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[protege-discussion] Fwd: Protege 3.4.4 (579) 64-bit max heap size

Len Yabloko protege at ontospace.net
Fri Sep 3 13:33:24 PDT 2010


When I use run_protete.bat the memory is allocated in full, but JVM still maxout at 2.5G

Protege 3.4.4 Build 579, JVM 1.6.0_21-b07, memory=5965M, Windows 7, encoding=UTF
-8, language=en, country=US
Loaded plugin edu.stanford.smi.protegex.owl - OWL Plugin
Loaded plugin ca.uvic.cs.chisel.jambalaya - Jambalaya
Loaded plugin com.ngs.ontobase.protege - ONTOBaseTab
Loaded plugin dfki.protege.ontoviz
Loaded plugin edu.stanford.smi.protegex.standard_extensions - Graph Widget, Tabl
e Widget
Loaded plugin edu.stanford.bmir.protegex.bp.ref - BioPortal Reference Plugin
Loaded plugin edu.stanford.smi.protegex.rdf_backend - RDF Backend
Loaded plugin edu.stanford.smi.protegex.changes - Changes tab
Loaded plugin edu.stanford.smi.protegex.chatPlugin - Chat
Loaded plugin edu.stanford.smi.protege.collab - Collaborative Protege
Loaded plugin edu.stanford.smi.protege.script - Script Plugin
Loaded plugin edu.stanford.smi.protege.stringsearch - String Search Tab
Loaded plugin edu.stanford.smi.protegex.changeanalysis - Change Analysis Tab
Loaded plugin edu.stanford.smi.protegex.datamaster - DataMaster Tab
Loaded plugin edu.stanford.smi.protegex.pal_tabs - PAL Tabs
Loaded plugin edu.stanford.smi.protegex.ezpal - EZPal Tab
Loaded plugin edu.stanford.smi.protegex.facets_tab
Loaded plugin edu.stanford.smi.protegex.instance_tree
WARNING: Duplicate plugin: edu.stanford.smi.protege.widget.instance_tree.Knowled
geTreeTab -- PluginUtilities.checkPlugin()
WARNING: Duplicate plugin: edu.stanford.smi.protege.widget.instance_tree.Instanc
eTreeSlot -- PluginUtilities.checkPlugin()
WARNING: Duplicate plugin: edu.stanford.smi.protege.widget.instance_tree.Instanc
eTreeTab -- PluginUtilities.checkPlugin()
Loaded plugin edu.stanford.smi.protegex.prompt - PROMPT Tab
Loaded plugin edu.stanford.smi.protegex.metaanalysis - MetaAnalysis Tab
Loaded plugin edu.stanford.smi.protegex.owl.inference.pellet - Protege Pellet Re
asoner
Loaded plugin edu.stanford.smi.protegex.query.lucene - LuceneQueryTab
Loaded plugin edu.stanford.smi.protegex.umls_tab - UMLS Tab
Loaded plugin edu.stanford.smi.protegex.wordnet - WordNet Tab
Loaded plugin edu.stanford.smi.protegex.xml_tab - XML Tab
Loaded plugin org.algernon - Algernon
Loaded plugin org.protege.owl.axiome - Axiome Plugin
Loaded plugin org.protege.owl.mappingmaster - MappingMaster Plugin
Loaded plugin se.liu.ida.JessTab - JessTab Plugin
Loaded plugin uk.ac.iam.soton.akt.tgviztab - TGVizTab
Loaded plugin uk.ac.man.cs.mig.coode.debugger
Loaded plugin uk.ac.man.cs.mig.coode.manchesterowlsyntaxeditor
Loaded plugin uk.ac.man.cs.mig.coode.owldoc
Loaded plugin uk.ac.man.cs.mig.coode.owlindividualstab
Loaded plugin uk.ac.man.cs.mig.coode.owlviz
Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard - Basic Wizards
Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard.owl - OWL Wizards
Root: /C:/Program%20Files/Protege_3.4.4/plugins/com.ngs.ontobase.protege/
java.io.FileNotFoundException: log.txt (Access is denied)
        at java.io.RandomAccessFile.open(Native Method)
        at java.io.RandomAccessFile.<init>(RandomAccessFile.java:212)
        at com.ngs.ontobase.util.WriterLoggerDestination.prepareWriterLoggerDest
ination(WriterLoggerDestination.java:83)
        at com.ngs.ontobase.protege.ONTOBaseTab.initialize(ONTOBaseTab.java:86)
        at edu.stanford.smi.protege.widget.WidgetUtilities.createTabWidget(Unkno
wn Source)
        at edu.stanford.smi.protege.ui.ProjectView.addTab(Unknown Source)
        at edu.stanford.smi.protege.ui.ProjectView.createTabbedPane(Unknown Sour
ce)
        at edu.stanford.smi.protege.ui.ProjectView.<init>(Unknown Source)
        at edu.stanford.smi.protege.ui.ProjectManager.displayCurrentProject(Unkn
own Source)
        at edu.stanford.smi.protege.ui.ProjectManager.displayCurrentProject(Unkn
own Source)
        at edu.stanford.smi.protege.ui.ProjectManager.loadProject(Unknown Source
)
        at edu.stanford.smi.protege.ui.WelcomeDialog.doOpenProject(Unknown Sourc
e)
        at edu.stanford.smi.protege.ui.WelcomeDialog.access$400(Unknown Source)
        at edu.stanford.smi.protege.ui.WelcomeDialog$10.mouseClicked(Unknown Sou
rce)
        at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:25
3)
        at java.awt.Component.processMouseEvent(Component.java:6270)
        at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
        at java.awt.Component.processEvent(Component.java:6032)
        at java.awt.Container.processEvent(Container.java:2041)
        at java.awt.Component.dispatchEventImpl(Component.java:4630)
        at java.awt.Container.dispatchEventImpl(Container.java:2099)
        at java.awt.Component.dispatchEvent(Component.java:4460)
        at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577
)
        at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4247)

