Comfy Ubuntu/Pop!OS

Various bits of setup for a research machine


Ah, Ubuntu! The linux distro that realises that whilst we might tell ourselves we are lured to Linux by the promise of being lean, fast and secure, what really brings the crowds is something with bells, whistles, a V8 engine, flashing lights and a whiff of danger.

Ubuntu is a lowest-common-denominator system for Linux HOWTO guides to target because, AFAICT, there is a gigantic amount of crap pre-installed so odds are your software of choice is already there, or at least the dependencies for it are, so the documentation author can spend the least possible time arsing about with getting the necessities together. Also, I suspect, the kind of person who is exacting enough to run Archlinux or NixOS is intimidating to imagine trying to explain things to.

Using the rather busy Ubuntu default install to run some specialised app often feels like using a circular saw with integrated wiffle bat to crack a nut, though, and I have a vague inking that it’s probably not as secure as I hoped all this crap cannot be secure. I suppose this is intended welcoming to Windows users who pine for the default adware-and-weird-OEM-broadband-bundle home screen. Or something.

Because of my faint queasiness about all that I am interested in more minimalist approaches to Ubuntu than the mainline rolling mess, such as Elementary, Pop! or possibly even a super sleek hardened OS.

So actually Pop!OS

You can read two fannish histories of thie Ubuntu derivative here

I am experimenting with Pop!OS for the next laptop rebuild.

Basic

apt install libcurl4-openssl-dev build-essentials

apt or apt-get?

apt, unless you have a compelling reason.

Non-packaged apps: homebrew

homebrew is the goods:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Probably I want all the libraries which are too patent-encumbered to be bundled with my holier-than-me distribution. This means codecs and other content-related apps, e.g.

brew install libsamplerate libsndfile ffmpeg node pandoc

Linuxbrew is how you would install shiny hipster things s which get their value from new features that came out yesterday and which you like before they are cool. It claims to support julia, but AFAICT that doesn’t work. node.js does, though.

I would typically do

brew install hugo pandoc fish ffmpeg syncthing

Fish shell

Since I use fish shell as my default but ubuntu automatically executes the bash startup script .profile on login I ran into the following errors on login, when it tried to run the fish init in a bash process

bash: set: -g: invalid option
set: usage: set [-abefhkmnptuvxBCHP] [-o option-name] [--] [arg ...]
bash: set: -g: invalid option
...

This may be related to an intermittently reported bug in homebrew.

The fix is to change the automatically-added line in .profile to be

eval $(SHELL=bash /bin/brew shellenv)

and to add

eval (/bin/brew shellenv)

to ~/.config/fish/config.fish.

Note that this can cause surprising side effects; notably if I install homebrew python (and many homebrew apps need python and will install it for me) I will find my default user python is homebrew python, which breaks certain ubuntu apps that expect my default user python to be system python. I should probably file some bug reports for that for either homebrew or the affected packages; it undesirable. For now I recommend

brew unlink python

If there are problems with installing haskell packages with an error like

gcc-5: error: unrecognized command line option '-no-pie'

(e.g. pandoc) then try:

brew install gcc@6
HOMEBREW_CC=gcc-6 brew install pandoc

Setting it as a default shell, now? If brew installed, add /home/linuxbrew/.linuxbrew/bin/fish to /etc/shells. Then run

chsh -s /home/linuxbrew/.linuxbrew/bin/fish

Otherwise

apt-add-repository ppa:fish-shell/release-2
apt install fish
chsh -s /usr/bin/fish

From within fish, one should add a user script path

set -gx PATH ~/bin $PATH

Packaged apps

I mean, applications packaged in one of the special pre-rolled formats like snap or flatpak or AppImage.

Flatpak is built in to Pop!OS but not stock Ubuntu. For that you need

add-apt-repository ppa:alexlarsson/flatpak  # before 18.10
apt install flatpak
apt install gnome-software-plugin-flatpak  # Integrates into GNOME
flatpak remote-add --if-not-exists flathub \
   https://flathub.org/repo/flathub.flatpakrepo

Possibly one also should limit snap’s disk usage which I usually do, although I don’t know if there are downsides.

sudo snap set system refresh.retain=2

Networking

Firewall

Why would I not use at least a perfunctory firewall?

ufw enable

DNS

See DNS servers.

