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

Brice Sommacal brice.sommacal at gmail.com
Wed Jun 16 02:23:45 PDT 2010


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?


Brice

2010/6/15 Tania Tudorache <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>
>
>> 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>
>>
>>> 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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