Email:hpl@ifi.uio.no
INF5620 presents a lot of computer codes for solving partial differential equations. These codes are mostly written in Python, but apply sometimes computing intensive snippets in Cython, C, C++, or Fortran. The necessary software environment consists of
- Python and a range of mathematical packages
- LaTeX, imaging tools, version control systems
- C, C++, and Fortran compilers
More specifically, the following packages are needed:
- Eco system for scientific computing with Python:
- GNU Compilers: gcc, gfortran
Don't install all this software directly on Mac or Windows
The listed software is complex and non-trivial to install on Mac OS X or Windows 7/8. It requires much experience to get all pieces to work together, so unless you have extensive experience with building and installing complex mathematical packages on Windows or Mac, stay away from it and rely on Ubuntu.
VMWare Fusion virtual machine
A virtual machine allows you to run another complete computer system in a separate window. For Mac users, I recommend VMWare Fusion over VirtualBox for running a Linux (or Windows) virtual machine. (VMWare Fusion's hardware integration seems superior to that of VirtualBox.) VMWare Fusion is commercial software, but there is a free trial version you can start with. Alternatively, you can use the simpler VMWare Player, which is free for personal use.
Installing Ubuntu
The following recipe will install a Ubuntu virtual machine under VMWare Fusion.
Download Ubuntu. Choose a version that is compatible with your computer, usually a 64-bit version nowadays (I recommend 16.04).
Launch VMWare Fusion (the instructions here are for version 7).
Click on File - New and choose to Install from disc or image.
Click on Use another disc or disc image and choose your .iso file with the Ubuntu image.
Choose Easy Install, fill in password, and check the box for sharing files with the host operating system.
Choose Customize Settings and make the following settings (these settings can be changed later, if desired):
- Processors and Memory: Set a minimum of 2 Gb memory, but not more than half of your computer's total memory. The virtual machine can use all processors.
- Hard Disk: Choose how much disk space you want to use inside the virtual machine (20 Gb is considered a minimum).
Choose where you want to store virtual machine files on the hard disk. The default location is usually fine. The directory with the virtual machine files needs to be frequently backed up so make sure you know where it is.
Ubuntu will now install itself without further dialog, but it will take some time.
You may need to define a higher resolution of the display in the Ubuntu machine. Find the System settings icon on the left, go to Display, choose some display (you can try several, click Keep this configuration when you are satisfied).
- You can have multiple keyboards on Ubuntu. Launch System settings, go to Keyboard, click the Text entry hyperlink, add keyboard(s) (Input sources to use), and choose a shortcut, say Ctrl+space or Ctrl+backslash, in the Switch to next source using field. Then you can use the shortcut to quickly switch keyboard.
- A terminal window is key for programmers. Click on the Ubuntu icon on the top of the left pane, search for gnome-terminal, right-click its new icon in the left pane and choose Lock to Launcher such that you always have the terminal easily accessible when you log in. The gnome-terminal can have multiple tabs (Ctrl+shift+t to make a new tab).
File sharing
The Ubuntu machine can see the files on your host system if you download VMWare Tools. Go to the Virtual Machine pull-down menu in VMWare Fusion and choose Install VMWare Tools. A tarfile is downloaded. Click on it and it will open a folder vmware-tools-distrib, normally in your home folder. Move to the new folder and run sudo perl vmware-install.pl. You can go with the default answers to all the questions.
On a Mac, you must open Virtual Machine - Settings... and choose Sharing to bring up a dialog where you can add the folders you want to be visible in Ubuntu. Just choose your home folder. Then turn on the file sharing button (or turn off and on again). Go to Ubuntu and check if you can see all your host system's files in /mnt/hgfs/.
If you later detect that /mnt/hgfs/ folder has become empty, VMWare Tools must be reinstalled by first turning shared folders off, and then running:
Terminal> sudo /usr/bin/vmware-config-tools.pl
Occasionally it is necessary to do a full reinstall by sudo perl vmware-install.pl as above.
Backup of a VMWare virtual machine on a Mac
The entire Ubuntu machine is a folder on the host computer, typically with a name like Documents/Virtual Machines/Ubuntu 64-bit. Backing up the Ubuntu machine means backing up this folder. However, if you use tools like Time Machine and work in Ubuntu during backup, the copy of the state of the Ubuntu machine is likely to be corrupt. You are therefore strongly recommended to shut down the virtual machine prior to running Time Machine or simply copying the folder with the virtual machine to some backup disk.
If something happens to your virtual machine, it is usually a straightforward task to make a new machine and import data and software automatically from the previous machine.
VirtualBox virtual machine
VirtualBox is free software that allows you to run a virtual machine with, e.g., the Ubuntu operating system. Download and install VirtualBox. Choose the version according to the operating system on the host. On Mac OS X, choose VirtualBox x.y.z for OS X hosts, where x.y.z is the version number of VirtualBox. Double click the downloaded .dmg file to install Vagrant. Those who work on a Windows machine will select VirtualBox x.y.z for Windows hosts, which downloads an .exe file to be double clicked to perform the installation.
Installing software on a Ubuntu machine
You need to install additional software for scientific computing with Python:
Terminal> sudo apt-get install python-setuptools python-pip mercurial Terminal> sudo pip install numpy sympy scipy nose pytest Terminal> sudo apt-get install python-matplotlib Terminal> sudo pip install ipython --upgrade
You will also need to install FEniCS as follows:
Terminal> sudo add-apt-repository ppa:fenics-packages/fenics Terminal> sudo apt-get update Terminal> sudo apt-get install --no-install-recommends fenics Terminal> sudo apt-get dist-upgrade