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

@@ -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"]

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