September 25, 2022

Setting up the Ubuntu 22.04 LTS server, desktop, and RStudio server at home

Why? I want to set up a computer on my home network dedicated to running code. You may want to do this if:

  • You want to run code that takes a long time to complete. Let it run on the server computer so you can use your main computer for other things.
  • Your main computer is low on hard drive space. Upload all the data files to the server and run your analysis on the server.

Who? Programmers comfortable with Linux who need to run code on a separate computer they don't mind reformatting. You don't need to be an expert Linux user. "Comfortable with Linux" can just mean comfortable searching the internet to find out what to type into a terminal. DON'T do this on your main computer. This will completely erase and rewrite the hard drive.

What? Ubuntu server 22.04 LTS with Ubuntu desktop, RStudio server and R 4.3 (or the latest versions)

Cost? All the software is free. For hardware, you need the following:


  • "Main" computer
    • To download files, prepare the USB drives, check that the server works, and search the internet for help
    • I used my regular personal computer
  • Second computer to become the server - this will be erased/overwritten
    • Save anything you want to keep somewhere else, including data and software licenses. Everything will be erased during the setup process.
    • I used an old desktop computer. They sell special server computers (more expensive due to faster processors and better RAM), but I strongly suggest using an old desktop you already have for a first time project. 
  • Empty USB drive
    • This will be erased/overwritten to make bootable USB drives to erase & install things on the server computer
    • Afterward, you can reformat back to a regular USB drive for file storage
    • The storage amount is dictated by the .iso file you are installing: 
      • 4 GB is ok for Ubuntu server 
      • 8 GB is needed for Ubuntu desktop since it has more software
  • Ethernet cable and wired access to the internet for the server (at least for the setup steps)
  • Keyboard, mouse, and monitor (only necessary for setup)
    • Directly connect your regular keyboard, mouse, and monitor to avoid buying more. This can be temporary just for setup steps.
    • Alternatively: I used a Linux-compatible USB switch and cheap no brand VGA switch so I could use the same keyboard, mouse, and monitor for both my Window and Linux server computers. 
    • Alternatively 2: You can also use a tiny $9 keyboard+touchpad combo for the server computer. I tried this but didn't like it long-term because it is too small and uncomfortably slow to use.

How?


Table of contents


Prepare an executable USB drive to install the Ubuntu server or desktop

  • Detailed instructions with screenshots [WikiHow]
  • Download an .iso file of the Ubuntu server or desktop, e.g. Ubuntu Server 22.04.3 LTS
    • Select "Option 2: Manual install"
    • Download the .iso file anywhere (main computer or USB flash drive ok)
    • LTS = long-term support, good so you don't need to upgrade as often
    • .iso files are packaged files that can be used to make installation CD-ROMs or executable USB drive
    • You can start with either server or desktop, then install the other later
  • Get a >4 GB USB drive that you're ok erasing completely. This will become the executable USB.
    • If you downloaded the .iso file to a USB flash drive, then you need a second USB flash drive that you are ok erasing. You can't use the same USB flash drive.
      • First USB=storage of the downloaded .iso file, does not need to be erased. 
      • Second USB=to be erased and rewritten with the .iso file contents.
  • Using Rufus (freeware), the .iso file, and your USB drive that you are ok erasing completely, make an executable USB drive to install the Ubuntu server.
    • Run Rufus on your main computer, with your USB drive plugged in
    • Install the .iso file onto the USB that you want to make executable. Use default settings, plus one addition from advanced settings: check the box for "Add fixes for old BIOSes (extra partition, align, etc.)"
    • If Rufus says your .iso file needs a different Grub and asks if it can download it for you, say yes and continue.
    • The final executable USB can used during computer start up to run the .iso data, but is safe to plug into a computer that is already turned on (won't run the .iso data).
Image shows installation of Ubuntu Studio, not Ubuntu server, but it's very similar. "Device" is your USB drive. Use "Select" to load your ISO file.



