UW AMath High Performance Scientific Computing
AMath 483/583 Class Notes
Spring Quarter, 2013

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Virtual Machine for this class [2014 Edition]

We are using a wide variety of software in this class, much of which is probably not found on your computer. It is all open source software (see licences) and links/instructions can be found in the section Downloading and installing software for this class.

An alternative, which many will find more convenient, is to download and install the [VirtualBox] software and then download a Virtual Machine (VM) that has been built specifically for this course. VirtualBox will run this machine, which will emulate a specific version of Linux that already has installed all of the software packages that will be used in this course.

You can find the VM on the class webpage in the file uwhpsc.zip.

Note that the file is quite large (approximately 803 MB compressed), and if possible you should download it from on-campus to shorten the download time. The TA’s will also have the VM on memory sticks for transferring.

System requirements

The VM is around 2 GB in size, uncompressed, and the virtual disk image may expand to up to 8 GB, depending on how much data you store in the VM. Make sure you have enough free space available before installing. You can set how much RAM is available to the VM when configuring it, but it is recommended that you give it at least 512 MB; since your computer must host your own operating system at the same time, it is recommended that you have at least 1 GB of total RAM.

Setting up the VM in VirtualBox

Once you have downloaded and uncompressed the virtual machine disk image from the class web site, you can set it up in VirtualBox, by doing the following:

  1. Start VirtualBox
  2. Click the New button near the upper-left corner
  3. Click Next at the starting page
  4. Enter a name for the VM (put in whatever you like); for OS Type, select “Linux”, and for Version, select “Ubuntu”. Click Next.
  5. Enter the amount of memory to give the VM, in megabytes. 512 MB is the recommended minimum. Click Next.
  6. Click Use existing hard disk, then click the folder icon next to the disk list. In the Virtual Media Manager that appears, click Add, then select the virtual machine disk image you downloaded from the class web site. Ignore the message about the recommended size of the boot disk, and leave the box labeled “Boot Hard Disk (Primary Master)” checked. Once you have selected the disk image, click Next.
  7. Review the summary VirtualBox gives you, then click Finish. Your new virtual machine should appear on the left side of the VirtualBox window.

Starting the VM

Once you have configured the VM in VirtualBox, you can start it by double-clicking it in the list of VM’s on your system. The virtual machine will take a little time to start up; as it does, VirtualBox will display a few messages explaining about mouse pointer and keyboard capturing, which you should read.

After the VM has finished booting, it will present you with a login screen; the login and password are both uwhpsc. (We would have liked to set up a VM with no password, but many things in Linux assume you have one.)

Note that you will also need this password to quit the VM.

Running programs

You can access the programs on the virtual machine through the Applications Menu (the mouse on an X symbol in the upper-left corner of the screen), or by clicking the quick-launch icons next to the menu button. By default, you will have quick-launch icons for a command prompt window (also known as a terminal window), a text editor, and a web browser. After logging in for the first time, you should start the web browser to make sure your network connection is working.

Fixing networking issues

When a Linux VM is moved to a new computer, it sometimes doesn’t realize that the previous computer’s network adaptor is no longer available.

Also, if you move your computer from one wireless network to another while the VM is running, it may lose connection with the internet.

If this happens, it should be sufficient to shut down the VM (with the 0/1 button on the top right corner) and then restart it. On shutdown, a script is automatically run that does the following, which in earlier iterations of the VM had to be done manually...

$ sudo rm /etc/udev/rules.d/70-persistent-net.rules

This will remove the incorrect settings; Linux should then autodetect and correctly configure the network interface it boots.

Shutting down

When you are done using the virtual machine, you can shut it down by clicking the 0/1 button on the top-right corner of the VM. You will need the password uwhpsc.

Cutting and pasting

If you want to cut text from one window in the VM and paste it into another, you should be able to highlight the text and then type ctrl-c (or in a terminal window, ctrl-shift-C, since ctrl-c is the interrupt signal). To paste, type ctrl-v (or ctrl-shift-V in a terminal window).

If you want to be able to cut and paste between a window in the VM and a window on your host machine, click on Machine from the main VitualBox menu (or Settings in the Oracle VM VirtualBox Manager window), then click on General and then Advanced. Select Bidirectional from the Shared Clipboard menu.

Shared Folders

If you create a file on the VM that you want to move to the file system of the host machine, or vice versa, you can create a “shared folder” that is seen by both.

