I am trying to do an EMM upgrade from baseline 6.2 to 6.5, in order to use the launchpad v4.
The instructions from the launchpad seems very clear, if I am using Essential OS and I am in version 6.2, as I am, I have to do a two steps upgrade, from 6.2 to 6.4 and from 6.4 to 6.5 later.
The first step worked fine, but the second did not, a NullPointerException is thrown in the console.
I have try it in windows 7 and in Lubuntu 19.04 with the same results, any idea about what could be the solution, or the error done in my process?
Thanks a lot in advance
Environment Lubuntu 19.04
Protégé 3.5
Essential Baseline Meta Model 6.2
Essential Viewer 6.2
Java: openjdk version "11.0.4"
Tomcat 9
Environment Windows 7 Professional
Protégé 3.5
Essential Baseline Meta Model 6.2
Essential Viewer 6.2
Java: java version "1.8.0_221"
Tomcat 8.5
Upgrade Instructions followed
Log for the upgrade Step 2
Error applying EMM 65 upgrade EUP file in Protégé 3.5
-
ddiegomercado
- Posts: 5
- Joined: 11 Sep 2019, 11:39
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-
jonathan.carter
- Posts: 1087
- Joined: 04 Feb 2009, 15:44
Thanks for the stack trace. We're looking into this.
Is there any more of the stack trace below line 47?
I can see where the Null Pointer exception is occurring but I think there is some more information about where this started.
Thanks
Jonathan
Is there any more of the stack trace below line 47?
I can see where the Null Pointer exception is occurring but I think there is some more information about where this started.
Thanks
Jonathan
Essential Project Team
-
jonathan.carter
- Posts: 1087
- Joined: 04 Feb 2009, 15:44
Hi,
I’ve just followed the process that you described, starting with the baseline 6.2 repository and applied the 6.2 to 6.4 upgrade pack.
This completed successfully and next, without saving the repository, I then applied the 6.4 to 6.5 upgrade pack. This took some minutes (8 minutes for the last update) to run but completed successfully.
The exception message that you’ve posted suggests a couple of options that I’d like to check with you.
I’ve just followed the process that you described, starting with the baseline 6.2 repository and applied the 6.2 to 6.4 upgrade pack.
This completed successfully and next, without saving the repository, I then applied the 6.4 to 6.5 upgrade pack. This took some minutes (8 minutes for the last update) to run but completed successfully.
The exception message that you’ve posted suggests a couple of options that I’d like to check with you.
- When you installed Protege, did you select the option to install all the suggested ‘widgets’? In particular, is the GraphWidget installed? (It should be!)
- Have you made the configuration changes to increase the Java memory for Protege? The repository itself will be pushing the out-of-the-box Protege configuration and these updates are performing a lot of operations on a large ontology. All this means that it is likely that Protege will run out of Java memory whilst performing these updates. If you haven’t already, please follow these instructions for setting the Protege memory configuration.
Essential Project Team
-
ddiegomercado
- Posts: 5
- Joined: 11 Sep 2019, 11:39
Thanks a lot Jonathan for the response, I'm going to verify and test your suggestions, I think I did a correct memory configuration, at least in windows, and all widgets were installed, but let me do a double check.
I tried to attach the full stack trace as file, but I was not able to do, let me share it as plain text in this response
FINE: Exception caught -- java.lang.NullPointerException
at edu.stanford.smi.protegex.widget.graph.GraphWidget.getValues(Unknown
Source)
at edu.stanford.smi.protege.widget.AbstractSlotWidget$1.templateFacetVal
ueChanged(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchClsEvent(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchFrameEventAsClsFacetEvent(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchEvent(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchEvents(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchEvents(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchEvents(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.set
DirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.undo.SetDirectOwnSlotValues
Command.doIt(Unknown Source)
at edu.stanford.smi.protege.model.framestore.undo.UndoFrameStore.simpleC
ommandExecute(Unknown Source)
at edu.stanford.smi.protege.model.framestore.undo.UndoFrameStore.execute
(Unknown Source)
at edu.stanford.smi.protege.model.framestore.undo.UndoFrameStore.setDire
ctOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.
setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.ChangeMonitorFrameStore.set
DirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.cleandispatch.DefaultDispat
ch.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.cleandispatch.CleanDispatch
FrameStore.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.setDirect
OwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.setDirect
OwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.DefaultKnowledgeBase.setDirectOwnSlotV
alues(Unknown Source)
at edu.stanford.smi.protege.model.DefaultKnowledgeBase.setDocumentation(
Unknown Source)
at edu.stanford.smi.protege.model.DefaultSlot.setDocumentation(Unknown S
ource)
at sun.reflect.GeneratedMethodAccessor45.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.python.core.PyReflectedFunction.__call__(Unknown Source)
at org.python.core.PyMethod.__call__(Unknown Source)
at org.python.core.PyObject.__call__(Unknown Source)
at org.python.core.PyInstance.invoke(Unknown Source)
at org.python.pycode._pyx33674.CreateSlot$1(<unknown>:7)
at org.python.pycode._pyx33674.call_function(<unknown>)
at org.python.core.PyTableCode.call(Unknown Source)
at org.python.core.PyTableCode.call(Unknown Source)
at org.python.core.PyFunction.__call__(Unknown Source)
at org.python.core.PyObject.__call__(Unknown Source)
at org.python.pycode._pyx35231.f$0(<unknown>:1)
at org.python.pycode._pyx35231.call_function(<unknown>)
at org.python.core.PyTableCode.call(Unknown Source)
at org.python.core.PyCode.call(Unknown Source)
at org.python.core.Py.runCode(Unknown Source)
at com.sun.script.jython.JythonScriptEngine.evalCode(JythonScriptEngine.
