Merge pull request #91 from precice/develop

Release v202404.0.0

Author: MakisH

.github/workflows/build.yml

@@ -42,7 +42,7 @@ jobs:
 
     - name: Run vagrant up
       run: |
-        vagrant up --provider=${{ matrix.provider }}
+        VAGRANT_DISABLE_VBOXSYMLINKCREATE=1 vagrant up --provider=${{ matrix.provider }}
 
     - name: Package Vagrant box
       run: vagrant package --base "preCICE-VM" --output preCICE.box

.gitignore

@@ -1,2 +1,5 @@
 .vagrant
-vagrant
+vagrant
+
+# Editors
+settings.json

README.md

@@ -25,7 +25,7 @@ You can afterwards also see and manage the produced VM in VirtualBox.
 A few things you may need:
 
 - The username and password are `vagrant`/`vagrant`
-- The keyboard layout is US English (QWERTY). You can change this in [`install-basics.sh`](./install-basics.sh) or through the keyboard setting shortcut on `~/Desktop`.
+- The keyboard layout is US English (QWERTY). You can change this in [`install-basics.sh`](./provisioning/install-basics.sh) or through the keyboard setting shortcut on `~/Desktop`.
 - Find scripts to install additional software on `~/Desktop/shared`.
 
 ### What else can I do?
@@ -40,25 +40,29 @@ A few things you may need:
 
 ## What is included?
 
-This box is based on the [generic/ubuntu2004](https://github.com/lavabit/robox/tree/master/scripts/ubuntu2004) base box and installs:
+This box is based on the ~~[generic/ubuntu2004](https://github.com/lavabit/robox/tree/master/scripts/ubuntu2004)~~ [bento/ubuntu-20.04](https://github.com/chef/bento) base box and installs:
 
 - Xubuntu-core (Xfce desktop environment) and related tools
 - VirtualBox guest additions
 - Terminator (a nice split-window terminal emulator, find it in `Applications > System`)
 - Git, CMake, ccmake
 - Editors: nano, vim, gedit
-- preCICE latest for the master branch
-- preCICE config visualizer (master)
+- Diff viewer: meld
+- preCICE latest from the master branch (built in release-with-debug-info mode)
+- preCICE config visualizer with its GUI (master)
 - preCICE Python bindings (PIP)
 - preCICE Julia bindings (Pkg)
-- OpenFOAM v2112 and the OpenFOAM-preCICE adapter (master)
+- preCICE Rust bindings (Cargo)
+- preCICE FMI Runner (PIP)
+- preCICE Micro Manager (PIP)
+- OpenFOAM v2312 and the OpenFOAM-preCICE adapter (master)
 - deal.II 9.3 from the official backports and the deal.II-preCICE adapter (master)
-- CalculiX 2.19 from source and the CalculiX-preCICE adapter (master)
+- CalculiX 2.20 from source and the CalculiX-preCICE adapter (master)
 - FEniCS latest from the FEniCS PPA and the FEniCS-preCICE adapter (PIP)
-- Nutils latest from PIP
-- SU2 6.0.0 and the SU2-preCICE adapter (master)
+- SU2 7.5.1 and the SU2-preCICE adapter (master)
 - code_aster 14.6 and the code_aster-preCICE adapter (master)
-- DUNE 2.8 and the experimental DUNE-preCICE adapter (master)
+- DUNE 2.9.1 and the experimental DUNE-preCICE adapter (main)
+- DuMuX 3.8 and the DuMuX-preCICE adapter (v2.0.0)
 - ASTE (master)
 - Paraview from APT
 - Gnuplot
@@ -117,6 +121,11 @@ vagrant box remove test-box
 If you require a more responsive experience, lower overhead, or exotic features such as GPU pass through, then the `libvirt` vagrant box is for you.
 This allows you to run the vagrant box via libvirt and QEMU as a Kernerl Virtual Machine (KVM).
 