Graphics etc

I suppose one should have gimp installed. May be worth installing a fancy version from PPA to ensure version 2.10 or greater which has necessities such as WebP support.

add-apt-repository ppa:otto-kesselgulasch/gimp
apt install gimp

OTOH the flatpack distribution of GIMP has a lot more plugins.

flatpak install flathub org.gimp.GIMP
flatpak install flathub org.gimp.GIMP.Plugin.GMic
flatpak install flathub org.gimp.GIMP.Plugin.Fourier
flatpak install flathub org.gimp.GIMP.Plugin.Resynthesizer
flatpak install flathub org.gimp.GIMP.Plugin.LiquidRescale
flatpak install flathub org.gimp.GIMP.Plugin.LensFun
flatpak install flathub org.gimp.GIMP.Plugin.BIMP

Krita is a better image editor in from a UX perspective, although missing some hardcore nerd features.

snap install krita

For desktop publishing, Scribus

add-apt-repository ppa:scribus/ppa
apt install scribus-ng

Academic necessities

TeX

Of course I need LaTeX. This comes baked into Ubuntu if I want it, but that version is not flexible or current and wastes disk space. I recommend TinyTex, Yihui Xie’s excellent mini distro for modern workflows.

Fonts

See also fonts.

There are many in the ubuntu repos these days

apt install fonts-ebgaramond \
  fonts-cmu fonts-firacode \
  fonts-lmodern fonts-stix fonts-powerline \
  fonts-texgyre \
  font-noto

Citations

Zotero of course.

Developer stuff

R

RStudio can be downloaded from its site. R is already in the repository. One might want a fresher version but nothing has made that worth the bother for me yet.

# Basic essentials
apt install r-base r-base-dev
# Specific packages I use need these extras
apt install libatlas3-base libopenblas-base libv8-dev libfontconfig1-dev libcairo2-dev libprotobuf-dev protobuf-compiler libjq-dev 

Julia

My current favourite numerical software! I download julia as a plain installer package; It’s too rapidly evolving for anything else.

Python

I give in, and just run anaconda. It is easy of science stuff. Also, running homebrew python caused me problems.

Download e.g. x64 Miniconda, from the download page.

bash Miniconda3-latest-Linux-x86_64.sh
# simulate login/logout here
exec bash -
# don’t be so aggressive conda
conda config --set auto_activate_base false 
conda init fish  # fish users
conda activate base

The minimal conda base setup for me is just a jupyter host with multikernel support and some basic utils

conda install ipykernel nbstripout

Bonus: then I get pytorch and and other such tricky-GPU-dependency packages without messing about.

conda install pytorch torchvision cudatoolkit=10.1 -c pytorch

GPU config

See budget GPU configuration.

Git gui

Sublime merge is a handy git GUI.

wget -qO - https://download.sublimetext.com/sublimehq-pub.gpg | sudo apt-key add -
echo "deb https://download.sublimetext.com/ apt/stable/" | sudo tee /etc/apt/sources.list.d/sublime-text.list
sudo apt update
sudo apt install sublime-merge

File syncing

See also file sync/backup.

rclone

One of these:

apt install rclone
brew install rclone

Syncthing

There is a medium-fresh version of syncthing in the Ubuntu repository, so one can simply

sudo apt install syncthing

Or, a little fresher,

brew install syncthing

If I want an even fresher version I can choose, bonus apt PPAs.

# Add the release PGP keys:
curl -s https://syncthing.net/release-key.txt | sudo apt-key add -
# Add the "stable" channel to your APT sources:
echo "deb https://apt.syncthing.net/ syncthing stable" | \
    sudo tee /etc/apt/sources.list.d/syncthing.list
# Update and install syncthing:
sudo apt install syncthing

Now choose my autostart method. I probably want to do this as a user, not as a system service, because root access is from a different devops era. As such it makes sense to put (assming snap installed syncthing)

/snap/bin/syncthing

as a user startup application.