First create a folder (i.e. directory) on the host machine, e.g. via:

$ mkdir ~/uwhpsc_shared

This creates a new subdirectory in your home directory on the host machine.

In the VirtualBox menu click on Devices, then click on Shared Folders. Click the + button on the right side and then type in the full path to the folder you want to share under Folder Path, including the folder name, and then the folder name itself under Folder name. If you click on Auto-mount then this will be mounted every time you start the VM.

Then click OK twice.

Then, in the VM (at the linux prompt), type the following commands:

sharename=uwhpsc_shared   # or whatever name the folder has
sudo mkdir /mnt/$sharename
sudo chmod 777 /mnt/$sharename
sudo mount -t vboxsf -o uid=1000,gid=1000 $sharename /mnt/$sharename

You may need the password uwhpsc for the first sudo command.

The folder should now be found in the VM in /mnt/$sharename. (Note $sharename is a variable set in the first command above.)

If auto-mounting doesn’t work properly, you may need to repeat the final sudo mount ... command each time you start the VM.

Enabling more processors

If you have a reasonably new computer with a multi-core processor and want to be able to run parallel programs across multiple cores, you can tell VirtualBox to allow the VM to use additional cores. To do this, open the VirtualBox Settings. Under System, click the Processor tab, then use the slider to set the number of processors the VM will see. Note that some older multi-core processors do not support the necessary extensions for this, and on these machines you will only be able to run the VM on a single core.

Problems enabling multiple processors...

Users may encounter several problems with enabling mutliple processors. Some users may not be able to change this setting (it will be greyed out). Other users when may find no improved performance after enabling multiple processors. Still others may encounter an error such as:


All of these problems indicate that virtualization has not been enabled on your processors.

Fortunately this has an easy fix. You just have to enable virtualization in your BIOS settings.

1. To access the BIOS settings you must restart your computer and press a certain button on startup. This button will depend on the company that manufactures your computer (for example for Lenovo’s it appears to be the f1 key).

2. Next you must locate a setting that will refer to either virtualization, VT, or VT-x. Again the exact specifications will depend on the computer’s manufacturer, however it should be found in the Security section (or the Performance section if you are using a Dell).

3. Enable this setting, then save and exit the bios settings.After your computer reboots you should be able to start the VM using multiple processors now.

4. If your BIOS does not have any settings like this it is possible that your BIOS is set up to hide this option from you, and you may need to follow the advice here: http://mathy.vanvoorden.be/blog/2010/01/enable-vt-x-on-dell-laptop/

Note: Unfortunately some older hardware does not support virtualization, and so if these solutions don’t work for you it may be that this is the case for your processors. There also may be other possible problems...so don’t be afraid to ask the TAs for help!

Changing guest resolution/VM window size

See also

The section Guest Additions, which makes this easier.

It’s possible that the size of the VM’s window may be too large for your display; resizing it in the normal way will result in not all of the VM desktop being displayed, which may not be the ideal way to work. Alternately, if you are working on a high-resolution display, you may want to increase the size of the VM’s desktop to take advantage of it. In either case, you can change the VM’s display size by going to the Applications menu in the upper-left corner, pointing to Settings, then clicking Display. Choose a resolution from the drop-down list, then click Apply.

Setting the host key

See also

The section Guest Additions, which makes this easier.

When you click on the VM window, it will capture your mouse and future mouse actions will apply to the windows in the VM. To uncapture the mouse you need to hit some control key, called the host key. It should give you a message about this. If it says the host key is Right Control, for example, that means the Control key on the right side of your keyboard (it does not mean to click the right mouse button).

On some systems, the host key that transfers input focus between the VM and the host operating system may be a key that you want to use in the VM for other purposes. To fix this, you can change the host key in VirtualBox. In the main VirtualBox window (not the VM’s window; in fact, the VM doesn’t need to be running to do this), go to the File menu, then click Settings. Under Input, click the box marked “Host Key”, then press the key you want to use.

Guest Additions

While we have installed the VirtualBox guest additions on the class VM, the guest additions sometimes stop working when the VM is moved to a different computer, so you may need to reinstall them. Do the following so that the VM will automatically capture and uncapture your mouse depending on whether you click in the VM window or outside it, and to make it easier to resize the VM window to fit your display.

