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:[EMAIL PROTECTED] |Sent: Monday, October 29, 2007 12:35 PM |To: Bernd Jagla |Cc: r-help@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" <[EMAIL PROTECTED]> 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]] |> |> ______________________________________________ |> R-help@r-project.org mailing list |> https://stat.ethz.ch/mailman/listinfo/r-help |> PLEASE do read the posting guide http://www.R-project.org/posting- |guide.html |> and provide commented, minimal, self-contained, reproducible code. | |-- |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 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.