java:289)
at com.sun.script.jython.JythonScriptEngine.eval(JythonScriptEngine.java
:170)
at javax.script.AbstractScriptEngine.eval(Unknown Source)
at com.enterprise_architecture.essential.scripting.ScriptJob.execute(Scr
iptJob.java:268)
at com.enterprise_architecture.essential.update.EssentialScriptEngine.pr
ocessScript(EssentialScriptEngine.java:344)
at com.enterprise_architecture.essential.update.EssentialScriptEngine.ex
ecute(EssentialScriptEngine.java:201)
at com.enterprise_architecture.essential.update.EssentialUpdateTab$2.con
struct(EssentialUpdateTab.java:1049)
at com.enterprise_architecture.essential.update.SwingWorker$2.run(SwingW
orker.java:110)
at java.lang.Thread.run(Unknown Source)
WARNING: Exception caught java.lang.NullPointerException -- EventDispatchFrameSt
ore.dispatchEvents()
WARNING: use fine logging for more details -- EventDispatchFrameStore.dispatchEv
ents()
FINE: Exception caught -- java.lang.NullPointerException
at edu.stanford.smi.protegex.widget.graph.GraphWidget.getValues(Unknown
Source)
at edu.stanford.smi.protege.widget.AbstractSlotWidget$1.templateFacetVal
ueChanged(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchClsEvent(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchFrameEventAsClsFacetEvent(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchEvent(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchEvents(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchEvents(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchEvents(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.set
DirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.undo.SetDirectOwnSlotValues
Command.doIt(Unknown Source)
at edu.stanford.smi.protege.model.framestore.undo.UndoFrameStore.simpleC
ommandExecute(Unknown Source)
at edu.stanford.smi.protege.model.framestore.undo.UndoFrameStore.execute
(Unknown Source)
at edu.stanford.smi.protege.model.framestore.undo.UndoFrameStore.setDire
ctOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.
setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.ChangeMonitorFrameStore.set
DirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.cleandispatch.DefaultDispat
ch.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.cleandispatch.CleanDispatch
FrameStore.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.setDirect
OwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.setDirect
OwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.DefaultKnowledgeBase.setValueTypeValue
s(Unknown Source)
at edu.stanford.smi.protege.model.DefaultKnowledgeBase.setAllowedClses(U
nknown Source)
at edu.stanford.smi.protege.model.DefaultSlot.setAllowedClses(Unknown So
urce)
at sun.reflect.GeneratedMethodAccessor58.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.python.core.PyReflectedFunction.__call__(Unknown Source)
at org.python.core.PyMethod.__call__(Unknown Source)
at org.python.core.PyObject.__call__(Unknown Source)
at org.python.core.PyInstance.invoke(Unknown Source)
at org.python.pycode._pyx33842.ResetAddAllowedClass$1(<unknown>:11)
at org.python.pycode._pyx33842.call_function(<unknown>)
at org.python.core.PyTableCode.call(Unknown Source)
at org.python.core.PyTableCode.call(Unknown Source)
at org.python.core.PyFunction.__call__(Unknown Source)
at org.python.pycode._pyx35234.f$0(<unknown>:1)
at org.python.pycode._pyx35234.call_function(<unknown>)
at org.python.core.PyTableCode.call(Unknown Source)
at org.python.core.PyCode.call(Unknown Source)
at org.python.core.Py.runCode(Unknown Source)
at com.sun.script.jython.JythonScriptEngine.evalCode(JythonScriptEngine.
