dealii-vm

Generate a virtualbox machine from scratch for deal.II and ASPECT

binaries available online at http://www.math.clemson.edu/~heister/dealvm/

Howto:

1. Get candi:

   git clone https://github.com/dealii/candi
   

2. Get vagrant from https://www.vagrantup.com/ and the vagrant disksize plugin:

   vagrant plugin install vagrant-disksize
   vagrant up
   

3. compilation:

   cd ~/libs && ./setup.sh
   cd ~/deal.II/ && ./setup.sh && make clean
   cd ~/aspect && ./_setup.sh && make && mv aspect aspect.debug && make clean && mv aspect.debug aspect
   

4. Manual setup:

• add shortcuts to terminal, firefox, leafpad to menu bar
• settings->power: disable all energy saving stuff
• add deal.II parameter-gui binary to ~/bin/, download from https://github.com/tjhei/parameter_gui/releases
• in firefox:
  • show bookmark bar
  • default homepage: info.html
  • dealii.org
  • deal.II docs: https://dealii.org/current/doxygen/deal.II/index.html
  • ASPECT: https://aspect.geodynamics.org/
  • about:config browser.sessionstore.resume_from_crash = false
• download aspect manual.pdf and put on desktop: cd Desktop; wget https://github.com/geodynamics/aspect/releases/download/v2.2.0/aspect-manual-2.2.0.pdf
• add firefox to autostart: settings->session and startup->add
• disable screensaver in "light locker settings"
• install qtcreator: https://www.qt.io/download-open-source/#section-6 or https://download.qt.io/official_releases/qtcreator/3.6/3.6.1/ install into ~/bin/ add to path add deal.II style: https://github.com/dealii/dealii/wiki/QtCreator
• install https://github.com/rfjakob/earlyoom and test
• install vscode https://code.visualstudio.com/download plugins: c/c++, cmake, cmake tools apply fix: max fs watches
• edit /etc/default/grub.d/50-cloudimg-settings.cfg and remove console=ttyS0 sudo update-grub and then disable serial port 1 in machine settings also remove cidata second hd image
• set reasonable defaults for txt, prm, cc files (mousepad, vscode)
• install clang format: cd deal.II && ./contrib/utilities/download_clang_format && cd clang-6/ && mv clang-format ~/bin/

6. For releasing the image:
   • update software: apt-get update && apt-get upgrade && apt-get autoremove && apt-get autoclean
   • remove deal.II build files
   • run zerofree to remove disk size (need to boot into safe mode using ESC): reboot into recovery systemctl stop systemd-journald.socket systemctl stop systemd-journald.service echo u >/proc/sysrq-trigger mount -n -o remount,ro -t ext4 /dev/sda1 / zerofree -v /dev/sda1 also see https://wiki.ubuntu.com/RecoveryMode
   • remove shared vagrant folder
   • set to 2 cores, 7GB RAM
   • serial port: disconnected
   • export virtual machine after shutting down: product URL: https://www.math.clemson.edu/~heister/dealvm/ name: deal.II VM
   • git tag -s -m "Version 1.15.0" v1.15.0 && git push mygithub HEAD v1.15.0