just a few mouse clicks (e.g. AFNI_, Caret_, FSL_, PyMVPA_).
.. _virtual machine: http://en.wikipedia.org/wiki/Virtual_machine
-.. _AFNI: http://afni.nimh.nih.gov/afni/
-.. _Caret: http://brainvis.wustl.edu/wiki/index.php/Caret:About
-.. _FSL: http://www.fmrib.ox.ac.uk/fsl/
-.. _PyMVPA: http://www.pymvpa.org
Downloads
---------
-* `NeuroDebian 6.0.1 image (32bit)
- <http://neuro.debian.net/debian/vm/neurodebian_6.0.1_i386.zip>`_ [~560MB]
+Stable (6.x series)
+~~~~~~~~~~~~~~~~~~~
+
+Based on current stable `Debian 6.0 (squeeze)`_ release. This VM
+provides a stable, well tested environment with the most of the recent
+releases available from NeuroDebian.
+
+* `NeuroDebian 6.0.6 image (32bit)
+ <http://neuro.debian.net/debian/vm/NeuroDebian_6.0.6_i386.ova>`_ [~559MB]
*This image should work on virtually all systems that are supported by*
VirtualBox_ *and can be used whenever the, otherwise preferable, 64bit image
is not compatible with a host machine.*
-* `NeuroDebian 6.0.1 image (64bit)
- <http://neuro.debian.net/debian/vm/neurodebian_6.0.1_amd64.zip>`_ [~570MB]
+* `NeuroDebian 6.0.6 image (64bit)
+ <http://neuro.debian.net/debian/vm/NeuroDebian_6.0.6_amd64.ova>`_ [~576MB]
*This image only works on 64bit host machines with active hardware
virtualization support. The should include all recent Apple hardware and most
64bit Windows systems.*
+Development (to be 7.x series)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Based on upcoming `Debian 7.0 (wheezy)`_ release. Although already
+quite stable, there might be outstanding issues. This VM also
+switches from GNOME_ (v.2) desktop environment to XFCE4_. We
+recommend this VM over a stable one for anyone needing recent releases
+of tools not available for the stable VM (e.g. recent pandas) --
+**getting a complete "Scientific Python" stack with 100s of other
+Python modules was never easier**. Moreover your feedback might also
+be valuable to polish upcoming Debian wheezy release and NeuroDebian
+VM 7.0.
+
+* `NeuroDebian 6.999.b4.20121231 image (32bit)
+ <http://neuro.debian.net/debian/vm/NeuroDebian_6.999.b4.20121231_i386.ova>`_ [~656MB]
+
+* `NeuroDebian 6.999.b4.20121231 image (64bit)
+ <http://neuro.debian.net/debian/vm/NeuroDebian_6.999.b4.20121231_amd64.ova>`_ [~660MB]
+
+
+Historical
+~~~~~~~~~~
+
+Virtual appliances above carry guest additions for 4.x series of the
+VirtualBox. If you still have VirtualBox 3.x, use previous 6.0.2
+virtual appliances:
+
+* `NeuroDebian 6.0.2 image (32bit)
+ <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]
+
+* `NeuroDebian 6.0.2 image (64bit)
+ <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]
+
+.. note::
+
+ This older virtual appliances are distributed as a `zip` file. Please
+ extract all files from the `.zip` file, using appropriate software
+ for your operating system.
+
.. note::
You can verify that you have downloaded archives correctly using
*This webpage offers installers of the VirtualBox application, as well as the
documentation.*
+Changes
+-------
+
+6.999.b4.20121231 -- 31 Dec 2012
+
+ * Based on beta 4 release of debian-installer_ for wheezy
+ * Comes with XFCE4_ instead of GNOME_
+
+6.0.6 -- 01 Oct 2012
+
+ * Updated core system to Debian squeeze 6.0.6
+
+6.0.5 -- 10 Nov 2011
+
+ * Updated core system to Debian squeeze 6.0.3
+ * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.10
+
+ - ``~/host`` is now symlinked to correct path ``/media/sf_host``
+ - ``brain`` user is added to ``vboxsf`` group so mounted host
+ directories should become readily available
+
+ * Root partition size and swap space got doubled in size (40GB
+ and 2GB correspondingly). Space is allocated dynamically so
+ the actual size of the virtual drive should not grow unless
+ you use it
+
+6.0.4 -- 13 Jun 2011
+
+ * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.4
+
+6.0.3 -- 12 Jun 2011 [Superseded in the archive by 6.0.4]
+
+ * Updated to Debian squeeze 6.0.1
+ * Updated VirtualBox guest additions to 4.0.4 from backports.debian.org
+ * Appliance is available as a single file (.ova) ready for the import
+
+6.0.2 -- 08 Feb 2011
+
+6.0.1 -- 01 Dec 2010
Documentation
-------------
whole operating system, as well as from software updates for
neuroscience-related packages.
