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

[Martin Morgan]

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
>
>
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>
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-- 
Martin Morgan
Computational Biology Shared Resource Director
Fred Hutchinson Cancer Research Center
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