3 NeuroDebian Virtual Machine
4 ===========================
10 For those who are not yet running a Debian-based operation system we offer a
11 `virtual machine`_ that can be used with `VirtualBox`_, allowing users to benefit
12 from a Debian-based research environment on other operating systems.
13 This virtual machine initially comes as a compact Debian installation that can,
14 once installed, be equipped with a large variety of neuroscience software with
15 just a few mouse clicks (e.g. AFNI_, Caret_, FSL_, PyMVPA_).
17 .. _virtual machine: http://en.wikipedia.org/wiki/Virtual_machine
18 .. _AFNI: http://afni.nimh.nih.gov/afni/
19 .. _Caret: http://brainvis.wustl.edu/wiki/index.php/Caret:About
20 .. _FSL: http://www.fmrib.ox.ac.uk/fsl/
21 .. _PyMVPA: http://www.pymvpa.org
27 * `NeuroDebian 6.0.6 image (32bit)
28 <http://neuro.debian.net/debian/vm/NeuroDebian_6.0.6_i386.ova>`_ [~559MB]
30 *This image should work on virtually all systems that are supported by*
31 VirtualBox_ *and can be used whenever the, otherwise preferable, 64bit image
32 is not compatible with a host machine.*
34 * `NeuroDebian 6.0.6 image (64bit)
35 <http://neuro.debian.net/debian/vm/NeuroDebian_6.0.6_amd64.ova>`_ [~576MB]
37 *This image only works on 64bit host machines with active hardware
38 virtualization support. The should include all recent Apple hardware and most
39 64bit Windows systems.*
41 Virtual appliances above carry guest additions for 4.x series of the
42 VirtualBox. If you still have VirtualBox 3.x, use previous 6.0.2
45 * `NeuroDebian 6.0.2 image (32bit)
46 <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]
48 * `NeuroDebian 6.0.2 image (64bit)
49 <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]
53 This older virtual appliances are distributed as a `zip` file. Please
54 extract all files from the `.zip` file, using appropriate software
55 for your operating system.
59 You can verify that you have downloaded archives correctly using
61 <http://neuro.debian.net/debian/vm/MD5SUMS>`_ . You can also verify
62 the authenticity of the `MD5SUMS
63 <http://neuro.debian.net/debian/vm/MD5SUMS>`_ itself using `gpg
65 <http://neuro.debian.net/debian/vm/MD5SUMS.gpg>`_ signed with
66 NeuroDebian archive key.
68 * `VirtualBox download page <http://www.virtualbox.org/wiki/Downloads>`_ (Windows, Linux, Mac,
71 *This webpage offers installers of the VirtualBox application, as well as the
79 * Updated core system to Debian squeeze 6.0.6
83 * Updated core system to Debian squeeze 6.0.3
84 * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.10
86 - ``~/host`` is now symlinked to correct path ``/media/sf_host``
87 - ``brain`` user is added to ``vboxsf`` group so mounted host
88 directories should become readily available
90 * Root partition size and swap space got doubled in size (40GB
91 and 2GB correspondingly). Space is allocated dynamically so
92 the actual size of the virtual drive should not grow unless
97 * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.4
99 6.0.3 -- 12 Jun 2011 [Superseded in the archive by 6.0.4]
101 * Updated to Debian squeeze 6.0.1
102 * Updated VirtualBox guest additions to 4.0.4 from backports.debian.org
103 * Appliance is available as a single file (.ova) ready for the import
112 The virtual machine contains an installation of `Debian 6.0 (squeeze)`_ with a
113 GNOME_ desktop environment. All installed software comes from standard Debian
114 packages, or prospective Debian packages from NeuroDebian. This means that all
115 contained software is readily available for any system running a Debian
116 operating system (or a recent Ubuntu release). The virtual machine can be seen
117 as a showcase of what Debian for neuroscience research feels like. Moreover,
118 once downloaded this virtual machine can be kept up to date, just as any other
119 Debian installation. Using convenient graphical package management tools users
120 will benefit from security bug fixes provided by the Debian project for the
121 whole operating system, as well as from software updates for
122 neuroscience-related packages.
124 .. _Debian 6.0 (squeeze): http://www.debian.org/releases/squeeze
125 .. _GNOME: http://www.gnome.org/
131 The following video shows how to get the NeuroDebian virtual machine running
132 on your machine. The installation is shown for Mac OS X. It should, however, be
133 very similar on a Windows box. If you cannot watch the video, please take a
134 look at the written instructions below.
138 <iframe title="YouTube video player"
139 class="youtube-player"
143 src="http://www.youtube.com/embed/eqfjKV5XaTE?hd=1"
144 frameborder="0"></iframe>
146 First download and install a recent version of VirtualBox_. VirtualBox is a
147 virtualization software that is freely available for Windows, MacOS X, Solaris,
148 and Linux. VirtualBox comes with a comprehensive manual that should answer
149 potential questions regarding installation and maintenance.
151 .. _VirtualBox: http://www.virtualbox.org
153 Next, download the most recent version of the NeuroDebian virtual machine from
154 the Downloads_ section. Start VirtualBox and select "Import Appliance" from the file
157 .. image:: pics/vm_import_app.jpg
159 The next dialog will ask you to choose a virtual machine. Please navigate to the
160 extracted NeuroDebian download and select the `.ova` (or extracted
161 `.ovf` for older appliances shipped as `.zip`) file.
