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.
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
1 2 sudo apt upgrade ubuntu-drivers autoinstall
These are most likely installed already, but you can check anyway:
1 2 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.
1 sudo apt install vim
/etc/gdm3/custom.conf by uncommenting
This will forces the computer to use the Xorg display server, ie the one that actually works.
1 GRUB_CMDLINE_LINUX_DEFAULT="quiet splash"
1 GRUB_CMDLINE_LINUX_DEFAULT="quiet splash nomodeset"
This will disable video drivers until the kernel has started. Update with:
1 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.
1 2 3 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
1 2 3 4 5 sudo ufw default deny incoming sudo ufw default allow outgoing sudo ufw allow ssh sudo systemctl start ufw sudo systemctl enable ufw
Later, you can set up SSH keys.
1 ssh-keygen -t rsa -b 4096
To copy your details over to other places:
1 ssh-copy-id username@destination
4. Checkinstall, GCC (optional)
checkinstall is a useful tool that replaces
make install. It build a .deb package that is easily removable with:
1 dpkg -r yourpackagename
1 sudo apt install checkinstall
5. Environment modules
Install dependencies. Here the latest tcl-dev is 8.6, but check.
1 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.
1 cd modules-4.2.3/
Make folders to store the modulefiles and packages
1 mkdir /store/packages /store/modules
Set up the build, make, and checkinstall it.
1 2 3 ./configure make sudo checkinstall
/etc/profile.d/modules.csh already exist, skip this step. Otherwise, copy or symlink them.
1 2 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/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
1 code .
Create a new environment with
1 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.