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[protege-owl] Protege server - java.awt.HeadlessException

Tania Tudorache tudorache at stanford.edu
Wed Jun 16 08:23:10 PDT 2010


On 06/16/2010 02:23 AM, Brice Sommacal wrote:
> Thank you again Tania.
>
> I will test it on our server and let you know how it goes.
>
> It may be a silly question, but are we able to use database backend 
> AND file based with Protege server?

Yes. It is a good question :)

Tania

>
>
> Brice
>
> 2010/6/15 Tania Tudorache <tudorache at stanford.edu 
> <mailto:tudorache at stanford.edu>>
>
>     Hi Brice,
>
>     We are using for our production servers the run_protege_server.sh
>     that comes with Protege. We usually have to adjust the heap size,
>     and it seems you also have to. We have some guidelines on how
>     large the heap size can be here:
>
>     http://protegewiki.stanford.edu/wiki/Setting_Heap_Size
>
>     To adjust the heap size for the server, just edit the -Xmx string.
>
>     If you are using files projects (which is not recommended), you
>     should also enable the
>
>     SAVE_INTERVAL=-saveIntervalSec=120
>
>     The recommended backend to be used with the Protege server is the
>     database backend. This is explained on the wiki (also the auto-save):
>
>     http://protegewiki.stanford.edu/wiki/Protege_Client_Server_Tutorial_Setup#Which_type_of_back-end_to_use_.28database_vs._file-based.29_in_client-server_mode
>
>     If you run with file projects, the protege server will load all
>     ontologies into memory, and you may not have enough memory to load
>     all the 10 ontologies at the same time. This is a reason more to
>     use the database backend. Also, if something happens to the
>     Protege server, or the machine goes down, it is much safer to have
>     the ontologies stored in a database (you won't lose any data),
>     rather than files - which are in memory, and most likely some of
>     the changes will be lost.
>
>     Tania
>
>
>     On 06/15/2010 08:42 AM, Brice Sommacal wrote:
>>     Hello Tania,
>>
>>     Thank you for this clear explanation :-)
>>
>>     I deleted the unicode_panel.jar from the classpath, and from now,
>>     I have the following error.
>>
>>     From this,I have to increase the Xmx value, isn't it?
>>     But, I already did that, and my java heap size is set to 512.
>>
>>     I have also got an Java heap space error when shutting down the
>>     server.
>>
>>     Could you share with us what java configuration do you have?
>>
>>     (We have enter about 10 projects, and we are using Protege server
>>     for mainly 4 people)
>>
>>     BR,
>>
>>
>>     Brice
>>     --------------------------------------------------------------------------------------------------------------------------
>>
>>     Exception in thread "main" java.lang.OutOfMemoryError: Java heap
>>     space
>>             at java.nio.CharBuffer.wrap(CharBuffer.java:350)
>>             at java.nio.CharBuffer.wrap(CharBuffer.java:373)
>>             at
>>     java.lang.StringCoding$StringDecoder.decode(StringCoding.java:138)
>>             at java.lang.StringCoding.decode(StringCoding.java:173)
>>             at java.lang.String.<init>(String.java:443)
>>             at java.util.jar.Manifest.parseName(Manifest.java:252)
>>             at java.util.jar.Manifest.read(Manifest.java:206)
>>             at java.util.jar.Manifest.<init>(Manifest.java:52)
>>             at
>>     java.util.jar.JarFile.getManifestFromReference(JarFile.java:167)
>>             at java.util.jar.JarFile.getManifest(JarFile.java:148)
>>             at
>>     sun.misc.URLClassPath$JarLoader$2.getManifest(URLClassPath.java:696)
>>             at
>>     java.net.URLClassLoader.defineClass(URLClassLoader.java:228)
>>             at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
>>             at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
>>             at java.security.AccessController.doPrivileged(Native Method)
>>             at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>>             at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>>             at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
>>             at
>>     edu.stanford.smi.protegex.owl.ui.properties.types.AbstractPropertyTypesWidget$TypeCheckBox.<init>(Unknown
