Hotfix/docker notebooks (#80)

* Fix to get notebooks working in docker --------- Co-authored-by: Frank Malatino <[email protected]>
NOAA-GFDL · Apr 18, 2024 · b8c8c53 · b8c8c53
1 parent 7e435fa
commit b8c8c53
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Showing 9 changed files with 779 additions and 2,176 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -2,12 +2,16 @@ FROM python:3.8.13-bullseye@sha256:2a01d88a1684e6d7f08030cf5ae73b536926c64076cab
 
 RUN apt-get update && apt-get install -y make \
     software-properties-common \
+    libgeos-dev \
     libopenmpi3 \
     libopenmpi-dev \
     libboost-all-dev \
     libhdf5-serial-dev \
     netcdf-bin \
     libnetcdf-dev \
+    libproj-dev \
+    proj-bin \
+    proj-data \
     python3 \
     python3-pip
 
@@ -22,5 +26,26 @@ COPY . /pace
 RUN cd /pace && \
     pip3 install -r /pace/requirements_dev.txt -c /pace/constraints.txt
 
+RUN cd / && \
+    git clone https://github.com/ai2cm/fv3net
+
+ENV CFLAGS="-I/usr/include -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H=1"
+
+RUN python3 -m pip install \
+    numpy==1.21.2 \
+    netCDF4==1.5.7 \
+    mpi4py==3.1.1 \
+    matplotlib==3.5.2 \
+    ipyparallel==8.4.1 \
+    jupyterlab==3.4.4 \
+    shapely==1.8.5 \
+    cartopy==0.18.0 \
+    jupyterlab_code_formatter==1.5.2 \
+    isort==5.10.1 \
+    black==22.3.0 \
+    /fv3net/external/vcm
+
+ENV PYTHONPATH=/fv3net/external/fv3viz:/pace/external/gt4py/src
+
 ENV OMPI_ALLOW_RUN_AS_ROOT=1
 ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
diff --git a/Makefile b/Makefile
@@ -20,12 +20,16 @@ BROWSER := python -c "$$BROWSER_PYSCRIPT"
 DOCKER_BUILDKIT=1
 SHELL=/bin/bash
 CWD=$(shell pwd)
+CMD ?=bash
 PULL ?=True
 DEV ?=y
 CHECK_CHANGED_SCRIPT=$(CWD)/changed_from_main.py
 CONTAINER_CMD?=docker
 SAVEPOINT_SETUP=pip3 list
 
+PORT ?=8888
+APP_NAME ?=Pace_dev
+
 VOLUMES ?=
 BUILD_FLAGS ?=
 
@@ -91,13 +95,19 @@ _force_build:
 
 enter:
 	docker run --rm -it \
-		--network host \
 		$(VOLUMES) \
-	$(PACE_IMAGE) bash
+		-p=$(PORT):$(PORT) \
+		--name="$(APP_NAME)" \
+	$(PACE_IMAGE) $(CMD)
 
 dev:
 	DEV=y $(MAKE) enter
 
+notebook:
+	CMD="jupyter notebook --ip 0.0.0.0 --no-browser --allow-root --notebook-dir=/pace/examples/notebooks" \
+	DEV=y \
+	$(MAKE) enter
+
 test_util:
 	if [ $(shell $(CHECK_CHANGED_SCRIPT) util) != false ]; then \
 		$(MAKE) -C util test; \

diff --git a/examples/Dockerfile b/examples/Dockerfile
diff --git a/examples/Makefile b/examples/Makefile
diff --git a/examples/README.md b/examples/README.md
@@ -4,11 +4,11 @@ This directory serves as a demo of how you can develop and run individual compon
 
 ## Getting started
 
-The easiest way of running these demos is using a Docker container. If you do not already have Docker installed, it can be downloaded directly from [Docker](https://www.docker.com/). Once Docker is set up, you can build and run the container:
+The easiest way of running these demos is using a Docker container. If you do not already have Docker installed, it can be downloaded directly from [Docker](https://www.docker.com/). Once Docker is set up, you can build and run the container from the root Pace directory:
 
 ```
 make build
-make run
+make notebook
 ```
 
 Once the docker container is running, you can connect to the Jupyter notebook server by copying and pasting the URLs into any browser on your machine. An example output is shown below:

diff --git a/examples/notebooks/functions.py b/examples/notebooks/functions.py
@@ -272,7 +272,9 @@ def configure_domain(
     quantity_factory = QuantityFactory.from_backend(sizer=sizer, backend=backend)
 
     metric_terms = MetricTerms(
-        quantity_factory=quantity_factory, communicator=communicator
+        quantity_factory=quantity_factory,
+        communicator=communicator,
+        eta_file="eta79.nc",
     )
 
     # workaround for single layer