From cf30a35d0c6f7f11cdd87de4a20a7693f16dea5b Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Wed, 5 Oct 2022 11:34:08 +0200
Subject: [PATCH 01/50] Fix preCICE branch name (master->main renaming)

---
 provisioning/install-precice.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/provisioning/install-precice.sh b/provisioning/install-precice.sh
index af4c0ed..f4a3812 100644
--- a/provisioning/install-precice.sh
+++ b/provisioning/install-precice.sh
@@ -5,10 +5,10 @@ set -ex
 sudo apt-get install -y cmake libeigen3-dev libxml2-dev libboost-all-dev petsc-dev python3-dev python3-numpy
 
 # Get preCICE from GitHub:
-# - Always get the latest master, no need for versioning
+# - Always get the latest main branch, no need for versioning
 # - Build in Debug mode, so that users can report bugs
 if [ ! -d "precice/" ]; then
-    git clone --depth=1 --branch master https://github.com/precice/precice.git
+    git clone --depth=1 --branch main https://github.com/precice/precice.git
 fi
 (
     cd precice

From bea07007e6036d4e3c8cda31d7c31b875c8ba035 Mon Sep 17 00:00:00 2001
From: David Schneider <david.schneider@ipvs.uni-stuttgart.de>
Date: Mon, 14 Nov 2022 17:23:46 +0100
Subject: [PATCH 02/50] Add ASTE recipe for the latest ASTE release (#47)

* Add ASTE recipe for the latest ASTE release

* Add corresponding aste version

* Use branch name instead of version

Co-authored-by: Gerasimos Chourdakis <makishourdakis@gmail.com>
---
 README.md                    |  1 +
 Vagrantfile                  |  1 +
 provisioning/install-aste.sh | 23 +++++++++++++++++++++++
 3 files changed, 25 insertions(+)
 create mode 100644 provisioning/install-aste.sh

diff --git a/README.md b/README.md
index fb78dd0..6ded08e 100644
--- a/README.md
+++ b/README.md
@@ -58,6 +58,7 @@ This box is based on the [generic/ubuntu2004](https://github.com/lavabit/robox/t
 - SU2 6.0.0 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)
+- ASTE (master)
 - Paraview from APT
 - Gnuplot
 
diff --git a/Vagrantfile b/Vagrantfile
index 275e6cd..18d951d 100644
--- a/Vagrantfile
+++ b/Vagrantfile
@@ -55,6 +55,7 @@ Vagrant.configure("2") do |config|
   config.vm.provision "shell", path: "provisioning/install-code_aster.sh", privileged: false
   config.vm.provision "shell", path: "provisioning/install-dune.sh", privileged: false
   config.vm.provision "shell", path: "provisioning/install-paraview.sh", privileged: false
+  config.vm.provision "shell", path: "provisioning/install-aste.sh", privileged: false
 
   # Post-installation steps
   config.vm.provision "shell", path: "provisioning/post-install.sh", privileged: false
diff --git a/provisioning/install-aste.sh b/provisioning/install-aste.sh
new file mode 100644
index 0000000..392e3f8
--- /dev/null
+++ b/provisioning/install-aste.sh
@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+set -ex
+
+# Install the C++ vtk library
+sudo apt-get -y install libvtk7-dev
+sudo apt-get -y install libmetis-dev
+
+python3 -m pip install sympy scipy jinja2
+
+# Get aste
+if [ ! -d "aste/" ]; then
+    git clone --depth=1 --branch master https://github.com/precice/aste.git
+fi
+(
+    cd aste
+    git pull
+    mkdir -p build && cd build
+    cmake .. && make -j "$(nproc)"
+)
+
+# Add aste to PATH and libmetis to the library path
+echo "export PATH=\"\${HOME}/aste:\${PATH}\"" >>~/.bashrc
+echo "export LD_LIBRARY_PATH=\"\${HOME}/aste:\${LD_LIBRARY_PATH}\"" >>~/.bashrc

From a694fe4813345acf79196e8b5d33de789db8c5ab Mon Sep 17 00:00:00 2001
From: erikscheurer <84399192+erikscheurer@users.noreply.github.com>
Date: Tue, 15 Nov 2022 16:30:12 +0100
Subject: [PATCH 03/50] Add Julia bindings to vm (#48)

Co-authored-by: Gerasimos Chourdakis <makishourdakis@gmail.com>
Co-authored-by: Ishaan Desai <ishaandesai@gmail.com>
Co-authored-by: Ishaan Desai <ishaan.desai@ipvs.uni-stuttgart.de>
---
 README.md                              |  1 +
 Vagrantfile                            |  1 +
 provisioning/install-julia-bindings.sh | 11 +++++++++++
 3 files changed, 13 insertions(+)
 create mode 100644 provisioning/install-julia-bindings.sh

diff --git a/README.md b/README.md
index 6ded08e..f28ed0a 100644
--- a/README.md
+++ b/README.md
@@ -50,6 +50,7 @@ This box is based on the [generic/ubuntu2004](https://github.com/lavabit/robox/t
 - preCICE latest for the master branch
 - preCICE config visualizer (master)
 - preCICE Python bindings (PIP)
+- preCICE Julia bindings (Pkg)
 - OpenFOAM v2112 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)
diff --git a/Vagrantfile b/Vagrantfile
index 18d951d..e38f3a9 100644
--- a/Vagrantfile
+++ b/Vagrantfile
@@ -55,6 +55,7 @@ Vagrant.configure("2") do |config|
   config.vm.provision "shell", path: "provisioning/install-code_aster.sh", privileged: false
   config.vm.provision "shell", path: "provisioning/install-dune.sh", privileged: false
   config.vm.provision "shell", path: "provisioning/install-paraview.sh", privileged: false
+  config.vm.provision "shell", path: "provisioning/install-julia-bindings.sh", privileged: false
   config.vm.provision "shell", path: "provisioning/install-aste.sh", privileged: false
 
   # Post-installation steps
diff --git a/provisioning/install-julia-bindings.sh b/provisioning/install-julia-bindings.sh
new file mode 100644
index 0000000..00d8d07
--- /dev/null
+++ b/provisioning/install-julia-bindings.sh
@@ -0,0 +1,11 @@
+#!/usr/bin/env bash
+
+# install latest julia
+pip3 install jill
+jill install --confirm
+
+# install preCICE bindings
+julia -e 'using Pkg; Pkg.add("PreCICE")'
+
+# to test the installation, run the following command:
+# julia -e 'using Pkg; Pkg.test("PreCICE")'

From 94c5979bc01587f453a7564a05e31a86a80da43a Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Fri, 18 Nov 2022 15:18:38 +0100
Subject: [PATCH 04/50] Upgrade OpenFOAM to v2206 (#46)

---
 Vagrantfile                                     |  2 +-
 provisioning/install-openfoam.sh                | 14 +++++++-------
 provisioning/post-install.sh                    |  2 +-
 provisioning/prebuilt/swak4Foam/README.txt      | 17 ++++++++++++++++-
 .../prebuilt/swak4Foam/swak4Foam.tar.gz         |  4 ++--
 5 files changed, 27 insertions(+), 12 deletions(-)

diff --git a/Vagrantfile b/Vagrantfile
index e38f3a9..761339e 100644
--- a/Vagrantfile
+++ b/Vagrantfile
@@ -46,7 +46,7 @@ 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-v2112/platforms/linux64GccDPInt32Opt/swak4Foam.tar.gz"
+  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
diff --git a/provisioning/install-openfoam.sh b/provisioning/install-openfoam.sh
index 56ff2d8..acb2b62 100644
--- a/provisioning/install-openfoam.sh
+++ b/provisioning/install-openfoam.sh
@@ -4,10 +4,10 @@ set -ex
 # Add the signing key, add the repository, update:
 wget -q -O - https://dl.openfoam.com/add-debian-repo.sh | sudo bash
 
-# Install OpenFOAM v2112:
-sudo apt-get install -y openfoam2112-dev
+# Install OpenFOAM v2206:
+sudo apt-get install -y openfoam2206-dev
 # Enable OpenFOAM by default:
-echo ". /usr/lib/openfoam/openfoam2112/etc/bashrc" >> ~/.bashrc
+echo ". /usr/lib/openfoam/openfoam2206/etc/bashrc" >> ~/.bashrc
 
 # Get the OpenFOAM-preCICE adapter
 if [ ! -d "openfoam-adapter/" ]; then
@@ -16,7 +16,7 @@ fi
 (
     cd openfoam-adapter
     git pull
-    openfoam2112 ./Allwmake
+    openfoam2206 ./Allwmake
 )
 
 # Get swak4Foam (provides groovyBC, needed for the turek-hron-fsi3 tutorial)
@@ -27,7 +27,7 @@ fi
 # (
 #     cd swak4Foam
 #     hg checkout develop
-#     openfoam2112 ./AllwmakeAll
+#     openfoam2206 ./AllwmakeAll
 # )
 #
 # # Remove some swak4Foam files to save space (approx. 150MB)
@@ -35,7 +35,7 @@ fi
 # sudo apt-get purge --autoremove -y mercurial # This also removes Python2, yipieh!
 #
 # # Option 2: Use pre-built binaries
-# # (see Vagrantfile and post-install.sh, rebuild and update for OpenFOAM version other than v2112)
+# # (see Vagrantfile and post-install.sh, rebuild and update for OpenFOAM version other than v2206)
 
 # Build the tutorials partitioned-heat-conduction solver
-cd ~/tutorials/partitioned-heat-conduction/openfoam-solver && openfoam2112 wmake
+cd ~/tutorials/partitioned-heat-conduction/openfoam-solver && openfoam2206 wmake
diff --git a/provisioning/post-install.sh b/provisioning/post-install.sh
index 8bed9e7..c3e4253 100644
--- a/provisioning/post-install.sh
+++ b/provisioning/post-install.sh
@@ -3,7 +3,7 @@ set -ex
 
 # Setup swak4Foam
 (
-    cd "${HOME}/OpenFOAM/vagrant-v2112/platforms/linux64GccDPInt32Opt/"
+    cd "${HOME}/OpenFOAM/vagrant-v2206/platforms/linux64GccDPInt32Opt/"
     tar -xzvf swak4Foam.tar.gz
 )
 
diff --git a/provisioning/prebuilt/swak4Foam/README.txt b/provisioning/prebuilt/swak4Foam/README.txt
index e30f332..a8b587f 100644
--- a/provisioning/prebuilt/swak4Foam/README.txt
+++ b/provisioning/prebuilt/swak4Foam/README.txt
@@ -1,2 +1,17 @@
-Prebuilt libraries and tools of swak4Foam for Ubuntu 20.04 and OpenFOAM v2112, based on commit ea7680cdcf8b (December 2021).
+Prebuilt libraries and tools of swak4Foam for Ubuntu 20.04 and OpenFOAM v2206, based on the develop branch of swak4Foam (built on November 2022):
+
+```bash
+vagrant@precicevm:~/swak4Foam$ hg tip
+changeset:   3999:481d96f16780
+branch:      develop
+tag:         tip
+parent:      3997:4d33e38246ad
+parent:      3998:12dad7c691d1
+user:        Bernhard F.W. Gschaider <bgschaid@hfd-research.com>
+date:        Mon Jul 04 01:06:48 2022 +0200
+summary:     flow: Promoted <feature> 'port/of9' (12dad7c691d1) to 'develop'.
+```
+
+The files are extracted from `/home/vagrant/OpenFOAM/vagrant-<version>/platforms/` and copied there.
+
 Find the source code on http://hg.code.sf.net/p/openfoam-extend/swak4Foam/rev/ea7680cdcf8b
diff --git a/provisioning/prebuilt/swak4Foam/swak4Foam.tar.gz b/provisioning/prebuilt/swak4Foam/swak4Foam.tar.gz
index 45be87b..1e469cd 100644
--- a/provisioning/prebuilt/swak4Foam/swak4Foam.tar.gz
+++ b/provisioning/prebuilt/swak4Foam/swak4Foam.tar.gz
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:a6150a56f3670a237e2dbff936a5f99f900d4c71c82fa08bce9dad2795ebfae0
-size 19974607
+oid sha256:284da0859454c970ebbc208e477a8572060280eff4ba6252cd33ed24b25c4fd1
+size 20097408

From 43ca14145ffda4db7b30761ed7d31a6f7fcee78f Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Fri, 18 Nov 2022 16:37:55 +0100
Subject: [PATCH 05/50] Update CalculiX to v2.20

---
 provisioning/install-calculix.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/provisioning/install-calculix.sh b/provisioning/install-calculix.sh
index 27a6204..613b803 100644
--- a/provisioning/install-calculix.sh
+++ b/provisioning/install-calculix.sh
@@ -5,9 +5,9 @@ set -ex
 sudo apt-get install -y libarpack2-dev libspooles-dev libyaml-cpp-dev
 
 # Install CalculiX
-wget --quiet http://www.dhondt.de/ccx_2.19.src.tar.bz2
-tar xvjf ccx_2.19.src.tar.bz2
-rm -fv ccx_2.19.src.tar.bz2
+wget --quiet http://www.dhondt.de/ccx_2.20.src.tar.bz2
+tar xvjf ccx_2.20.src.tar.bz2
+rm -fv ccx_2.20.src.tar.bz2
 
 # Get the CalculiX-preCICE adapter
 if [ ! -d "calculix-adapter/" ]; then

From 7d5e890a4b8938b18fdfaf8eda1018a3170f6037 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Mon, 21 Nov 2022 19:28:53 +0100
Subject: [PATCH 06/50] fix-aste-path

---
 provisioning/install-aste.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/provisioning/install-aste.sh b/provisioning/install-aste.sh
index 392e3f8..1dbae5a 100644
--- a/provisioning/install-aste.sh
+++ b/provisioning/install-aste.sh
@@ -19,5 +19,5 @@ fi
 )
 
 # Add aste to PATH and libmetis to the library path
-echo "export PATH=\"\${HOME}/aste:\${PATH}\"" >>~/.bashrc
-echo "export LD_LIBRARY_PATH=\"\${HOME}/aste:\${LD_LIBRARY_PATH}\"" >>~/.bashrc
+echo "export PATH=\"\${HOME}/aste/build:\${PATH}\"" >>~/.bashrc
+echo "export LD_LIBRARY_PATH=\"\${HOME}/aste/build:\${LD_LIBRARY_PATH}\"" >>~/.bashrc

From 0d5fe51d4fc4e08ddc17a5487a221bc80a77b8f8 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Mon, 21 Nov 2022 19:37:28 +0100
Subject: [PATCH 07/50] Add pandas (#59)

---
 provisioning/install-precice.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/provisioning/install-precice.sh b/provisioning/install-precice.sh
index f4a3812..49fe124 100644
--- a/provisioning/install-precice.sh
+++ b/provisioning/install-precice.sh
@@ -55,6 +55,9 @@ sudo apt-get install -y python3-pip
 pip3 install --upgrade pip
 pip3 install --user pyprecice
 
+# Additional python packages
+pip3 install --user pandas # Needed for the post-processing script of the oscillator tutorial
+
 # Get the Python solverdummy into the examples
 if [ ! -d "python-bindings/" ]; then
     git clone --depth=1 --branch master https://github.com/precice/python-bindings.git

From bed63fb7c0e32f90d8c9a397d27da5d40329a429 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Mon, 21 Nov 2022 19:38:52 +0100
Subject: [PATCH 08/50] Add dune-fem (#58)

---
 provisioning/install-dune.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/provisioning/install-dune.sh b/provisioning/install-dune.sh
index 432ca9c..792e736 100755
--- a/provisioning/install-dune.sh
+++ b/provisioning/install-dune.sh
@@ -68,5 +68,9 @@ echo "export DUNE_CONTROL_PATH=\"\${HOME}/dune\"" >> ~/.bashrc
 # 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
 
+# Install dune-fem from PIP
+
+pip3 install --user dune-fem==2.8
+
 # We are done with DUNE, let's do back home
 cd ~

From c6e7137c30f7b360e299a4f7651c5619b1023432 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Mon, 21 Nov 2022 19:47:34 +0100
Subject: [PATCH 09/50] Build elastic-tube-1d (#60)

Closes #53.
---
 provisioning/install-precice.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/provisioning/install-precice.sh b/provisioning/install-precice.sh
index 49fe124..68e83e4 100644
--- a/provisioning/install-precice.sh
+++ b/provisioning/install-precice.sh
@@ -40,6 +40,10 @@ if [ ! -d "tutorials/" ]; then
     git clone --depth=1 --branch master https://github.com/precice/tutorials.git
     ln -sf ~/tutorials ~/Desktop/
 fi
+(
+    cd tutorials/elastic-tube-1d/fluid-cpp/ && mkdir build && cd build && cmake .. && make && cd ../..
+    cd solid-cpp/ && mkdir build && cd build && cmake .. && make
+)
 (
     cd tutorials/quickstart/solid-cpp/ && cmake . && make
 )

From 8661219da36bf5a52533c36566b3a59a127f206c Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Mon, 21 Nov 2022 20:33:39 +0100
Subject: [PATCH 10/50] Replace PDF reader (evince -> atril)

closes #36
---
 provisioning/install-basics.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/provisioning/install-basics.sh b/provisioning/install-basics.sh
index 281d54c..ff78f0b 100644
--- a/provisioning/install-basics.sh
+++ b/provisioning/install-basics.sh
@@ -11,7 +11,7 @@ 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 evince firefox firefox-locale-en baobab catfish
+sudo apt-get install -y thunar xfce4-terminal terminator bash-completion tree atril firefox firefox-locale-en baobab catfish
 
 # Setup auto-login for the graphical session
 # Disabled due to https://github.com/precice/vm/issues/40

From a22e921edf31e9dd0518eed6b25c24e7903455cc Mon Sep 17 00:00:00 2001
From: Ishaan Desai <ishaandesai@gmail.com>
Date: Mon, 21 Nov 2022 21:09:02 +0100
Subject: [PATCH 11/50] Make the vm install Nutils v7.0 instead of v6.3 (#56)

---
 provisioning/install-nutils.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/provisioning/install-nutils.sh b/provisioning/install-nutils.sh
index d9f007e..dd2b068 100644
--- a/provisioning/install-nutils.sh
+++ b/provisioning/install-nutils.sh
@@ -2,4 +2,4 @@
 set -ex
 
 # Install Nutils from PIP (we will also need matplotlib in our examples)
-pip3 install --user matplotlib nutils==6.3
+pip3 install --user matplotlib nutils==7.0

From 76f47ace172e4da642d720c3a09a880263c22b96 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Mon, 21 Nov 2022 21:43:28 +0100
Subject: [PATCH 12/50] Add venv with Nutils 6 for perpendicular-flap (#62)

Closes #61
---
 provisioning/install-precice.sh | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/provisioning/install-precice.sh b/provisioning/install-precice.sh
index 68e83e4..906ddd4 100644
--- a/provisioning/install-precice.sh
+++ b/provisioning/install-precice.sh
@@ -62,6 +62,19 @@ pip3 install --user pyprecice
 # Additional python packages
 pip3 install --user pandas # Needed for the post-processing script of the oscillator tutorial
 
+# Temporary workaround for https://github.com/precice/vm/issues/61
+# Remove as soon as https://github.com/precice/tutorials/issues/217 gets resolved
+sudo apt-get install -y python3.8-venv
+(
+    cd tutorials/perpendicular-flap/fluid-nutils/
+    python3 -m venv nutils6-env
+    # shellcheck source=/dev/null
+    source nutils6-env/bin/activate
+    pip3 install nutils==6.3 pyprecice
+    sed -i "s/python3/nutils6-env\/bin\/python3/g" ./run.sh
+    deactivate
+)
+
 # Get the Python solverdummy into the examples
 if [ ! -d "python-bindings/" ]; then
     git clone --depth=1 --branch master https://github.com/precice/python-bindings.git

From 900f746ac91aacbc7f49f3f71b34fc9259cb8b15 Mon Sep 17 00:00:00 2001
From: Ishaan Desai <ishaandesai@gmail.com>
Date: Tue, 22 Nov 2022 14:21:36 +0100
Subject: [PATCH 13/50] Manually uninstall fenics-ufl package to avoid fenics
 not working (#64)

---
 provisioning/install-fenics.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/provisioning/install-fenics.sh b/provisioning/install-fenics.sh
index 8348604..c09eede 100644
--- a/provisioning/install-fenics.sh
+++ b/provisioning/install-fenics.sh
@@ -9,3 +9,6 @@ sudo apt-get -y install --no-install-recommends fenics
 
 # Install the FEniCS-preCICE adapter from PIP
 pip3 install --user fenicsprecice
+
+# Remove fenics-ufl package manually
+pip3 uninstall -y fenics-ufl

From 7b4d268fa177e7f8a3d9c73ae898c14e777962b7 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 22 Nov 2022 15:37:11 +0100
Subject: [PATCH 14/50] Move fenics-ufl uninstall step to post-install.sh

Investigating why it was previously giving a permission issue.
---
 provisioning/install-fenics.sh | 3 ---
 provisioning/post-install.sh   | 4 ++++
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/provisioning/install-fenics.sh b/provisioning/install-fenics.sh
index c09eede..8348604 100644
--- a/provisioning/install-fenics.sh
+++ b/provisioning/install-fenics.sh
@@ -9,6 +9,3 @@ sudo apt-get -y install --no-install-recommends fenics
 
 # Install the FEniCS-preCICE adapter from PIP
 pip3 install --user fenicsprecice
-
-# Remove fenics-ufl package manually
-pip3 uninstall -y fenics-ufl
diff --git a/provisioning/post-install.sh b/provisioning/post-install.sh
index c3e4253..ce34535 100644
--- a/provisioning/post-install.sh
+++ b/provisioning/post-install.sh
@@ -7,6 +7,10 @@ set -ex
     tar -xzvf swak4Foam.tar.gz
 )
 
+# Remove fenics-ufl package
+# Workaround for https://github.com/precice/vm/issues/4
+pip3 uninstall -y fenics-ufl
+
 # Create a link to the default shared folder
 ln -sf /vagrant/ ~/Desktop/shared
 

From c40ecab6927465587f821b5685ed539743e1a7b2 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 16 Apr 2024 14:05:53 +0200
Subject: [PATCH 15/50] Install meld

Closes #67
---
 provisioning/install-devel.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/provisioning/install-devel.sh b/provisioning/install-devel.sh
index 9757a40..883f9d1 100644
--- a/provisioning/install-devel.sh
+++ b/provisioning/install-devel.sh
@@ -5,4 +5,6 @@ sudo apt-get install -y build-essential git cmake cmake-curses-gui
 
 sudo apt-get install -y nano vim gedit
 
+sudo apt-get install -y meld
+
 sudo apt-get install -y ipython3

From 062fe4269d1eecc70741f2b0e52d3444313d7086 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Tue, 16 Apr 2024 14:10:19 +0200
Subject: [PATCH 16/50] Remove dune-fem (#70)

Closes #68
---
 provisioning/install-dune.sh | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/provisioning/install-dune.sh b/provisioning/install-dune.sh
index 792e736..432ca9c 100755
--- a/provisioning/install-dune.sh
+++ b/provisioning/install-dune.sh
@@ -68,9 +68,5 @@ echo "export DUNE_CONTROL_PATH=\"\${HOME}/dune\"" >> ~/.bashrc
 # 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
 
-# Install dune-fem from PIP
-
-pip3 install --user dune-fem==2.8
-
 # We are done with DUNE, let's do back home
 cd ~

From f004994063f21f5106abd40d67d2a6fab5d0c0c3 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 16 Apr 2024 14:52:49 +0200
Subject: [PATCH 17/50] Switch preCICE to RelWithDebInfo

Closes #41
---
 provisioning/install-precice.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/provisioning/install-precice.sh b/provisioning/install-precice.sh
index 906ddd4..0a091ec 100644
--- a/provisioning/install-precice.sh
+++ b/provisioning/install-precice.sh
@@ -14,7 +14,7 @@ fi
     cd precice
     git pull
     mkdir -p build && cd build/
-    cmake -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=Debug -DBUILD_TESTING=OFF -Wno-dev ..
+    cmake -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=RelWithDebInfo -DBUILD_TESTING=OFF -Wno-dev ..
     make -j "$(nproc)"
     rm -fv ./*.deb && make package
     sudo apt-get install -y ./libprecice2_*.deb

From aa12205c7c393ac2d4f8e5421a942c49df00a4fa Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 16 Apr 2024 15:00:54 +0200
Subject: [PATCH 18/50] Add settings.json to gitignore

---
 .gitignore | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 87f6b1f..a14106b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,5 @@
 .vagrant
-vagrant
\ No newline at end of file
+vagrant
+
+# Editors
+settings.json

From ef1c609016ae4c34d2b132afe683b6b0a1401621 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Tue, 16 Apr 2024 15:25:59 +0200
Subject: [PATCH 19/50] Remove Nutils (#71)

It is now installed in each tutorial separately
---
 README.md                       |  1 -
 Vagrantfile                     |  1 -
 provisioning/install-nutils.sh  |  5 -----
 provisioning/install-precice.sh | 13 -------------
 4 files changed, 20 deletions(-)
 delete mode 100644 provisioning/install-nutils.sh

diff --git a/README.md b/README.md
index f28ed0a..2f4f977 100644
--- a/README.md
+++ b/README.md
@@ -55,7 +55,6 @@ This box is based on the [generic/ubuntu2004](https://github.com/lavabit/robox/t
 - 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)
 - 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)
 - code_aster 14.6 and the code_aster-preCICE adapter (master)
 - DUNE 2.8 and the experimental DUNE-preCICE adapter (master)
diff --git a/Vagrantfile b/Vagrantfile
index 761339e..300dbad 100644
--- a/Vagrantfile
+++ b/Vagrantfile
@@ -50,7 +50,6 @@ Vagrant.configure("2") do |config|
   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-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
diff --git a/provisioning/install-nutils.sh b/provisioning/install-nutils.sh
deleted file mode 100644
index dd2b068..0000000
--- a/provisioning/install-nutils.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/usr/bin/env bash
-set -ex
-
-# Install Nutils from PIP (we will also need matplotlib in our examples)
-pip3 install --user matplotlib nutils==7.0
diff --git a/provisioning/install-precice.sh b/provisioning/install-precice.sh
index 0a091ec..42e6495 100644
--- a/provisioning/install-precice.sh
+++ b/provisioning/install-precice.sh
@@ -62,19 +62,6 @@ pip3 install --user pyprecice
 # Additional python packages
 pip3 install --user pandas # Needed for the post-processing script of the oscillator tutorial
 
-# Temporary workaround for https://github.com/precice/vm/issues/61
-# Remove as soon as https://github.com/precice/tutorials/issues/217 gets resolved
-sudo apt-get install -y python3.8-venv
-(
-    cd tutorials/perpendicular-flap/fluid-nutils/
-    python3 -m venv nutils6-env
-    # shellcheck source=/dev/null
-    source nutils6-env/bin/activate
-    pip3 install nutils==6.3 pyprecice
-    sed -i "s/python3/nutils6-env\/bin\/python3/g" ./run.sh
-    deactivate
-)
-
 # Get the Python solverdummy into the examples
 if [ ! -d "python-bindings/" ]; then
     git clone --depth=1 --branch master https://github.com/precice/python-bindings.git

From 62a89a3091e1a998a4db56bf82e236aab418ec10 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Tue, 16 Apr 2024 15:39:18 +0200
Subject: [PATCH 20/50] Remove swak4Foam (#72)

---
 Vagrantfile                                    |  1 -
 provisioning/install-openfoam.sh               | 18 ------------------
 provisioning/prebuilt/swak4Foam/README.txt     | 17 -----------------
 .../prebuilt/swak4Foam/swak4Foam.tar.gz        |  3 ---
 4 files changed, 39 deletions(-)
 delete mode 100644 provisioning/prebuilt/swak4Foam/README.txt
 delete mode 100644 provisioning/prebuilt/swak4Foam/swak4Foam.tar.gz

diff --git a/Vagrantfile b/Vagrantfile
index 300dbad..7351c3e 100644
--- a/Vagrantfile
+++ b/Vagrantfile
@@ -46,7 +46,6 @@ 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
diff --git a/provisioning/install-openfoam.sh b/provisioning/install-openfoam.sh
index acb2b62..2e9e96e 100644
--- a/provisioning/install-openfoam.sh
+++ b/provisioning/install-openfoam.sh
@@ -19,23 +19,5 @@ fi
     openfoam2206 ./Allwmake
 )
 
-# Get swak4Foam (provides groovyBC, needed for the turek-hron-fsi3 tutorial)
-#
-# # Option 1: Build from source
-# sudo apt-get install -y mercurial
-# hg clone http://hg.code.sf.net/p/openfoam-extend/swak4Foam swak4Foam
-# (
-#     cd swak4Foam
-#     hg checkout develop
-#     openfoam2206 ./AllwmakeAll
-# )
-#
-# # Remove some swak4Foam files to save space (approx. 150MB)
-# rm -rfv .~swak4Foam
-# sudo apt-get purge --autoremove -y mercurial # This also removes Python2, yipieh!
-#
-# # Option 2: Use pre-built binaries
-# # (see Vagrantfile and post-install.sh, rebuild and update for OpenFOAM version other than v2206)
-
 # Build the tutorials partitioned-heat-conduction solver
 cd ~/tutorials/partitioned-heat-conduction/openfoam-solver && openfoam2206 wmake
diff --git a/provisioning/prebuilt/swak4Foam/README.txt b/provisioning/prebuilt/swak4Foam/README.txt
deleted file mode 100644
index a8b587f..0000000
--- a/provisioning/prebuilt/swak4Foam/README.txt
+++ /dev/null
@@ -1,17 +0,0 @@
-Prebuilt libraries and tools of swak4Foam for Ubuntu 20.04 and OpenFOAM v2206, based on the develop branch of swak4Foam (built on November 2022):
-
-```bash
-vagrant@precicevm:~/swak4Foam$ hg tip
-changeset:   3999:481d96f16780
-branch:      develop
-tag:         tip
-parent:      3997:4d33e38246ad
-parent:      3998:12dad7c691d1
-user:        Bernhard F.W. Gschaider <bgschaid@hfd-research.com>
-date:        Mon Jul 04 01:06:48 2022 +0200
-summary:     flow: Promoted <feature> 'port/of9' (12dad7c691d1) to 'develop'.
-```
-
-The files are extracted from `/home/vagrant/OpenFOAM/vagrant-<version>/platforms/` and copied there.
-
-Find the source code on http://hg.code.sf.net/p/openfoam-extend/swak4Foam/rev/ea7680cdcf8b
diff --git a/provisioning/prebuilt/swak4Foam/swak4Foam.tar.gz b/provisioning/prebuilt/swak4Foam/swak4Foam.tar.gz
deleted file mode 100644
index 1e469cd..0000000
--- a/provisioning/prebuilt/swak4Foam/swak4Foam.tar.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:284da0859454c970ebbc208e477a8572060280eff4ba6252cd33ed24b25c4fd1
-size 20097408

From b96f545ac24e04ac382d5fb7388cf41538de936b Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 16 Apr 2024 15:40:08 +0200
Subject: [PATCH 21/50] Update preCICE version in Debian package name

---
 provisioning/install-precice.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/provisioning/install-precice.sh b/provisioning/install-precice.sh
index 42e6495..9e7286d 100644
--- a/provisioning/install-precice.sh
+++ b/provisioning/install-precice.sh
@@ -17,7 +17,7 @@ fi
     cmake -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=RelWithDebInfo -DBUILD_TESTING=OFF -Wno-dev ..
     make -j "$(nproc)"
     rm -fv ./*.deb && make package
-    sudo apt-get install -y ./libprecice2_*.deb
+    sudo apt-get install -y ./libprecice3_*.deb
     # Remove generated packages to save space (approx. 70MB)
     rm -rfv ./*.deb ./*.tar.gz _CPack_Packages
 )

From e25abe2cdc1968d2d1328d98e1901241d007c77c Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 16 Apr 2024 15:40:45 +0200
Subject: [PATCH 22/50] Remove more code related to swak4Foam

---
 provisioning/post-install.sh | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/provisioning/post-install.sh b/provisioning/post-install.sh
index ce34535..9c52fc1 100644
--- a/provisioning/post-install.sh
+++ b/provisioning/post-install.sh
@@ -1,12 +1,6 @@
 #!/usr/bin/env bash
 set -ex
 
-# Setup swak4Foam
-(
-    cd "${HOME}/OpenFOAM/vagrant-v2206/platforms/linux64GccDPInt32Opt/"
-    tar -xzvf swak4Foam.tar.gz
-)
-
 # Remove fenics-ufl package
 # Workaround for https://github.com/precice/vm/issues/4
 pip3 uninstall -y fenics-ufl

From b19df640ff07649b1b6b577c68a771b7fdb0ac1a Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 16 Apr 2024 15:41:22 +0200
Subject: [PATCH 23/50] Do not build the elastic-tube-1d solvers

They are now built automatically on the first run of the tutorial.
---
 provisioning/install-precice.sh | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/provisioning/install-precice.sh b/provisioning/install-precice.sh
index 9e7286d..036a4ee 100644
--- a/provisioning/install-precice.sh
+++ b/provisioning/install-precice.sh
@@ -40,10 +40,6 @@ if [ ! -d "tutorials/" ]; then
     git clone --depth=1 --branch master https://github.com/precice/tutorials.git
     ln -sf ~/tutorials ~/Desktop/
 fi
-(
-    cd tutorials/elastic-tube-1d/fluid-cpp/ && mkdir build && cd build && cmake .. && make && cd ../..
-    cd solid-cpp/ && mkdir build && cd build && cmake .. && make
-)
 (
     cd tutorials/quickstart/solid-cpp/ && cmake . && make
 )

From d13fbaf7d75e0f7bba55d6de2b4b4ebfbe4cd368 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 16 Apr 2024 15:41:49 +0200
Subject: [PATCH 24/50] Install matplotlib

Needed in several post-processing scripts, previously installed next to Nutils.
---
 provisioning/install-precice.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/provisioning/install-precice.sh b/provisioning/install-precice.sh
index 036a4ee..f0d07d5 100644
--- a/provisioning/install-precice.sh
+++ b/provisioning/install-precice.sh
@@ -56,7 +56,7 @@ pip3 install --upgrade pip
 pip3 install --user pyprecice
 
 # Additional python packages
-pip3 install --user pandas # Needed for the post-processing script of the oscillator tutorial
+pip3 install --user pandas matplotlib # Needed for the post-processing scripts
 
 # Get the Python solverdummy into the examples
 if [ ! -d "python-bindings/" ]; then

From d55d48817f726bc93cf1bf9638d15c6cea2d3ea8 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Tue, 16 Apr 2024 17:06:20 +0200
Subject: [PATCH 25/50] Install FMI runner (#77)

Closes #74
---
 Vagrantfile                 | 1 +
 provisioning/install-fmi.sh | 5 +++++
 2 files changed, 6 insertions(+)
 create mode 100644 provisioning/install-fmi.sh

diff --git a/Vagrantfile b/Vagrantfile
index 7351c3e..4710712 100644
--- a/Vagrantfile
+++ b/Vagrantfile
@@ -49,6 +49,7 @@ Vagrant.configure("2") do |config|
   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-fmi.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
diff --git a/provisioning/install-fmi.sh b/provisioning/install-fmi.sh
new file mode 100644
index 0000000..3a59461
--- /dev/null
+++ b/provisioning/install-fmi.sh
@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+set -ex
+
+# Install the FMI runner from PIP
+pip3 install --user fmiprecice

From dd9af1bc1981b2accf9413a4f6268ac797e61cee Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 16 Apr 2024 17:18:30 +0200
Subject: [PATCH 26/50] Rename install-fmi.sh to install-fmiprecice.sh

---
 Vagrantfile                                            | 2 +-
 provisioning/{install-fmi.sh => install-fmiprecice.sh} | 0
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename provisioning/{install-fmi.sh => install-fmiprecice.sh} (100%)

diff --git a/Vagrantfile b/Vagrantfile
index 4710712..ec8ba9b 100644
--- a/Vagrantfile
+++ b/Vagrantfile
@@ -49,7 +49,7 @@ Vagrant.configure("2") do |config|
   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-fmi.sh", privileged: false
+  config.vm.provision "shell", path: "provisioning/install-fmiprecice.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
diff --git a/provisioning/install-fmi.sh b/provisioning/install-fmiprecice.sh
similarity index 100%
rename from provisioning/install-fmi.sh
rename to provisioning/install-fmiprecice.sh

From 2013ae53f099c630f9b6ec281174b471bb9892e5 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Tue, 16 Apr 2024 18:39:04 +0200
Subject: [PATCH 27/50] Update SU2 (#78)

---
 provisioning/install-su2.sh | 23 +++++++++++------------
 1 file changed, 11 insertions(+), 12 deletions(-)

diff --git a/provisioning/install-su2.sh b/provisioning/install-su2.sh
index 69dc370..935d257 100644
--- a/provisioning/install-su2.sh
+++ b/provisioning/install-su2.sh
@@ -1,15 +1,18 @@
 #!/usr/bin/env bash
 set -ex
 
-# Get SU2 6.0.0 from GitHub
-wget --quiet https://github.com/su2code/SU2/archive/v6.0.0.tar.gz
-tar -xzf v6.0.0.tar.gz
-rm -fv v6.0.0.tar.gz
+# Install dependencies
+pip3 install --user mpi4py
+
+# Get SU2 7.5.1 from GitHub
+wget --quiet  https://github.com/su2code/SU2/archive/refs/tags/v7.5.1.tar.gz
+tar -xzf v7.5.1.tar.gz
+rm -fv v7.5.1.tar.gz
 
 # Add SU2 to PATH and apply.
 # We first export to a separate script, so that we can load it here (non-interactive shell).
 {
-    echo "export SU2_HOME=\"\${HOME}/SU2-6.0.0\""
+    echo "export SU2_HOME=\"\${HOME}/SU2-7.5.1\""
     echo "export SU2_RUN=\"\${SU2_HOME}/SU2_CFD/bin\""
     echo "export PATH=\"\${SU2_RUN}:\${PATH}\""
     echo "export PYTHONPATH=\"\${SU2_RUN}:\${PYTHONPATH}\""
@@ -32,13 +35,9 @@ fi
 # Configure and build the SU2 adapter
 (
     cd "${SU2_HOME}"
-    ./configure --disable-metis --disable-parmetis --disable-cgns --disable-DOT \
-        --disable-MSH --disable-DEF --disable-SOL --disable-GEO \
-        --prefix="${SU2_RUN}" CXXFLAGS='-std=c++11'
-    make -j "$(nproc)"
-    # We still need sudo for whatever reason
-    sudo make install
+    ./meson.py build -Denable-pywrapper=true --prefix="${SU2_RUN}" &&\
+    ./ninja -C build install
 )
 
 # Remove the libSU2Core.a library to save space (approx. 500MB)
-rm -fv ~/SU2-6.0.0/SU2_CFD/obj/libSU2Core.a
+rm -fv ~/SU2-7.5.1/SU2_CFD/obj/libSU2Core.a

From 663aba492fe10264c79a38b86cfa1b5bba8b4124 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Tue, 16 Apr 2024 21:12:52 +0200
Subject: [PATCH 28/50] Add cargo (Rust) (#80)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Frédéric Simonis <simonisfrederic@gmail.com>
---
 provisioning/install-devel.sh   | 3 +++
 provisioning/install-precice.sh | 6 ++++++
 2 files changed, 9 insertions(+)

diff --git a/provisioning/install-devel.sh b/provisioning/install-devel.sh
index 883f9d1..0a3d005 100644
--- a/provisioning/install-devel.sh
+++ b/provisioning/install-devel.sh
@@ -3,6 +3,9 @@ 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
diff --git a/provisioning/install-precice.sh b/provisioning/install-precice.sh
index f0d07d5..fd8498c 100644
--- a/provisioning/install-precice.sh
+++ b/provisioning/install-precice.sh
@@ -43,6 +43,12 @@ fi
 (
     cd tutorials/quickstart/solid-cpp/ && cmake . && make
 )
+(
+    cd tutorials/elastic-tube-1d/solid-rust/ && mkdir -p .cargo && cargo vendor > .cargo/config.toml
+)
+(
+    cd tutorials/elastic-tube-1d/fluid-rust/ && mkdir -p .cargo && cargo vendor > .cargo/config.toml
+)
 (
     cd tutorials/heat-exchanger && ./download-meshes.sh
 )

From 33d8b963979b01f43a76e13e54600d70615e5cf4 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Tue, 16 Apr 2024 21:59:14 +0200
Subject: [PATCH 29/50] Install config-visualizer-gui, move Python installation
 to basics (#76)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Frédéric Simonis <simonisfrederic@gmail.com>
---
 provisioning/install-basics.sh            |  1 +
 provisioning/install-config-visualizer.sh | 26 +++++++++++++----------
 2 files changed, 16 insertions(+), 11 deletions(-)

diff --git a/provisioning/install-basics.sh b/provisioning/install-basics.sh
index ff78f0b..05d54c4 100644
--- a/provisioning/install-basics.sh
+++ b/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
 
 # Setup auto-login for the graphical session
 # Disabled due to https://github.com/precice/vm/issues/40
diff --git a/provisioning/install-config-visualizer.sh b/provisioning/install-config-visualizer.sh
index 06359ac..81d0551 100644
--- a/provisioning/install-config-visualizer.sh
+++ b/provisioning/install-config-visualizer.sh
@@ -1,18 +1,22 @@
 #!/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 libcairo2-dev libgirepository1.0-dev gcc libcairo2-dev pkg-config gir1.2-gtk-4.0
+
+# Get the config-visualizer from PIP
+pipx install precice-config-visualizer
+pipx install precice-config-visualizer-gui
 
 # 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/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/

From c879fc8eff249a1df574d889aa1bb062d9d21411 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Tue, 16 Apr 2024 22:01:40 +0200
Subject: [PATCH 30/50] Add missing venv

---
 provisioning/install-basics.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/provisioning/install-basics.sh b/provisioning/install-basics.sh
index 05d54c4..d3939b8 100644
--- a/provisioning/install-basics.sh
+++ b/provisioning/install-basics.sh
@@ -12,7 +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
+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

From 876cf15339e0170f813145b1a4d7c23941905732 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 16 Apr 2024 22:05:48 +0200
Subject: [PATCH 31/50] Update README

---
 README.md | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 2f4f977..e69d1b4 100644
--- a/README.md
+++ b/README.md
@@ -47,15 +47,18 @@ This box is based on the [generic/ubuntu2004](https://github.com/lavabit/robox/t
 - 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)
+- preCICE Rust bindings (Cargo)
+- preCICE FMI Runner (PIP)
 - OpenFOAM v2112 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)
 - FEniCS latest from the FEniCS PPA and the FEniCS-preCICE adapter (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)
 - ASTE (master)

From 58a99fcfa205607f637d022eb77a7838e3a31040 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 16 Apr 2024 22:09:46 +0200
Subject: [PATCH 32/50] Install micro-manager

---
 Vagrantfile                           | 1 +
 provisioning/install-micro-manager.sh | 4 ++++
 2 files changed, 5 insertions(+)
 create mode 100644 provisioning/install-micro-manager.sh

diff --git a/Vagrantfile b/Vagrantfile
index ec8ba9b..c1c5474 100644
--- a/Vagrantfile
+++ b/Vagrantfile
@@ -50,6 +50,7 @@ Vagrant.configure("2") do |config|
   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-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
diff --git a/provisioning/install-micro-manager.sh b/provisioning/install-micro-manager.sh
new file mode 100644
index 0000000..bf0ea3b
--- /dev/null
+++ b/provisioning/install-micro-manager.sh
@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+set -ex
+
+pip install --user micro-manager-precice

From 2a4188db05a7b91ee62eefac7b0b90a989ab9a7b Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 16 Apr 2024 23:23:54 +0200
Subject: [PATCH 33/50] Add Micro-Manager in the README.md

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index e69d1b4..2bb743b 100644
--- a/README.md
+++ b/README.md
@@ -54,6 +54,7 @@ This box is based on the [generic/ubuntu2004](https://github.com/lavabit/robox/t
 - preCICE Julia bindings (Pkg)
 - preCICE Rust bindings (Cargo)
 - preCICE FMI Runner (PIP)
+- preCICE Micro Manager (PIP)
 - OpenFOAM v2112 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)

From 9e0a47f97b024ad834fc9b514619817521dbacea Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Wed, 17 Apr 2024 12:11:00 +0200
Subject: [PATCH 34/50] Revert back to bento/ubuntu-20.04 (#84)

---
 README.md   | 7 ++++++-
 Vagrantfile | 4 +++-
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 2bb743b..6ac24b6 100644
--- a/README.md
+++ b/README.md
@@ -40,7 +40,7 @@ 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
@@ -120,6 +120,11 @@ 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:
 ```
diff --git a/Vagrantfile b/Vagrantfile
index c1c5474..a2878d3 100644
--- a/Vagrantfile
+++ b/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.

From 86805973b190d3353c164f81fe7c47ad2b934420 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Wed, 17 Apr 2024 12:17:04 +0200
Subject: [PATCH 35/50] Fix the config visualizer in the vm (#86)

---
 provisioning/install-config-visualizer.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/provisioning/install-config-visualizer.sh b/provisioning/install-config-visualizer.sh
index 81d0551..d10d879 100644
--- a/provisioning/install-config-visualizer.sh
+++ b/provisioning/install-config-visualizer.sh
@@ -4,11 +4,11 @@ set -ex
 # Install CLI dependencies
 sudo apt-get install -y graphviz
 # Install GUI depedencies
-sudo apt-get install -y libcairo2-dev libgirepository1.0-dev gcc libcairo2-dev pkg-config gir1.2-gtk-4.0
+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
-pipx install precice-config-visualizer
-pipx install precice-config-visualizer-gui
+pipx install precice-config-visualizer==1.1.3
+pipx install precice-config-visualizer-gui==0.1.0
 
 # Add the config-visualizer to PATH
 # shellcheck disable=SC2016

From 627496670771d856b7dff697d40f6e36a89efc36 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= <simonisfrederic@gmail.com>
Date: Thu, 18 Apr 2024 16:44:33 +0200
Subject: [PATCH 36/50] Fix link

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 6ac24b6..b544a59 100644
--- a/README.md
+++ b/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?

From 2bf0132cb7c62c9167bd2d88beb8da4f8263ace7 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Fri, 19 Apr 2024 12:04:08 +0200
Subject: [PATCH 37/50] Reinstall config-visualizer if already installed

To support continuing from a previously failed build
---
 provisioning/install-config-visualizer.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/provisioning/install-config-visualizer.sh b/provisioning/install-config-visualizer.sh
index d10d879..2915857 100644
--- a/provisioning/install-config-visualizer.sh
+++ b/provisioning/install-config-visualizer.sh
@@ -7,8 +7,8 @@ sudo apt-get install -y graphviz
 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
-pipx install precice-config-visualizer==1.1.3
-pipx install precice-config-visualizer-gui==0.1.0
+pipx install --force precice-config-visualizer==1.1.3
+pipx install --force precice-config-visualizer-gui==0.1.0
 
 # Add the config-visualizer to PATH
 # shellcheck disable=SC2016

From cb73901eea6f576c64b79e5640d62789aafb32a9 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Fri, 19 Apr 2024 12:04:46 +0200
Subject: [PATCH 38/50] Update OpenFOAM

---
 README.md                        |  2 +-
 provisioning/install-openfoam.sh | 11 ++++++-----
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index b544a59..64388af 100644
--- a/README.md
+++ b/README.md
@@ -55,7 +55,7 @@ This box is based on the ~~[generic/ubuntu2004](https://github.com/lavabit/robox
 - preCICE Rust bindings (Cargo)
 - preCICE FMI Runner (PIP)
 - preCICE Micro Manager (PIP)
-- OpenFOAM v2112 and the OpenFOAM-preCICE adapter (master)
+- 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)
 - FEniCS latest from the FEniCS PPA and the FEniCS-preCICE adapter (PIP)
diff --git a/provisioning/install-openfoam.sh b/provisioning/install-openfoam.sh
index 2e9e96e..10c6b8a 100644
--- a/provisioning/install-openfoam.sh
+++ b/provisioning/install-openfoam.sh
@@ -4,10 +4,10 @@ set -ex
 # Add the signing key, add the repository, update:
 wget -q -O - https://dl.openfoam.com/add-debian-repo.sh | sudo bash
 
-# Install OpenFOAM v2206:
-sudo apt-get install -y openfoam2206-dev
+# Install OpenFOAM v2312:
+sudo apt-get install -y openfoam2312-dev
 # Enable OpenFOAM by default:
-echo ". /usr/lib/openfoam/openfoam2206/etc/bashrc" >> ~/.bashrc
+echo ". /usr/lib/openfoam/openfoam2312/etc/bashrc" >> ~/.bashrc
 
 # Get the OpenFOAM-preCICE adapter
 if [ ! -d "openfoam-adapter/" ]; then
@@ -16,8 +16,9 @@ fi
 (
     cd openfoam-adapter
     git pull
-    openfoam2206 ./Allwmake
+    openfoam2312 ./Allclean
+    openfoam2312 ./Allwmake
 )
 
 # Build the tutorials partitioned-heat-conduction solver
-cd ~/tutorials/partitioned-heat-conduction/openfoam-solver && openfoam2206 wmake
+cd ~/tutorials/partitioned-heat-conduction/solver-openfoam && openfoam2312 wmake

From dce8f24a06ba8bdf6be38e5dc7d2fc6bd70c792c Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Fri, 19 Apr 2024 12:05:35 +0200
Subject: [PATCH 39/50] Correct CalculiX version in README

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 64388af..0669516 100644
--- a/README.md
+++ b/README.md
@@ -57,7 +57,7 @@ This box is based on the ~~[generic/ubuntu2004](https://github.com/lavabit/robox
 - 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)
 - SU2 7.5.1 and the SU2-preCICE adapter (master)
 - code_aster 14.6 and the code_aster-preCICE adapter (master)

From 8cc36bfa84ff0c314a0cc44e051120afc0bf287a Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Fri, 19 Apr 2024 12:06:30 +0200
Subject: [PATCH 40/50] Disable uninstalling fenics-ufl

---
 provisioning/post-install.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/provisioning/post-install.sh b/provisioning/post-install.sh
index 9c52fc1..6f082c2 100644
--- a/provisioning/post-install.sh
+++ b/provisioning/post-install.sh
@@ -3,7 +3,7 @@ set -ex
 
 # Remove fenics-ufl package
 # Workaround for https://github.com/precice/vm/issues/4
-pip3 uninstall -y fenics-ufl
+# pip3 uninstall -y fenics-ufl
 
 # Create a link to the default shared folder
 ln -sf /vagrant/ ~/Desktop/shared

From a714000df1758c592a8ce8b37c931059d6b10863 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Fri, 19 Apr 2024 12:34:01 +0200
Subject: [PATCH 41/50] Fix pipx venv path for config-visualizer

---
 provisioning/install-config-visualizer.sh | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/provisioning/install-config-visualizer.sh b/provisioning/install-config-visualizer.sh
index 2915857..6538322 100644
--- a/provisioning/install-config-visualizer.sh
+++ b/provisioning/install-config-visualizer.sh
@@ -7,8 +7,10 @@ sudo apt-get install -y graphviz
 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
-pipx install --force precice-config-visualizer==1.1.3
-pipx install --force precice-config-visualizer-gui==0.1.0
+PRECEICE_CONFIG_VISUALIZER_VERSION=1.1.3
+PRECEICE_CONFIG_VISUALIZER_GUI_VERSION=0.1.0
+pipx install --force precice-config-visualizer==${PRECEICE_CONFIG_VISUALIZER_VERSION}
+pipx install --force precice-config-visualizer-gui==${PRECEICE_CONFIG_VISUALIZER_GUI_VERSION}
 
 # Add the config-visualizer to PATH
 # shellcheck disable=SC2016
@@ -17,6 +19,6 @@ echo 'export PATH="${HOME}/.local/bin:${PATH}"' >> ~/.bashrc
 # Add the GUI in the apps menu
 mkdir -p ~/.local/share/applications ~/.local/share/icons
 
-CV_LOC_SHARE=~/.local/pipx/venvs/precice-config-visualizer-gui/share
+CV_LOC_SHARE=~/.local/pipx/venvs/precice-config-visualizer-gui\=\=${PRECEICE_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/

From e12ca135d962fd48a2840773be5c788d52dda75f Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Fri, 19 Apr 2024 13:09:44 +0200
Subject: [PATCH 42/50] Fix shellcheck complaints

---
 provisioning/install-config-visualizer.sh | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/provisioning/install-config-visualizer.sh b/provisioning/install-config-visualizer.sh
index 6538322..2e2bde0 100644
--- a/provisioning/install-config-visualizer.sh
+++ b/provisioning/install-config-visualizer.sh
@@ -7,10 +7,10 @@ sudo apt-get install -y graphviz
 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
-PRECEICE_CONFIG_VISUALIZER_VERSION=1.1.3
-PRECEICE_CONFIG_VISUALIZER_GUI_VERSION=0.1.0
-pipx install --force precice-config-visualizer==${PRECEICE_CONFIG_VISUALIZER_VERSION}
-pipx install --force precice-config-visualizer-gui==${PRECEICE_CONFIG_VISUALIZER_GUI_VERSION}
+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
 # shellcheck disable=SC2016
@@ -19,6 +19,6 @@ echo 'export PATH="${HOME}/.local/bin:${PATH}"' >> ~/.bashrc
 # Add the GUI in the apps menu
 mkdir -p ~/.local/share/applications ~/.local/share/icons
 
-CV_LOC_SHARE=~/.local/pipx/venvs/precice-config-visualizer-gui\=\=${PRECEICE_CONFIG_VISUALIZER_GUI_VERSION}/share
+CV_LOC_SHARE=~/.local/pipx/venvs/precice-config-visualizer-gui==${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/

From 7cdf04af7514b048d32ba36dead0fe0a7ae6b260 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Fri, 19 Apr 2024 14:20:02 +0200
Subject: [PATCH 43/50] Fix SU2 paths

---
 provisioning/install-su2.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/provisioning/install-su2.sh b/provisioning/install-su2.sh
index 935d257..35eb466 100644
--- a/provisioning/install-su2.sh
+++ b/provisioning/install-su2.sh
@@ -9,13 +9,13 @@ wget --quiet  https://github.com/su2code/SU2/archive/refs/tags/v7.5.1.tar.gz
 tar -xzf v7.5.1.tar.gz
 rm -fv v7.5.1.tar.gz
 
-# Add SU2 to PATH and apply.
+# Add SU2 and the SU2 adapter to PATH and apply.
 # We first export to a separate script, so that we can load it here (non-interactive shell).
 {
     echo "export SU2_HOME=\"\${HOME}/SU2-7.5.1\""
-    echo "export SU2_RUN=\"\${SU2_HOME}/SU2_CFD/bin\""
-    echo "export PATH=\"\${SU2_RUN}:\${PATH}\""
-    echo "export PYTHONPATH=\"\${SU2_RUN}:\${PYTHONPATH}\""
+    echo "export SU2_RUN=\"\${SU2_HOME}/SU2_CFD\""
+    echo "export PATH=\"\${SU2_RUN}/bin/:\${HOME}/su2-adapter/run/:\${PATH}\""
+    echo "export PYTHONPATH=\"\${SU2_RUN}/bin/:\${PYTHONPATH}\""
 } >> ~/.su2-bashrc
 
 echo ". \${HOME}/.su2-bashrc" >> ~/.bashrc

From 6fb6393da9781a924d7b6e139d0758b707963908 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Fri, 19 Apr 2024 14:21:28 +0200
Subject: [PATCH 44/50] Update config-visualizer aliases

---
 provisioning/.alias | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/provisioning/.alias b/provisioning/.alias
index 4831f56..17c3eac 100644
--- a/provisioning/.alias
+++ b/provisioning/.alias
@@ -1,12 +1,12 @@
 # preCICE config visualizer
 function preciceToPNG(){
-  cat "${1:-precice-config.xml}" | precice-config-visualizer | dot -Tpng > precice-config.png
+  precice-config-visualizer "${1:-precice-config.xml}" | dot -Tpng > precice-config.png
 }
 
 function preciceToPDF(){
-  cat "${1:-precice-config.xml}" | precice-config-visualizer | dot -Tpdf > precice-config.pdf
+  precice-config-visualizer "${1:-precice-config.xml}" | dot -Tpdf > precice-config.pdf
 }
 
 function preciceToSVG(){
-  cat "${1:-precice-config.xml}" | precice-config-visualizer | dot -Tsvg > precice-config.svg
+  precice-config-visualizer "${1:-precice-config.xml}" | dot -Tsvg > precice-config.svg
 }

From ab7279e39a0ee797db00bf493aed0bf551b8310a Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Sat, 20 Apr 2024 07:41:03 +0200
Subject: [PATCH 45/50] Disable VBOXSYMLINKCREATE for GitHub Actions

Debugging
---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index b298d37..47114cc 100644
--- a/.github/workflows/build.yml
+++ b/.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

From de16019a5e375dae3818be48210fe8ba90474501 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Tue, 23 Apr 2024 17:13:04 +0200
Subject: [PATCH 46/50] Add DuMux 3.8 and update DUNE to 2.9.1 (#87)

---
 README.md                    |  3 +-
 provisioning/install-dune.sh | 63 +++++++++++++++++++++++-------------
 2 files changed, 42 insertions(+), 24 deletions(-)

diff --git a/README.md b/README.md
index 0669516..a52559f 100644
--- a/README.md
+++ b/README.md
@@ -61,7 +61,8 @@ This box is based on the ~~[generic/ubuntu2004](https://github.com/lavabit/robox
 - FEniCS latest from the FEniCS PPA and the FEniCS-preCICE adapter (PIP)
 - 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
diff --git a/provisioning/install-dune.sh b/provisioning/install-dune.sh
index 432ca9c..2507ae5 100755
--- a/provisioning/install-dune.sh
+++ b/provisioning/install-dune.sh
@@ -1,72 +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
+
+# 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
+
+# Build DuMux
+CMAKE_FLAGS="$CMAKE_FLAGS -DCMAKE_DISABLE_FIND_PACKAGE_Kokkos=TRUE" ./dune-common/bin/dunecontrol --only=dumux all
+
+if [ ! -d "dumux-adapter/" ]; then
+    git clone  --depth 1 --branch v2.0.0 https://github.com/precice/dumux-adapter.git
+fi
+
+# Build the DuMux-preCICE adapter
+CMAKE_FLAGS="$CMAKE_FLAGS -DCMAKE_DISABLE_FIND_PACKAGE_Kokkos=TRUE" ./dune-common/bin/dunecontrol --only=dumux-precice all
 
 # Set the DUNE_CONTROL_PATH (DUNE recursively finds modules in this directory)
-echo "export DUNE_CONTROL_PATH=\"\${HOME}/dune\"" >> ~/.bashrc
+echo "export DUNE_CONTROL_PATH=\"\${HOME}/dune-dumux\"" >> ~/.bashrc
 
 # 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
+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 ~

From 03eb24fd8236ecc9ebc609de476da540e179375d Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Tue, 23 Apr 2024 18:16:37 +0200
Subject: [PATCH 47/50] Version-agnostic apt install of preCICE Debian package
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Frédéric Simonis <simonisfrederic@gmail.com>
---
 provisioning/install-precice.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/provisioning/install-precice.sh b/provisioning/install-precice.sh
index fd8498c..51e7711 100644
--- a/provisioning/install-precice.sh
+++ b/provisioning/install-precice.sh
@@ -17,7 +17,7 @@ fi
     cmake -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=RelWithDebInfo -DBUILD_TESTING=OFF -Wno-dev ..
     make -j "$(nproc)"
     rm -fv ./*.deb && make package
-    sudo apt-get install -y ./libprecice3_*.deb
+    sudo apt-get install -y ./libprecice*_*.deb
     # Remove generated packages to save space (approx. 70MB)
     rm -rfv ./*.deb ./*.tar.gz _CPack_Packages
 )

From c08fdcc8b2d754ee4b000de6e1f83a2134ac72ad Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Tue, 23 Apr 2024 18:17:09 +0200
Subject: [PATCH 48/50] Install polars
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Frédéric Simonis <simonisfrederic@gmail.com>
---
 provisioning/install-precice.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/provisioning/install-precice.sh b/provisioning/install-precice.sh
index 51e7711..4c760f7 100644
--- a/provisioning/install-precice.sh
+++ b/provisioning/install-precice.sh
@@ -62,7 +62,7 @@ pip3 install --upgrade pip
 pip3 install --user pyprecice
 
 # Additional python packages
-pip3 install --user pandas matplotlib # Needed for the post-processing scripts
+pip3 install --user pandas matplotlib polars # Needed for the post-processing scripts
 
 # Get the Python solverdummy into the examples
 if [ ! -d "python-bindings/" ]; then

From 235bd037a471fd0a36b2ba0806c5dd322b40e4a3 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <chourdak@in.tum.de>
Date: Tue, 23 Apr 2024 18:20:15 +0200
Subject: [PATCH 49/50] Simplify config-visualizer aliases
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

co-authored-by: Frédéric Simonis <simonisfrederic@gmail.com>
---
 provisioning/.alias | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/provisioning/.alias b/provisioning/.alias
index 17c3eac..67234b9 100644
--- a/provisioning/.alias
+++ b/provisioning/.alias
@@ -1,12 +1,12 @@
 # preCICE config visualizer
 function preciceToPNG(){
-  precice-config-visualizer "${1:-precice-config.xml}" | dot -Tpng > precice-config.png
+  precice-config-visualizer -o precice-config.png "${1:-precice-config.xml}"
 }
 
 function preciceToPDF(){
-  precice-config-visualizer "${1:-precice-config.xml}" | dot -Tpdf > precice-config.pdf
+  precice-config-visualizer -o precice-config.pdf "${1:-precice-config.xml}"
 }
 
 function preciceToSVG(){
-  precice-config-visualizer "${1:-precice-config.xml}" | dot -Tsvg > precice-config.svg
+  precice-config-visualizer -o precice-config.svg "${1:-precice-config.xml}"
 }

From 8f4fc38b94a78741cc55d17967e8623b0e03e4ca Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <makishourdakis@gmail.com>
Date: Tue, 23 Apr 2024 18:23:32 +0200
Subject: [PATCH 50/50] Enable debug log in preCICE
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Frédéric Simonis <simonisfrederic@gmail.com>
---
 provisioning/install-precice.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/provisioning/install-precice.sh b/provisioning/install-precice.sh
index 4c760f7..cda6d35 100644
--- a/provisioning/install-precice.sh
+++ b/provisioning/install-precice.sh
@@ -14,7 +14,7 @@ fi
     cd precice
     git pull
     mkdir -p build && cd build/
-    cmake -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=RelWithDebInfo -DBUILD_TESTING=OFF -Wno-dev ..
+    cmake -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=RelWithDebInfo -DPRECICE_RELEASE_WITH_DEBUG_LOG=ON -DBUILD_TESTING=OFF -Wno-dev ..
     make -j "$(nproc)"
     rm -fv ./*.deb && make package
     sudo apt-get install -y ./libprecice*_*.deb