Merge pull request #117 from dynamicslab/lp/patch-1

Improvement of Developer's Experience

.devcontainer/devcontainer.json

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+{
+	"name": "HydroGym Devpod",
+
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	// 	pulling from Dockerhub
+	"image": "lpaehler/hydrogym-devpod:stable",
+	"features": {
+		"ghcr.io/devcontainers-contrib/features/black:2": {},
+		"ghcr.io/devcontainers-contrib/features/poetry:2": {},
+		"ghcr.io/devcontainers-contrib/features/ruff:1": {}
+	},
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// Setting up an editable version of HydroGym
+	"postCreateCommand": "pip install -e ."
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.packaging/Dockerfile.devpod

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+# Full Firedrake pre-installed with all of it enabled
+FROM lpaehler/hydrogym-env:stable
+
+# Activation of the virtual environment
+RUN bash -c "source firedrake/bin/activate"
+
+# Clone HydroGym
+RUN bash -c "git clone https://github.com/dynamicslab/hydrogym.git"
+
+# Installation of HydroGym's dependencies, and only the
+# the dependencies
+RUN bash -c "cd hydrogym && pip install -r requirements.txt"

.packaging/Dockerfile.firedrake_env

@@ -0,0 +1,167 @@
+# DockerFile for an environment into which firedrake can be installed.
+#   entirely based on:
+#   https://github.com/firedrakeproject/firedrake/blob/master/docker/Dockerfile.env
+FROM ubuntu:22.04
+
+# Update and install required packages for Firedrake
+USER root
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+RUN apt-get update \
+    && apt-get -y dist-upgrade \
+    && DEBIAN_FRONTEND=noninteractive apt-get -y install tzdata \
+    && apt-get -y install curl vim docker.io \
+                 openssh-client build-essential autoconf automake \
+                 cmake gfortran git libopenblas-serial-dev \
+                 libtool python3-dev python3-pip python3-tk python3-venv \
+                 python3-requests zlib1g-dev libboost-dev sudo gmsh \
+                 bison flex \
+                 liboce-ocaf-dev \
+                 swig graphviz \
+                 libcurl4-openssl-dev libxml2-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Use a more sane locale
+ENV LC_ALL C.UTF-8
+
+# Set up user so that we do not run as root
+RUN useradd -m -s /bin/bash -G sudo firedrake && \
+    echo "firedrake:docker" | chpasswd && \
+    echo "firedrake ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers && \
+    ldconfig
+
+USER firedrake
+WORKDIR /home/firedrake
+
+# Fetch PETSc, SLEPc and eigen
+RUN git clone https://github.com/firedrakeproject/petsc.git
+RUN git clone https://github.com/firedrakeproject/slepc.git
+
+# Build MPICH manually because we don't want PETSc to build it twice
+RUN bash -c 'cd petsc; \
+    ./configure \
+        --COPTFLAGS=-O3 -march=native -mtune=native \
+        --CXXOPTFLAGS=-O3 -march=native -mtune=native \
+        --FOPTFLAGS=-O3 -march=native -mtune=native \
+        --with-c2html=0 \
+        --with-debugging=0 \
+        --with-fortran-bindings=0 \
+        --with-make-np=12 \
+        --with-shared-libraries=1 \
+        --with-zlib \
+        --download-chaco \
+        --download-fftw \
+        --download-hdf5 \
+        --download-hwloc \
+        --download-hypre \
+        --download-metis \
+        --download-ml \
+        --download-mumps \
+        --download-mpich \
+        --download-mpich-device=ch3:sock \
+        --download-netcdf \
+        --download-pastix \
+        --download-pnetcdf \
+        --download-ptscotch \
+        --download-scalapack \
+        --download-suitesparse \
+        --download-superlu_dist \
+        PETSC_ARCH=packages; \
+        mv packages/include/petscconf.h packages/include/old_petscconf.nope;'
+# Don't run make here, we only want MPICH and HWLOC
+# It is also necessary to move `petscconf.h` so packages isn't treated like a working PETSc
+
+# Build default Firedrake PETSc
+RUN bash -c 'export PACKAGES=/home/firedrake/petsc/packages; \
+    cd petsc; \
+    ./configure \
+        --COPTFLAGS=-O3 -march=native -mtune=native \
+        --CXXOPTFLAGS=-O3 -march=native -mtune=native \
+        --FOPTFLAGS=-O3 -march=native -mtune=native \
+        --with-c2html=0 \
+        --with-debugging=0 \
+        --with-fortran-bindings=0 \
+        --with-make-np=12 \
+        --with-shared-libraries=1 \
+        --with-bison \
+        --with-flex \
+        --with-zlib \
+        --with-chaco-dir=$PACKAGES \
+        --with-fftw-dir=$PACKAGES \
+        --with-hdf5-dir=$PACKAGES \
+        --with-hwloc-dir=$PACKAGES \
+        --with-hypre-dir=$PACKAGES \
+        --with-metis-dir=$PACKAGES \
+        --with-ml-dir=$PACKAGES \
+        --with-mpi-dir=$PACKAGES \
+        --with-mumps-dir=$PACKAGES \
+        --with-netcdf-dir=$PACKAGES \
+        --with-pastix-dir=$PACKAGES \
+        --with-pnetcdf-dir=$PACKAGES \
+        --with-ptscotch-dir=$PACKAGES \
+        --with-scalapack-dir=$PACKAGES \
+        --with-suitesparse-dir=$PACKAGES \
+        --with-superlu_dist-dir=$PACKAGES \
+        PETSC_ARCH=default; \
+    make PETSC_DIR=/home/firedrake/petsc PETSC_ARCH=default all;'
+
+# Build default Firedrake SLEPc
+RUN bash -c 'export PETSC_DIR=/home/firedrake/petsc; \
+    export PETSC_ARCH=default; \
+    cd slepc; \
+    ./configure; \
+    make SLEPC_DIR=/home/firedrake/slepc PETSC_DIR=/home/firedrake/petsc PETSC_ARCH=default;'
+
+# Additionally build complex PETSc for Firedrake
+RUN bash -c 'export PACKAGES=/home/firedrake/petsc/packages; \
+    cd petsc; \
+    ./configure \
+        --COPTFLAGS=-O3 -march=native -mtune=native \
+        --CXXOPTFLAGS=-O3 -march=native -mtune=native \
+        --FOPTFLAGS=-O3 -march=native -mtune=native \
+        --with-c2html=0 \
+        --with-debugging=0 \
+        --with-fortran-bindings=0 \
+        --with-make-np=12 \
+        --with-scalar-type=complex \
+        --with-shared-libraries=1 \
+        --with-bison \
+        --with-flex \
+        --with-zlib \
+        --with-chaco-dir=$PACKAGES \
+        --with-fftw-dir=$PACKAGES \
+        --with-hdf5-dir=$PACKAGES \
+        --with-hwloc-dir=$PACKAGES \
+        --with-metis-dir=$PACKAGES \
+        --with-mpi-dir=$PACKAGES \
+        --with-mumps-dir=$PACKAGES \
+        --with-netcdf-dir=$PACKAGES \
+        --with-pastix-dir=$PACKAGES \
+        --with-pnetcdf-dir=$PACKAGES \
+        --with-ptscotch-dir=$PACKAGES \
+        --with-scalapack-dir=$PACKAGES \
+        --with-suitesparse-dir=$PACKAGES \
+        --with-superlu_dist-dir=$PACKAGES \
+        PETSC_ARCH=complex; \
+    make PETSC_DIR=/home/firedrake/petsc PETSC_ARCH=complex all;'
+
+# Build complex Firedrake SLEPc
+RUN bash -c 'export PETSC_DIR=/home/firedrake/petsc; \
+    export PETSC_ARCH=complex; \
+    cd slepc; \
+    ./configure; \
+    make SLEPC_DIR=/home/firedrake/slepc PETSC_DIR=/home/firedrake/petsc PETSC_ARCH=complex;'
+
+# Clean up unnecessary files
+RUN rm -rf /home/firedrake/petsc/**/externalpackages \
+    && rm -rf /home/firedrake/petsc/src/docs \
+    && rm -f /home/firedrake/petsc/src/**/tutorials/output/* \
+    && rm -f /home/firedrake/petsc/src/**/tests/output/*
+
+# Set some useful environment variables
+ENV PETSC_DIR /home/firedrake/petsc
+ENV SLEPC_DIR /home/firedrake/slepc
+ENV MPICH_DIR /home/firedrake/petsc/packages/bin
+ENV HDF5_DIR /home/firedrake/petsc/packages
+ENV HDF5_MPI ON
+ENV OMP_NUM_THREADS 1
+ENV OPENBLAS_NUM_THREADS 1