java:289)
at com.sun.script.jython.JythonScriptEngine.eval(JythonScriptEngine.java
:170)
at javax.script.AbstractScriptEngine.eval(Unknown Source)
at com.enterprise_architecture.essential.scripting.ScriptJob.execute(Scr
iptJob.java:268)
at com.enterprise_architecture.essential.update.EssentialScriptEngine.pr
ocessScript(EssentialScriptEngine.java:344)
at com.enterprise_architecture.essential.update.EssentialScriptEngine.ex
ecute(EssentialScriptEngine.java:201)
at com.enterprise_architecture.essential.update.EssentialUpdateTab$2.con
struct(EssentialUpdateTab.java:1049)
at com.enterprise_architecture.essential.update.SwingWorker$2.run(SwingW
orker.java:110)
at java.lang.Thread.run(Unknown Source)
WARNING: Exception caught java.lang.NullPointerException -- EventDispatchFrameSt
ore.dispatchEvents()
WARNING: use fine logging for more details -- EventDispatchFrameStore.dispatchEv
ents()
I tried to attach the full stack trace as file, but I was not able to do, let me share it as plain text in this response
FINE: Exception caught -- java.lang.NullPointerException
at edu.stanford.smi.protegex.widget.graph.GraphWidget.getValues(Unknown
Source)
at edu.stanford.smi.protege.widget.AbstractSlotWidget$1.templateFacetVal
ueChanged(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchClsEvent(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchFrameEventAsClsFacetEvent(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchEvent(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchEvents(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchEvents(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchEvents(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.set
DirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.undo.SetDirectOwnSlotValues
Command.doIt(Unknown Source)
at edu.stanford.smi.protege.model.framestore.undo.UndoFrameStore.simpleC
ommandExecute(Unknown Source)
at edu.stanford.smi.protege.model.framestore.undo.UndoFrameStore.execute
(Unknown Source)
at edu.stanford.smi.protege.model.framestore.undo.UndoFrameStore.setDire
ctOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.
setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.ChangeMonitorFrameStore.set
DirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.cleandispatch.DefaultDispat
ch.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.cleandispatch.CleanDispatch
FrameStore.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.setDirect
OwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.setDirect
OwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.DefaultKnowledgeBase.setDirectOwnSlotV
alues(Unknown Source)
at edu.stanford.smi.protege.model.DefaultKnowledgeBase.setDocumentation(
Unknown Source)
at edu.stanford.smi.protege.model.DefaultSlot.setDocumentation(Unknown S
ource)
at sun.reflect.GeneratedMethodAccessor45.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.python.core.PyReflectedFunction.__call__(Unknown Source)
at org.python.core.PyMethod.__call__(Unknown Source)
at org.python.core.PyObject.__call__(Unknown Source)
at org.python.core.PyInstance.invoke(Unknown Source)
at org.python.pycode._pyx33674.CreateSlot$1(<unknown>:7)
at org.python.pycode._pyx33674.call_function(<unknown>)
at org.python.core.PyTableCode.call(Unknown Source)
at org.python.core.PyTableCode.call(Unknown Source)
at org.python.core.PyFunction.__call__(Unknown Source)
at org.python.core.PyObject.__call__(Unknown Source)
at org.python.pycode._pyx35231.f$0(<unknown>:1)
at org.python.pycode._pyx35231.call_function(<unknown>)
at org.python.core.PyTableCode.call(Unknown Source)
at org.python.core.PyCode.call(Unknown Source)
at org.python.core.Py.runCode(Unknown Source)
at com.sun.script.jython.JythonScriptEngine.evalCode(JythonScriptEngine.
java:289)
at com.sun.script.jython.JythonScriptEngine.eval(JythonScriptEngine.java
:170)
at javax.script.AbstractScriptEngine.eval(Unknown Source)
at com.enterprise_architecture.essential.scripting.ScriptJob.execute(Scr
iptJob.java:268)
at com.enterprise_architecture.essential.update.EssentialScriptEngine.pr
ocessScript(EssentialScriptEngine.java:344)
at com.enterprise_architecture.essential.update.EssentialScriptEngine.ex
ecute(EssentialScriptEngine.java:201)
at com.enterprise_architecture.essential.update.EssentialUpdateTab$2.con
struct(EssentialUpdateTab.java:1049)
at com.enterprise_architecture.essential.update.SwingWorker$2.run(SwingW
orker.java:110)
at java.lang.Thread.run(Unknown Source)
WARNING: Exception caught java.lang.NullPointerException -- EventDispatchFrameSt
ore.dispatchEvents()
WARNING: use fine logging for more details -- EventDispatchFrameStore.dispatchEv
ents()
FINE: Exception caught -- java.lang.NullPointerException
at edu.stanford.smi.protegex.widget.graph.GraphWidget.getValues(Unknown
Source)
at edu.stanford.smi.protege.widget.AbstractSlotWidget$1.templateFacetVal
ueChanged(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchClsEvent(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchFrameEventAsClsFacetEvent(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchEvent(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchEvents(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchEvents(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dis
patchEvents(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.set
DirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.undo.SetDirectOwnSlotValues
Command.doIt(Unknown Source)
at edu.stanford.smi.protege.model.framestore.undo.UndoFrameStore.simpleC
ommandExecute(Unknown Source)
at edu.stanford.smi.protege.model.framestore.undo.UndoFrameStore.execute
(Unknown Source)
at edu.stanford.smi.protege.model.framestore.undo.UndoFrameStore.setDire
ctOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.
setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.ChangeMonitorFrameStore.set
DirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.cleandispatch.DefaultDispat
ch.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.cleandispatch.CleanDispatch
FrameStore.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.setDirect
OwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.setDirect
OwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.DefaultKnowledgeBase.setValueTypeValue
s(Unknown Source)
at edu.stanford.smi.protege.model.DefaultKnowledgeBase.setAllowedClses(U
nknown Source)
at edu.stanford.smi.protege.model.DefaultSlot.setAllowedClses(Unknown So
urce)
at sun.reflect.GeneratedMethodAccessor58.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.python.core.PyReflectedFunction.__call__(Unknown Source)
at org.python.core.PyMethod.__call__(Unknown Source)
at org.python.core.PyObject.__call__(Unknown Source)
at org.python.core.PyInstance.invoke(Unknown Source)
at org.python.pycode._pyx33842.ResetAddAllowedClass$1(<unknown>:11)
at org.python.pycode._pyx33842.call_function(<unknown>)
at org.python.core.PyTableCode.call(Unknown Source)
at org.python.core.PyTableCode.call(Unknown Source)
at org.python.core.PyFunction.__call__(Unknown Source)
at org.python.pycode._pyx35234.f$0(<unknown>:1)
at org.python.pycode._pyx35234.call_function(<unknown>)
at org.python.core.PyTableCode.call(Unknown Source)
at org.python.core.PyCode.call(Unknown Source)
at org.python.core.Py.runCode(Unknown Source)
at com.sun.script.jython.JythonScriptEngine.evalCode(JythonScriptEngine.
java:289)
at com.sun.script.jython.JythonScriptEngine.eval(JythonScriptEngine.java
:170)
at javax.script.AbstractScriptEngine.eval(Unknown Source)
at com.enterprise_architecture.essential.scripting.ScriptJob.execute(Scr
iptJob.java:268)
at com.enterprise_architecture.essential.update.EssentialScriptEngine.pr
ocessScript(EssentialScriptEngine.java:344)
at com.enterprise_architecture.essential.update.EssentialScriptEngine.ex
ecute(EssentialScriptEngine.java:201)
at com.enterprise_architecture.essential.update.EssentialUpdateTab$2.con
struct(EssentialUpdateTab.java:1049)
at com.enterprise_architecture.essential.update.SwingWorker$2.run(SwingW
orker.java:110)
at java.lang.Thread.run(Unknown Source)
WARNING: Exception caught java.lang.NullPointerException -- EventDispatchFrameSt
ore.dispatchEvents()
WARNING: use fine logging for more details -- EventDispatchFrameStore.dispatchEv
ents()
-
ddiegomercado
- Posts: 5
- Joined: 11 Sep 2019, 11:39
After doing the memory setting of protege at 2 Gb, even while the exception was thrown again, I was able to do the model update to version 6.5.
However I was not able to publish the new model after the essential viewer update (downloaded from https://github.com/essentialproject/essential_viewer), I was able to update the viewer but the model can not be published for that viewer from the protege, the trace on protege says the following:
"Rendering repository...
Sending repository snapshot...
Checking for access...
Sending XML snapshot...
Failed to send snapshot to the Report Service :
Essential Viewer ReportService encountered an internal error while receiving your repository snapshot. Contact your system administrator and check Essential Viewer server logs for errors, e.g. memory exceptions."
The tomcat memory is set to 2GB as well.
I was not able to locate other trace in protege or tomcat server, that is all the information the tool says, any idea about that?
Thanks a lot in advance.
Regards.
David.
However I was not able to publish the new model after the essential viewer update (downloaded from https://github.com/essentialproject/essential_viewer), I was able to update the viewer but the model can not be published for that viewer from the protege, the trace on protege says the following:
"Rendering repository...
Sending repository snapshot...
Checking for access...
Sending XML snapshot...
Failed to send snapshot to the Report Service :
Essential Viewer ReportService encountered an internal error while receiving your repository snapshot. Contact your system administrator and check Essential Viewer server logs for errors, e.g. memory exceptions."
The tomcat memory is set to 2GB as well.
I was not able to locate other trace in protege or tomcat server, that is all the information the tool says, any idea about that?
Thanks a lot in advance.
Regards.
David.
-
ddiegomercado
- Posts: 5
- Joined: 11 Sep 2019, 11:39
Any suggestions about the issue I have?
Thanks a lot in advance.
Regards
David.
Thanks a lot in advance.
Regards
David.
-
jonathan.carter
- Posts: 1087
- Joined: 04 Feb 2009, 15:44
Hi David,
Thanks for the stack traces. I can see that this is failing whilst trying to make a configuration change to one of the widgets in Protege. Unfortunately, I can't tell where (amongst 1000's of lines of updates) this is happening.
Have you ticked the option on the update tab to present detailed output?
Also, how have you installed Essential Open Source? The Viewer is included in the open source installer but yet you mention downloading it from Git.
If you haven't already, I recommend using the open source installer, as described in these instructions, and then try again.
I can't replicate this issue and it may be that you have an incomplete installation.
Once all the above have been reviewed, we can set the update tab into debug mode, where it writes out each line as it performs the update and we can see which line of the update pack is causing the problem:
Thanks for the stack traces. I can see that this is failing whilst trying to make a configuration change to one of the widgets in Protege. Unfortunately, I can't tell where (amongst 1000's of lines of updates) this is happening.
