How to set-up Ubuntu 19.04

NOTE: this has now been moved to a permanent group resource

Maybe it’s time to upgrade. Maybe your Python environment’s just a limping zombie at this point. Maybe you thought it’d be a good idea to mount a network drive at boot so undergraduate students wouldn’t need either sudo permissions or to borrow a postgrad whenever they need to access the drive, and so you tested it on your own computer and it worked fine, and then as soon as you touched /etc/fstab on the honours student’s computer it just up and died and nothing you do for love nor God can get it to boot up again. Here is how to set up Ubuntu 19.04 on a computer to work, the first time.

Basics

0. Obtain a Ubuntu USB drive

You need to somehow create a bootable USB stick. This is easiest in Ubuntu and there are many tutorials already, so I won’t clutter it up.

1. Install Ubuntu and drivers

Stick the USB in and boot up the computer. You need to change the boot order to boot off the USB stick first. This differs across operating systems; on our old Ubuntu 16.04s, we hit F10 to bring up Boot Options.

You can choose a normal installation or a minimal one. Out of convenience, we go with the normal installation; the only weirdly irritating thing it installs is Amazon. This shouldn’t take long – ours was under 10 min.

The computer will reboot after this.

Do not reboot again before Step 3.

2. Reconfiguring grub and the display server

sudo apt upgrade
ubuntu-drivers autoinstall

These are most likely installed already, but you can check anyway:

sudo apt install build-essential
sudo apt install linux-headers-$(uname -r)

We found that if we rebooted our computer off the default installation, the displays wouldn’t work. It turns out this is probably because of the buggy Wayland display server, but we didn’t sit down to disentangle Wayland vs. Nvidia drivers (another common source of issues) vs. buggy video drivers as a whole.

You may like to install vim.

sudo apt install vim

Edit /etc/gdm3/custom.conf by uncommenting # WaylandEnable=false. This will forces the computer to use the Xorg display server, ie the one that actually works.

Edit /etc/default/grub. Replace:

GRUB_CMDLINE_LINUX_DEFAULT="quiet splash"

with

GRUB_CMDLINE_LINUX_DEFAULT="quiet splash nomodeset"

This will disable video drivers until the kernel has started. Update with:

sudo update-grub

Still do not reboot before Step 3.

3. Configure SSH

Before you reboot, set up SSH so you can get in if your displays die. This installs openssh-server, enables the service and starts the service.

sudo apt install openssh-server
sudo systemctl enable ssh
sudo systemctl start ssh

Test your access by ssh-ing in. To set up a firewall, first check that this line IPV6=yes is in /etc/default/ufw.

sudo ufw default deny incoming
sudo ufw default allow outgoing
sudo ufw allow ssh
sudo systemctl start ufw
sudo systemctl enable ufw

SSH keys

Later, you can set up SSH keys.

ssh-keygen -t rsa -b 4096

To copy your details over to other places:

ssh-copy-id username@destination

Extras

4. Checkinstall, GCC (optional)

Checkinstall

checkinstall is a useful tool that replaces make install. It build a .deb package that is easily removable with:

dpkg -r yourpackagename

sudo apt install checkinstall

5. Environment modules

Install dependencies. Here the latest tcl-dev is 8.6, but check.

sudo apt-get install tcl tcl8.6-dev

Download and unzip the latest Environment Modules. Here it’s 4.2.3. Navigate to the directory.

cd modules-4.2.3/

Make folders to store the modulefiles and packages

mkdir /store/packages /store/modules

Set up the build, make, and checkinstall it.

./configure
make
sudo checkinstall

If /etc/profile.d/modules.sh and /etc/profile.d/modules.csh already exist, skip this step. Otherwise, copy or symlink them.

sudo ln -s /usr/local/Modules/init/profile.sh /etc/profile.d/modules.sh
sudo ln -s /usr/local/Modules/init/profile.csh /etc/profile.d/modules.csh

Now, when you install applications, try to install them into /packages. Modulefiles are included in the repo for your convenience.

Note that the default path for modulefiles is /usr/local/Modules/modulefiles. Edit /usr/local/Modules/init/modulerc and add module use /store/modules to use the directory you made above.

6. Anaconda and Python

Download and install Anaconda before you do anything with Python. This will likely install Visual Studio Code as well, which is super helpful. Open a folder in VS Code with

code .

Environments

Create a new environment with

conda create --name myenv [python=3.6] [scipy=0.15.0]

Use the options in brackets if you need a specific version of Python and/or specific packages. You can also activate it and install directly into it.

Computational chemistry stuff

For information on compiling GROMACS, AMBER, and possibly other packages, go here.