Ubuntu no x11 display variable was set, but this program performed an operation which requires it.

unread,

Aug 31, 2011, 6:29:27 AM8/31/11



Sign in to reply to author

You do not have permission to delete messages in this group

Sign in to report message as abuse

Either email addresses are anonymous for this group or you need the view member email addresses permission to view the original message

Hello, I am attempting to use Tree Annotator on a Linux machine, as I encounter an out of memory error when using a Windows machine (1 billion generations, sampled every 1000 generations, so 1000000 trees with 50000 trees as burnin). I keep getting an error pertaining to X11 which is not installed on my machine. Is there any way to run TREEANNOTATOR and BEAST without X11 on Linux? Here is the error: [lab@BTUC10 bin]$ ./treeannotator JRI not available. Using Java bivariate attributes Exception in thread "main" java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java: 173) at java.awt.Window.<init>(Window.java:437) at java.awt.Frame.<init>(Frame.java:419) at java.awt.Frame.<init>(Frame.java:384) at javax.swing.JFrame.<init>(JFrame.java:174) at jam.framework.AbstractFrame.<init>(Unknown Source) at jam.framework.DocumentFrame.<init>(Unknown Source) at jam.console.ConsoleFrame.<init>(Unknown Source) at jam.console.ConsoleApplication.<init>(Unknown Source) at jam.console.ConsoleApplication.<init>(Unknown Source) at dr.app.tools.TreeAnnotator.main(Unknown Source) Thank you.

-Crystal

unread,

Aug 31, 2011, 7:28:35 AM8/31/11



Sign in to reply to author

You do not have permission to delete messages in this group

Sign in to report message as abuse

Either email addresses are anonymous for this group or you need the view member email addresses permission to view the original message

to

Hey crystal,

You need to install Xming windows server available on source forge. Turn Xming once installed, Customize putty by checking X11 in putty settings and localhost:0 in the display field.

unread,

Aug 31, 2011, 7:44:20 AM8/31/11



Sign in to reply to author

You do not have permission to delete messages in this group

Sign in to report message as abuse

Either email addresses are anonymous for this group or you need the view member email addresses permission to view the original message

to

Dear Crystal,

TreeAnnotator (as well as the other BEAST components) will only try to bring up a user interface if you give them no command line options.

Try typing:

./treeannotator -help

1,000,000 trees is likely to be too much for most computers and is probably more than you need. You can use logcombiner to down sample to a more manageable number (we usually suggest 10,000).

Andrew

unread,

Aug 31, 2011, 4:23:45 PM8/31/11



Sign in to reply to author

You do not have permission to delete messages in this group

Sign in to report message as abuse

Either email addresses are anonymous for this group or you need the view member email addresses permission to view the original message

to

Hi Crystal If you are running a custom installation of any GNU/Linux distribution, you will probably have some kind of  X-server installed. Therefore, I think it is just the DISPLAY variable that is not set correctly. Try setting this variable with the command: export DISPLAY=localhost:0 ... and then try starting treeannotator again. Hope this helps #Mats

unread,

Sep 1, 2011, 11:40:41 AM9/1/11



Sign in to reply to author

You do not have permission to delete messages in this group

Sign in to report message as abuse

Either email addresses are anonymous for this group or you need the view member email addresses permission to view the original message

Dear Dr. Rambaut, Thank you. I see that the memory can be increased for BEAST in Linux via the command line, but can the same be done for TreeAnnotator? Also, is tree annotator limited, like BEAST is, on the amount of memory it is allowed to use? Or is the limitation the amount of memory the computer has? Thanks again! > > For more options, visit this group athttp://groups.google.com/group/beast-users?hl=en.

> > ___________________________________________________________________ >   Andrew Rambaut                 >   Institute of Evolutionary Biology       University of Edinburgh >   Ashworth Laboratories                         Edinburgh EH9 3JT