Update main, v202104.1.0

.github/workflows/build.yml

@@ -0,0 +1,38 @@
+name: Build and package
+on:
+  pull_request:
+    types: [ready_for_review]
+jobs:
+  vagrant-up:
+    runs-on: macos-10.15
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Cache Vagrant boxes
+      uses: actions/cache@v2
+      with:
+        path: ~/.vagrant.d/boxes
+        key: ${{ runner.os }}-vagrant-${{ hashFiles('Vagrantfile') }}
+        restore-keys: |
+          ${{ runner.os }}-vagrant-
+
+    - name: Show Vagrant version
+      run: vagrant --version
+
+    - name: Run vagrant up
+      run: vagrant up
+
+    - name: Package Vagrant box
+      run: vagrant package --base "preCICE-VM" --output preCICE.box
+
+    - name: Generate Vagrant box SHA256 hash
+      run: shasum -a 256 preCICE.box
+
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v2
+      with:
+          name: precice-vagrant-box
+          path: preCICE.box
+          retention-days: 7
+

.github/workflows/check-shell.yml

@@ -0,0 +1,12 @@
+name: Lint scripts
+on: [push, pull_request]
+jobs:
+  check_shell:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v2
+      - name: Lint shell scripts (shellcheck)
+        uses: ludeeus/action-shellcheck@master
+        with:
+          ignore: Vagrantfile

README.md

@@ -23,6 +23,7 @@ Ready-to-use boxes are available on [Vagrant Cloud](https://app.vagrantup.com/pr
 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`.
 - Find scripts to install additional software on `~/Desktop/shared`.
@@ -40,27 +41,33 @@ A few things you may need:
 ## What is included?
 
 This box is based on the [bento/ubuntu-20.04](https://github.com/chef/bento/blob/master/packer_templates/ubuntu/ubuntu-20.04-amd64.json) 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 latest from the master branch
-- preCICE Python bindings
-- OpenFOAM v2012 and the OpenFOAM-preCICE adapter
-- deal.II 9.2 from the official backports and the deal.II-preCICE adapter (you still need to copy the compiled executables wherever you need them)
-- CalculiX 2.16 from source and the CalculiX-preCICE adapter
-- FEniCS latest from the FEniCS PPA and the FEniCS-preCICE adapter
+- 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)
+- 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 from source
+- 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
+- Gnuplot
+
+It then adds to the `/home/vagrant/`:
 
-It then adds on the `/home/vagrant/Desktop`:
 - The preCICE examples (solverdummies), including a copy of the Python solverdummy.
 - The preCICE tutorials from the `precice/tutorials`
 
 The adapter repositories remain in `/home/vagrant/`.
+It also adds a few shortcuts on the Desktop (see `post-install.sh`).
+At the end, it cleans up all object files and the APT cache (see `cleanup.sh`).
 
 ## Troubleshooting
 
@@ -77,3 +84,27 @@ Usually running again (e.g. with `vagrant up --provision`) helps.
 ### There is no GUI
 
 In case you killed the session before provisioning finished, the setup of your VM might be incomplete. You might still be able to interact with the VM without the GUI. In that case, run `vagrant up --provision`.
+
+## 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.
+
+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:
+
+```bash
+vagrant box add test-box precice-vagrant-box/preCICE.box 
+```
+
+You can then start a VM by going into an empty directory and executing:
+
+```bash
+vagrant init test-box
+vagrant up
+```
+
+Afterwards, you probably want to destroy everything to save storage space:
+
+```bash
+vagrant destroy
+vagrant box remove test-box
+```

Vagrantfile

@@ -26,32 +26,37 @@ Vagrant.configure("2") do |config|
   end
 
   # Install a desktop environment and basic tools
-  config.vm.provision "shell", path: "provisioning/install-basics.sh"
+  config.vm.provision "shell", path: "provisioning/install-basics.sh", privileged: false
 
   # Install common development tools
-  config.vm.provision "shell", path: "provisioning/install-devel.sh"
+  config.vm.provision "shell", path: "provisioning/install-devel.sh", privileged: false
 
   # Install preCICE
-  config.vm.provision "shell", path: "provisioning/install-precice.sh"
+  config.vm.provision "shell", path: "provisioning/install-precice.sh", privileged: false
 
   # Install solvers, adapters, and related tools
-  config.vm.provision "shell", path: "provisioning/install-config-visualizer.sh"
-  config.vm.provision "shell", path: "provisioning/install-openfoam.sh"
-  config.vm.provision "shell", path: "provisioning/install-dealii.sh"
-  config.vm.provision "shell", path: "provisioning/install-calculix.sh"
-  config.vm.provision "shell", path: "provisioning/install-fenics.sh"
-  config.vm.provision "shell", path: "provisioning/install-nutils.sh"
-  config.vm.provision "shell", path: "provisioning/install-su2.sh"
-  config.vm.provision "shell", path: "provisioning/install-paraview.sh"
+  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 "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-paraview.sh", privileged: false
 