+> Note
+> The libvirt variant does not work with the `bento/ubuntu-20.04` base image, but also the VirtualBox variant does not at the moment work with the `generic/ubuntu2004` image.
+> Change the base image in the beginning of the Vagrantfile if you need this feature.
+> See https://github.com/precice/vm/issues/83 for details.
+
 To use this box, first install the vagrant plugin `vagrant-libvirt` following the [official installation instructions](https://github.com/vagrant-libvirt/vagrant-libvirt#installation).
 Then you follow the normal usage instructions above, but you need to tell vagrant to use the `libvirt` box by passing one additional option:
 ```

Vagrantfile

@@ -4,7 +4,9 @@
 Vagrant.configure("2") do |config|
   # The generic/ images support virtualbox as well as libvirt and hyperv.
   # This allows us to create performance oriented images for Linux (libvirt) and Windows (hyperv).
-  config.vm.box = "generic/ubuntu2004"
+  # However, it does not build: https://github.com/precice/vm/issues/83
+  # config.vm.box = "generic/ubuntu2004"
+  config.vm.box = "bento/ubuntu-20.04"
 
   # We don't want the box to automatically update every time it starts.
   # We can instead handle updates internally, without destroying the machine.
@@ -46,11 +48,11 @@ Vagrant.configure("2") do |config|
   # Install solvers, adapters, and related tools
   config.vm.provision "shell", path: "provisioning/install-config-visualizer.sh", privileged: false
   config.vm.provision "shell", path: "provisioning/install-openfoam.sh", privileged: false
-  config.vm.provision "file", source: "provisioning/prebuilt/swak4Foam/swak4Foam.tar.gz", destination: "~/OpenFOAM/vagrant-v2206/platforms/linux64GccDPInt32Opt/swak4Foam.tar.gz"
   config.vm.provision "shell", path: "provisioning/install-dealii.sh", privileged: false
   config.vm.provision "shell", path: "provisioning/install-calculix.sh", privileged: false
   config.vm.provision "shell", path: "provisioning/install-fenics.sh", privileged: false
-  config.vm.provision "shell", path: "provisioning/install-nutils.sh", privileged: false
+  config.vm.provision "shell", path: "provisioning/install-fmiprecice.sh", privileged: false
+  config.vm.provision "shell", path: "provisioning/install-micro-manager.sh", privileged: false
   config.vm.provision "shell", path: "provisioning/install-su2.sh", privileged: false
   config.vm.provision "shell", path: "provisioning/install-code_aster.sh", privileged: false
   config.vm.provision "shell", path: "provisioning/install-dune.sh", privileged: false

provisioning/.alias

@@ -1,12 +1,12 @@
 # preCICE config visualizer
 function preciceToPNG(){
-  cat "${1:-precice-config.xml}" | precice-config-visualizer | dot -Tpng > precice-config.png
+  precice-config-visualizer -o precice-config.png "${1:-precice-config.xml}"
 }
 
 function preciceToPDF(){
-  cat "${1:-precice-config.xml}" | precice-config-visualizer | dot -Tpdf > precice-config.pdf
+  precice-config-visualizer -o precice-config.pdf "${1:-precice-config.xml}"
 }
 
 function preciceToSVG(){
-  cat "${1:-precice-config.xml}" | precice-config-visualizer | dot -Tsvg > precice-config.svg
+  precice-config-visualizer -o precice-config.svg "${1:-precice-config.xml}"
 }

provisioning/install-basics.sh

@@ -12,6 +12,7 @@ sudo apt-get upgrade -qy
 # Install the Xfce desktop environment and basic applications
 sudo apt-get install -y xubuntu-core^
 sudo apt-get install -y thunar xfce4-terminal terminator bash-completion tree atril firefox firefox-locale-en baobab catfish
+sudo apt-get install -y python3-dev pipx python-is-python3 python3-venv
 
