From 6efdddb16ef0fcc79db8d4cda32543e6959b8227 Mon Sep 17 00:00:00 2001 From: d33bs Date: Fri, 17 Apr 2026 15:47:39 -0600 Subject: [PATCH 1/4] add uv instructions for alpin Co-Authored-By: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> --- internal/computer_setup.md | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/internal/computer_setup.md b/internal/computer_setup.md index dcac506..5fc4e88 100644 --- a/internal/computer_setup.md +++ b/internal/computer_setup.md @@ -66,3 +66,23 @@ Sudo usermod -aG docker $USER newgrp docker docker run hello-world + +## Using uv on CU Anschutz HPC Alpine (early 2026) + +`uv` is not currently a standard, always-available Alpine module (as of early 2026). +Load it from the Way Lab module path, then set storage locations on project storage before creating environments or installing tools. + +If you skip the storage exports below, `uv` may write into default home locations and cause storage/quota issues. + +```bash +module use --append /pl/active/koala/software/lmod-files +module load uv +# test that uv loaded +uv -v + +# uv paths on HPC project storage +export UV_BASE=/projects/$USER/uv +export UV_CACHE_DIR="$UV_BASE/cache" +export UV_PYTHON_INSTALL_DIR="$UV_BASE/python" +export UV_TOOL_DIR="$UV_BASE/tools" +``` From 154d67459130a3b4bf2e74873ef0c13100c0c314 Mon Sep 17 00:00:00 2001 From: Dave Bunten Date: Fri, 8 May 2026 13:58:04 -0600 Subject: [PATCH 2/4] Update internal/computer_setup.md Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> --- internal/computer_setup.md | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/internal/computer_setup.md b/internal/computer_setup.md index 5fc4e88..8716035 100644 --- a/internal/computer_setup.md +++ b/internal/computer_setup.md @@ -85,4 +85,14 @@ export UV_BASE=/projects/$USER/uv export UV_CACHE_DIR="$UV_BASE/cache" export UV_PYTHON_INSTALL_DIR="$UV_BASE/python" export UV_TOOL_DIR="$UV_BASE/tools" -``` + +# set the exact path to the bin +# if you do not set this then alpine will assume that the binary is found in their default location +# this is important when running anything from scratch space +ENV_PATH="/projects/mlippincott@xsede.org/software/uv/envs/nf1_uv_env/.venv" + +# This assigns the python binary path in the correct uv env +PYTHON_BIN="$ENV_PATH/bin/python3" + +# this calls the python kernel from the correct env +"$PYTHON_BIN" python_script.py From 5c65d2b420f257331bcf13d6928da89ecb16706d Mon Sep 17 00:00:00 2001 From: d33bs Date: Fri, 8 May 2026 13:59:22 -0600 Subject: [PATCH 3/4] Update computer_setup.md --- internal/computer_setup.md | 1 + 1 file changed, 1 insertion(+) diff --git a/internal/computer_setup.md b/internal/computer_setup.md index 8716035..5c6cf0e 100644 --- a/internal/computer_setup.md +++ b/internal/computer_setup.md @@ -96,3 +96,4 @@ PYTHON_BIN="$ENV_PATH/bin/python3" # this calls the python kernel from the correct env "$PYTHON_BIN" python_script.py +``` From 7d97650d071ada2d46d7c080efe7f2f9b533d6b8 Mon Sep 17 00:00:00 2001 From: d33bs Date: Fri, 8 May 2026 13:59:49 -0600 Subject: [PATCH 4/4] Update computer_setup.md --- internal/computer_setup.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/internal/computer_setup.md b/internal/computer_setup.md index 5c6cf0e..e22ecb8 100644 --- a/internal/computer_setup.md +++ b/internal/computer_setup.md @@ -87,7 +87,7 @@ export UV_PYTHON_INSTALL_DIR="$UV_BASE/python" export UV_TOOL_DIR="$UV_BASE/tools" # 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 +# 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"