-.. _Debian 6.0 (squeeze): http://www.debian.org/releases/squeeze
-.. _GNOME: http://www.gnome.org/
Installation
.. _VirtualBox: http://www.virtualbox.org
Next, download the most recent version of the NeuroDebian virtual machine from
-the Downloads_ section. The machine is distributed as a zip file. Please
-extract this file, using appropriate software for your operating system.
-Once extracted, start VirtualBox and select "Import Appliance" from the file
+the Downloads_ section. Start VirtualBox and select "Import Appliance" from the file
menu.
.. image:: pics/vm_import_app.jpg
The next dialog will ask you to choose a virtual machine. Please navigate to the
-extracted NeuroDebian download and select the `.ovf` file.
+extracted NeuroDebian download and select the `.ova` (or extracted
+`.ovf` for older appliances shipped as `.zip`) file.
.. image:: pics/vm_import_wizard.jpg
you'll have a chance to configure the machine. You can assign the amount of RAM
that should be made available to it (for serious fMRI data processing, please
allow at least 2 GB). If you have a recent computer with multiple CPU cores,
-you can also decide how many cores should be used by the virtual machine. If
-you have a large screen you should increase the display memory to 32 MB in the
-*Display* settings.
+you can also decide how many cores should be used by the virtual machine.
.. image:: pics/vm_add_host_folder.jpg
network to access it. The virtual machine is preconfigured to access a shared
folder named labeled "host". Click on the *add* button to select a folder that
shall be accessible by the machine (e.g. your home directory) and put "host" as
-the folder name. Note, the folder name is simply a label. Your directory will
+the folder name and mark it to be auto-mounted. Note, the folder name is simply a label. Your directory will
not be renamed.
.. image:: pics/vm_host_folder.jpg
+If you have a large screen you should increase the display memory to
+32 MB in the *Display* settings. Also you might like to enable the
+support for 3D Acceleration
+
+.. image:: pics/vm_settings_display.jpg
+
Finally, close the settings dialog. You have now completed the setup, and you
can start the virtual machine by hitting the *Start* button. A new window will
appear showing the boot process. After a short while the NeuroDebian desktop
frameborder="0"></iframe>
+.. _chap_vm_troubleshooting:
+
Troubleshooting
~~~~~~~~~~~~~~~
+Updating the VM or installing new packages doesn't work.
+
+ The VM uses as service that tries to figure out the best/closest package
+ repository for you. In some network environments this service might not work
+ well, or not at all. To check if this is a problem, you can modify the
+ respective configuration by hand. Edit ``/etc/apt/sources.list`` (you need to
+ use ``sudo`` for that) and replace the package repository URL with a mirror
+ close to you. A comprehensive list of mirrors is available at:
+ http://www.debian.org/mirror/list
+
+ Pick one and replace all ``geomirror.debian.net`` URLs with the new mirror
+ URL. For example, in Canada you might want to change::
+
+ deb http://i386-geomirror.debian.net/debian squeeze main non-free contrib
+
+ to::
+
+ deb http://ftp.ca.debian.org/debian/ squeeze main non-free contrib
+
+ Only modify lines that refer to ``geomirror`` (all of them), but do **not**
+ modify entries for ``security.debian.org``.
+
I cannot hear sounds played in the virtual machine.
By default the sound is muted. To enable playback launch the mixer applet by
the "Master" and "PCM" channels and raise the volume as desired. You should
now be able to hear sounds played within the virtual machines through your
host computer's speakers.
+
+I have upgraded VirtualBox from 3.x series to 4.x, and my VM lost
+mounted host directories.
+
+ NeuroDebian VMs prior 6.0.3 were shipped with guest additions from
+ 3.x series of VirtualBox and some initial versions of VirtualBox in
+ 4.x series have failed to mount host directories properly.
+ VirtualBox 4.0.8 seems to work fine with guest additions from 3.x
+ series. If you nevertheless want to upgrade guest additions within
+ NeuroDebian VM, please rebuild the version available from the
+ backports::
+
+ sudo apt-get install -y linux-headers-2.6-amd64 # or -686 for 32bit
+ sudo apt-get install -y -t squeeze-backports virtualbox-ose-guest-dkms \
+ virtualbox-ose-guest-utils virtualbox-ose-guest-x11
+
+ and reboot VM.
+
+.. include:: link_names.txt
projects / neurodebian.git / blobdiff