.packaging/Dockerfile.hydrogym

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+# Dockerfile with HydroGym included
+#   --> highly unstable for now.
+
+FROM lpaehler/hydrogym-env:stable
+
+USER firedrake
+WORKDIR /home/firedrake
+
+# Activation of the virtual environment
+RUN bash -c "source firedrake/bin/activate"
+
+# Clone HydroGym
+RUN bash -c "git clone https://github.com/dynamicslab/hydrogym.git"
+
+# Installation of HydroGym
+RUN bash -c "cd hydrogym && pip install ."
+
+#RUN bash -c ". $VENV/bin/activate && pip install -e /home/hydrogym"
+#RUN bash -c ". $VENV_COMPLEX/bin/activate && pip install -e /home/hydrogym"

.packaging/Dockerfile.hydrogym_env

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+# Dockerfile for a fully enabled Firedrake as base environment for HydroGym
+#   Based on:
+#   https://github.com/firedrakeproject/firedrake/blob/master/docker/Dockerfile.vanilla
+#   https://github.com/firedrakeproject/firedrake/blob/master/docker/Dockerfile.firedrake
+
+FROM lpaehler/hydrogym-firedrake-env:stable
+
+USER firedrake
+WORKDIR /home/firedrake
+
+ENV PETSC_ARCH default
+
+# Installation of basic Firedrake.
+RUN curl -O https://raw.githubusercontent.com/firedrakeproject/firedrake/master/scripts/firedrake-install
+RUN bash -c "python3 firedrake-install \
+    --no-package-manager \
+    --disable-ssh \
+    --torch \
+    --honour-petsc-dir \
+    --mpicc=$MPICH_DIR/mpicc \
+    --mpicxx=$MPICH_DIR/mpicxx \
+    --mpif90=$MPICH_DIR/mpif90 \
+    --mpiexec=$MPICH_DIR/mpiexec"
+
+# Installation of extra Firedrake components.
+RUN bash -c "source firedrake/bin/activate; \
+    firedrake-update \
+        --documentation-dependencies \
+        --netgen \
+        --slepc \
+        --tinyasm \
+        --install femlium \
+        --install fascd \
+        --install gusto \
+        --install icepack \
+        --install irksome \
+        --install thetis"