Re: [R] Qsub - unable to open connection to X11 display
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@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. __ 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.
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.
Re: [R] Qsub - unable to open connection to X11 display
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.
Re: [R] Qsub - unable to open connection to X11 display
But doesn't it suffice to replace png() by bitmap()? b On Oct 29, 2007, at 12:47 PM, Duncan Murdoch wrote: 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@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. __ 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. __ 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.
Re: [R] Qsub - unable to open connection to X11 display
That is great, bitmap works. Now I have the problem that the gray levels are too bright. I tried using col=black in the hist function, but that only fills the bars. The tick marks etc are all in a fainting gray... Any idea on how to get those darker??? Thanks again, Bernd |-Original Message- |From: Benilton Carvalho [mailto:[EMAIL PROTECTED] |Sent: Monday, October 29, 2007 1:26 PM |To: Duncan Murdoch |Cc: Bernd Jagla; r-help@r-project.org |Subject: Re: [R] Qsub - unable to open connection to X11 display | |But doesn't it suffice to replace png() by bitmap()? |b | |On Oct 29, 2007, at 12:47 PM, Duncan Murdoch wrote: | | 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@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. | | __ | 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. __ 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.
