How to access Python for doing scientific computing

 

 

 

Much of the material in this document is taken from Appendix H.1 in the book A Primer on Scientific Programming with Python, 4th edition, by the same author, published by Springer, 2014.

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.

  1. Go to http://goo.gl/nSeBCg and download a full-blown Ubuntu box for scientific computing: ubuntu-14.04-amd64-vmware.ova (6.7 Gb!).
  2. Launch VMWare Fusion.
  3. Click on File - Import, then Choose file, and browse to the to the ubuntu-14.04-amd64-vmware.ova file you downloaded.
  4. Type your chosen name of the virtual machine in the Save As text box and rely on the default location. Your entire virtual machine is stored in this file, and backing up the machine means backing up the file.
  5. Click Import.
  6. Press Command+E (or go to Virtual Machine - Settings...). Specify the following:
  7. Start up the virtual Ubuntu machine. The username and password for this machine are fenics.
  8. 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).
  9. 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.
  10. 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).
Pre-i3/5/7 Intel processors and 32 vs. 64 bit. If your computer has a pre-i3/5/7 Intel processor and the processor does not have VT-x enabled, you cannot use the pre-packaged 64-bit virtual machines. Instead, you have to download a plain 32-bit image (from http://www.ubuntu.com/download/desktop and install the necessary software (see next section). To check if your computer has VT-x (hardware virtualization) enabled, you can use this tool: URL: https://www.grc.com/securable.htm.

Installing software on a minimalistic Ubuntu machine

If you have a minimalistic Ubuntu machine downloaded from the Ubuntu site, 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 spyder
Terminal> sudo pip install ipython --upgrade
Terminal> sudo pip install tornado --upgrade
Terminal> sudo pip install pyzmq --upgrade
Terminal> sudo pip install -e \ 
          git+https://github.com/hplgit/scitools.git#egg=scitools

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.