Have you ticked the option on the update tab to present detailed output?
Also, how have you installed Essential Open Source? The Viewer is included in the open source installer but yet you mention downloading it from Git.
If you haven't already, I recommend using the open source installer, as described in these instructions, and then try again.
I can't replicate this issue and it may be that you have an incomplete installation.
Once all the above have been reviewed, we can set the update tab into debug mode, where it writes out each line as it performs the update and we can see which line of the update pack is causing the problem:
- Stop Protege
- Open the file: <PROTEGE_INSTALL>/plugins/com.enterprise_architecture.essential.update/updatetab.properties
- Edit the updatetab.output.debugtrace property to be true (updatetab.output.debugtrace=on)
- Save the file and restart Protege
- Run the update and watch the command line trace output
Essential Project Team
-
ddiegomercado
- Posts: 5
- Joined: 11 Sep 2019, 11:39
Thanks a lot Jonathan for your support
Let me try to explain better:
I did the process of updating the model in two steps: from 6.2 to 6.4, and from 6.4 to 6.5 as indicated in the launchpad_v4 instructions. In the same document it was indicated that the model should be update one more time with the “launchpad_loader.dup” file, and later, the viewer application had to be updated from the GitHub, since the installer packaged you indicated does not have the last viewer application version. After that: Model updates in protege, and last viewer app installed, the model had to be published from the protege's viewer plugin to the viewer deployed on Tomcat, this is the final step that fails, it was started from the protege's tab “essential viewer”, not from the “essential update” tab.
Therefore, although I have enabled the traces as indicated, as these are for the update plugin, instead for the viewer plugin, I do not get any more traces, and I also cannot find the configuration for the viewer plugin
I try to attach the instructions that I am following “Essential Launchpad v4 Step-by-Step for OS Users.pdf” of the package “Essential_Launchpad_V41_IMPORT.zip”, and the photo of the plugin I am using and where it is failing
Any idea?
Best regards
David
Let me try to explain better:
I did the process of updating the model in two steps: from 6.2 to 6.4, and from 6.4 to 6.5 as indicated in the launchpad_v4 instructions. In the same document it was indicated that the model should be update one more time with the “launchpad_loader.dup” file, and later, the viewer application had to be updated from the GitHub, since the installer packaged you indicated does not have the last viewer application version. After that: Model updates in protege, and last viewer app installed, the model had to be published from the protege's viewer plugin to the viewer deployed on Tomcat, this is the final step that fails, it was started from the protege's tab “essential viewer”, not from the “essential update” tab.
Therefore, although I have enabled the traces as indicated, as these are for the update plugin, instead for the viewer plugin, I do not get any more traces, and I also cannot find the configuration for the viewer plugin
I try to attach the instructions that I am following “Essential Launchpad v4 Step-by-Step for OS Users.pdf” of the package “Essential_Launchpad_V41_IMPORT.zip”, and the photo of the plugin I am using and where it is failing
Any idea?
Best regards
David
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-
neil.walsh
- Posts: 445
- Joined: 16 Feb 2009, 13:45
- Contact:
Hi David,
We have done some work to improve the install guide and improve the downloads for open source users.
The GitHub downloads by default can't just be renamed from ZIP to WAR as they wrap the content in a folder. This is a likely cause of the issue you are experiencing. You can now however download the correctly packaged WAR directly from our site.
https://www.enterprise-architecture.org/os_download.php
We have today released version 6.7 which has many improvement and should be a lot easier to get installed.
Let me know if this resolves the issues for you
Cheers
Neil
We have done some work to improve the install guide and improve the downloads for open source users.
The GitHub downloads by default can't just be renamed from ZIP to WAR as they wrap the content in a folder. This is a likely cause of the issue you are experiencing. You can now however download the correctly packaged WAR directly from our site.
https://www.enterprise-architecture.org/os_download.php
We have today released version 6.7 which has many improvement and should be a lot easier to get installed.
Let me know if this resolves the issues for you
Cheers
Neil
I'm trying to do the update to the repository as well but encountered the same out of memory errors applying the 6.4 to 6.5 EUP upgrade. Opening the newer essential_baseline_v6.7.pprj in Protege appears to do nothing but the terminal output (see below) shows the "Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: GC overhead limit exceeded" error.