 # Setup auto-login for the graphical session
 # Disabled due to https://github.com/precice/vm/issues/40

provisioning/install-config-visualizer.sh

@@ -1,18 +1,24 @@
 #!/usr/bin/env bash
 set -ex
 
-# Get the config-visualizer from GitHub
-if [ ! -d "config-visualizer/" ]; then
-    git clone --depth=1 --branch master https://github.com/precice/config-visualizer.git
-fi
-pip3 install --user -e config-visualizer
+# Install CLI dependencies
+sudo apt-get install -y graphviz
+# Install GUI depedencies
+sudo apt-get install -y build-essential pkg-config python3-dev libcairo2-dev libgirepository1.0-dev gir1.2-gtk-3.0
+
+# Get the config-visualizer from PIP
+PRECICE_CONFIG_VISUALIZER_VERSION=1.1.3
+PRECICE_CONFIG_VISUALIZER_GUI_VERSION=0.1.0
+pipx install --force precice-config-visualizer==${PRECICE_CONFIG_VISUALIZER_VERSION}
+pipx install --force precice-config-visualizer-gui==${PRECICE_CONFIG_VISUALIZER_GUI_VERSION}
 
 # Add the config-visualizer to PATH
-echo "export PATH=\"\${HOME}/config-visualizer/bin:\${PATH}\"" >>~/.bashrc
+# shellcheck disable=SC2016
+echo 'export PATH="${HOME}/.local/bin:${PATH}"' >> ~/.bashrc
 
-# By default, there is no `python` executable, there is only `python3`,
-# which causes issues to the config-visualizer
-sudo apt-get install -y python-is-python3
+# Add the GUI in the apps menu
+mkdir -p ~/.local/share/applications ~/.local/share/icons
 
-# Install graphviz, which provides dot, an almost required package to make this useful
-sudo apt-get install -y graphviz
+CV_LOC_SHARE=~/.local/pipx/venvs/precice-config-visualizer-gui==${PRECICE_CONFIG_VISUALIZER_GUI_VERSION}/share
+cp $CV_LOC_SHARE/applications/org.precice.config_visualizer.desktop ~/.local/share/applications/
+cp $CV_LOC_SHARE/icons/hicolor/scalable/apps/org.precice.config_visualizer.svg ~/.local/share/icons/

provisioning/install-devel.sh

@@ -3,6 +3,11 @@ set -ex
 
 sudo apt-get install -y build-essential git cmake cmake-curses-gui
 
+# For the Rust bindings of preCICE, installed by the elastic-tube-1d tutorial
+sudo apt-get install -y cargo
+
 sudo apt-get install -y nano vim gedit
 
+sudo apt-get install -y meld
+
 sudo apt-get install -y ipython3

provisioning/install-dune.sh

@@ -1,76 +1,89 @@
 #!/usr/bin/env bash
 set -ex
 
-# Make a folder to collect all DUNE-related code (-p to allow re-provisioning)
-mkdir -p dune && cd dune
+# Make a folder to collect all DUNE-related code
+mkdir -p dune-dumux && cd dune-dumux
 
-# Get required DUNE modules
+# Modules used by DUNE and DuMux
+# While the installdumux.py script clones these as well,
+# we explicitly clone them to control the versions.
 if [ ! -d "dune-common/" ]; then
-    git clone --branch v2.8.0 --depth=1 https://gitlab.dune-project.org/core/dune-common.git
+    git clone --depth 1 --branch v2.9.1 https://gitlab.dune-project.org/core/dune-common.git
 fi
 
 if [ ! -d "dune-istl/" ]; then
-    git clone --branch v2.8.0 --depth=1 https://gitlab.dune-project.org/core/dune-istl.git
+    git clone --depth 1 --branch v2.9.1 https://gitlab.dune-project.org/core/dune-istl.git
 fi
 
 if [ ! -d "dune-localfunctions/" ]; then
-    git clone --branch v2.8.0 --depth=1 https://gitlab.dune-project.org/core/dune-localfunctions.git
+    git clone --depth 1 --branch v2.9.1 https://gitlab.dune-project.org/core/dune-localfunctions.git
 fi
 
 if [ ! -d "dune-grid/" ]; then
-    git clone --branch v2.8.0 --depth=1 https://gitlab.dune-project.org/core/dune-grid.git
+    git clone --depth 1 --branch v2.9.1 https://gitlab.dune-project.org/core/dune-grid.git
 fi
 
 if [ ! -d "dune-geometry/" ]; then
-    git clone --branch v2.8.0 --depth=1 https://gitlab.dune-project.org/core/dune-geometry.git
