[R] Qsub - unable to open connection to X11 display

[Bernd Jagla]

Thanks for the comments/suggestions.

R is running smoothly on the head node with a small sample script. 
We are using the grid engine qsub system. There is no -X option available
for that one.

Can't I just disable the X11? There is such an option in Matlab, so I
thought R would have something similar...

-B

|-----Original Message-----
|From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
|Sent: Monday, October 29, 2007 12:35 PM
|To: Bernd Jagla
|Cc: r-help at r-project.org
|Subject: Re: [R] Qsub - unable to open connection to X11 display
|
|Hi Bernd,
|
|A little speculation / uninformed input on my part, but I'm guessing
|that the R on your nodes is compiled without X11 support, probably
|because the cluster nodes have X11, but not the X11 header files
|required by R when it is built. Probably
|
|> capabilities()[["X11"]]
|[1] FALSE
|
|One solution would build the R nodes with X11 support, this might
|require cooperation from the cluster administrator (to install X11
|headers?).
|
|If X11 support is compiled in, then have you added -X to qsub?
|
|Martin
|
|"Bernd Jagla" <baj2107 at columbia.edu> writes:
|
|> Hi there,
|>
|>
|>
|> I want to run an R script on a cluster with qsub. Obviously I don't want
|to
|> display any X window, but I want use png() or something else to write out
|> images.
|>
|> Unfortunately I get the following error message:
|>
|>
|>
|>> png(filename = " ALL.png", width = 480, height = 480, pointsize = 12, bg
|=
|> "white", res = NA)
|>
|> Error in X11(paste("png::", filename, sep = ""), width, height,
|pointsize,
|> :
|>
|>         unable to start device PNG
|>
|> In addition: Warning message:
|>
|> unable to open connection to X11 display ''
|>
|> Execution halted
|>
|>
|>
|> When X11 is working everything works fine.
|>
|>
|>
|> Is there a way to make this work without X11?
|>
|>
|>
|> Or, how would I simulate an X11 environment (including the correct
|DISPLAY
|> variable) on a cluster node?
|>
|>
|>
|> I appreciate any comments or suggestions.
|>
|>
|>
|> Thanks,
|>
|>
|>
|> Bernd
|>
|>
|> 	[[alternative HTML version deleted]]
|>
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|
|--
|Martin Morgan
|Computational Biology Shared Resource Director
|Fred Hutchinson Cancer Research Center
|1100 Fairview Ave. N.
|PO Box 19024 Seattle, WA 98109
|
|Location: Arnold Building M2 B169
|Phone: (206) 667-2793