Install the server or desktop

  • Use an old desktop that you are ok erasing completely
    • Beware: you shouldn't have any files or software you want to keep on it!
    • You will lose the Windows or iOS operating systems, too!
  • Optional (recommended if donating the computer): erase the hard drive with DBAN software
    • Download the DBAN .iso file (free) and create an executable USB drive using Rufus
    • Optional step because installing the Ubuntu server overwrites the hard drive anyway
    • But using DBAN overwrites the hard drive several times and ensures your original data can't be recovered
  • Reboot the computer
    • Disable "fast restart" if you have Windows 8 or later
    • Starting with Windows 8, computers have a "fast restart" mode that skips your opportunity to enter the BIOS menu when you start it again.
  • Enter the BIOS menu by holding down the F2 or F12 key as soon as you press the power button. Keep holding it for several seconds until the BIOS menu appears.
    • Search the internet for your computer's instructions. It might be the F1 key or another key.
    • May require rebooting the computer several times to get it right
    • If you see the Windows screen, shut down and try again
    • Timing is key! Your opportunity to enter the BIOS is a really short window at the very beginning of start up
  • Edit the BIOS settings to boot from USB first, before booting from the hard drive
    • Turn off BIOS safety settings that prevent booting from USB, if any
    • Turn off Windows secure boot
    • Change the boot order to boot from USB before anything else (hard drive, CD, etc)
    • Usually this is the most difficult part because it is very computer-specific
    • Don't quit at this step! The rest is easier!
  • Shut down the computer completely after adjusting BIOS settings
  • Connect the computer to the internet before the Ubuntu setup process
  • Plug in the executable USB drive that you created with Rufus and the Ubuntu server .iso installation file
  • Turn on the computer
    • It should boot from the USB and start the Ubuntu server installation.
    • If not, try holding F2 or F12 when turning on the computer. You may need to adjust more BIOS settings until it works.
  • Follow installation instructions. The first few minutes are just waiting for the screen of automatic tasks to complete. Eventually you get a text screen that says welcome.
  • For Ubuntu Server: here is what I selected. [x] means I checked that box:
    • Language: [x] English
    • Choose type of install: [x] Ubuntu server, [x] Search for additional third party drivers
    • Network connections: Connect to ethernet "eth" (preferred)
    • [x] Use entire disk, [x] set disk up at LVM group
    • Accept default storage configurations
    • Select a username and server name (make each one word, no spaces)
    • [x] Install OpenSSH
    • Featured server snaps: keep all default 
  • For Ubuntu Desktop: I accepted all defaults
  • Remove the executable USB drive once the installation is complete. 
    • If you don't, the computer will restart and boot from the USB again. You will get a message to "remove installation media" (remove the USB). Do so and hit [Enter] to continue.
    • Keep the installation drive nearby until you finish and everything works. If something goes wrong, you can re-install.
  • After all is done, you can reformat (erase) the executable USB with your main computer to use it like a normal USB storage drive again.
    • It is safe to plug in when the computer is already turned on. It was created to execute on start up and will not execute when you plug it in any other time.
    • Just in case, if your main computer is confused and asks if you want to import contents or run the ISO, click "Cancel" or "No". If your main computer asks if you want to reformat the USB drive, say "OK" or "Yes".

If you started with Ubuntu Server:
Set up a desktop (GUI) for the server

  • By default, the Ubuntu server just has the command line interface. Set up a desktop to make life easier. This requires internet so make sure your ethernet cord is connected.

  • Install tasksel, then open it to see what it can install. Check boxes with the [spacebar] and move to "OK" using the [tab] key. Use Ctrl+Z to exit tasksel.
    • sudo apt update
    • sudo apt upgrade
    • sudo apt-get install tasksel
    • tasksel

  • Install a GUI (a desktop style) from the command line using tasksel or the default apt get method. You only need one GUI.

    • Ubuntu Studio desktop is nice if hard drive space isn't an issue. It comes with audio, video, and graphical editing software. Good if you want to use the server computer as an extra desktop.
      • sudo tasksel install ubuntustudio-desktop
      • During the installation of jackd2 (an audio server installed with Ubuntu Studio), you will get this message: "Enable realtime process priority?" I said no.

    • MATE desktop is fine also. It comes with useful software and takes up less space than Ubuntu Studio. (Don't run both, pick one):
      • sudo tasksel install ubuntu-mate
      • sudo apt install ubuntu-mate-desktop

    • MATE core desktop is a barebones version of MATE. Useful if you want to save hard drive space and only use the computer as a server. It works for that, but I hated it whenever I had to log into the server computer. For notekeeping purposes only, this is the command for it:
      • sudo tasksel install ubuntu-mate-core

    • Lubuntu desktop is the lightest desktop (smallest file size). When I installed it, I lost access to the terminal window via the GUI or keyboard shortcuts. I had to reinstall the server using the executable USB drive. Not recommended!

  • Select and install a display manager (pick one) that works with the GUI you want:
    • sudo apt install lightdm # lightweight, default for Ubuntu 22.04 LTS with Ubuntu Studio
    • sudo apt install gdm3     # heavier, default for Ubuntu 22.04 LTS with MATE
    • sudo apt install slim -y   # lightweight, recommended for Ubuntu 24.04 LTS

  • Enter the GUI and celebrate when the all text terminal turns into a colorful desktop with ONE of the following commands to start the desktop software (don't run all, pick one):
    • sudo service lightdm start
    • sudo service gdm3 start 
    • sudo service slim start

  • Log in with your username and password, then check the desktop environment.
    • Make sure you can open a terminal window
    • Make sure you can access the internet. 
    • Connect to wifi at this point if desired.
    • If your password doesn't work, check if it works in the terminal: 
      • Ctrl + Alt + F1
      • Ctrl + Alt + F2
      • Try either one. To go back to the GUI, try either one again.

