Re: [Rd] R "capabilities" on a cluster node

From: Hin-Tak Leung <hin-tak.leung_at_cimr.cam.ac.uk>
Date: Mon, 01 Oct 2007 19:30:26 +0100

The double '//' is harmless. What you are failing at is that your R-build-host has the system X11 runtime libraries (libSM.so.6 and friends) while your execution hosts don't have them, and R_X11.so depends on the system X11 libraries which R cannot find on the execution hosts.

So - ask your grid engine administrator to install the X11 runtime libraries on the grid nodes, or ask him/her to build a special version of R which doesn't depend on X11. (the former is the recommended approach, but your admins may think the latter suit their policies).

Yes, pdf/ps are always available. (they are just save-to-file devices using R's own pdf/ps writing code).

The png/jpeg situation are similar to but separate from X11. On the R build host, you need both the development headers (libpng-devel, libjpeg-devel, libX11-devel & other libX*-devel packages for redhat systems) as well as the runtime libraries (libpng, libjpeg, libX*) to build R with each of the support for these 3. On the execution hosts, you need just the runtime libraries.

The reason why you are missing jpeg/png is probably because your build host doesn't have the headers. (it is relatively rare not to have jpeg/png runtime, but the headers are normally not installed).

We (used to?) have a similiar situation on our sun grid - my desktop R can do png but our cluster grid R cannot. (ghostscript and a few other software can convert ps/pdf to png so it is not a big loss, just a minor inconvenience).

Earl F. Glynn wrote:
> R version 2.5.1 (2007-06-27)
>
> I' running some simple R jobs via the Sun Grid Engine on our Linux cluster
> in preparation for some bigger ones.
>
> I checked R's capabilities on the cluster nodes (after failing to create a
> png file) and am getting the following warning message:
> [Run on a cluster node using qrsh:]
>
>
>

>> capabilities()

>
> jpeg png tcltk X11 http/ftp sockets libxml fifo
>
> FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE
>
> cledit iconv NLS profmem
>
> TRUE TRUE TRUE FALSE
>
> Warning message:
>
> unable to load shared library
> '/n/site/inst/Linux-i686/bioinfo/R/2.5.1/lib/R/modules//R_X11.so':
>
> libSM.so.6: cannot open shared object file: No such file or directory in:
> capabilities()
>
>
>
>
>
> Is the double slash (//) in the path above a bug in how we've configured R
> here (the /n/site/inst/ directory is shared but is platform specific), or a
> bug in how the capabilities command works? The file does exist if the
> double slash in the path had not caused the warning above.
>
>
>
>
>
>
> How can one programmatically get the info from ?Devices, which appears to be
> dynamic based on one's system? Is it safe to assume that pdf's or
> postscript files are always available in R since they're not listed in
> capabilities and seem to be shown everywhere under ?Devices ?
>
>
>
>
>
> Part of the ?Devices output on a cluster node says this:
>
>
>
> The following devices will be available if R was compiled to use
>
> them:
>
>
>
> * 'X11' The graphics driver for the X11 Window system
>
>
>
> * 'png' PNG bitmap device
>
>
>
> * 'jpeg' JPEG bitmap device
>
>
>
> We can just recompile to get png or jpeg support? Are X11 libraries used on
> cluster nodes while running "headless"? Can I create pngs or jpegs without
> X11?
>
>
>
> Thanks for any advice about this.
>
>
>
> efg
>
>
>
> Earl F. Glynn
>
> Scientific Programmer
> Stowers Institute for Medical Research
>
> ______________________________________________
> R-devel_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel


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