   # Post-installation steps
-  config.vm.provision "shell", path: "provisioning/post-install.sh"
-  config.vm.provision "file", source: "provisioning/install-vscode.sh", destination: "~/Desktop/install-vscode.sh"
+  config.vm.provision "shell", path: "provisioning/post-install.sh", privileged: false
+  config.vm.provision "file", source: "provisioning/install-vscode.sh", destination: "~/install-vscode.sh"
+  config.vm.provision "file", source: "provisioning/get-started.desktop", destination: "~/Desktop/get-started.desktop"
+  config.vm.provision "file", source: "provisioning/.alias", destination: "~/.alias"
 
   # Pre-packaging steps
+  config.vm.provision "shell", path: "provisioning/cleanup.sh", privileged: false
   # Add the default Vagrant insecure public key to the authorized keys
   config.vm.provision "file", source: "provisioning/vagrant.pub", destination: "~/.ssh/vagrant.pub"
   config.vm.provision "shell", inline: <<-SHELL
     cat /home/vagrant/.ssh/vagrant.pub >> /home/vagrant/.ssh/authorized_keys
   SHELL
+
 end

provisioning/.alias

@@ -0,0 +1,12 @@
+# preCICE config visualizer
+function config-visualizer-pdf(){
+  cat $1 | precice-config-visualizer | dot -Tpdf > precice-config.pdf
+}
+
+function config-visualizer-svg(){
+  cat $1 | precice-config-visualizer | dot -Tsvg > precice-config.svg
+}
+
+function config-visualizer(){
+  cat $1 | precice-config-visualizer | dot -Tpng > precice-config.png
+}

provisioning/cleanup.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+set -ex
+
+# Cleanup the APT cache to save space
+sudo apt-get clean
+
+# Cleanup all object files from compilation
+find "${HOME}" -type f -name '*.o' -exec rm -fv {} \;

provisioning/get-started.desktop

@@ -0,0 +1,6 @@
+[Desktop Entry]
+Encoding=UTF-8
+Name=Get started
+Type=Link
+URL=https://precice.org/installation-vm.html
+Icon=text-html

provisioning/install-basics.sh

@@ -1,11 +1,9 @@
-#!/bin/sh
+#!/usr/bin/env bash
 set -ex
 
-USER="vagrant"
-
 # We (may) need the multiverse repository for the VBox Guest Additions
 sudo apt-add-repository multiverse
-apt-get update
+sudo apt-get update
 sudo apt-get upgrade -qy
 
 # Install the Xfce desktop environment and basic applications
@@ -15,16 +13,14 @@ sudo apt-get install -y thunar xfce4-terminal terminator bash-completion tree ev
 # Install the VirtualBox guest additions
 sudo apt-get install -y virtualbox-guest-dkms virtualbox-guest-utils virtualbox-guest-x11
 
-# Create /home/${USER}/desktop
-sudo -u ${USER} mkdir -p /home/${USER}/Desktop
-chown ${USER}:${USER} /home/${USER}/Desktop
+# Create Desktop
+mkdir -p ~/Desktop
 
 # Use US-English keyboard layout
 L='us' && sudo sed -i 's/XKBLAYOUT=\"\w*"/XKBLAYOUT=\"'$L'\"/g' /etc/default/keyboard
 # Add a shortcut to the keyboard options on the Desktop
-cp /usr/share/applications/xfce-keyboard-settings.desktop /home/${USER}/Desktop/
-chmod +x /home/${USER}/Desktop/xfce-keyboard-settings.desktop
-chown ${USER}:${USER} /home/${USER}/Desktop/xfce-keyboard-settings.desktop
+cp /usr/share/applications/xfce-keyboard-settings.desktop ~/Desktop/
+chmod +x ~/Desktop/xfce-keyboard-settings.desktop
 
 # Set a hostname
 echo "precicevm" | sudo tee /etc/hostname

provisioning/install-calculix.sh

@@ -1,23 +1,23 @@
-#!/bin/sh
+#!/usr/bin/env bash
 set -ex
 
-USER="vagrant"
-
 # Install dependencies
 sudo apt-get install -y libarpack2-dev libspooles-dev libyaml-cpp-dev
 
-# Install CalculiX 
-cd /home/${USER}/
+# Install CalculiX
 wget --quiet http://www.dhondt.de/ccx_2.16.src.tar.bz2
-tar xvjf ccx_2.16.src.tar.bz2 
+tar xvjf ccx_2.16.src.tar.bz2
+rm -fv ccx_2.16.src.tar.bz2
 
 # Get the CalculiX-preCICE adapter
 if [ ! -d "calculix-adapter/" ]; then
-    sudo -u ${USER} git clone --depth=1 --branch master https://github.com/precice/calculix-adapter.git
+    git clone --depth=1 --branch master https://github.com/precice/calculix-adapter.git
 fi
-cd calculix-adapter
-git pull
-sudo -u ${USER} -s bash -c "make -j 2"
+(
+    cd calculix-adapter
+    git pull
+    make -j 2
+)
 