        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
        at java.awt.Container.dispatchEventImpl(Container.java:2085)
        at java.awt.Window.dispatchEventImpl(Window.java:2478)
        at java.awt.Component.dispatchEvent(Component.java:4460)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThre
ad.java:269)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.
java:184)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.
java:178)
        at java.awt.Dialog$1.run(Dialog.java:1046)
        at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:597)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThre
ad.java:269)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.
java:184)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre
ad.java:174)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)

        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)

        at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Protege Wizards v1.0 beta build 15
Loaded standard Protege wizards library
WARNING: java.io.FileNotFoundException: C:\Program Files\Protege_3.4.4\protege.p
roperties (Access is denied) -- ApplicationProperties.flush()
Load time for file:\C:\Users\Len\Desktop\stores7.pprj = 0 sec (project) + 5 sec
(ui)



>
>On 09/03/2010 12:55 PM, Len Yabloko wrote:
>> I got 8G on Windows 7 Professional 64-bit
>>
>> However, when I run Protege 3.3.4 64-bit with protege.lax set
>> lax.nl.java.option.java.heap.size.max=6400000000
>> I only get 1871M allocated as show below
>>
>> cwd: C:\Program Files\Protege_3.4.4
>> cmd: "C:\Program Files\Java\jdk1.6.0_21\bin\java.exe" -Xms262144000 -Xmx2105032704 -classpath "C:\Program Files\Protege_3.4.4\protege.jar;C:\Program Files\Prote
>> ge_3.4.4\looks.jar;C:\Program Files\Protege_3.4.4\unicode_panel.jar;C:\Program F
>> iles\Protege_3.4.4\driver.jar;C:\Program Files\Protege_3.4.4\driver0.jar;C:\Prog
>> ram Files\Protege_3.4.4\driver1.jar;C:\Program Files\Protege_3.4.4\driver2.jar$;
>> C:\Program Files\Protege_3.4.4\lax.jar;" com.zerog.lax.LAX "C:/Program Files/Pro
>> tege_3.4.4/Protege.lax" "C:/Users/Len/AppData/Local/Temp/laxEB4C.tmp"
>> Protege 3.4.4 Build 579, JVM 1.6.0_21-b07, memory=1871M, Windows 7, encoding=UTF
>> -8, language=en, country=US
>>    
>
>So I may  know about this issue. I believe that I remember a problem 
>with install anywhere where it does not  properly handle the Windows 7 
>64-bit case.  If you start Protege without using install-anywhere (e.g. 
>by setting the right memory allocation in the run_protege.bat and 
>running that) then you won't have  this problem.
>
>This seems like it must be (??) a different problem than you originally 
>reported because in the original message  you had  said:
>
>> I have this code running inside my tab plugin:
>>
>> public static long test = Runtime.getRuntime().maxMemory()/1014;
>>      static {
>>      	System.out.println("Total memory : " +test+ " KB");
>>      }
>> }
>>
>> It results in: Total memory : 5515235 KB
>>    
>
>This is pretty much the code that Protege runs when it reports the 
>memory the following output (SystemUtilities.logSystemInfo):
>
>> Protege 3.4.4 Build 579, JVM 1.6.0_21-b07, memory=1871M, Windows 7, encoding=UTF
>> -8, language=en, country=US
>
>
>-Timothy
>
>
>>
>>
>>
>>
>>
>>
>>    
