbox menu press Device > Insert Guest Addition CD image

If during the installation some screen pop-up asking some question just accept the default option. Rather if nothing is appending try to install " Virtual Box guest edition with the CL" (see below). 

The download procedure will start and a screen will pop up:

pres "cancel".

![title](GuestAddition2.png)

Open the terminal and type:

    cd /media/user/VBox_GAs_*
    sudo ./VBoxLinuxAdditions.run

At this point you can reboot your machine. Now all screen setting, screen scale (View -> Auto-resize Guest Display) and drag/drop should work properly.


### Install the Virtual Box guest edition with the CL 

If for some reason you were not able to install "Virtual Box guest edition with the GUI" you can try with the "Virtual Box guest edition with the CL". 


    sudo apt-get install virtualbox-guest-additions-iso
    sudo mkdir -p /media/user/VBox_GAs 
    sudo mount -o loop /usr/share/virtualbox/VBoxGuestAdditions.iso /media/user/VBox_GAs
    cd /media/user/VBox_GAs
    sudo bash ./VBoxLinuxAdditions.run

At this point you can reboot.

Guest Additions in VirtualBox enable better performance and functionality in virtual machines, including shared clipboard/drag and drop, shared folders, improved graphics support, and seamless app windows. **Thus, it is very important that you install it correctly.** 

Use *lsmod* from the command line, as it will tell you not only if it's installed, but properly loaded:

    lsmod | grep vboxguest 

vboxguest    57344  6 vboxsf   # the number can be different

### Use "arandr" for setting a customized resolution (probably not needed)

For some OS the "Auto-resize Guest Display" is not working properly. Therefore is possible to select a customized resolution by installing *arandr*. Anyway follow this route only if "Virtual Box guest edition" did not solve the problem. 

Open the terminal and type:

    sudo apt install arandr

then run arandr in the terminal 

    arandr

and following the below figure, select the best resolution that suitable for your screen. Select in such a way that you have the full screen cover without sliding lateral bars or white areas.

![title](screenresolution1.png)

You can also save the screen settings by "Layout -> Save as" ->  leaving a default directory (~/.screenlayout/) 

![title](screenresolution2.png)

Now the script screen_vm.sh need to be run every time that you boot the machine. The easy way is to add to the ~/.bashrc. **But you will need to open the terminal to allow the enlargement**  

    echo "bash ~/.screenlayout/screen_vm.sh"  >> ~/.bashrc

--->

## Test your shared folder

Another test that you should do, is to see if the shared folder is correctly done. Open a bash terminal and run 

    ls /media/sf_LVM_shared
   
If are able to list the folder then means that the sharing folder operation is properly done. Moreover try to insert a file from your host OS in the LVM_shared folder and see if visible in the Ubuntu 24.04 LTS. 

If you get an error "ls: cannot access '/media/sf_LVM_shared': No such file or directory" means that you did not correctly done the sharing folder operation or the Virtual Box Guest Additions installation, thus try to redo it.


If you get permission denied in accessing '/media/sf_LVM_shared' run this commands

    sudo usermod -a -G vboxsf osboxes
    sudo chown -R osboxes:osboxes /media/sf_LVM_shared

**You will need to reboot to make the folder accessible.**

## Populate Ubuntu 24.04 LTS with additional software
### Install geo-software
At this point the Ubuntu 24.04 LTS Virtual Machine is ready to install additional software and data for running Spatial Ecology courses. In the bash terminal run the following lines 

    cd /tmp/
    wget https://raw.githubusercontent.com/selvaje/SE_data/refs/heads/master/exercise/install_additional_sw_data_4SE_courses.sh 
    sudo bash ./install_additional_sw_data_4SE_courses.sh

as before the sudo password is **osboxes.org**.

**If a prompt asks for user input, just use the arrow keys to select the default option and press Enter.**


### Test installed additional software

In the bash terminal run the following lines one by one. Close the window that each time pop-up.

Test [gdal](https://gdal.org/en/stable/#)

    gdal_translate --version 

You should see the gdal version GDAL 3.8.4, released 2024/02/08

Test [pktools](http://pktools.nongnu.org/html/index.html)

    pkfilter --help
 
You should see the pkfilter manual instructions.
 
Test [OpenEV](http://openev.sourceforge.net)
 
    source ~/.bashrc
    openev

You should see the openev software popup. 

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Test  [R studio](https://rstudio.com)

    rstudio

You should see the rstudio software pop-up

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## Git Settings 

The below instructions together with the [Git Setting for the Spatial Ecology courses YouTube video](https://www.youtube.com/watch?v=QzMNHEStG0U&t=6s) can guide along the full procedure to retrieve dataset and material for the courses.   


We are going to retrieve dataset and material for the first time using *git clone*.

    
    cd                                 # enter in user home
    git clone https://github.com/selvaje/SE_data  # download the data 

If the download succeed you should see the *SE_data* folder 

    ls -l $HOME/SE_data 

Now we need copy the $HOME/SE_data to an independent directory the:  
*/media/sf\_\LVM\_shared/my\_SE\_data*

    rsync -hvrPt --ignore-existing ~/SE_data/* /media/sf_LVM_shared/my_SE_data
    cd /media/sf_LVM_shared/my_SE_data

The */media/sf_LVM_shared/my_SE_data* is your working directory. Do not touch the *~/SE_data* folder!! 

---

Every time that we need to download more data from the git repository, follow this procedure 


    cd $HOME/SE_data
    git pull
    rsync -hvrPt --ignore-existing $HOME/SE_data/* /media/sf_LVM_shared/my_SE_data
    cd /media/sf_LVM_shared/my_SE_data

Now you should be ready to follow the lectures of the Spatial Ecology courses.  
Remember always to work on */media/sf\_LVM\_shared/my\_SE\_data*

---

If for any reason the *git pull* commands give a synchronized error you need to remove the *$HOME/SE_data* and repeat the *git clone* and *rsync* operation.

    cd
    rm -ry $HOME/SE_data
    git clone https://github.com/selvaje/SE_data
    rsync -hvrPt --ignore-existing $HOME/SE_data/* /media/sf_LVM_shared/my_SE_data
    cd /media/sf_LVM_shared/my_SE_data


## Install jupyter lab

We are going to use jupyter lab as main scripting editor. Here how to install 

    sudo apt install pipx
    pipx ensurepath
    pipx install jupyterlab
    echo 'export PATH=$PATH:$HOME/.local/bin' >> ~/.bashrc
    source ~/.bashrc

Test jupyter lab

    jupyter-lab /media/sf_LVM_shared/my_SE_data/exercise/grass_hydro.ipynb

Get familiar with the jupyter lab GUI.

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## Settings for running jupyterlab

The below instructions are needed to create a python virtual environment (in this case juplab_env) that need to be activate via "source ~/juplab__env/bin/activate" everytime that you wanna use jupyterlab 

    sudo apt install python3.8-venv
    python3 -m venv juplab_env
    ## allow to use system python packages
    sed 's/false/true/g' ~/juplab_env/pyvenv.cfg > ~/juplab_env/pyvenv_tmp.cfg ;
    mv ~/juplab_env/pyvenv_tmp.cfg ~/juplab_env/pyvenv.cfg
    
    source ~/juplab_env/bin/activate    ### run this line everytime wanna use jupyterlab
    pip install -U pip
    pip3 install jupyterlab

--->