Setup
The setup guide walks you through the process of setting up your developer environment on the SODAS server.
Projects
All compute projects are stored in the /projects/folder.
abc123@sodashead01fl /projects/main_compute-AUDIT $ tree -L 1
.
├── apps
├── data
├── people
└── scratch
Warning
Since the compute server (which is accessed via Slurm) does not have access to other network drives (i.e. h-drive and s-drives), you must store your project data and code in a compute project directory.
You can make a request for a new project at the UCPH service portal. Select FS-sodas under FS system
Configuration
Shared cache
TBD
Install custom software
uv
Install uv:
There are two different strategies for managing your virtual environments.
You can either do it by creating named environments in the ~/.virtualenvs/
folder, or by creating them locally in a .venv folder in your project.
TBD: Test what is fastest
Python projects
To make uv work on the network drives properly, you have to change the following setting first.
To get the full benefit of uv, you should initialize your python projects in the desired folder. This could be /projects/my_project/people/abc123/python/ or /projects/my_project/apps/python/.
When you have navigated to the desired folder, you can run
This will create some boiler plate, which will allow you to take advantage of uv's dependency management.
Then, to add a project dependency, you can run:
This will add the dependency to the uv.lock and pyproject.toml files, and install it into the venv.
Tip
uv stores venvs in .venv folder in the project directory, and initializes
them automatically with the above steps. You can also create a venv
manually by running uv venv
If you later found it it isn't needed for your project, you can remove it with:
To run your scripts, you can use the uv run command:
Using your environments
First you must activate your environment.
Tip
Add a function to your to easily activate virtual environments either named or local from anywhere on the server:
echo 'function activate() { if [ -n "$1" ]; then source ~/.virtualenvs/"$1"/bin/activate; else source ./.venv/bin/activate; fi; }' >> ~/.bashrc
This function will activate the virtual environment in the current directory, or from the name of the virtual environment.
You can then activate the environment by running activate or activate my-project.
Named environments
If you prefer named virtual environments, you can store them in ~/.virtualenvs/.
Here you can create new named virtual environments
JupyterLab
Warning
The following steps do not fully work, since
uv havn't added --include-deps flag yet
To install jupyterlab system-wide, we can run:
echo "alias jlab=\"jupyter-lab --port=8880 --ip=10.84.10.216 --no-browser\"" >> ~/.bashrc
echo "alias jadd=\"python -m ipykernel install --user --display-name \${PWD} --name \${PWD##*/}\"" >> ~/.bashrc
zsh
In this step of the guide, we will take you throw setting up zsh as your default shell, and installing oh-my-zsh
Building from source
Make directories for local installations and downloads
Download the latest version of zsh
Unpack the tarball
Build zsh from source
Remove the downloaded files
Find configuration examples online.
Starship
To get a better prompt, you can install starship:
And add the following to your ~/.zshrc:
Example
Here is an example of a starship.toml configuration file, it can be saved
in ~/.config/starship.toml
format = """
[](#9A348E)\
$username\
$hostname\
[](bg:#DA627D fg:#9A348E)\
$directory\
[](fg:#DA627D bg:#FCA17D)\
$git_branch\
$git_status\
[](fg:#FCA17D bg:#86BBD8)\
$nodejs\
$python\
[](fg:#86BBD8 bg:#06969A)\
$docker_context\
[](fg:#06969A bg:blue)\
$custom\
[](fg:blue) \
"""
right_format="""
$status $cmd_duration $time
"""
# Disable the blank line at the start of the prompt
add_newline = false
# You can also replace your username with a neat symbol like or disable this
# and use the os module below
[username]
show_always = true
style_user = "bg:#9A348E"
style_root = "bg:#9A348E"
format = "[$user]($style fg:black)"
disabled = false
[hostname]
ssh_symbol="@"
style="bg:#9A348E"
format="[$ssh_symbol$hostname]($style fg:black)"
[directory]
style = "bg:#DA627D fg:black"
format = "[ $path ]($style)"
truncation_length = 3
truncation_symbol = "…/"
# Here is how you can shorten some long paths by text replacement
# similar to mapped_locations in Oh My Posh:
[directory.substitutions]
"Documents" = " "
"Downloads" = " "
"Music" = " "
"Pictures" = " "
# Keep in mind that the order matters. For example:
# "Important Documents" = " "
# will not be replaced, because "Documents" was already substituted before.
# So either put "Important Documents" before "Documents" or use the substituted version:
# "Important " = " "
[docker_context]
symbol = " "
style = "bg:#06969A"
format = '[ $symbol $context ]($style)'
[git_branch]
symbol = ""
style = "bg:#FCA17D black"
format = '[ $symbol $branch ]($style)'
[git_status]
style = "bg:#FCA17D black"
format = '[$all_status$ahead_behind ]($style)'
[nodejs]
symbol = ""
style = "bg:#86BBD8"
format = '[ $symbol ($version) ]($style)'
[python]
style = "bg:#86BBD8 black"
symbol = " "
format = '[${symbol}($virtualenv) ]($style)'
[status]
format = '[$symbol$common_meaning$signal_name$maybe_int]($style) '
map_symbol = true
disabled = false
[cmd_duration]
min_time = 500
format = '[$duration](bold yellow)'
[time]
disabled = false
time_format = "%R" # Hour:Minute Format
style = ""
format = '[ $time]($style)'
[custom.slurm]
command = """
if [ ! -z "${SLURM_JOB_ID}" ]; then
echo " ${SLURM_JOB_ID}"
fi
"""
when = "[ ! -z \"${SLURM_JOB_ID}\" ]"
description = "Display current Slurm job ID"
style = "bg:blue black"
format = "[ $output ]($style)"
Environment Variables
TBD
Github
Generate SSH key
Follow the guide at GitHub.
SSH Config
Create a config file at ~/.ssh/config and add the following lines: