Release v202202.0.0

MakisH · web-flow · commit 1045afd56138 · 2022-02-13T11:53:43.000+01:00
Merge Request #29
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,2 @@
+*.so filter=lfs diff=lfs merge=lfs -text
+*.tar.gz filter=lfs diff=lfs merge=lfs -text
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -2,12 +2,16 @@ name: Build and package
 on:
   pull_request:
     types: [ready_for_review]
+  workflow_dispatch:
+    
 jobs:
   vagrant-up:
     runs-on: macos-10.15
 
     steps:
     - uses: actions/checkout@v2
+      with:
+        lfs: true
 
     - name: Cache Vagrant boxes
       uses: actions/cache@v2
diff --git a/README.md b/README.md
@@ -50,14 +50,15 @@ This box is based on the [bento/ubuntu-20.04](https://github.com/chef/bento/blob
 - preCICE latest for the master branch
 - preCICE config visualizer (master)
 - preCICE Python bindings (PIP)
-- OpenFOAM v2012 and the OpenFOAM-preCICE adapter (master)
-- deal.II 9.2 from the official backports and the deal.II-preCICE adapter (master)
-- CalculiX 2.16 from source and the CalculiX-preCICE adapter (master)
+- 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)
 - 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)
-- Paraview from the official binaries
+- DUNE 2.8 and the experimental DUNE-preCICE adapter (master)
+- Paraview from APT
 - Gnuplot
 
 It then adds to the `/home/vagrant/`:
@@ -87,7 +88,7 @@ In case you killed the session before provisioning finished, the setup of your V
 
 ## Testing before publishing
 
-We now have a GitHub action that can build the Vagrant box. This workflow only runs for pull requests that are marked as "ready for review" (i.e. not "draft"), as it takes significant time to complete (~1.5h). If you already submitted a normal PR but the workflow is not triggered, convert the PR to draft and then to "ready for review" again.
+We now have a GitHub action that can build the Vagrant box. This workflow only runs for pull requests that are marked as "ready for review" (i.e. not "draft"), as it takes significant time to complete (~1.5h). If you already submitted a normal PR but the workflow is not triggered, you can manually trigger it from the "Actions" tab.
 
 The workflow uploads the resulting box as an artifact and it also prints its SHA256 checksum before that. Download the job artifact and unzip it. Then run add the box to Vagrant:
 
diff --git a/Vagrantfile b/Vagrantfile
@@ -37,12 +37,14 @@ 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 "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
   config.vm.provision "shell", path: "provisioning/install-paraview.sh", privileged: false
 
   # Post-installation steps
diff --git a/provisioning/cleanup.sh b/provisioning/cleanup.sh
@@ -6,3 +6,6 @@ sudo apt-get clean
 
 # Cleanup all object files from compilation
 find "${HOME}" -type f -name '*.o' -exec rm -fv {} \;
+
+# Remove the cache
+rm -rfv ~/.cache
diff --git 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
+sudo apt-get install -y thunar xfce4-terminal terminator bash-completion tree evince firefox firefox-locale-en baobab catfish
 
 # Install the VirtualBox guest additions
 sudo apt-get install -y virtualbox-guest-dkms virtualbox-guest-utils virtualbox-guest-x11
diff --git 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_2.16.src.tar.bz2
-tar xvjf ccx_2.16.src.tar.bz2
-rm -fv ccx_2.16.src.tar.bz2
+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
 
 # Get the CalculiX-preCICE adapter
 if [ ! -d "calculix-adapter/" ]; then
@@ -16,7 +16,7 @@ fi
 (
     cd calculix-adapter
     git pull
-    make -j 2
+    make -j "$(nproc)"
 )
 
 # Add the CalculiX adapter to PATH
diff --git a/provisioning/install-code_aster.sh b/provisioning/install-code_aster.sh
@@ -29,6 +29,11 @@ fi
     ln -sf "${HOME}/code_aster-adapter/cht/adapter.py" .
 )
 
+# Remove the code_aster tests to save space (approx. 500MB)
+rm -rfv ~/code_aster/14.6/share/aster/tests
+# Remove some documentation to save space (~100MB)
+rm -rfv ~/code_aster/public/med-4.00/share/doc
+
 # Optional: Update the tutorials exchange directory (needs to be absolute) and generate the export file.
 (
     cd "${HOME}/tutorials/flow-over-heated-plate-steady-state"
diff --git a/provisioning/install-dealii.sh b/provisioning/install-dealii.sh
@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 set -ex
 