But wait! Does it report my disk is full when I try to use filesystem monitors? I need to allocate more resources to that.

$ cat /proc/sys/fs/inotify/max_user_watches
8192
$ sudo sh -c 'echo 204800 > /proc/sys/fs/inotify/max_user_watches'
$ echo "fs.inotify.max_user_watches=204800" | sudo tee -a /etc/sysctl.conf
$ cat /proc/sys/fs/inotify/max_user_watches
204800

Multimedia

apt install graphicsmagick-imagemagick-compat graphicsmagick

Mail client

I like mailspring but there are [others](./email_clients

Browser

A nice browser is necessary, no?

I use firefox. Google Chromium is also OK, or Brave. Chrome seems to be getting creepy these days. If I nonetheless want Chrome for profile sync or some other features not in plain chromium, askubuntu says:

sudo bash
wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | \
    apt-key add -
echo "deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main" >> \
    /etc/apt/sources.list.d/google.list
apt install google-chrome-stable

Standard disclaimer: the other features that are not in plain chromium may include Google spyware.

Maybe you would like to sidestep that issue with the possibly-better crypto privacy dotcom buzzword browser Brave?

sudo apt install apt-transport-https curl
sudo curl -fsSLo /usr/share/keyrings/brave-browser-archive-keyring.gpg https://brave-browser-apt-release.s3.brave.com/brave-browser-archive-keyring.gpg
echo "deb [signed-by=/usr/share/keyrings/brave-browser-archive-keyring.gpg arch=amd64] https://brave-browser-apt-release.s3.brave.com/ stable main"|sudo tee /etc/apt/sources.list.d/brave-browser-release.list
sudo apt update
sudo apt install brave-browser

Editors

Not all the good editors are packaged by the system. The fashionable ones are installed separately.

I like vs code

Once the right editor is there, set it as default either system wide

update-alternatives --config editor

or per-user

alias editor=code

or per-user-per-MIMETYPE:

xdg-mime default code.desktop text/plain

Password manager

Obviously password managers are essential. passwordstore:

apt install pass

Bitwarden comes as a flatpak.

Clipboard

The usual clipboard stuff.

Recent ubuntu is missing the essential utility xclip:

apt install xclip

CopyQ (every desktop) seem most popular and works well.

apt install software-properties-common
add-apt-repository ppa:hluk/copyq
apt install copyq

It seems to be available as a packaged app too although it was being buggy for me; lots of errors in the notification log.

flatpak install --user --from https://flathub.org/repo/appstream/com.github.hluk.copyq.flatpakref
flatpak run com.github.hluk.copyq

The app reveal shortcuts do not work for me in recent ubuntu, but a workaround is to put the command copyq toggle into a keyboard shortcut.

Useful: CopyQ Keyboard shortcuts.

Alternatively, Zazu offers a clipboard manager.

See also clipboard managers for some in-depth and cross-platform comparison nand some security warning about these.

Terminal

How best to emulate 1970s hardware on Ubuntu as modern practice dictates? Hmmm. I like hyper (deb download of unknown provenance). Terminator seems to be an acceptable default option for a pure native app without many bells or whistles.

Launching applications

One could use a custom launcher, e.g. Zazu or do. But the built-in launcher on Gnome at least is pretty good, so I do not bother.

Mouse

Also trackpad buttons. For my Razer Blade there were extra things to do. There are also some tips there about making settings persist.

Kai Koenig reveals that I can have the button assignments different between mouse and keyboard. This is useful for me, since I mouse left-handed and trackpad right-handed, for reasons of avoiding RSI.

This needs the xinput trick

xinput -list

to find the name of my mouse, then

xinput set-button-map "2.4G Mouse" 3 2 1 &&

Making it work generically for all peripherals and not each specific mouse requires fancier footwork.

If I just broke my right touchpad button but am too lazy/cheap/busy to fix it, I can enable simulated right clicks in the universal access menu, which works in most apps. Like most accessibility features, the right click simulation works a lot of the time but some apps clearly have not thought about it and the clicks go weird.