  • Prevent the server from going to sleep with this sequence (not a terminal command)
    • Settings > Power > Automatic Suspend > Off
    • This keeps the server accessible 

  • Make a file of system specifications
    • sudo lshw -html > server_specs.html
    • This creates an .html file with information on your hard drive, memory, graphics and sound cards, wifi card, etc.

  • Exit the GUI (not recommended unless you're replacing it). This removes the desktop and takes you back to a terminal only interface. You don't need to do this to access the terminal. This is just for reference:
    • sudo service <DisplayManager> stop
    • where <DisplayManager> is either lightdm or gdm3 or slim


If you started with Ubuntu Desktop:
Install OpenSSH

sudo apt update && sudo apt upgrade
sudo apt install openssh-server


ssh -V 


Change the ssh port from the default 22 to something else (pick a number, e.g. 23). 
sudo nano /etc/ssh/sshd_config
  • Find the line that says "#Port 22". 
  • Remove the hashtag and change the number to something other than 22.
  • Don't use these ports for ssh. They are used for something else already:
    • 20 (ftp-data)
    • 21 (ftp server)
    • 22 (default ssh port, often targeted by bots and hackers)
    • 23 (telnet server)
    • 25 (email server)
    • 53 (DNS server port for rerouting internet traffic)
    • 69 (tftp server)
    • 80 (internet http port)
    • 110 (POP3 server)
    • 123 (NTP server)
    • 443 (internet https port)
    • 8787 (RStudio server port)
    • 8888 (Jupyterlab server port)
  • To save changes: Ctrl+O
  • To exit the text editor: Ctrl+X

Start and/or reload the sshd service to apply changes, then check status:

sudo systemctl start ssh
sudo systemctl reload ssh
sudo systemctl status ssh 
Cntr+Z to quit the status window 
 

If the status message still says that the server is listening on the default port, port 22, then stop and restart the ssh server a different way:  

sudo systemctl stop ssh
sudo systemctl start ssh
sudo systemctl status ssh 
Cntr+Z to quit the status window 

You should see that the server is listening on your desired port now.


Enable the firewall and allow traffic through specific ports:

sudo ufw enable #turns on the firewall
sudo ufw allow www #allow internet access
sudo ufw allow 53/tcp #allow DNS queries to route internet traffic
sudo ufw allow 80/tcp #allows http access
sudo ufw allow 443/tcp #allows https access
sudo ufw allow 8787/tcp #RStudio server port

Open up the port you are using for ssh access, but only allow access from your local home network IP addresses. Example with port 25:

sudo ufw allow from 192.168.0.0/24 to any port 22
sudo ufw allow from 192.168.1.0/24 to any port 22

Replace "22" with whichever port you are using for ssh access. The default port is 22.

Replace the IP address with your home network range if needed, though 192.168.0.x and 192.168.1.x are common patterns. This is not the same as your public IP address visible to people on the internet. The "/24" at the end is the same as saying the last number can vary.

DON'T do the "ufw allow from" version of the terminal command for the internet ports or you may lose internet access.

Reload the firewall to apply the rules:

sudo ufw reload #apply the rules 

View which ports are open:

sudo ufw status verbose #more details
sudo ufw status numbered #supplies a numbered list

Delete any rules you don't want using the line <number> (without the greater/less than signs):

sudo ufw delete <number> 

I suggest deleting any lines for port 22, which may have been opened automatically if at any point you ran "sudo ufw enable ssh".


To delete all ufw rules and start over:

sudo ufw reset
sudo ufw enable #turns on the firewall again

 

Also recommended is the package "fail2ban" which automatically blocks IP addresses that try to brute force login into your server with multiple attempts. After a certain number of failed attempts, fail2ban prevents further tries.

sudo apt install fail2ban

systemctl status fail2ban.service # check status info. It will be inactive by default. Ctrl+Z to return to terminal.

Read the configuration instructions before enabling it.

 

Set up a static IP address for the server computer

What is a static IP and why is it useful? It is an IP address that does not change. Having a static IP address is useful for a server computer (or printer) so that other computers have a known address to interact with it. Setting up a static IP is accomplished on a private network by telling the internet router to always assign the same local IP address to a specific MAC address (the physical hardware identification). Reserving an IP address for the server computer makes certain things easier, such as accessing the server via ssh or RStudio server web interface.

There are two IP addresses for internet-connected equipment:
  • Local IP address - assigned by your internet router to everything that connects to it, usually starts with 192.168.0.x, or 192.168.1.x, where the number x varies. This local address changes as things get disconnected and re-connected, but you can reserve specific local IP addresses for specific equipment MAC addresses for free. 

  • Public IP address - assigned by your internet service provider, find yours at whatismyIP.com. This is what websites see when you visit them. Unless you pay for premium internet service, your public IP is not static.

For the purposes of a private home Ubuntu server, you only need a static local IP address. It doesn't matter if your public IP address changes. 

