[ome-users] Hamamatsu export kCGErrorFailure

Tue Dec 3 11:03:58 GMT 2013

Hi Andreas,  

(Sending this back to the list so that other’s can chime in…)

My apologies on assuming your were using Xgrid. In my past experience, I’ve only ever seen “Can’t connect to window server” errors on an Xserve in two situations: running a process as user “nobody” under Xgrid (or some other grid computing platform), or if your Xserve has no graphics processor. The second situation is unlikely, as most of the Intel Xserves shipped with an integrated Intel graphics processor, so even if you don’t have a discreet graphics card installed you would still have graphics capabilities.

That said, after discussing the issue with Melissa, this is all a moot point. The most recent version of Bio-Formats shouldn’t even touch the libraries that are causing your issues. So Melissa’s original assessment was correct: somehow you’re not running the most recent version of Bio-Formats. Try double-checking your binary path and make sure that “bfconvert -version” reports “5.0.0-beta1” as the Bio-Formats version.

Cheers,

Josh

On Wednesday, November 27, 2013 at 15:56, Andreas Heindl wrote:

> Hi Josh,
> Thanks for your mail. I connect to the XServe via ssh and as far as I  
> know I haven't set up Xgrid. I use HTCondor to distribute jobs but that  
> shouldn't interfere with bfconvert because I launched it right after I  
> logged in via ssh (using my account (with admin rights))? Do I have to  
> create a Xgrid to get rid of that problem?
> Thanks in advance,
> Andreas
>  
> On 26/11/13 15:40, Joshua Ballanco wrote:
> > Hi Andreas,
> >  
> > I believe the issue you are seeing is a symptom of your Xgrid configuration. If you are not using Xgrid with authentication enabled, then jobs run under user “nobody” by default. Unfortunately, user “nobody” does not have access to the window server, which is required for a variety of different graphics processing routines. The simplest fix would be to set up a dedicated “xgrid” user on your Xgrid nodes and use password or kerberos-based authentication between the Xgrid controller and the nodes.
> >  
> > Cheers,
> >  
> > Josh
> >  
> >  
> > On Tuesday, November 26, 2013 at 16:47, Andreas Heindl wrote:
> >  
> > > Dear Melissa,
> > > I upgraded to the latest version which didn't solve the problem.
> > > However, on Linux (Ubuntu, 64bit) it works fine.
> > > On our XServe (Java[1]) it still crashed with the error beneath:
> > >  
> > > 012A-2013-11-18_15.06.56.ndpi
> > > Reading IFDs
> > > Populating metadata
> > > Populating OME metadata
> > > [Hamamatsu NDPI] -> ./012A-2013-11-18_15.06.56/Tile0.jpg [JPEG]
> > > Mon Nov 25 16:39:42 yy1.local java[37867] <Error>: kCGErrorFailure:
> > > Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are
> > > logged.
> > > Exception in thread "main" java.lang.InternalError: Can't connect to
> > > window server - not enough permissions.
> > > at java.lang.ClassLoader$NativeLibrary.load(Native Method)
> > > at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1833)
> > > at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1730)
> > > at java.lang.Runtime.loadLibrary0(Runtime.java:823)
> > > at java.lang.System.loadLibrary(System.java:1044)
> > > at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50)
> > > at java.security.AccessController.doPrivileged(Native Method)
> > > at java.awt.Toolkit.loadLibraries(Toolkit.java:1605)
> > > at java.awt.Toolkit.<clinit>(Toolkit.java:1627)
> > > at loci.formats.codec.JPEGTileDecoder.initialize(JPEGTileDecoder.java:136)
> > > at loci.formats.in.NDPIReader.setupService(NDPIReader.java:365)
> > > at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:114)
> > > at loci.formats.FormatReader.openBytes(FormatReader.java:781)
> > > at loci.formats.ImageReader.openBytes(ImageReader.java:400)
> > > at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:544)
> > > at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:486)
> > > at loci.formats.tools.ImageConverter.main(ImageConverter.java:672)
> > >  
> > >  
> > >  
> > >  
> > > [1]
> > > java version "1.6.0_65"
> > > Java(TM) SE Runtime Environment (build 1.6.0_65-b14-462-10M4609)
> > > Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-462, mixed mode)
> > >  
> > >  
> > >  
> > > On 25/11/13 18:34, Melissa Linkert wrote:
> > > > Hi Andreas,
> > > >  