>>     Source)
>>             at
>>     edu.stanford.smi.protegex.owl.ui.properties.types.AbstractPropertyTypesWidget.initialize(Unknown
>>     Source)
>>             at
>>     edu.stanford.smi.protegex.owl.ui.properties.types.RDFPropertyTypesWidget.initialize(Unknown
>>     Source)
>>             at
>>     edu.stanford.smi.protege.widget.WidgetUtilities.setupSlotWidget(Unknown
>>     Source)
>>             at
>>     edu.stanford.smi.protege.widget.WidgetUtilities.createSlotWidget(Unknown
>>     Source)
>>             at
>>     edu.stanford.smi.protege.widget.FormWidget.createWidget(Unknown
>>     Source)
>>             at
>>     edu.stanford.smi.protege.widget.FormWidget.createWidgets(Unknown
>>     Source)
>>             at
>>     edu.stanford.smi.protege.widget.FormWidget.initializeWidgets(Unknown
>>     Source)
>>             at
>>     edu.stanford.smi.protege.widget.FormWidget.initialize(Unknown Source)
>>             at
>>     edu.stanford.smi.protege.widget.WidgetUtilities.createClsWidget(Unknown
>>     Source)
>>             at
>>     edu.stanford.smi.protege.model.Project.getDesignTimeClsWidget(Unknown
>>     Source)
>>             at
>>     edu.stanford.smi.protegex.owl.ui.forms.AbsoluteFormsLoader.addFormWidget(Unknown
>>     Source)
>>             at
>>     edu.stanford.smi.protegex.owl.ui.forms.AbsoluteFormsLoader.load(Unknown
>>     Source)
>>             at
>>     edu.stanford.smi.protegex.owl.ui.forms.AbsoluteFormsLoader.loadAll(Unknown
>>     Source)
>>
>>
>>     2010/6/10 Tania Tudorache <tudorache at stanford.edu
>>     <mailto:tudorache at stanford.edu>>
>>
>>         Forgot to mention one thing:
>>
>>         I recommend that you use Protege 3.4.4.
>>
>>         The classpath in the script should look like:
>>
>>         CLASSPATH=protege.jar:looks.jar:driver.jar:driver0.jar:driver1.jar:driver2.jar
>>
>>         Tania
>>
>>
>>         On 06/10/2010 12:00 PM, Tania Tudorache wrote:
>>>         Hi Brice,
>>>
>>>         The headless mode is used for machines that do not have a
>>>         graphical system (e.g. no monitor, no graphic card), or on
>>>         Unix system, for the cases you do not have a X display.
>>>
>>>         You can read more about the headless mode here:
>>>         http://java.sun.com/developer/technicalArticles/J2SE/Desktop/headless/
>>>
>>>         The Protege server is usually run on servers that do not
>>>         have an X display or a graphical system, so that is why the
>>>         headless flag is enabled by default in the
>>>         run_protege_server script.
>>>
>>>         You get the exception because Protege is trying to load the
>>>         forms of your OWL file from the .forms files (which it
>>>         doesn't make sense in a server environment). There is a
>>>         misbehaving piece of code that tries to access the graphical
>>>         display, when it shouldn't. To fix this problem, remove the
>>>         "unicode_panel.jar" from the classpath variable in the
>>>         run_protege_server.sh.
>>>
>>>         I'll fix the script for the next Protege 3.4 release.
>>>
>>>         Thanks!
>>>         Tania
>>>
>>>
>>>
>>>         On 06/10/2010 02:50 AM, Brice Sommacal wrote:
>>>>         Hello Tania,
>>>>
>>>>         You're right. The headless flag is in run_protege_server.sh.
>>>>         But the error still be displayed.
>>>>
>>>>         Could you please have a look at my script to chek that
>>>>         everything is ok?
>>>>         What is the goal of the headless flag?
>>>>
>>>>         Thanks again for your support,
>>>>         BR,
>>>>
>>>>
>>>>         Brice
>>>>
>>>>         2010/6/9 Tania Tudorache <tudorache at stanford.edu
>>>>         <mailto:tudorache at stanford.edu>>
>>>>
>>>>             Yes, indeed, you need the headless flag. The server
>>>>             start script run_protege_server.sh already contains it.
>>>>
>>>>             Tania
>>>>
>>>>
>>>>             On 06/09/2010 02:58 AM, simon wrote:
>>>>
>>>>                 Hi Brice,
>>>>
>>>>                 Try playing around with the
>>>>                 "-Djava.awt.headless=true" tomcat/java startup
>>>>                 option.
>>>>
>>>>                 Cheers
>>>>                 Simon
>>>>
>>>>
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>>>
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