  • Identify the MAC addresses for the Ubuntu server computer with this terminal command:
    • ip a

  • MAC addresses look like letter and number pairs in this format, A0:A0:A0:A0:A0:A0 
    • Ethernet and wifi have different MAC addresses
    • Write down both and then see which one is connected to the internet router

  • Log into your internet router's admin website to set up a static IP address ("reserve an IP address") for the Ubuntu server
    • This requires administrative access to the internet router. Ask whoever set up the internet for help, or check the back of your internet router for default login information.
    • Here are default router addresses, usernames, and passwords
    • Instructions to reserve IP addresses vary by manufacturer
    • Search "how to reserve IP address printer __[your router model]__" and follow those instructions for the Ubuntu server instead. Printers are the most common equipment that needs a static IP, so printers will have the most help pages on this topic.
    • Check under "LAN Setup" and find a section called "Address Reservation"

Log into the server via ssh from the main computer

  • On the server computer, turn on ssh access and check ssh server status (should be active)
    • sudo systemctl start ssh
    • sudo systemctl status ssh
    • Cntr+Z to quit the status window

  • On the server computer, ssh into the "localhost" (not an IP address, do not replace) and then exit
    • ssh localhost -p <port>
    • Where <port> is replaced by your ssh port, default is 22
    • Say "yes" when asked if you want to add the localhost to a list of known hosts
    • exit

  • On the main computer, open a terminal.
    • On Windows, you can open a terminal like this:
      • WindowsKey + R, then type "cmd"
      • Or search "cmd" and click Command Prompt
    • Alternatively, use MobaXterm software (free version) or PuTTY (freeware) to interact with the server. 

  • On the main computer, open a terminal and type something like: 
    • ssh user@192.168.0.10 
      • Replace "user" with your server username
      • Replace "192.168.0.10" with your specific Ubuntu server's local static IP address
      • This example assumes the default ssh port (port 22). 
    • ssh user@192.168.0.10 -p <port>
      • Where <port> is your ssh port number. See the section on increasing server security by changing the ssh port number.
    • If using MobaXterm or PuTTY, fill in the boxes for username, IP, and port number.

  • First time message will look something like this: "The authenticity of host '[192.168.0.10]:22 ([192.168.0.10]:22)' can't be established. ECDSA key fingerprint is...."
    • Say "yes", you want to continue connecting. 

  • The terminal should ask for server login information

  • SECURITY NOTE: the server does not yet have a firewall installed. I suggest continuing with defaults and checking that everything works before enabling the firewall (instructions for that are at the end). 
    • If you are taking a break, you can turn off the ssh server with this:
      • sudo systemctl stop ssh
    • Then turn it back on when you come back:
      • sudo systemctl start ssh
    • Or just turn off the server computer until you are ready to add additional security

Troubleshoot ssh issues

  • https://likegeeks.com/ssh-connection-refused/
  • https://www.webservertalk.com/troubleshoot-ssh-connection-refused
  • https://ubuntu.com/server/docs/service-openssh
  • Check the server IP address to verify that you are attempting to ssh to the correct IP
    • ip route
  • Check that the server computer has internet access at all
    • ping 8.8.8.8 -c2 
    • This sends two packets to check for a connection. Note: there is no space between c and 2
    • Check for 0% packet loss which means the internet works
    • If there is packet loss, then troubleshoot your internet connection
  • Check that the server computer DNS is rerouting internet traffic correctly
    • ping google.com -c2
    • Check for 0% packet loss which means the DNS is working correctly AND you have internet
    • If the ping to 8.8.8.8 works, but the ping to google.com fails, then you have a DNS resolution error. This happened to me after rebooting my original Ubuntu server 20.04 LTS computer and I ended up reinstalling the whole server because nothing seemed to fix it. If it happens to you, try rebooting the internet router! I did not try that.
  • If you have a firewall enabled on the server computer (instructions for that later), make sure you opened the ssh port.
    • sudo ufw allow ssh #enables default port 22
    • sudo ufw allow 25/tcp #where 25 should be replaced with whatever port you are using for ssh if not the default port 22
  • Disable the server firewall if enabled - does that allow you to ssh into the server computer? If so, you will need to edit the firewall rules.
    • sudo ufw disable
  • Check that your main computer's firewall allows internet access to whatever program you are using to ssh into the server, examples:
    • Windows command prompt (cmd.exe)
    • Windows Subsystem Linux (wsl.exe)
    • PuTTY - a free ssh client that you may want to try if the Windows command prompt isn't working and you don't have Windows Subsystem Linux
  • Create a second server account with less privileges and attempt to ssh from that account
    • otheruser@serverIP #assumes default port 22
    • otheruser@serverIP -p 25 #tries port 25 (replace "25" with your ssh port number) 
  • Remove OpenSSH and reinstall. Don't type the #comments
    • sudo apt-get purge openssh-server
    • sudo apt-get autoremove #cleans up dependencies not used by anything else
    • sudo apt-get autoclean #cleans up more leftover files
    • sudo apt-get update 
    • sudo apt-get upgrade
    • sudp apt install openssh-server #reinstall
    • sudo systemctl start ssh #start the ssh server
    • sudo systemctl status ssh #check status
  • If using your main account, try permitting root login temporarily. Not recommended as a long-term solution since it makes the server less secure. 
    • sudo nano /etc/ssh/sshd_config
    • Type this line without any hashtag (#) in front:
      • PermitRootLogin yes
    • [Ctrl+O], [Ctlr+X] to save and exit
    • sudo systemctl restart ssh
    • Set up a firewall rule limiting IP addresses to the ssh port if you want to keep this setting.
  • Reboot the internet router if nothing else works. When I had ssh issues, rebooting the internet router fixed these error messages:
    • "Resource temporarily unavailable" from Windows Subsystem Linux
    • "Connection timed out" from Windows 10 command prompt