+    git clone --depth 1 --branch v2.9.1 https://gitlab.dune-project.org/core/dune-geometry.git
 fi
 
-if [ ! -d "dune-functions/" ]; then
-    git clone --branch v2.8.0 --depth=1 https://gitlab.dune-project.org/staging/dune-functions.git
+if [ ! -d "dune-foamgrid/" ]; then
+    # The missing v in the tag in this module originates from the project itself
+    git clone --depth 1 --branch 2.9.1 https://gitlab.dune-project.org/extensions/dune-foamgrid.git
 fi
 
-if [ ! -d "dune-uggrid/" ]; then
-    git clone --branch v2.8.0 --depth=1 https://gitlab.dune-project.org/staging/dune-uggrid.git
+if [ ! -d "dune-functions/" ]; then
+    git clone --depth 1 --branch v2.9.1 https://gitlab.dune-project.org/staging/dune-functions.git
 fi
 
 if [ ! -d "dune-typetree/" ]; then
-    git clone --branch v2.8.0 --depth=1 https://gitlab.dune-project.org/staging/dune-typetree.git
+    git clone --depth 1 --branch v2.9.1 https://gitlab.dune-project.org/staging/dune-typetree.git
 fi
 
-if [ ! -d "dune-foamgrid/" ]; then
-    git clone --branch releases/2.8 --depth=1 https://gitlab.dune-project.org/extensions/dune-foamgrid.git
+if [ ! -d "dune-uggrid/" ]; then
+    git clone --depth 1 --branch v2.9.1 https://gitlab.dune-project.org/staging/dune-uggrid.git
 fi
 
-# Get the dune-elastodynamics module (solid solver)
+# Get the dune-elastodynamics module (solid solver for the plain dune adapter)
 if [ ! -d "dune-elastodynamics/" ]; then
-    git clone --branch master --depth=1 https://github.com/maxfirmbach/dune-elastodynamics.git
+    git clone --depth 1 --branch master https://github.com/maxfirmbach/dune-elastodynamics.git
 fi
 (
     cd dune-elastodynamics
     git pull
 )
 
-# Get the DUNE-preCICE adapter
+# Get the plain DUNE-preCICE adapter
 if [ ! -d "dune-adapter/" ]; then
-    git clone --branch main --depth=1 https://github.com/precice/dune-adapter.git
+    git clone --depth 1 --branch main https://github.com/precice/dune-adapter.git
 fi
 (
     cd dune-adapter/dune-precice
     git pull
 )
 
-# Build all the DUNE and DUNE-preCICE related modules
-DUNE_CONTROL_PATH=~/dune ./dune-common/bin/dunecontrol all
+./dune-common/bin/dunecontrol all
 
-# Set the DUNE_CONTROL_PATH (DUNE recursively finds modules in this directory)
-echo "export DUNE_CONTROL_PATH=\"\${HOME}/dune\"" >> ~/.bashrc
+# Get DuMux and the DuMux-preCICE adapter
+if [ ! -d "dumux/" ]; then
+    git clone --depth 1 --branch releases/3.8 https://git.iws.uni-stuttgart.de/dumux-repositories/dumux.git
+fi
 
-# Copy the built example code to the tutorials
-cp ~/dune/dune-adapter/dune-precice-howto/build-cmake/examples/dune-perpendicular-flap ~/tutorials/perpendicular-flap/solid-dune
+# Build DuMux
+CMAKE_FLAGS="$CMAKE_FLAGS -DCMAKE_DISABLE_FIND_PACKAGE_Kokkos=TRUE" ./dune-common/bin/dunecontrol --only=dumux all
+
+if [ ! -d "dumux-adapter/" ]; then
+    git clone  --depth 1 --branch v2.0.0 https://github.com/precice/dumux-adapter.git
+fi
 
-# Install dune-fem from PIP
+# Build the DuMux-preCICE adapter
+CMAKE_FLAGS="$CMAKE_FLAGS -DCMAKE_DISABLE_FIND_PACKAGE_Kokkos=TRUE" ./dune-common/bin/dunecontrol --only=dumux-precice all
 
-pip3 install --user dune-fem==2.8
+# Set the DUNE_CONTROL_PATH (DUNE recursively finds modules in this directory)
+echo "export DUNE_CONTROL_PATH=\"\${HOME}/dune-dumux\"" >> ~/.bashrc
+
+# Copy the built example code to the tutorials
+cp ~/dune-dumux/dune-adapter/dune-precice-howto/build-cmake/examples/dune-perpendicular-flap ~/tutorials/perpendicular-flap/solid-dune
 
 # We are done with DUNE, let's do back home
 cd ~

provisioning/install-fmiprecice.sh

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+set -ex
+
+# Install the FMI runner from PIP
+pip3 install --user fmiprecice