beerninr@DEV_VM7:/opt/protege$ sh run_protege.sh
DARWIN = false
JAVA_HOME = /usr/lib/jvm/java-8-openjdk-amd64
JAVA_PATH = /usr/lib/jvm/java-8-openjdk-amd64/jre/bin
Protege 3.5 Build 663, JVM 1.8.0_222-8u222-b10-1ubuntu1~16.04.1-b10, memory=466M, Linux, encoding=UTF-8, language=en, country=NZ
Loaded plugin edu.stanford.smi.protegex.owl - OWL Plugin
Loaded plugin edu.stanford.smi.protegex.pal_tabs - PAL Tabs
Loaded plugin se.liu.ida.JessTab - JessTab Plugin
Loaded plugin uk.ac.man.cs.mig.coode.debugger
Loaded plugin uk.ac.man.cs.mig.coode.owldoc
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.standard_extensions - Graph Widget, Table Widget
Loaded plugin edu.stanford.smi.protegex.chatPlugin - Chat
Loaded plugin edu.stanford.smi.protege.collab - Collaborative Protege
Loaded plugin edu.stanford.smi.protegex.changeanalysis - Change Analysis Tab
Loaded plugin edu.stanford.smi.protegex.ezpal - EZPal Tab
Loaded plugin edu.stanford.bmir.protegex.bp.ref - BioPortal Reference Plugin, BioPortal Import Plugin
Loaded plugin edu.stanford.smi.protegex.prompt - PROMPT Tab
Loaded plugin uk.ac.man.cs.mig.coode.manchesterowlsyntaxeditor
Loaded plugin dfki.protege.ontoviz
Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard - Basic Wizards
Loaded plugin com.enterprise_architecture.essential.update - Essential Update Tab
Loaded plugin edu.stanford.smi.protegex.metaanalysis - MetaAnalysis Tab
Loaded plugin uk.ac.iam.soton.akt.tgviztab - TGVizTab
Loaded plugin org.protege.owl.mappingmaster - MappingMaster Plugin
Loaded plugin com.enterprise_architecture.essential.integration.widgets - Essential Integration Tab
Loaded plugin org.protege.owl.axiome - Axiome Plugin
Loaded plugin edu.stanford.smi.protege.stringsearch - String Search Tab
Loaded plugin edu.stanford.smi.protegex.instance_tree
Loaded plugin edu.stanford.smi.protegex.datamaster - DataMaster Tab
Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard.owl - OWL Wizards
Loaded plugin com.enterprise_architecture.essential.snapshot - Essential Snapshot Tab
Loaded plugin uk.ac.man.cs.mig.coode.owlviz
Loaded plugin edu.stanford.smi.protege.script - Script Plugin
Loaded plugin edu.stanford.smi.protegex.query.lucene - LuceneQueryTab
Loaded plugin edu.stanford.smi.protegex.xml_tab - XML Tab
Loaded plugin uk.ac.man.cs.mig.coode.owlindividualstab
Loaded plugin edu.stanford.smi.protegex.facets_tab
Loaded plugin ca.uvic.cs.chisel.jambalaya - Jambalaya
Loaded plugin com.enterprise_architecture.essential.widgets - Essential Viewer Tab
Loaded plugin edu.stanford.smi.protegex.owl.inference.pellet - Protege Pellet Reasoner
Loaded 5000 instances: essential_baseline_6.5.4_ProjectKB_Class14734
Loaded 6000 instances: essential_baseline_6.5.4_ProjectKB_Class15490
Loaded 7000 instances: essential_baseline_6.5.4_ProjectKB_Class16725
Set type on 5000 instances: essential_baseline_6.5.4_ProjectKB_Class17070
Loaded 8000 instances: essential_baseline_6.5.4_ProjectKB_Class17558
Set type on 6000 instances: essential_baseline_6.5.4_ProjectKB_Class18082
Loaded 9000 instances: essential_baseline_6.5.4_ProjectKB_Class18498
Set type on 7000 instances: essential_baseline_6.5.4_ProjectKB_Class19110
Loaded 10000 instances: essential_baseline_6.5.4_ProjectKB_Class19577
Set type on 8000 instances: essential_baseline_6.5.4_ProjectKB_Class20126
Loaded 11000 instances: essential_baseline_6.5.4_ProjectKB_Class20614
Set type on 9000 instances: essential_baseline_6.5.4_ProjectKB_Class21338
Loaded 12000 instances: essential_baseline_6.5.4_ProjectKB_Class21613
Set type on 10000 instances: essential_baseline_6.5.4_ProjectKB_Class22361
Loaded 13000 instances: essential_baseline_6.5.4_ProjectKB_Class22689
Set type on 11000 instances: essential_baseline_6.5.4_ProjectKB_Class23418
Loaded 14000 instances: essential_baseline_6.5.4_ProjectKB_Class23612
Set type on 12000 instances: essential_baseline_6.5.4_ProjectKB_Class24434
Loaded 15000 instances: essential_baseline_6.5.4_ProjectKB_Class24820
Set type on 13000 instances: essential_baseline_6.5.4_ProjectKB_Class25445
Loaded 16000 instances: essential_baseline_6.5.4_ProjectKB_Class25621
Set type on 14000 instances: essential_baseline_6.5.4_ProjectKB_Class26477