Keyboard

This mapping

 key <HOME> {    [  Prior        ]   };
 key <PGUP> {    [  Home         ]   };
 key  <END> {    [  Next         ]   };
 key <PGDN> {    [  End          ]   };

is an ideak xkb mapping for my silly keyboard design. (see also).

Desktop could be nicer

Ubuntu 17.0 or later: GNOME

Oh wait Unity desktop is over now I need to convert all the classic tweaking to GNOME. See comfy GNOME shell.

Ubuntu before 17.10: Unity

Here are the keyboard shortcuts needed to have a civilised desktop experience.

The default OS switcher is configurable

apt install compizconfig-settings-manager compiz-plugins

I simply don’t like the default Unity alt-tab application switcher. It may work for a lot of people, but it just slows me down. For me it’s faster to have a single application switcher that cycles through all open windows, possibly within one desktop, but I’m not sure about that. I am really not compatible with the default unity switcher that groups windows, for example terminals, together so when hitting alt-tab you can’t (in an effective way) switch between terminals. Having a different key combo for that slows my brain down. […] Open compizconfig-settings-manager with alt-F2, type ccsm.

Scroll down to Ubuntu Unity Plugin. Choose the tab Switcher. Disable the alt-tab and shift-alt-tab key bindings. (Key to start the switcher and Key to switch to the previous window in the Switcher. Click the Back button.

Scroll down to the Window management section. Here you can select another switcher. I enable the Static Application Switcher, resolve any potential conflicts by setting the setting for Static Application Switcher. Now you can tweak the switcher by clicking on it. I have changed alt-tab and shift-alt-tab to Next window (All windows) and Prev window (All windows).

Unity tweak tool does unity-specific tweaks of this kind of nonsense.

# Only if you want the very fresh version
add-apt-repository ppa:freyja-dev/unity-tweak-tool-daily
apt install unity-tweak-tool

See also the nifty run-or-raise hack.

Encryption and identity

ssh setup:

ssh-keygen -t ed25519 -o -a 100
ssh-keygen -t rsa -b 4096 -o -a 100

Verify debian

apt install debian-keyring  ## keys of extra-paranoid nerds
add-apt-repository ppa:tails-team/tails-installer
apt install tails-installer  ## for installing the paranoid tails OS
apt install pius signing-party  ## citizen identity verification

One should always have the utilities Cryptomator and zulucrypt on hand.

One way of getting cryptomator:

add-apt-repository ppa:sebastian-stenzel/cryptomator
apt update
apt install cryptomator

zulucrypt is

apt install zulucrypt

Or one can download slightly fancier version from the package creator.

Encrypted home folders/disks

See linux fs hacks.

Dual-booting with windows

See dual boot: windows/linux

Offline documentation

Zeal is not bad.

add-apt-repository ppa:zeal-developers/ppa
apt install zeal

Razer-specific

See comfy razer.

Virtual machines

I want to run virtual machines?? Be aware Ubuntu may have special needs wrt config.

virtualbox is passable. These days I prefer libvirt, unless there is some particular machine image that I need that only runs on virtualbox for some reason. ATM there are none.

libvirt

Easyish! Fastish! Open! Badly documented!

apt install virt-manager qemu-kvm

Virtualbox

Semi-open! Confusing! Circuitous! Opaque! Hard to remove! Well-documented! Has the best UI FWIW!

wget -q https://www.virtualbox.org/download/oracle_vbox_2016.asc -O- | \
  sudo apt-key add -
wget -q https://www.virtualbox.org/download/oracle_vbox.asc -O- | \
  sudo apt-key add -
sudo add-apt-repository 'https://download.virtualbox.org/virtualbox/debian contrib'
sudo apt install virtualbox virtualbox-ext-pack

If only I could temporarily disable lock screen

Caffeine.

apt install caffeine

Mounting that Windows partition on login

By default the various disks that I plug in to my machine are visible in the sidebar, but util I click on them they are not actually mounted so I can’t use the files. “Clicking on stuff” is not a satisfactory workflow, especially if you have other scripts which depend on data on my external drive. So fix that.

GUI automount

I believe we need to set the gnome config variable org.gnome.desktop.media-handling set automount to True.

