Clean up precice/adapter Dockerfiles

adapters/Dockerfile.calculix-adapter

@@ -1,10 +1,14 @@
+# Dockerfile for building the calculix-adapter for preCICE
+# NOTE: Built for CalculiX v2.16
+
+# Building on top of the latest preCICE-build
 ARG branch=develop
 ARG from=precice/precice-ubuntu1804.home-${branch}
 FROM $from
 
 USER root
 
-# ( since we are importing form the precice image )
+# Install dependencies
 RUN apt-get -qq update && apt-get -qq install \
     build-essential \
     gfortran \
@@ -19,20 +23,24 @@ RUN apt-get -qq update && apt-get -qq install \
     libyaml-cpp-dev && \
     rm -rf /var/lib/apt/lists/*
 
+# Rebuild image from here if `force_rebuild` is enabled
 ARG CACHEBUST
 
 USER precice
-# get calculix source
+
+# Get calculix source (using version 2.16)
 WORKDIR /home/precice
 RUN curl -s http://www.dhondt.de/ccx_2.16.src.tar.bz2 | tar -xj
+
+# Get adapter source
 ARG adapter_branch=develop
 RUN git clone --depth 1 --branch $adapter_branch https://github.com/precice/calculix-adapter.git
 
-# build adapter
+# Build adapter
 WORKDIR calculix-adapter/
 RUN make -j $(nproc)
 
-# create directory for input/out/exchange
+# Create directory for input/out/exchange
 WORKDIR /home/precice
 RUN mkdir -p Logs Data/Input Data/Output Data/Exchange
 ENV PATH="/home/precice/calculix-adapter/bin:${PATH}"

adapters/Dockerfile.codeaster-adapter

@@ -1,3 +1,6 @@
+# Dockerfile for building the codeaster-adapter for preCICE
+
+# Building on top of the latest preCICE-build
 ARG branch=develop
 ARG from=precice/precice-ubuntu1804.home-${branch}
 ARG base_solver=precice/codeaster
@@ -7,20 +10,18 @@ FROM $from
 USER root
 ENV USER=root
 
-# Install dependecies
+# Install dependencies
 RUN apt-get -qq update && apt-get -qq install \
     git \
     locales \
     python3-pip \
     python3-numpy && \
     rm -rf /var/lib/apt/lists/*
 
-RUN locale-gen en_US.UTF-8
-ENV LANG en_US.UTF-8
-ENV LANGUAGE en_US:en
-ENV LC_ALL en_US.UTF-8
+# Rebuild image from here if `force_rebuild` is enabled
+ARG CACHEBUST
 
-# Building Code_Aster-adapter
+# Build Code_Aster-adapter
 USER precice
 WORKDIR /home/precice
 
@@ -38,6 +39,6 @@ RUN \
 RUN \
     mkdir Data Logs && cd Data && mkdir Exchange Input Output
 
-# Installing python bindings for preCICE
+# Install python bindings for preCICE
 RUN \
     pip3 install --upgrade pip && pip3 install --user pyprecice

adapters/Dockerfile.dealii-adapter

@@ -1,21 +1,29 @@
+# Dockerfile for building the dealii-adapter for preCICE
+# NOTE: Built with dimension argument set to 2.
+
+# Building on top of the latest preCICE-build
 ARG branch=develop
 ARG from=precice/precice-ubuntu1804.home-${branch}
 ARG base_solver=precice/deal.ii
 FROM ${base_solver} as deal.ii
 FROM $from
 
+# Rebuild image from here if `force_rebuild` is enabled
 ARG CACHEBUST
 
+# Get solver
 COPY --from=deal.ii /home/precice/dealii/ /home/precice/dealii/
 COPY --from=deal.ii /home/precice/dealii_build/ /home/precice/dealii_build/
 
 USER precice
 WORKDIR /home/precice
 RUN mkdir -p Logs Data/Input Data/Output Data/Exchange
 
+# Get adapter source
 ARG adapter_branch=develop
 RUN git clone --depth 1 --branch $adapter_branch https://github.com/precice/dealii-adapter.git
 