 # Add the CalculiX adapter to PATH
-echo "export PATH=\"/home/${USER}/calculix-adapter/bin:\${PATH}\"" >> /home/${USER}/.bashrc
+echo "export PATH=\"\${HOME}/calculix-adapter/bin:\${PATH}\"" >>~/.bashrc

provisioning/install-code_aster.sh

@@ -0,0 +1,77 @@
+#!/usr/bin/env bash
+set -ex
+
+# Install dependencies
+sudo apt-get install -y bison cmake make flex g++ gcc gfortran \
+    grace liblapack-dev libblas-dev \
+    libboost-numpy-dev libboost-python-dev \
+    python3 python3-dev python3-numpy \
+    tk zlib1g-dev
+
+# Install code_aster 14.6 - skip to save time if target dir exists
+if [ ! -d "code_aster/" ]; then
+    wget --quiet https://www.code-aster.org/FICHIERS/aster-full-src-14.6.0-1.noarch.tar.gz
+    tar xvzf aster-full-src-14.6.0-1.noarch.tar.gz && rm -fv aster-full-src-14.6.0-1.noarch.tar.gz
+    (
+        cd aster-full-src-14.6.0
+        yes | python3 setup.py install --prefix="${HOME}/code_aster"
+    )
+    echo ". ${HOME}/code_aster/etc/codeaster/profile.sh" >>~/.bashrc
+    rm -rf ./aster-full-src-14.6.0/
+fi
+
+# Get the code_aster-preCICE adapter
+if [ ! -d "code_aster-adapter/" ]; then
+    git clone --depth=1 --branch master https://github.com/precice/code_aster-adapter.git
+fi
+(
+    cd "${HOME}/code_aster/14.6/lib/aster/Execution"
+    ln -sf "${HOME}/code_aster-adapter/cht/adapter.py" .
+)
+
+# Optional: Update the tutorials exchange directory (needs to be absolute) and generate the export file.
+(
+    cd "${HOME}/tutorials/flow-over-heated-plate-steady-state"
+
+    sed -i "s|exchange-directory=\"..\"|exchange-directory=\"$(pwd)\"|g" precice-config.xml
+
+    cd ./solid-codeaster
+    if [ ! -f "solid.export" ]; then
+        {
+            echo "P actions make_etude"
+            echo "P aster_root /code_aster"
+            echo "P consbtc oui"
+            echo "P debug nodebug"
+            echo "P display precicevm:0"
+            echo "P follow_output yes"
+            echo "P mclient precicevm"
+            echo "P memjob 524288"
+            echo "P memory_limit 512.0"
+            echo "P mode interactif"
+            echo "P ncpus 1"
+            echo "P nomjob linear-thermic"
+            echo "P origine salomemeca_asrun 1.10.0"
+            echo "P protocol_copyfrom asrun.plugins.server.SCPServer"
+            echo "P protocol_copyto asrun.plugins.server.SCPServer"
+            echo "P protocol_exec asrun.plugins.server.SSHServer"
+            echo "P rep_trav /tmp/root-23129e00f0db-interactif_4800"
+            echo "P serveur localhost"
+            echo "P soumbtc oui"
+            echo "P time_limit 600.0"
+            echo "P tpsjob 11"
+            echo "P uclient precicevm"
+            echo "P username precicevm"
+            echo "P version stable"
+            echo "A memjeveux 64.0"
+            echo "A tpmax 600.0"
+            echo "F comm ${HOME}/code_aster-adapter/cht/adapter.comm D 1"
+            echo "F libr $(pwd)/config.comm D 90"
+            echo "F libr $(pwd)/def.comm D 91"
+            echo "F mmed $(pwd)/solid.mmed D 20"
+            echo "R repe $(pwd)/REPE_OUT D 0"
+            echo "R repe $(pwd)/REPE_OUT R 0"
+            echo "F mess $(pwd)/solid.mess R 6"
+            echo "F resu $(pwd)/solid.resu R 8"
+        } >>solid.export
+    fi
+)

provisioning/install-config-visualizer.sh

@@ -1,20 +1,18 @@
-#!/bin/sh
+#!/usr/bin/env bash
 set -ex
 
-USER="vagrant"
-
 # Get the config-visualizer from GitHub
 if [ ! -d "config-visualizer/" ]; then
-    sudo -u ${USER} git clone --depth=1 --branch master https://github.com/precice/config-visualizer.git
+    git clone --depth=1 --branch master https://github.com/precice/config-visualizer.git
 fi
-sudo -u ${USER} -s bash -c "pip3 install --user -e config-visualizer"
+pip3 install --user -e config-visualizer
 
 # Add the config-visualizer to PATH
-echo "export PATH=\"/home/${USER}/config-visualizer/bin:${PATH}\"" >> /home/${USER}/.bashrc
+echo "export PATH=\"\${HOME}/config-visualizer/bin:\${PATH}\"" >>~/.bashrc
 
 # By default, there is no `python` executable, there is only `python3`,
 # which causes issues to the config-visualizer
-apt-get install -y python-is-python3
+sudo apt-get install -y python-is-python3
 
 # Install graphviz, which provides dot, an almost required package to make this useful
-apt-get install -y graphviz
+sudo apt-get install -y graphviz