  1. Boot the VM, and log in.
  2. In the VirtualBox menu bar on your host system, select Devices –> Install Guest Additions... (Note: click on the window for the class VM itself to get this menu, not on the main “Sun VirtualBox” window.)
  3. A CD drive should appear on the VM’s desktop, along with a popup window. (If it doesn’t, see the additional instructions below.) Select “Allow Auto-Run” in the popup window. Then enter the password you use to log in.
  4. The Guest Additions will begin to install, and a window will appear, displaying the progress of the installation. When the installation is done, the window will tell you to press ‘Enter’ to close it.
  5. Right-click the CD drive on the desktop, and select ‘Eject’.
  6. Restart the VM.

If step 3 doesn’t work the first time, you might need to:

Alternative Step 3:
  1. Reboot the VM.
  2. Mount the CD image by right-clicking the CD drive icon, and clicking ‘Mount’.
  3. Double click the CD image to open it.
  4. Double click ‘autorun.sh’.
  5. Enter the VM password to install.

How This Virtual Machine was made

  1. Download Ubuntu 12.04 PC (Intel x86) alternate install ISO from http://cdimage.ubuntu.com/xubuntu/releases/12.04.2/release/xubuntu-12.04.2-alternate-i386.iso

  2. Create a new virtual box

  3. Set the system as Ubuntu

  4. Use defualt options

  5. After that double click on your new virtual machine...a dropdown box should appear where you can select your ubuntu iso

  6. As you are installing...at the first menu hit F4 and install a command line system

  7. Let the install proceed following the instructions as given. On most options the default answer will be appropriate. When it comes time to format the hard drive, choose the manual option. Format all the free space and set it as the mount point. From the next list choose root (you dont need a swap space).

  8. Install the necessary packages

    # $UWHPSC/notes/install.sh
    sudo apt-get update
    sudo apt-get upgrade
    sudo apt-get install xfce4
    sudo apt-get install jockey-gtk
    sudo apt-get install xdm
    sudo apt-get install ipython
    sudo apt-get install python-numpy
    sudo apt-get install python-scipy
    sudo apt-get install python-matplotlib
    sudo apt-get install python-dev
    sudo apt-get install git
    sudo apt-get install python-sphinx
    sudo apt-get install gfortran
    sudo apt-get install openmpi-bin
    sudo apt-get install liblapack-dev
    sudo apt-get install thunar
    sudo apt-get install xfce4-terminal
    # some packages not installed on the VM 
    # that you might want to add:
    sudo apt-get install gitk               # to view git history
    sudo apt-get install xxdiff             # to compare two files
    sudo apt-get install python-sympy       # symbolic python
    sudo apt-get install imagemagick        # so you can "display plot.png"
    sudo apt-get install python-setuptools  # so easy_install is available
    sudo easy_install nose                  # unit testing framework
    sudo easy_install StarCluster           # to help manage clusters on AWS
  9. To setup the login screen edit the file Xresources so that the greeting line says.:

    xlogin*greeting: Login and Password are uwhpsc
  10. Create the file uwhpscvm-shutdown.:

#Finish up Script--does some cleanup then shuts down

#prevent network problems
rm -f /etc/udev/rules.d/70-persistent-net.rules

shutdown -h now
  1. Save it at.:

  2. Execute the following command command.:

    $ sudo chmod +x /usr/local/bin/uwhpscvm-shutdown
  3. Right click on the upper panel and select add new items and choose to add a new launcher.

  4. Name the new launcher something like shutdown and in the command blank copy the following line.:

    gksudo /usr/local/bin/uwhpscvm-shutdown
  5. Go to preferred applications and select Thunar for file managment and the xfce4 terminal.

  6. Run jockey-gtk and install guest-additions.

  7. Go to Applications then Settings then screensaver and select “disable screen saver” mode

  8. In the settings menu select the general settings and hit the advanced tab. Here you can set the clipboard and drag and drop to allow Host To Guest.

  9. Shutdown the machine and then go to the main virtualbox screen. Click on the virtualmachine and then hit the settings button.

  10. After, in the system settings click on the processor tab. This may let you allow the virtual machine to use more than one processor (depending on your computer). Choose a setting somewhere in the green section of the Processors slider.

About the VM

The class virtual machine is running XUbuntu 12.04, a variant of Ubuntu Linux (http://www.ubuntu.com), which itself is an offshoot of Debian GNU/Linux (http://www.debian.org). XUbuntu is a stripped-down, simplified version of Ubuntu suitable for running on smaller systems (or virtual machines); it runs the xfce4 desktop environment.