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

Tania Tudorache tudorache at stanford.edu
Tue Jun 15 12:52:09 PDT 2010


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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