+# Build adapter
 RUN cd dealii-adapter/linear_elasticity/ && \
     cmake -DDEAL_II_DIR=$HOME/dealii_build -DDIM=2 -DCMAKE_BUILD_TYPE=Release . && \
     make -j $(nproc)

adapters/Dockerfile.dealii-adapter_3D

@@ -1,21 +1,29 @@
+# Dockerfile for building the dealii-adapter for preCICE
+# NOTE: Built with dimension argument set to 3.
+
+# Building on top of the latest preCICE-build
 ARG branch=develop
 ARG from=precice/precice-ubuntu1804.home-${branch}
 ARG base_solver=precice/deal.ii
 FROM ${base_solver} as deal.ii
 FROM $from
 
+# Rebuild image from here if `force_rebuild` is enabled
 ARG CACHEBUST
 
+# Get solver
 COPY --from=deal.ii /home/precice/dealii/ /home/precice/dealii/
 COPY --from=deal.ii /home/precice/dealii_build/ /home/precice/dealii_build/
 
 USER precice
 WORKDIR /home/precice
 RUN mkdir -p Logs Data/Input Data/Output Data/Exchange
 
+# Get adapter source
 ARG adapter_branch=develop
 RUN git clone --branch $adapter_branch https://github.com/precice/dealii-adapter.git
 
+# Build adapter
 RUN cd dealii-adapter/linear_elasticity/ && \
     cmake -DDEAL_II_DIR=$HOME/dealii_build -DDIM=3 -DCMAKE_BUILD_TYPE=Release . && \
     make -j $(nproc)

adapters/Dockerfile.fenics-adapter

@@ -1,4 +1,9 @@
-# System testing preCICE with fenics-adapter
+# Dockerfile for building the fenics-adapter for preCICE
+# NOTE: At the moment, fenics has some dependency issues, which
+#       requires us to use some workarounds for building the adapter.
+#       At a later point, these workarounds should be removed:
+#         1. precice-Ubuntu1804.package being built with outdated PETSc version
+#         2. Manually uninstalling the fenics-ufl package (in this file)
 
 # Building on top of the latest preCICE-build
 ARG branch=develop
@@ -9,7 +14,7 @@ USER root
 ENV USER=root
 ENV DEBIAN_FRONTEND=noninteractive
 
-# Installing necessary dependencies
+# Install necessary dependencies
 RUN apt-get -qq update && apt-get -qq install \
     apt-utils && \
     apt-get -qq install \
@@ -32,17 +37,16 @@ RUN pip3 install --user cython # TODO: can we put this dependency into requireme
 
 USER precice
 
-
-# Rebuild image if force_rebuild after that command
+# Rebuild image from here if `force_rebuild` is enabled
 ARG CACHEBUST
 
 ARG bindings_branch=develop
 ARG adapter_branch=develop
 
-# Builds the precice python bindings for python3
+# Build the precice python bindings for python3
 RUN pip3 install --user https://github.com/precice/python-bindings/archive/$bindings_branch.zip
 
-# Building fenics-adapter
+# Build fenics-adapter
 RUN pip3 install --user numpy==1.14.5 https://github.com/precice/fenics-adapter/archive/$adapter_branch.zip
 
 

adapters/Dockerfile.openfoam-adapter

@@ -1,3 +1,6 @@
+# Dockerfile for building the openfoam-adapter for preCICE
+# NOTE: Built for OpenFOAM v2006
+
 ARG branch=develop
 ARG from=precice/precice-ubuntu1804.home-${branch}
 # ARG base_solver=precice/openfoam
@@ -7,26 +10,22 @@ FROM $from
 USER root
 ENV USER=root
 
-# Install dependecies
+# Install dependencies
 RUN apt-get -qq update && apt-get -qq install \
     software-properties-common \
     wget apt-transport-https && \
     rm -rf /var/lib/apt/lists/*
 
 
-
+# Rebuild image from here if `force_rebuild` is enabled
 ARG CACHEBUST
 
 # Install OpenFOAM v2006
 # see https://github.com/precice/openfoam-adapter/wiki/Notes-on-OpenFOAM#get-openfoam
 RUN wget -q -O - https://dl.openfoam.com/add-debian-repo.sh | bash && \
     apt-get install -y openfoam2006-default
 