-# Install deal.II from the deal.II 9.2.0 backports PPA
-sudo add-apt-repository ppa:ginggs/deal.ii-9.2.0-backports
+# Install deal.II from the deal.II 9.3.0 backports PPA
+sudo add-apt-repository ppa:ginggs/deal.ii-9.3.0-backports
 sudo apt-get update
 sudo apt-get install -y libdeal.ii-dev
 
@@ -13,7 +13,7 @@ fi
 (
     cd dealii-adapter
     git pull
-    cmake . && make -j 2
+    cmake . && make -j "$(nproc)"
 )
 
 # Add the deal.II adapter to PATH
diff --git a/provisioning/install-dune.sh b/provisioning/install-dune.sh
@@ -0,0 +1,72 @@
+#!/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
+
+# Get required DUNE modules
+if [ ! -d "dune-common/" ]; then
+    git clone --branch v2.8.0 --depth=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
+fi
+
+if [ ! -d "dune-localfunctions/" ]; then
+    git clone --branch v2.8.0 --depth=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
+fi
+
+if [ ! -d "dune-geometry/" ]; then
+    git clone --branch v2.8.0 --depth=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
+fi
+
+if [ ! -d "dune-uggrid/" ]; then
+    git clone --branch v2.8.0 --depth=1 https://gitlab.dune-project.org/staging/dune-uggrid.git
+fi
+
+if [ ! -d "dune-typetree/" ]; then
+    git clone --branch v2.8.0 --depth=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
+fi
+
+# Get the dune-elastodynamics module (solid solver)
+if [ ! -d "dune-elastodynamics/" ]; then
+    git clone --branch master --depth=1 https://github.com/maxfirmbach/dune-elastodynamics.git
+fi
+(
+    cd dune-elastodynamics
+    git pull
+)
+
+# Get the DUNE-preCICE adapter
+if [ ! -d "dune-adapter/" ]; then
+    git clone --branch main --depth=1 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
+
+# Set the DUNE_CONTROL_PATH (DUNE recursively finds modules in this directory)
+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
+
+# We are done with DUNE, let's do back home
+cd ~
diff --git 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
+pip3 install --user matplotlib nutils==6.3
diff --git 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 v2012:
-sudo apt-get install -y openfoam2012-dev
+# Install OpenFOAM v2112:
+sudo apt-get install -y openfoam2112-dev
 # Enable OpenFOAM by default:
-echo ". /usr/lib/openfoam/openfoam2012/etc/bashrc" >> ~/.bashrc
+echo ". /usr/lib/openfoam/openfoam2112/etc/bashrc" >> ~/.bashrc
 
 # Get the OpenFOAM-preCICE adapter
 if [ ! -d "openfoam-adapter/" ]; then
@@ -16,5 +16,26 @@ fi
 (
     cd openfoam-adapter
     git pull
-    openfoam2012 ./Allwmake
+    openfoam2112 ./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
+#     openfoam2112 ./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 v2112)
+
+# Build the tutorials partitioned-heat-conduction solver
+cd ~/tutorials/partitioned-heat-conduction/openfoam-solver && openfoam2112 wmake
diff --git a/provisioning/install-paraview.sh b/provisioning/install-paraview.sh
@@ -1,11 +1,4 @@
 #!/usr/bin/env bash
 set -ex
 
-if [ ! -d "paraview" ]; then
-    mkdir paraview
-    PARAVIEW_URL="https://www.paraview.org/paraview-downloads/download.php?submit=Download&version=v5.8&type=binary&os=Linux&downloadFile=ParaView-5.8.1-MPI-Linux-Python3.7-64bit.tar.gz"
-    wget --no-check-certificate --quiet -O - "${PARAVIEW_URL}" | tar -xz -C paraview
-    ln -sf ~/paraview/ParaView-5.8.1-MPI-Linux-Python3.7-64bit/bin/paraview ~/Desktop/
-    # Add ParaView to PATH
-    echo "export PATH=\"\${HOME}/paraview/ParaView-5.8.1-MPI-Linux-Python3.7-64bit/bin:\${PATH}\"" >>~/.bashrc
-fi
+sudo apt-get install -y paraview
diff --git a/provisioning/install-precice.sh b/provisioning/install-precice.sh
@@ -15,17 +15,37 @@ fi
     git pull
     mkdir -p build && cd build/
     cmake -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=Debug -DBUILD_TESTING=OFF -Wno-dev ..
-    make -j 2
+    make -j "$(nproc)"
     rm -fv ./*.deb && make package
     sudo apt-get install -y ./libprecice2_*.deb
+    # Remove generated packages to save space (approx. 70MB)
+    rm -rfv ./*.deb ./*.tar.gz _CPack_Packages
 )
 