163 .. image:: pics/vm_import_wizard.jpg
165 You can finish importing of NeuroDebian by clicking on *next* a couple of
166 times. There is no need to change anything, as we will get through the
167 settings in a second. Importing of the virtual machine will take a short
168 while, as it is distributed in a compressed format that now gets extracted
169 (total extracted size about 2 GB). Once imported, the NeuroDebian virtual
170 machine will appear in the list of available machines. Do **not** start it yet,
171 but select NeuroDebian and hit the *Settings* button. In the following dialog
172 you'll have a chance to configure the machine. You can assign the amount of RAM
173 that should be made available to it (for serious fMRI data processing, please
174 allow at least 2 GB). If you have a recent computer with multiple CPU cores,
175 you can also decide how many cores should be used by the virtual machine.
177 .. image:: pics/vm_add_host_folder.jpg
179 However, most important is the *Shared Folders* setup. Shared folders allow the
180 virtual machine to access the local harddrive of the host computer. This is an
181 easy way to access data on the computer without duplicating it or using the
182 network to access it. The virtual machine is preconfigured to access a shared
183 folder named labeled "host". Click on the *add* button to select a folder that
184 shall be accessible by the machine (e.g. your home directory) and put "host" as
185 the folder name and mark it to be auto-mounted. Note, the folder name is simply a label. Your directory will
188 .. image:: pics/vm_host_folder.jpg
190 If you have a large screen you should increase the display memory to
191 32 MB in the *Display* settings. Also you might like to enable the
192 support for 3D Acceleration
194 .. image:: pics/vm_settings_display.jpg
196 Finally, close the settings dialog. You have now completed the setup, and you
197 can start the virtual machine by hitting the *Start* button. A new window will
198 appear showing the boot process. After a short while the NeuroDebian desktop
199 will appear, and a setup wizard will guide your through the final steps of the
200 configuration. You can now explore the system. The virtual machine is connected
201 with your host computer, and shares its Internet connection. Via this
202 connection you can update the contained software packages at any time.
204 .. image:: pics/vm_settings.jpg
206 The virtual machine logs yourself in automatically. The name of the virtual
207 machine user is `brain` and the password is `neurodebian`. The *root* password
208 is also `neurodebian`. In most cases, however, you should not be forced to type
209 the password, since `sudo` is configured to work without it.
213 For increased security you might want to change the default password. You can
214 do so by opening a terminal window and running the ``passwd`` command.
217 Working with the virtual machine
218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
220 The next video is a demonstration of some basic desktop integration features.
221 It shows how to use the virtual machine in full-screen and seamless mode, shared
222 folder access, software installation, as well as suspending and resuming the
227 <iframe title="YouTube video player"
228 class="youtube-player"
232 src="http://www.youtube.com/embed/OV7fYSEoOeQ?hd=1"
233 frameborder="0"></iframe>
236 .. _chap_vm_troubleshooting:
241 Updating the VM or installing new packages doesn't work.
243 The VM uses as service that tries to figure out the best/closest package
244 repository for you. In some network environments this service might not work
245 well, or not at all. To check if this is a problem, you can modify the
246 respective configuration by hand. Edit ``/etc/apt/sources.list`` (you need to
247 use ``sudo`` for that) and replace the package repository URL with a mirror
248 close to you. A comprehensive list of mirrors is available at:
249 http://www.debian.org/mirror/list
251 Pick one and replace all ``geomirror.debian.net`` URLs with the new mirror
252 URL. For example, in Canada you might want to change::
254 deb http://i386-geomirror.debian.net/debian squeeze main non-free contrib
258 deb http://ftp.ca.debian.org/debian/ squeeze main non-free contrib
260 Only modify lines that refer to ``geomirror`` (all of them), but do **not**
261 modify entries for ``security.debian.org``.
263 I cannot hear sounds played in the virtual machine.
265 By default the sound is muted. To enable playback launch the mixer applet by
266 clicking on the mixer icon in the task bar. Unmute the master volume control.
267 Now click on the "Volume control" to load the channel mixer dialog. Unmute
268 the "Master" and "PCM" channels and raise the volume as desired. You should
269 now be able to hear sounds played within the virtual machines through your
270 host computer's speakers.
272 I have upgraded VirtualBox from 3.x series to 4.x, and my VM lost
273 mounted host directories.
275 NeuroDebian VMs prior 6.0.3 were shipped with guest additions from
276 3.x series of VirtualBox and some initial versions of VirtualBox in
277 4.x series have failed to mount host directories properly.
278 VirtualBox 4.0.8 seems to work fine with guest additions from 3.x
279 series. If you nevertheless want to upgrade guest additions within
280 NeuroDebian VM, please rebuild the version available from the
283 sudo apt-get install -y linux-headers-2.6-amd64 # or -686 for 32bit
284 sudo apt-get install -y -t squeeze-backports virtualbox-ose-guest-dkms \
285 virtualbox-ose-guest-utils virtualbox-ose-guest-x11