Install R 4.4 or later (6/2024 update)

My instructions below are for Ubuntu Server 22.04.3 LTS, modified from the official R instructions [CRAN] and some from here to remove the old R version [thinkr.fr].


Check if you have R already (usually you won't)
R --version
 
 
Remove old R version if needed 
 
Don't type the #comments. Those are just notes for you.

sudo apt-get purge r-base* r-recommended r-cran-* #remove old pre-installed R version

sudo apt autoremove #remove dependencies not used by anything else

 

Install latest R version 

Don't skip installing the development packages. If you only install r-base, you will have problems with missing dependencies when you try installing R packages in the future.

sudo apt update 

wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc  # the qO has a capital letter O not number 0

sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" 

 This step tell Ubuntu where to download the newest R version.
Note, "focal" is for Ubuntu 20.x versions, "jammy" is for Ubuntu 22.x versions, but you may need a different version.

Using $(lsb_release -cs) automatically selects the correct release name.

sudo apt install r-base r-base-core r-recommended r-base-dev   #install R

sudo apt install libxml2-dev libcurl4-gnutls-dev libssl-dev cmake #development packages

sudo apt install libcurl4-openssl-dev4 libharfbuzz-dev libfribidi-dev ## optional, required for tidyverse R packages 

sudo apt install libmagick++-dev  ## optional, required for R package magick for graphics 

sudo apt install  libpoppler-cpp-dev ## optional, required for R package pdftools to use pdf files

sudo apt install libcairo2-dev ## optional, required for R package svglite to save .svg images

sudo apt install libtesseract-dev libleptonica-dev tesseract-ocr-eng ## optional, required for R package tesseract for image-to-text processing

R --version #check for R 4.3.1 (or whichever version is the most current at this time). If you have an older version, start over from the purge line. 

R #enter the R shell

 Type any R code you want in the R shell.

          q()  #exit R shell. Can also use Ctrl+Z to exit.


Keep watch for "ERROR: configuration failed" and "non-zero exit status" errors when installing R packages. Search the internet for those errors, the R package name, and "Ubuntu" to identify which additional development packages you need to install from the Linux terminal.

After this, I found that Ubuntu automatically updated my version of R when I ran regular maintenance updates with:

sudo apt update
sudo apt upgrade
sudo reboot #this restarts your computer so save any files you need!

Install RStudio server (6/2024 update)

Installation instructions for Ubuntu 22.04.3 LTS on 6/21/2024 (see link below for latest filename):
https://rstudio.com/products/rstudio/download-server/debian-ubuntu/

sudo apt install gdebi-core

wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2024.04.2-764-amd64.deb

sudo gdebi rstudio-server-2024.04.2-764-amd64.deb

sudo ufw allow 8787/tcp #optional, skip if you haven't enabled firewall yet

sudo systemctl status rstudio-server #check that it's working

Cntr+Z to exit the status window



Troubleshooting:

If you get an an error message about a missing dependency during the RStudio server installation for Ubuntu 22.04, you might need to install an old package from Ubuntu 20.04 and retry. 

echo "deb http://security.ubuntu.com/ubuntu focal-security main" | sudo tee /etc/apt/sources.list.d/focal-security.list

sudo apt update

sudo apt install libssl1.1

sudo rm /etc/apt/sources.list.d/focal-security.list

Check the RStudio server version:

rstudio-server version

First time setup for each user: ssh into the Ubuntu server from your main computer and add the server IP to your list of known hosts by answering yes to the question, "Are you sure you want to continue connecting (yes/no)?" You MUST be able to successfully ssh into the Ubuntu server before you can use the RStudio server.

From the main computer (not the server computer), either through the Windows 10 command prompt or ssh software (PuTTY or MobaXterm):
ssh user@serverIP #assuming the using default port 22
ssh user@serverIP -p 23 #example if ssh uses port 23

Log into the RStudio server from your main computer using a web browser, the server IP, and port 8787 [more info]:

http://<your server's IP>:8787

http://<your server name>:8787   # this also works

The login is your Ubuntu username and password.