Apparently this is equivalent to:

gsettings set org.gnome.desktop.media-handling automount true

or

dconf write /org/gnome/desktop/media-handling/automount true

There is also a gui, which I think is the officially recommended option:

apt install dconf-editor
dconf-editor
# make changes by clicking on things

GUIless automount

e.g. for the server. Install usbmount. I didn’t try this.

Manually

Userspace mounting is not hard but the command is not at all obvious. The virtue of this method is that it works also without root privileges, in principle. However, it also requires logging out and in again to test and frequently fails for me and I don’t know where the error logs go.

udisksctl mount --block-device /dev/disk/by-uuid/[uuid]

Or perhaps it is the slightly easier

/usr/bin/udisks --mount /dev/[sdc1 or something]

except that this one mounts it in the wrong place because otherwise it would be too useful.

But what is the UUID? Find it using blkid

sudo blkid

or if you are not root

ls /dev/disk/by-uuid

and apply some deduction.

NB: this could be slightly easier for external disks which have a label. Then it’s something like

udisksctl mount --block-device /dev/disk/by-label/[label]

This works on some of my Ubuntu machines but not others; can’t work out why.

Media

Playing music

Playing music: as not-quite-good as ever.

The built-in Rhythmbox is OK. I use Clementine or STrawberry, depending on what compiles this week.

Needed: unfashionable codecs:

apt install gst-plugins-ugly gst-plugins-bad

transcoding

Perhaps Handbrake.

add-apt-repository ppa:stebbins/handbrake-releases
apt-get install handbrake-gtk  handbrake-cli

VPN

Fiddly on Linux. See VPN

Comms

Signal desktop

The default safe chat client is Signal.

Note, be careful about installing this; The more instances of Signal you have, the bigger your attack surface, and Signal Desktop is not secure to be run on a non-encrypted FS.

Their recommended way is this:

curl -s https://updates.signal.org/desktop/apt/keys.asc | sudo apt-key add -
echo "deb [arch=amd64] https://updates.signal.org/desktop/apt xenial main" \
 | sudo tee -a /etc/apt/sources.list.d/signal-xenial.list
sudo apt install signal-desktop

This works only intermittently. If I am preapred to additionally trust Ubuntu I can get this more reliably via

snap install signal-desktop

Keybase

as per instructions.

curl --remote-name https://prerelease.keybase.io/keybase_amd64.deb
sudo apt install ./keybase_amd64.deb
run_keybase

Mounting android devices

I found that some newer/rarer MTPFS devices aren’t supported by 18.04 as filesystems. Should I try another MTPFS entirely, such as go-mtpfs?

Research ongoing for this one.

sudo apt install golang-go
sudo apt install libusb1-devel
mkdir /tmp/go
export GOPATH=/tmp/go
go get github.com/hanwen/go-mtpfs
mkdir xoom
go-mtpfs xoom &
cp -a ~/Music/Some-Album xoom/Music/
fusermount -u xoom

Additional config

journald

Ubuntu journald can get very big because there is no limit per default /etc/systemd/journald.conf:

SystemMaxUse=100M

Manual cleanup right now:

sudo journalctl --rotate
sudo journalctl --vacuum-time=2d

Booting and kernels

grub customizer customizes the GRUB2 boot menus without typos, if ones trust this developer to manage the boot setup.

sudo add-apt-repository ppa:danielrichter2007/grub-customizer # Optional on 19.10
sudo apt install grub-customizer

There is a version manager specifically for linux kernels (HT Abishek Prakash.) It is called UKUU.

sudo add-apt-repository ppa:teejee2008/ppa
sudo apt install ukuu

Power management

The arch guide explains the terminology. The TLP debugging guide and FAQ are also useful. Suspend is what I would normally call sleep where the computer just goes quiet and keeps the RAM powered up. Hibernate is when it suspends the whole state of the machine to RAM.

TLP and its GUI TLPUI can help tweaking power management for the non-power-management-obsessive. See also the system76 guide.

apt install tlp tlp-rdw --no-install-recommends
add-apt-repository ppa:linuxuprising/apps
apt install tlpui

You can do it more manually if desired, but it gets kinda complicated.

One could put a hibernate button in the shutdown menu if that seemed exciting.

