From e5df6b8b4753f9c04613287c81d4b12b08931aff Mon Sep 17 00:00:00 2001
From: gaelforget <gforget@mit.edu>
Date: Sun, 26 Jun 2022 18:30:15 -0400
Subject: [PATCH] add R, octave + kernels + compile MITgcm + README

---
 Dockerfile               | 13 ++++++++++++-
 README.md                |  7 ++++++-
 src/build_MITgcm_ECCO.sh | 16 ++++++++++++++++
 3 files changed, 34 insertions(+), 2 deletions(-)
 create mode 100644 src/build_MITgcm_ECCO.sh

diff --git a/Dockerfile b/Dockerfile
index b676edd..0c7e56d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -24,7 +24,8 @@ ENV JULIA_PROJECT ${USER_HOME_DIR}
 ENV JULIA_DEPOT_PATH ${USER_HOME_DIR}/.julia
 
 RUN conda config --env --add channels conda-forge
-RUN conda install numpy xarray dask pandas rise
+RUN conda config --env --add channels r
+RUN conda install numpy xarray dask pandas rise octave_kernel texinfo r-irkernel
 RUN julia -e "import Pkg; Pkg.Registry.update(); Pkg.instantiate();"
 
 USER root
@@ -32,6 +33,8 @@ USER root
 RUN apt-get update && \
     apt-get install -y --no-install-recommends build-essential && \
     apt-get install -y --no-install-recommends vim && \
+    apt-get install -y --no-install-recommends git && \
+    apt-get install -y --no-install-recommends unzip && \
     apt-get install -y --no-install-recommends gfortran && \
     apt-get install -y --no-install-recommends openmpi-bin && \
     apt-get install -y --no-install-recommends openmpi-doc && \
@@ -39,6 +42,11 @@ RUN apt-get update && \
     apt-get install -y --no-install-recommends mpich && \
     apt-get install -y --no-install-recommends libnetcdf-dev && \
     apt-get install -y --no-install-recommends libnetcdff-dev && \
+    apt-get install -y --no-install-recommends octave && \
+    apt-get install -y --no-install-recommends octave-doc && \
+    apt-get install -y --no-install-recommends octave-info && \
+    apt-get install -y --no-install-recommends octave-htmldoc && \
+    apt-get install -y --no-install-recommends liboctave-dev && \
     apt-get clean && rm -rf /var/lib/apt/lists/*
 
 USER ${NB_USER}
@@ -52,3 +60,6 @@ RUN jupyter labextension install @jupyterlab/server-proxy && \
 RUN julia --project=${mainpath} -e "import Pkg; Pkg.instantiate();"
 RUN julia ${mainpath}/src/download_stuff.jl
 
+ENV MPI_INC_DIR /usr/lib/x86_64-linux-gnu/openmpi/include
+RUN source ./src/build_MITgcm_ECCO.sh
+
diff --git a/README.md b/README.md
index 53f5930..6d95e4e 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,10 @@
 
-This repository is based on the Docker configuration in [JuliaClimate/Notebooks](https://github.com/JuliaClimate/Notebooks). It provides a [Docker image](https://www.docker.com) that makes it easy to analyze and run [NASA / ECCO](https://ecco-group.org) solutions.
+This [Docker image](https://www.docker.com) configuration makes it easy to analyze and run [NASA](https://ecco-group.org) ocean state estimates and other [MITgcm](http://mitgcm.org) model solutions. It derives from the [JuliaClimate/Notebooks](https://github.com/JuliaClimate/Notebooks) configuration and includes :
+
+- [MITgcm](https://mitgcm.readthedocs.io/en/latest/?badge=latest) (67z) compiled for [ECCOv4](https://eccov4.readthedocs.io/en/latest/) (r2)
+- gfortran, mpi, and netcdf libraries for MITgcm
+- Julia, R, and Python kernels (for Jupyter notebooks)
+- Support for Pluto notebook (+ Jupyter + terminal)
 
 !!! warning
     Work in progress...
diff --git a/src/build_MITgcm_ECCO.sh b/src/build_MITgcm_ECCO.sh
new file mode 100644
index 0000000..29323ae
--- /dev/null
+++ b/src/build_MITgcm_ECCO.sh
@@ -0,0 +1,16 @@
+#!/bin/sh
+
+git clone --depth 1 --branch checkpoint67z https://github.com/MITgcm/MITgcm
+git clone https://github.com/gaelforget/ECCOv4
+
+mkdir MITgcm/mysetups
+mv ECCOv4 MITgcm/mysetups/.
+
+#export MPI_INC_DIR=/usr/lib/x86_64-linux-gnu/openmpi/include
+
+cd MITgcm/mysetups/ECCOv4/build
+../../../tools/genmake2 -mods=../code -mpi
+make depend
+make -j 4
+cd ..
+