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]]
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]] > > ______________________________________________ > R-help at 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
On 10/29/2007 12:06 PM, Bernd Jagla wrote:> 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?Xvfb is the usual trick to fake an X11 environment without a display. (It's a "virtual frame buffer" X server.) I don't know if PNG works with it or not. Duncan Murdoch> > > > I appreciate any comments or suggestions. > > > > Thanks, > > > > Bernd > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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.