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Using X11

If you wish to work with interactive graphical programs on the grid, you will need a way to display the graphical output on your local machine. This is accomplished through a bit of software known as an X11 server, which receives requests from programs running on remote machines and renders graphical elements on your local desktop.

There are many X11 server implementations available. Our recommendations are as follows:

  • OS X - XQuartz (X.org for OS X). XQuartz is an improvement on the stock X11 server that ships with OS X. You can manage installation using MacPorts: first install MacPorts, then run '/opt/local/bin/port install xorg-server'. XQuartz will start automatically when an X11 connection is requested.
  • Linux - X.org X11 server. This will already be installed on a desktop-type computer.
  • Windows - Xming. Download and install the Xming and Xming-fonts packages. Xming must be started manually, either through the Program Files menu or the Quick Launch area. Once running, Xming will display an X icon in the System Tray. Good site for information on enabling X11 on Windows.

Once the X11 server is set up and running, you will need a tunnel via SSH for X11 traffic. Use the -X option of the ssh command-line client from OS X or Linux. Note that this is an upper-case -X, a lower-case -x will explicitly disable X11 tunneling.

Some people use the -Y option. This is not recommended as it tunnels X11 in trusted mode and is thus less secure than using -X.

Graphical clients such as the SSH Terminal on Windows will have a checkbox indicating an X11 tunnel is requested.

Troubleshooting

It is not unheard of for X11 connections to fail in seemingly mysterious ways. Typically, this is caused by minor misconfigurations that can be easily fixed. One common error is to try to run X11 through multiple network connections, e.g. ssh to ong0, then ssh to ong7, then run an X11 program. The correct way to resolve this is to ssh directly to the node on which you want to run the X11 program.

Some information may be provided by running your ssh session in verbose mode using the -v option. Up to three v's may be provided on the command line for increasing levels of verbosity.

Freesurfer

There is a known incompatibility between Freesurfer and XQuartz 2.7.9. At this time, no solution is known, but installing an earlier version of XQuartz provides an effective work-around.

There appears to be precedent for this type of breakage:

http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36960.html