Troubleshooting: if you can ssh into the Ubuntu server, but get a browser error saying the RStudio server website "took too long to respond", try this:

sudo systemctl status rstudio-server #check if RStudio is working
    Ctrl+Z keyboard shortcut (not terminal code!) to close out systemctl 

sudo systemctl start rstudio-server #only needed if status said it was inactive

sudo ufw allow 8787 #open up the port again if you have a firewall

Try to log in again. Make sure you are using "http://" and not "https://"

Install Perl, Python and JupyterLab

  • No need to install Perl and Python! They are already installed with Ubuntu Server 22.04.x LTS
  • Check the versions with 
    • python3 --version  #two hyphens
    • python2 --version 
    • perl --version
  • Install pip if needed for python
    • sudo apt install python3-pip
  • Upgrade pip
    • sudo apt update
    • python3 pip -m install --upgrade pip
  • To exit either terminal if you're stuck, use Ctrl+Z or quit()
    • ">>>" means you are in the Python shell
  • Install JupyterLab (a Python GUI):
    • pip3 install jupyterlab
  • Detailed video instructions for installing Jupyter for a server [YouTube 2019]
  • Install Spyder (a Python GUI):
    • sudo apt install spyder

Install Dropbox

OLD WAY: 

Manually download the latest .deb file (either 32-bit or 64-bit depending on your computer) from here: https://www.dropbox.com/install-linux

Don't follow the instructions to install from the terminal. It will partially work, but the installation code will freeze and you won't get a complete installation (my experience with Ubuntu 22.04 on 9/25/2022). 

Instead, right-click the .deb file from the Downloads folder and select "Open with Software Install". You won't see this option if you right-click from the browser's download list. [More details on how to use .deb files.]      

                         

NEW WAY (6/2024): 

sudo apt install nautilus-dropbox


After whichever install method you use, a pop-up window will come up. Sign in and select your preference settings.  

Check the status with:

dropbox status

After rebooting, Dropbox sometimes needs to be restarted manually. You can do this remotely from a terminal using:

dropbox start

To set up Dropbox to start automatically upon login, use this command:

dropbox autostart y

See more Dropbox terminal commands from the official source or with this command:

dropbox

 


Make your whole hard drive space available (8/2021)

Optional section when getting started! I did this only several months later when Dropbox surprisingly told me I was out of space, when I knew the drive shouldn't be full yet. 

Technical details: Your workspace inside the Ubuntu 20 server is a "logical volume" inside ext4-formatted partition sda3. Ubuntu automatically limits the aliquoted disk space to less than your total hard drive space.
 
Layman explanation: Ubuntu automatically limits the space available to your user account so that there is space available in case you add other users later. If you're the only user, though, you don't need this limitation. You can tell Ubuntu to give you all the space.

Check your storage allocations (doesn't change anything, just informational):
 
df -h #see file sizes in human readable format

cfdisk #shows all partitions on the hard drive and space used

Note: "sda" prefixes refer to your internal storage such as your hard drive, "sdb" prefixes refer to external storage such as USB drives.

du -sh ~/Downloads #see how much space your Downloads folder uses

du -sh ~/Dropbox #see how much space your Dropbox folder uses

df -h ~/Dropbox #see how much space is available, used, and free in this folder. Importantly, this also tells you where this folder is located on the hard drive.
 
sudo lsblk #shows virtual volume breakdown and which partition contains it

In my case, my Drobox folder was located in path "dev/mapper/ubuntu--vg-ubuntu--lv" (notice 2 hyphens, 1 hyphen, then 2 hyphens) in partition sda3. Write down the exact name of the virtual volume path because you will need it later! My system told me that 200 GB were available, even though my hard drive is 1 TB. 
 
Next, here are instructions that you should only follow after backing up your data (beware possible data loss if you have typos or mistakes):

I resized the logical volume (lv) to give it more space by following the instructions here, which I can confirm worked for Ubuntu server 20.04.2 on August 2021: https://slice2.com/2020/12/05/howto-easily-resize-the-default-lvm-volume-on-ubuntu-18-04/

Briefly, I first ran this test (-t) to see if I could resize the logical volume without errors:

sudo lvresize -t -v -l +100%FREE /dev/mapper/ubuntu--vg-ubuntu--lv
 
I checked the output and it told me no errors were found.

This is the start of real changes to your system (so make sure your data is backed up): I repeated the command  above with "-t" removed to run it for real, not as a test. 

After running, I checked the file system type (expect ext4) and size:
 
df -h -T | grep vg
 
Since ext4 was correct, I proceeded with the final resizing step:
 
sudo resize2fs -p /dev/mapper/ubuntu--vg-ubuntu--lv
 
Check that it worked by checking the file system size again: 

df -h -T |grep vg

Restart the server and you are done with this risky section.