> > > > > I recently noticed a new error message while extracting tiles from a
> > > > > ndpi (Hamamatsu) file. I'm using the most recent (stable)
> > > > > loci/bftools versions. Unfortunately, I couldn't find anything
> > > > > related to that error on google thus I hope you have an hint for me.
> > > > > It's running on a MacOSX XServe and the error message is attached
> > > > > here[1].
> > > >  
> > > >  
> > > >  
> > > >  
> > > > Are you using the 4.4.9 version of Bio-Formats? If so, I would very
> > > > much recommend that you try the 5.0.0-beta1 version instead:
> > > >  
> > > > http://downloads.openmicroscopy.org/bio-formats/5.0.0-beta1/
> > > >  
> > > > If 5.0.0-beta1 also produces an error message, please let us know.
> > > >  
> > > > Regards,
> > > > -Melissa
> > > >  
> > > > On Mon, Nov 25, 2013 at 04:46:33PM +0000, Andreas Heindl wrote:
> > > > > Dear all,
> > > > >  
> > > > > I recently noticed a new error message while extracting tiles from a
> > > > > ndpi (Hamamatsu) file. I'm using the most recent (stable)
> > > > > loci/bftools versions. Unfortunately, I couldn't find anything
> > > > > related to that error on google thus I hope you have an hint for me.
> > > > > It's running on a MacOSX XServe and the error message is attached
> > > > > here[1].
> > > > >  
> > > > > Thanks a lot and regards,
> > > > > Andreas
> > > > >  
> > > > >  
> > > > > [1]
> > > > >  
> > > > > 012A-2013-11-18_15.06.56.ndpi
> > > > > Reading IFDs
> > > > > Populating metadata
> > > > > Populating OME metadata
> > > > > [Hamamatsu NDPI] -> ./012A-2013-11-18_15.06.56/Tile0.jpg [JPEG]
> > > > > Mon Nov 25 16:39:42 yy1.local java[37867] <Error>: kCGErrorFailure:
> > > > > Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are
> > > > > logged.
> > > > > Exception in thread "main" java.lang.InternalError: Can't connect to
> > > > > window server - not enough permissions.
> > > > > at java.lang.ClassLoader$NativeLibrary.load(Native Method)
> > > > > at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1833)
> > > > > at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1730)
> > > > > at java.lang.Runtime.loadLibrary0(Runtime.java:823)
> > > > > at java.lang.System.loadLibrary(System.java:1044)
> > > > > at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50)
> > > > > at java.security.AccessController.doPrivileged(Native Method)
> > > > > at java.awt.Toolkit.loadLibraries(Toolkit.java:1605)
> > > > > at java.awt.Toolkit.<clinit>(Toolkit.java:1627)
> > > > > at loci.formats.codec.JPEGTileDecoder.initialize(JPEGTileDecoder.java:136)
> > > > > at loci.formats.in.NDPIReader.setupService(NDPIReader.java:365)
> > > > > at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:114)
> > > > > at loci.formats.FormatReader.openBytes(FormatReader.java:781)
> > > > > at loci.formats.ImageReader.openBytes(ImageReader.java:400)
> > > > > at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:544)
> > > > > at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:486)
> > > > > at loci.formats.tools.ImageConverter.main(ImageConverter.java:672)
> > > > >  
> > > > > The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
> > > > >  
> > > > > This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
> > > > > _______________________________________________
> > > > > ome-users mailing list
> > > > > ome-users at lists.openmicroscopy.org.uk (mailto:ome-users at lists.openmicroscopy.org.uk)
> > > > > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> > > >  
> > >  
> > >  
> > >  
> > >  
> > >  
> > >  
> > > --
> > > Division of Molecular Pathology
> > > The Institute of Cancer Research
> > > Chester Beatty Lab
> > > 237 Fulham Road
> > > SW3 6JB
> > > London
> > > Tel: 079-230-38499
> > >  
> > >  
> > > The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
> > >  
> > > This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
> > > _______________________________________________
> > > ome-users mailing list
> > > ome-users at lists.openmicroscopy.org.uk (mailto:ome-users at lists.openmicroscopy.org.uk)
> > > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >  
>  
>  
>  
>  
> --  
> Division of Molecular Pathology
> The Institute of Cancer Research
> Chester Beatty Lab
> 237 Fulham Road
> SW3 6JB
> London
> Tel: 079-230-38499
>  
>  
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
>  
> This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.  