Skip to content
Merged
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
31 changes: 31 additions & 0 deletions internal/computer_setup.md
Original file line number Diff line number Diff line change
Expand Up @@ -66,3 +66,34 @@ Sudo usermod -aG docker $USER
newgrp docker

docker run hello-world

## Using uv on CU Anschutz HPC Alpine (early 2026)

`uv` is not currently a standard, always-available Alpine module (as of early 2026).
Load it from the Way Lab module path, then set storage locations on project storage before creating environments or installing tools.

If you skip the storage exports below, `uv` may write into default home locations and cause storage/quota issues.

```bash
module use --append /pl/active/koala/software/lmod-files
module load uv
# test that uv loaded
uv -v
Comment thread
d33bs marked this conversation as resolved.

# uv paths on HPC project storage
export UV_BASE=/projects/$USER/uv
export UV_CACHE_DIR="$UV_BASE/cache"
export UV_PYTHON_INSTALL_DIR="$UV_BASE/python"
export UV_TOOL_DIR="$UV_BASE/tools"
Comment thread
d33bs marked this conversation as resolved.

# set the exact path to the bin
# if you do not set this then alpine will assume that the binary is found in their default location
# this is important when running anything from scratch space
ENV_PATH="/projects/mlippincott@xsede.org/software/uv/envs/nf1_uv_env/.venv"

# This assigns the python binary path in the correct uv env
PYTHON_BIN="$ENV_PATH/bin/python3"

# this calls the python kernel from the correct env
"$PYTHON_BIN" python_script.py
```
Loading