Install a remote desktop server


Install a Brother network printer using an IP address (6/2022 update)

Network printer = a printer connected to the internet. The printer is not connected to the computer via a USB cable or Ethernet cable.

  • Before starting, assign a static IP to your printer. This requires logging into the internet router admin page.
     
  • Install these dependencies on your computer before installing the printer drivers:
    • sudo apt install lib32zl #optional maybe
    • sudo apt install  lib32ncurses6 #replaces lib32ncurses5

  • Look up your specific printer on the Brother website, e.g. MFC-5460CN

  • Install the printer drivers [instructions, instructions from Brother]
    • Download the "Driver Install Tool" file, e.g. "linux-brprinter-installer-2.2.3-1.gz", to the Downloads folder
    • These instructions helped me set up a network printer with 32bit drivers on a 64bit computer
    • In a terminal to install the printer drivers:
      cd ~/Downloads && gunzip -v ~/Downloads/linux-brprinter*
      sudo bash ~/Downloads/linux-brprinter*       
    • Move some files to install the scanner files:
      sudo ln -sf /usr/lib64/libbrscandec*.so* /usr/lib
      sudo mkdir -p /usr/lib/sane
      sudo ln -sf /usr/lib64/sane/libsane-brother*.so* /usr/lib/sane
    • Add your username to the scanner user group, e.g. gonzalez:
      sudo usermod -a -G scanner gonzalez
    • If you get an error after a question about a proxy server, use the alternative method below.

  • Install the printer drivers -- alternative method if the above doesn't work. Installing the two .deb printer drivers separately.
    • From the Brother printer page, download the LPR printer driver and CUPSwrapper printer drivers separately (both .deb files). Install the LPR driver first, then the CUPSwrapper.
    • sudo mkdir /var/spool/lpd/
    • sudo mkdir /var/spool/lpd/mfc5460cn/
      • Replace the last step with whichever directory is missing. You'll see it as an error if you try to run the step below.
    • sudo dpkg -i --force-all mfc5460cnlpr-1.0.1-1.i386.deb
      • Replace the .deb filename with your specific LPR driver filename.
    • sudo dpkg -i --force-all mfc5460cncupswrapper-1.0.1-1.i386.deb
      • Replace the .deb filename with your specific CUPSwrapper driver filename.

  • You should see the printer installed (under "System > Printers"). Restart the computer if not.

  • The default printer settings assume you are connected by a USB cable. For a network printer, you need to change the device URI value. The default device URI value = usb:/dev/usb/lp0
  • If you have a static IP for your printer, change the device URI to specify the static IP address.
    • Go to "Printers" and right-click your device
    • Edit printer properties and find the device URI
    • Instructions: https://www.cups.org/doc/network.html
    • Example static IP = 192.168.0.3
    • The corresponding URI value = socket://192.168.0.3:9100

  • Print a test page.

Suggested software

Expanded security maintenance

Make an account to log into https://ubuntu.com/pro/dashboard

Under section "Free Personal Token", follow the instructions to attach your security token to your Ubuntu server and up to 4 other machines (5 total). The command looks like this:

sudo pro attach [your security token]

Doing this will enable the esm-apps repository which has extra bug fixes and security packages. 