>>> How much physical memory do you have?   You can allocate more than
>>> exits, so it just swaps pages in/out.
>>> Disk light on all time after you get to that point is a clear indicator.
>>> I would guess you have only 4gb real memory, so windows can only give
>>> the process about 2.5 to 3gb before it has to swap
>>>
>>> - Stanley
>>>
>>> -----Original Message-----
>>> From: protege-discussion-bounces at lists.stanford.edu
>>> [mailto:protege-discussion-bounces at lists.stanford.edu] On Behalf Of Len
>>> Yabloko
>>> Sent: Friday, September 03, 2010 12:12 PM
>>> To: User support for Core Protege and the Protege-Frames editor
>>> Subject: Re: [protege-discussion] Protege 3.4.4 (579) 64-bit max heap
>>> size
>>>
>>> Yes, I tried all variations and seems to corrently allocate memory.
>>>
>>> I have this code running inside my tab plugin:
>>>
>>> public static long test = Runtime.getRuntime().maxMemory()/1014;
>>>     static {
>>>     	System.out.println("Total memory : " +test+ " KB");
>>>     }
>>> }
>>>
>>> It results in: Total memory : 5515235 KB
>>>
>>> Windows 7 task manager show java.exe quickly climing to about 2G and
>>> stays there. What could explain this? Do I need a specialy compiled
>>> protege.jar?
>>>
>>>      
>>>> Had you tried -Xmx6000M?
>>>>
>>>> http://download.oracle.com/javase/6/docs/technotes/tools/windows/java.h
>>>>        
>>> tml
>>>      
>>>> -Xmsn
>>>> Specify the initial size, in bytes, of the memory allocation pool. This
>>>>        
>>>      
>>>> value must be a multiple of 1024 greater than 1MB. Append the letter k
>>>> or K to indicate kilobytes, or m or M to indicate megabytes. The
>>>>        
>>> default
>>>      
>>>> value is chosen at runtime based on system configuration.
>>>>
>>>> On 9/3/2010 10:57 AM, Len Yabloko wrote:
>>>>        
>>>>> Hello everyone,
>>>>>
>>>>> I am running latest Protege Frames version on Windows 7 64-bit and
>>>>>          
>>> trying to generate a very large frame ontology by loading data from
>>> MySQL database using frame API. I have allocated 6G to jvm and checked
>>> Runtime.maxMemory() to verify that is was correctly allocated. But for
>>> some reason when memory reaches about 2.5G (according to Windows task
>>> manager) it stops allocating and loading slows after about 15,000 frames
>>> loaded. I tried launching Protege with -vmargs -Xmx6g using 64-bit jvm,
>>> but no luck so far.
>>>      
>>>>> Can someone suggest what may be a cause of such behavior?
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> protege-discussion mailing list
>>>>> protege-discussion at lists.stanford.edu
>>>>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>>>>
>>>>> Instructions for unsubscribing:
>>>>>          
>>> http://protege.stanford.edu/doc/faq.html#01a.03
>>>      
>>>>>          
>>>>
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>>>>
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>>>>        
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>>>>        
>>>
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>>>      
>>
>>
>>
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>> protege-discussion mailing list
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>>
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>>    
>
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