Temperature monitoring and fan maangermen is via lm-sensors.

Power monitoring happens by powertop

apt install powertop
#reboot here, then calibrate
powertop -c

Script on wake

Running scripts on resume is an essential survival tool on my laptop.

gnome or some other bit of boring infrastructure flips the scrollwheel direction and remaps your keyboard every time the laptop sleeps? You are not alone. This is common, and has been annoying people since at least 2012.

Solution: work out a command that puts the system in the state you want, then run it upon resuming from suspend. This should be easy, but i find it annoyingly tricky because it changed at some point (2015 in ubuntu?) and so you get various scripts on the online forums which have aged badly.

Let’s say we want to fix the trackpad every time the laptop wakes. (**which is not needed since 19.04 AFAICT).

Answers about /usr/lib/pm-utils/sleep.d I believe are no longer current. Or I can supposedly create a system service, which seems like a lot of effort for a temporary hack.

What I believe I shoudl be creating is a a resume hook in /lib/systemd/system-sleep/fixthings.

Immediately before entering system suspend and/or hibernation systemd-suspend.service (and the other mentioned units, respectively) will run all executables in /usr/lib/systemd/system-sleep/ and pass two arguments to them. The first argument will be "pre", the second either "suspend", "hibernate", "hybrid-sleep", or "suspend-then-hibernate" depending on the chosen action. Immediately after leaving system suspend and/or hibernation the same executables are run, but the first argument is now "post". All executables in this directory are executed in parallel, and execution of the action is not continued until all executables have finished.

Note that scripts or binaries dropped in /usr/lib/systemd/system-sleep/ are intended for local use only and should be considered hacks. If applications want to react to system suspend/hibernation and resume, they should rather use the Inhibitor interface.

This resume hook looks simple enough.

Here is the /lib/systemd/system-sleep/fixthings hook script to set up my scrolling.

#!/bin/sh

case $1/$2 in
  pre/*)
    echo "Going to $2..."
    # Place your pre suspend commands here, or `exit 0`
    # if no pre suspend action required
    exit 0
    ;;
  post/*)
    echo "Waking up from $2..."
    # Place your post suspend (resume) commands here, or `exit 0`
    # if no post suspend action required
    sleep 15 # wait for my usb reset script to finish, hopefully
    xinput set-prop `xinput list --id-only "Bluetooth Mouse M336/M337/M535 Mouse"` 314 1  # logitech natural scroll
    setxkbmap -option compose:caps  #Caps lock is for typing diacritics
    ;;
esac

It must be rendered executable:

sudo chmod +x /lib/systemd/system-sleep/fixthings

Update: that script is no longer sufficient, since the property number changes.

Try this 76 line python script to keep the scrollwheel direction consistent.

Encrypt on sleep

It is unclear to me whether the default setup is safe for encryption. (i.e. can someone access your laboriously encrypted disk by making sure they steal your computer while it is in sleep mode?) It wasn’t, although various bugs have been closed now so maybe it is fine. Certainly encrypted hibernate is possible. But it does not seem fun and medium-paranoid people seem happy to do without it so maybe I am being too paranoid here.

Misc useful infrastructure

sudo apt install synaptic  # sometime I want old school debian style package manager
sudo apt install curl  # so many things depends on this why is it not there?

Accessing foreign file systems

See Linux FS hacks, but, in brief,

sudo apt install exfat-fuse exfat-utils ntfs-3g # interoperability for external drives

Installing and migrating

If you have encrypted and LVM layers on your disk there are a lot of steps to migrate disks. The official magical incantation is quite long, and include some surprising orderings. To reinstall grub there are some standard steps, but for encrypted drives there are some extras to get the boot partition in place.

mount /dev/sdXY /mnt
mount --bind /dev /mnt/dev &&
mount --bind /dev/pts /mnt/dev/pts &&
mount --bind /proc /mnt/proc &&
mount --bind /sys /mnt/sys
mount /dev/sdX2 /mnt/boot
mount /dev/sdX1 /mnt/boot/efi
chroot /mnt
grub-install /dev/sdX
grub-install --recheck /dev/sdX
update-grub

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