-# # Get OpenFOAM5 install via folder copy
-# COPY --from=openfoam /opt/openfoam5 /opt/openfoam5/
-# for of5, we need to also source the file at /opt/openfoam5/etc/bashrc
-
-# Building openfoam-adapter
+# Build openfoam-adapter
 USER precice
 SHELL ["/bin/bash", "-c"]  # without this command /opt/openfoam5/etc/bashrc cannot be sourced
 WORKDIR /home/precice

adapters/Dockerfile.su2-adapter

@@ -1,10 +1,14 @@
+# Dockerfile for building the su2-adapter for preCICE
+# NOTE: Built for SU2 v6.0.0
+
 ARG branch=develop
-ARG from=precice/precice-ubuntu1604.home-${branch}
+ARG from=precice/precice-ubuntu1804.home-${branch}
 FROM $from
 
 USER root
 ENV CXX="g++"
 
+# Install dependencies
 RUN apt-get -qq update && apt-get -qq install \
     dh-autoreconf \
     automake \
@@ -13,24 +17,30 @@ RUN apt-get -qq update && apt-get -qq install \
     ccache \
     time
 
+# Rebuild image from here if `force_rebuild` is enabled
 ARG CACHEBUST
 
 USER precice
+
+# Get solver
 WORKDIR /home/precice
 RUN mkdir -p Logs Data/Input Data/Output Data/Exchange
 RUN git clone --depth 1 --branch v6.0.0 https://github.com/su2code/SU2.git su2-source
 
+# Set solver environment variables
 ENV SU2_HOME="/home/precice/su2-source" \
     SU2_BIN="/home/precice/su2-bin" \
     SU2_RUN="/home/precice/su2-bin/bin" \
     PATH="/home/precice/su2-bin/bin:${PATH}" \
     PYTHONPATH="/home/precice/su2-bin/bin:${PYTHONPATH}"
 
+# Get adapter source
 ARG adapter_branch=develop
 RUN cd /home/precice && \
     git clone --depth 1 --branch $adapter_branch https://github.com/precice/su2-adapter.git && cd su2-adapter &&  \
     ./su2AdapterInstall
 
+# Build adapter
 WORKDIR /home/precice/su2-source
 RUN ./configure --disable-metis --disable-parmetis --disable-cgns --disable-DOT \
     --disable-MSH --disable-DEF --disable-SOL --disable-GEO \

precice/Dockerfile.Ubuntu1604.home

@@ -1,5 +1,11 @@
 # Dockerfile for building preCICE on ubuntu 16.04
 
+# #################
+# WARNING: As of 11.2020, images using Ubuntu 16.04 are no longer maintained.
+#          Attempting to build this dockerfile or using it as base image for
+#          other builds is likely to fail.
+# #################
+
 # Using ubuntu 16.04 as basis
 FROM ubuntu:16.04
 

precice/Dockerfile.Ubuntu1604.package

@@ -1,5 +1,11 @@
 # Dockerfile for building preCICE on ubuntu 16.04
 
+# #################
+# WARNING: As of 11.2020, images using Ubuntu 16.04 are no longer maintained.
+#          Attempting to build this dockerfile or using it as base image for
+#          other builds is likely to fail.
+# #################
+
 # Using ubuntu 16.04 as basis
 FROM ubuntu:16.04
 

precice/Dockerfile.Ubuntu1804.home

@@ -1,10 +1,17 @@
-# Dockerfile for building preCICE on Ubuntu 18.04
-# default setup, user set to 'precice', manual install
+# Dockerfile for building preCICE
+#   OS version:           Ubuntu 18.04
+#   User:                 precice
+#   PETSc install:        from source
+#   precice install:      default
+
 