Maintenance

Things to do occasionally to make things keep running well. Several of these things can be done through another computer logged in through ssh. After restarting, you may need physical access to the server or the internet router.
  • Identify your user account
    • whoami #returns your account name
  • Identify logged in users
    • w
  • Identify your Linux kernel (useful for hardware compatibility information) and Ubuntu version (useful for software compatibility):
    • uname -mrs && lsb_release -a
  • Identify external drive, USB flash drive, HDD, or SDD location
    • RStudio server web portal starting from the Home work directory:
      dir("../../[username]/media/") 
    • Linux terminal:
      ls ~/../../media/[username]/ 
    • #replace [username] with your own username without the square brackets
    • You should see your external drive name
  • Download & install updates (on the server computer or remotely)
    • sudo apt update #to check what is new, without installing anything
    • sudo apt upgrade #to install new versions of packages
    • sudo apt autoremove #to automatically remove packages that are no longer used
  • Restart if the ssh log in message says: "*** System restart required ***"
    • sudo reboot
    • You can do this remotely by ssh
    • You may need physical access to the server afterward if there are any issues with internet, firewall rules, or ssh. The most likely issue is that your need to check the IP address again if you didn't assign the server a static IP on the internet router yet.
  • Check your server IP address
    • ip a
    • enp2s0 = ethernet
    • wlp3s0 = wifi
  • Check devices connected to your local internet
    • sudo apt install arp-scan
    • sudo arp-scan --localnet
  • Check firewall rules
    • sudo ufw status
  • Restart Dropbox and check Dropbox status. I need to restart it often on Ubuntu server 20.04.03. It disconnects after a few hours of inactivity.
    • dropbox status
    • dropbox start
  • RStudio Server - check status, start if inactive, restart if it is active but not working well
    • systemctl status rstudio-server
    • systemctl start rstudio-server
    • systemctl restart rstudio-server
  • RStudio Server - "took too long to respond" browser error (on the server computer or remotely)
    • sudo ufw allow 8787 #reopen the 8787 port for the RStudio Server
    • If that doesn't work, check your server computer's internet access.
    • Check the RStudio Server link from the server computer itself (through a browser)
      • http://[your server IP address]:8787
      • http://192.168.0.100:8787 (example pattern)
    • Check that you can ssh into the server
  • Check status of the ssh service (on the server computer's terminal)
    • systemctl status ssh.service #check if it's active
    • systemctl restart ssh.service #restart if you're having issues
    • sudo service ssh restart #try restarting another way
    • sudo ufw status numbered #check which ports are open
      • sudo ufw allow <your ssh port> #reopen the ssh port if needed
  • Check that the server computer has internet access
    • sudo lshw -class network #shows network details
    • ping google.com -c2
      • Wait for results from the 2 packets. If the ping statistics say 0% packet loss, then you have internet working properly.
    • ping 8.8.8.8 -c2
      • Wait for results from the 2 packets. If the ping statistics say 0% packet loss, then you are connected to internet even if the DNS isn't working
      • If 100% packet loss, then you're not connected to internet (not a DNS problem)
    • If either ping fails and says "Temporary failure in name resolution" then the DNS is not routing internet traffic correctly.
    • Turn off the internet router for 30 seconds, then back on. This can fix several problems including router issues that affect every device, as well as IP assignment problems that don't affect server internet but prevent remote access through ssh or the RStudio browser url.
    • Reboot the computer.
    • Connect to ethernet and, if you get internet back, then download & install updates.
    • If you have tried everything and nothing works, wait 1 day to see if the problem fixes itself. If not, you may need to reinstall the server.
  • Check Linux kernel currently loaded. The kernel is the skeleton beneath your Ubuntu system. It is important for basic things like loading Ubuntu on startup and hardware compatibility.
    • uname -a
    • If you buy new hardware (e.g. wifi adapter), check that it is compatible with your Linux kernel.
  • Check Linux kernels available to you. [More info] 
    • dpkg --list | grep linux-image
    • That's two hypens before list
    • It's good to have a few old versions in case an update causes startup problems. You can power down the computer, then power it on and hold the F2 key to bring up the GRUB boot loader. If you can boot using an older kernel, you might be able to resolve problems with the new kernel without reinstalling your whole system.
  • Search available software by keywords, for example:
    • sudo apt search "video editor"
    • This will output a list of all software you have with this function
  • Stress test your RAM annually with memtester, per advice from Genome Spot 
  • 2/8/2022 issue with "initramfs" noted after a routine apt update and apt upgrade. Rebooting stopped with this error: "[end Kernel panic -  not syncing: VFS: unable to mount fs on unknown block c(0,0)]"
    • Solved on Ubuntu server 20.04.03 LTS using the following commands (adapted from here). I didn't need to mount any partitions beforehand because I was not using a live CD. I accessed the GRUB boot loader (screenshot examples) and booted using an older kernel (5.4.0-97-lowlatency), then used the terminal to fix the newer kernel's initramfs:
      • sudo update-initramfs -u -k 5.4.0-99-lowlatency
        • Change the underlined part to suit your needs
        • The underlined part was my newest Linux kernel that failed to load. That kernel was listed a few lines above the original "Kernel panic" error message. If you missed that information, identify your newest kernel using: 
          dpkg --list | grep linux-image
        • Your newest Linux kernel name may be different from mine!
      • sudo update-grub
      • sudo reboot
  • If login screen from the GUI doesn't work, how to access the terminal
    • Ctrl + Alt + F1 keys will bring up the terminal
  • Turn off the computer from the terminal:
    • sudo shutdown -r now

Good luck!

  • The key to success is following instructions, trial and error, checking for typos, and using the internet to find solutions for problems you'll encounter along the way
  • Patience is more important than being an expert Linux user or programmer
  • Break it up into a few days and stop to celebrate each completed step
  • You can do this as a beginner! It seems intimidating, but it's not that bad

If you get stuck after a terminal command, use Ctrl+Z

  • This is like the "Esc" key for Linux
  • Ctrl+Z will exit you out of any other shells (the python shell, the R shell) or file editing (vim, nano) that you might find yourself stuck in
  • Ctrl+Z stops processes and brings you back to the main terminal

Originally my notes for Ubuntu server 20.04 LTS (published December 20, 2020), but I copy/pasted and edited the notes when I installed Ubuntu server 22.04 LTS (9/25/2022). To be edited occasionally whenever I want to document down anything else I've found useful.  Last edited 6/20/2024 with GUI install notes and additional port information.
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