Loaded 17000 instances: essential_baseline_6.5.4_ProjectKB_Class26651
Set type on 15000 instances: essential_baseline_6.5.4_ProjectKB_Class27493
Loaded 18000 instances: essential_baseline_6.5.4_ProjectKB_Class27566
Loaded 19000 instances: essential_baseline_v1.1_ProjectKB_Class3936
Set type on 16000 instances: essential_baseline_v1.2_ProjectKB_Class16170
Loaded 20000 instances: essential_baseline_v1.2_ProjectKB_Class16648
Set type on 17000 instances: essential_baseline_v1.2_ProjectKB_Class17330
Loaded 21000 instances: essential_baseline_v1.2_ProjectKB_Class17685
Set type on 18000 instances: essential_baseline_v1.2_ProjectKB_Class18577
Loaded 22000 instances: essential_baseline_v1.2_ProjectKB_Class18629
Loaded 23000 instances: essential_baseline_v1.2_ProjectKB_Class19630
Set type on 19000 instances: essential_baseline_v1.2_ProjectKB_Class19687
Loaded 24000 instances: essential_baseline_v3.0.4_ProjectKB_Class15365
Set type on 20000 instances: essential_baseline_v1_ProjectKB_Instance_122
Loaded 25000 instances: essential_baseline_v1_ProjectKB_Instance_2124
Loaded 26000 instances: essential_baseline_v1_ProjectKB_Instance_24010
Set type on 21000 instances: essential_baseline_v1_ProjectKB_Instance_24041
Loaded 27000 instances: viewer3_dev_12032012_ProjectKB_Class12906
Set type on 22000 instances: essential_baseline_v1_ProjectKB_Instance_30472
Loaded 28000 instances: essential_baseline_v4.0_ProjectKB_Class25644
Set type on 23000 instances: essential_baseline_v1_ProjectKB_Instance_31922
Loaded 29000 instances: essential_baseline_v1_ProjectKB_Instance_33013
Loaded 30000 instances: essential_baseline_v1_ProjectKB_Instance_35615
Set type on 24000 instances: essential_baseline_v1_ProjectKB_Instance_36854
Loaded 31000 instances: essential_baseline_v1_ProjectKB_Instance_43358
Set type on 25000 instances: essential_baseline_v1_ProjectKB_Instance_4552
Loaded 32000 instances: essential_baseline_v3.0_ProjectKB_Class25232
Set type on 26000 instances: essential_baseline_v1_ProjectKB_Instance_49829
Loaded 33000 instances: store_1_ProjectKB_Class7103
Loaded 34000 instances: essential_baseline_v1_ProjectKB_Instance_5578
Set type on 27000 instances: essential_baseline_v1_ProjectKB_Instance_56372
Loaded 35000 instances: essential_baseline_v1_ProjectKB_Instance_57970
Set type on 28000 instances: essential_baseline_v1_ProjectKB_Instance_58401
Loaded 36000 instances: essential_baseline_v1_ProjectKB_Instance_61716
Set type on 29000 instances: essential_baseline_v1_ProjectKB_Instance_66060
Loaded 37000 instances: essential_baseline_v2.0_ProjectKB_Class114104
Loaded 38000 instances: essential_baseline_v1_ProjectKB_Instance_70100
Set type on 30000 instances: essential_baseline_v1_ProjectKB_Instance_70236
Loaded 39000 instances: essential_baseline_v2.0_ProjectKB_Class10011
Set type on 31000 instances: essential_baseline_v2.0_ProjectKB_Class10788
Loaded 40000 instances: viewer3_dev_12032012_ProjectKB_Class16872
Set type on 32000 instances: essential_baseline_v2.0_ProjectKB_Class12186
Loaded 41000 instances: store_1_ProjectKB_Class2666
Set type on 33000 instances: essential_baseline_v2.0_ProjectKB_Class136090
Loaded 42000 instances: essential_baseline_v2.0_ProjectKB_Class136140
Loaded 43000 instances: essential_baseline_v2.0_ProjectKB_Class145412
Set type on 34000 instances: essential_baseline_v2.0_ProjectKB_Class145432
Loaded 44000 instances: store_1_ProjectKB_Class710
Set type on 35000 instances: essential_baseline_v2.0_ProjectKB_Class22242
Loaded 45000 instances: essential_baseline_v64_ProjectKB_Class16171
Set type on 36000 instances: essential_baseline_v2.0_ProjectKB_Class2332
Loaded 46000 instances: essential_baseline_v2.0_ProjectKB_Class27128
Set type on 37000 instances: essential_baseline_v2.0_ProjectKB_Class27528
Loaded 47000 instances: essential_baseline_v2.0_ProjectKB_Class28125
Set type on 38000 instances: essential_baseline_v2.0_ProjectKB_Class28752
Loaded 48000 instances: essential_baseline_v2.0_ProjectKB_Class29288
Set type on 39000 instances: essential_baseline_v2.0_ProjectKB_Class29832
Loaded 49000 instances: essential_baseline_v2.0_ProjectKB_Class3222
