uclh-infrastructure-setup.md

UCLH Infrastructure setup instructions

Install shared miniforge installation if it doesn't exist

Follow the suggestion for installing a central miniforge installation to allow all users to be able to run modern python without having admin permissions.

# Create directory with correct structure (only if it doesn't exist yet)
mkdir /gae/miniforge3
chgrp -R docker /gae/miniforge3
chmod -R g+rwxs /gae/miniforge3  # inherit group when new directories or files are created
setfacl -R -m d:g::rwX /gae/miniforge3
# Install miniforge
wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh -p /gae/miniforge3
conda update -n base -c conda-forge conda
conda create -n pixl_dev python=3.10.*

The directory should now have these permissions

> ls -lah /gae/miniforge3/
total 88K
drwxrws---+  19 jstein01 docker 4.0K Nov 28 12:27 .
drwxrwx---.  18 root     docker 4.0K Dec  1 19:35 ..
drwxrws---+   2 jstein01 docker 8.0K Nov 28 12:27 bin
drwxrws---+   2 jstein01 docker   30 Nov 28 11:49 compiler_compat
drwxrws---+   2 jstein01 docker   32 Nov 28 11:49 condabin
drwxrws---+   2 jstein01 docker 8.0K Nov 28 12:27 conda-meta
-rw-rws---.   1 jstein01 docker   24 Nov 28 11:49 .condarc
...

If you haven't just installed the miniforge yourself, update your configuration

Edit ~/.bash_profile to add /gae/miniforge3/bin to the PATH. for example

PATH=$PATH:$HOME/.local/bin:$HOME/bin:/gae/miniforge3/bin

Run the updated profile (or reconnect to the GAE) so that conda is in your PATH

source ~/.bash_profile

Initialise conda

conda init bash

Run the updated profile (or reconnect to the GAE) so that conda is in your PATH

source ~/.bash_profile

Activate an existing pixl environment

conda activate pixl_dev

Create an instance for the GAE if it doesn't already exist

Select a place for the deployment. On UCLH infrastructure this will be in /gae, so /gae/pixl_dev for example.

mkdir /gae/pixl_dev
chgrp -R docker /gae/pixl_dev
chmod -R g+rwxs /gae/pixl_dev  # inherit group when new directories or files are created
setfacl -R -m d:g::rwX /gae/pixl_dev
# now clone the repository or copy an existing deployment