From cb7aab785edc8aafd94b721d2e13548925e5989f Mon Sep 17 00:00:00 2001
From: Fabian Zills <46721498+PythonFZ@users.noreply.github.com>
Date: Fri, 19 Apr 2024 14:31:23 +0200
Subject: [PATCH] update docker image (#288)

* update docker image

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update docker permission issues description

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* jupyter support

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 Dockerfile    | 19 +++++++++----------
 README.md     | 21 ++++++++++++++++++++-
 entrypoint.sh | 23 -----------------------
 3 files changed, 29 insertions(+), 34 deletions(-)
 delete mode 100644 entrypoint.sh

diff --git a/Dockerfile b/Dockerfile
index 78a598d7..a19dfff6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,17 +1,16 @@
-FROM pytorch/pytorch:2.1.2-cuda11.8-cudnn8-runtime
-RUN conda install git
+FROM python:3.11
+RUN apt update && apt install -y git
 
-COPY . /workspace/ipsuite
+# RUN python3 -m pip config set global.break-system-packages true
 
+COPY . /workspace/ipsuite
 WORKDIR /workspace/ipsuite
-RUN pip install .[comparison,gap,nequip,apax,allegro,mace]
-RUN pip install --upgrade torch --extra-index-url https://download.pytorch.org/whl/cu116
-RUN pip install --upgrade "jax[cuda11_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+
+RUN pip install .[comparison,gap,apax,mace]
+RUN pip install --upgrade torch torchvision torchaudio
+RUN pip install --upgrade "jax[cuda12_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
 RUN pip install git+https://github.com/PythonFZ/torch-dftd.git@patch-2
 RUN pip install dvc-s3
-
-COPY entrypoint.sh entrypoint.sh
-RUN chmod +x entrypoint.sh
+RUN pip install --no-cache-dir notebook jupyterlab
 
 WORKDIR /app
-ENTRYPOINT ["/workspace/ipsuite/entrypoint.sh"]
diff --git a/README.md b/README.md
index 91b3a85c..84ffbb2c 100644
--- a/README.md
+++ b/README.md
@@ -27,12 +27,31 @@ Examples can be found at:
 
 # Docker Image
 
-You can use IPSuite directly from within docker by calling it e.g. like:
+We provide an IPSuite docker image for Linux that includes the `apax`, `mace`
+and `gap` MLPs. You can use IPSuite directly from within the image by calling:
 
 ```sh
 docker run -it -v "$(pwd):/app" --gpus all pythonf/ipsuite dvc repro
 docker run -it -v "$(pwd):/app" --gpus all pythonf/ipsuite python
 docker run -it -v "$(pwd):/app" --gpus all pythonf/ipsuite zntrack list
+docker run -it -v "$(pwd):/app" --gpus all --rm -p 8888:8888 pythonf/ipsuite jupyter lab --ip=0.0.0.0 --port=8888 --allow-root
+```
+
+## Fix Permission Issues
+
+Running `dvc repro` via the docker container will create files owned by
+`root:root`. If you solely use docker this will not cause any issues. If you
+switch between docker and a `dvc` version on your host system, you might
+encounter permission errors. You can resolve them, by changing the ownership of
+the files. You can do this via the host `chown "$(id -u):$(id -g)" -R .` or from
+inside the docker container:
+
+```sh
+echo $(id -u):$(id -g)
+docker run -it -v "$(pwd):/app" pythonf/ipsuite /bin/bash
+addgroup --gid $GROUP_ID user
+adduser --disabled-password --gecos '' --uid $USER_ID --gid $GROUP_ID user
+chown user:user -R .
 ```
 
 # References
diff --git a/entrypoint.sh b/entrypoint.sh
deleted file mode 100644
index 7d9a532c..00000000
--- a/entrypoint.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/bin/bash
-
-# Check the command passed to the container
-case "$1" in
-  python)
-    # If "python" is passed, open a Python shell
-    exec python
-    ;;
-  dvc)
-    # If "dvc" is passed, run "dvc repro" with the rest of the arguments
-    shift
-    exec dvc "$@"
-    ;;
-  zntrack)
-    # If "zntrack" is passed, run "zntrack" with the rest of the arguments
-    shift
-    exec zntrack "$@"
-    ;;
-  *)
-    # Default: run the command as is
-    exec "$@"
-    ;;
-esac