 # Collect examples and tutorials
 cp -r /usr/share/precice/examples/ ./precice-examples
+(
+    cd precice-examples/solverdummies
+    cd c && cmake . && make && cd ..
+    cd cpp && cmake . && make && cd ..
+    cd fortran && cmake . && make && cd ..
+    if [ ! -d "fortran-module/" ]; then
+        git clone --depth=1 --branch master https://github.com/precice/fortran-module.git
+    fi
+    cd fortran-module && make
+    cd examples/solverdummy && make
+)
+
 if [ ! -d "tutorials/" ]; then
     git clone --depth=1 --branch master https://github.com/precice/tutorials.git
     ln -sf ~/tutorials ~/Desktop/
 fi
+(
+    cd tutorials/quickstart/solid-cpp/ && cmake . && make
+)
+(
+    cd tutorials/heat-exchanger && ./download-meshes.sh
+)
 sudo apt-get -y install gnuplot # needed for watchpoint scripts of tutorials
 
 
diff --git a/provisioning/install-su2.sh b/provisioning/install-su2.sh
@@ -35,7 +35,10 @@ fi
     ./configure --disable-metis --disable-parmetis --disable-cgns --disable-DOT \
         --disable-MSH --disable-DEF --disable-SOL --disable-GEO \
         --prefix="${SU2_RUN}" CXXFLAGS='-std=c++11'
-    make -j 2
+    make -j "$(nproc)"
     # We still need sudo for whatever reason
     sudo make install
 )
+
+# Remove the libSU2Core.a library to save space (approx. 500MB)
+rm -fv ~/SU2-6.0.0/SU2_CFD/obj/libSU2Core.a
diff --git a/provisioning/post-install.sh b/provisioning/post-install.sh
@@ -1,9 +1,19 @@
 #!/usr/bin/env bash
 set -ex
 
+# Setup swak4Foam
+(
+    cd "${HOME}/OpenFOAM/vagrant-v2112/platforms/linux64GccDPInt32Opt/"
+    tar -xzvf swak4Foam.tar.gz
+)
+
 # Create a link to the default shared folder
 ln -sf /vagrant/ ~/Desktop/shared
 
+# Add terminator on the desktop
+cp /usr/share/applications/terminator.desktop ~/Desktop/
+chmod +x ~/Desktop/terminator.desktop
+
 # Disable the screensaver and automatic screen lock
 {
     echo "xset s off -dpms"
diff --git a/provisioning/prebuilt/swak4Foam/README.txt b/provisioning/prebuilt/swak4Foam/README.txt
@@ -0,0 +1,2 @@
+Prebuilt libraries and tools of swak4Foam for Ubuntu 20.04 and OpenFOAM v2112, based on commit ea7680cdcf8b (December 2021).
+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
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a6150a56f3670a237e2dbff936a5f99f900d4c71c82fa08bce9dad2795ebfae0
+size 19974607

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+*.so filter=lfs diff=lfs merge=lfs -text`
	`2`	`+*.tar.gz filter=lfs diff=lfs merge=lfs -text`
Original file line number	Diff line number	Diff line change
`@@ -29,6 +29,11 @@ fi`
`29`	`29`	`ln -sf "${HOME}/code_aster-adapter/cht/adapter.py" .`
`30`	`30`	`)`
`31`	`31`
	`32`	`+# Remove the code_aster tests to save space (approx. 500MB)`
	`33`	`+rm -rfv ~/code_aster/14.6/share/aster/tests`
	`34`	`+# Remove some documentation to save space (~100MB)`
	`35`	`+rm -rfv ~/code_aster/public/med-4.00/share/doc`
	`36`	`+`
`32`	`37`	`# Optional: Update the tutorials exchange directory (needs to be absolute) and generate the export file.`
`33`	`38`	`(`
`34`	`39`	`cd "${HOME}/tutorials/flow-over-heated-plate-steady-state"`