 # Use official Ubuntu 18.04 as base
 FROM ubuntu:18.04
 
-# Installing necessary dependacies for preCICE, boost 1.65 from apt-get
+# Avoid timeouts during install due to interactive installs
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Install necessary dependencies for preCICE, Boost 1.65 from apt-get
 RUN apt-get -qq update && apt-get -qq install \
     build-essential \
     locales \
@@ -20,57 +27,53 @@ RUN apt-get -qq update && apt-get -qq install \
     cmake && \
     rm -rf /var/lib/apt/lists/*
 
-# create user precice
+# Create user precice
 ARG uid=1000
 ARG gid=1000
 RUN groupadd -g ${gid} precice \
-  && useradd -u ${uid} -g ${gid} -m -s /bin/bash precice
+    && useradd -u ${uid} -g ${gid} -m -s /bin/bash precice
 
-# set locale
+# Set locale
 RUN sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && \
     locale-gen
 ENV LANG en_US.UTF-8
 ENV LANGUAGE en_US:en
 ENV LC_NUMERIC en_US.UTF-8
 ENV LC_ALL en_US.UTF-8
 
-
-# Install PETSc from source
+# Install PETSc v3.12.5 from source (apt version too low)
 WORKDIR /petsc
 RUN wget -nv 'https://www.mcs.anl.gov/petsc/mirror/release-snapshots/petsc-3.12.5.tar.gz' -O - | tar xz && \
-  cd petsc-3.12.5 && \
-  ./configure && \
-  make all test
+cd petsc-3.12.5 && \
+./configure && \
+make all test
 RUN chown -R precice:precice /petsc
 
-# Rebuild image if force_rebuild after that command
+USER precice
+
+# Rebuild image from here on if `force_rebuild` is enabled
 ARG CACHEBUST
 
-USER precice
-WORKDIR /home/precice
-# Setting some environment variables for installing preCICE
+# Set some environment variables for installing preCICE
 ENV CPLUS_INCLUDE_PATH="$CPLUS_INCLUDE_PATH:/usr/include/eigen3" \
     CPATH="/usr/include/eigen3:${CPATH}" \
     PETSC_DIR="/petsc/petsc-3.12.5" \
     PETSC_ARCH="arch-linux2-c-debug" \
     LD_LIBRARY_PATH="/petsc/petsc-3.12.5/arch-linux2-c-debug/lib:${LD_LIBRARY_PATH}" \
     PKG_CONFIG_PATH="/petsc/petsc-3.12.5/arch-linux2-c-debug/lib/pkgconfig:${PKG_CONFIG_PATH}"
 
-
-# Building preCICE
+# Build preCICE
+WORKDIR /home/precice
 ARG branch=develop
 RUN git clone --depth 1 --branch $branch https://github.com/precice/precice.git /home/precice/precice
-WORKDIR /home/precice/precice
 
-# Some parameters for the build, you can set them in the build command e.g.
-# sudo docker build Dockerfile.precice --build-arg petsc_para=yes --build-arg mpi_para=yes .
-# this will result in
-# cmake -DPRECICE_PETScMapping=yes -DPRECICE_MPICommunication=yes -DPRECICE_PythonActions=no -DCMAKE_CXX_COMPILER=mpicxx -j2 /precice
+# Set parameters for the build, these can be overwritten by the docker build command
+# Example: `docker build --build-arg petsc_para=yes --build-arg mpi_para=yes .`
 ARG petsc_para=no
 ARG mpi_para=yes
 ARG python_para=no
 
-# Build preCICE and clean-up generated object files
+# Build preCICE and clean-up generated object files afterwards
 RUN mkdir /home/precice/precice-build && \
     cd /home/precice/precice-build && \
     mkdir /home/precice/precice-install && \
@@ -86,7 +89,7 @@ RUN mkdir /home/precice/precice-build && \
     make install && \
     rm -r /home/precice/precice-build
 
-# Setting preCICE environment variables
+# Set preCICE environment variables
 ENV PRECICE_ROOT="/home/precice/precice" \
     PKG_CONFIG_PATH="/home/precice/precice-install/lib/pkgconfig:${PKG_CONFIG_PATH}" \
     LD_LIBRARY_PATH="/home/precice/precice-install/lib:${LD_LIBRARY_PATH}" \