Set type on 40000 instances: essential_baseline_v2.0_ProjectKB_Class41993
Loaded 50000 instances: essential_baseline_v2.0_ProjectKB_Class42241
Set type on 41000 instances: essential_baseline_v2.0_ProjectKB_Class45639
Loaded 51000 instances: essential_baseline_v2.0_ProjectKB_Class45716
Loaded 52000 instances: essential_baseline_v2.0_ProjectKB_Class46645
Set type on 42000 instances: essential_baseline_v2.0_ProjectKB_Class46707
Loaded 53000 instances: essential_baseline_v2.0_ProjectKB_Class4918
Set type on 43000 instances: essential_baseline_v2.0_ProjectKB_Class5081
Loaded 54000 instances: essential_baseline_v2.0_ProjectKB_Class5415
Set type on 44000 instances: essential_baseline_v2.0_ProjectKB_Class5636
Loaded 55000 instances: store_1_ProjectKB_Class3709
Set type on 45000 instances: essential_baseline_v2.0_ProjectKB_Class6239
Loaded 56000 instances: essential_baseline_v2.0_ProjectKB_Class71892
Set type on 46000 instances: essential_baseline_v2.0_ProjectKB_Class71960
Loaded 57000 instances: essential_baseline_v2.0_ProjectKB_Class8108
Set type on 47000 instances: essential_baseline_v2.0_ProjectKB_Class81878
Set type on 48000 instances: essential_baseline_v2.0_ProjectKB_Class9079
Loaded 58000 instances: essential_baseline_v2.0_ProjectKB_Class9125
Set type on 49000 instances: essential_baseline_v2.0_ProjectKB_Class9841
Loaded 59000 instances: essential_baseline_v2.0_ProjectKB_Class9934
Loaded 60000 instances: store_1_ProjectKB_Class6649
Set type on 50000 instances: essential_baseline_v3.0.3_ProjectKB_Class14085
Loaded 61000 instances: essential_baseline_v3.0.4_ProjectKB_Class10894
Set type on 51000 instances: essential_baseline_v3.0.3_ProjectKB_Class72200
Loaded 62000 instances: essential_baseline_v3.0.3_ProjectKB_Class79440
Loaded 63000 instances: essential_baseline_v3.0.4_ProjectKB_Class11931
Set type on 52000 instances: essential_baseline_v3.0.4_ProjectKB_Class12283
Loaded 64000 instances: store_1_ProjectKB_Class5403
Set type on 53000 instances: essential_baseline_v3.0.4_ProjectKB_Class13304
Loaded 65000 instances: essential_baseline_v5_ProjectKB_Class20050
Loaded 66000 instances: essential_baseline_v3.0.4_ProjectKB_Class16416
Loaded 67000 instances: essential_baseline_v64_ProjectKB_Class23398
Loaded 68000 instances: essential_baseline_v3.0.4_ProjectKB_Class14138
Set type on 54000 instances: essential_baseline_v3.0.4_ProjectKB_Class14341
Loaded 69000 instances: essential_baseline_v3.0.4_ProjectKB_Class15056
Set type on 55000 instances: essential_baseline_v3.0.4_ProjectKB_Class15369
Set type on 56000 instances: essential_baseline_v3.0.4_ProjectKB_Class16394
Loaded 70000 instances: essential_baseline_v3.0.4_ProjectKB_Class2387
Set type on 57000 instances: essential_baseline_v3.0.4_ProjectKB_Class2423
Loaded 71000 instances: essential_baseline_v3.0.4_ProjectKB_Class3627
Loaded 72000 instances: essential_baseline_v3.0.4_ProjectKB_Class4699
Loaded 73000 instances: essential_baseline_v3.0.4_ProjectKB_Class5795
Loaded 74000 instances: essential_baseline_v3.0.4_ProjectKB_Class6833
Set type on 58000 instances: essential_baseline_v3.0.4_ProjectKB_Class7452
Loaded 75000 instances: essential_baseline_v3.0.4_ProjectKB_Class8497
Loaded 76000 instances: essential_baseline_v3.0.4_ProjectKB_Class9486
Set type on 59000 instances: essential_baseline_v3.0.6_ProjectKB_Class19527
Loaded 77000 instances: essential_baseline_v3.0.6_ProjectKB_Class19957
Set type on 60000 instances: essential_baseline_v3.0.6_ProjectKB_Class20549
Loaded 78000 instances: essential_baseline_v3.0.6_ProjectKB_Class20875
Set type on 61000 instances: essential_baseline_v3.0_ProjectKB_Class17288
Loaded 79000 instances: essential_baseline_v3.0_ProjectKB_Class17466
Set type on 62000 instances: essential_baseline_v3.0_ProjectKB_Class22080
Loaded 80000 instances: essential_baseline_v3.0_ProjectKB_Class2283
Set type on 63000 instances: essential_baseline_v3.0_ProjectKB_Class23405
Loaded 81000 instances: essential_baseline_v3.0_ProjectKB_Class23534
Set type on 64000 instances: essential_baseline_v3.0_ProjectKB_Class24553
Loaded 82000 instances: essential_baseline_v3.0_ProjectKB_Class24638
Set type on 65000 instances: essential_baseline_v3.0_ProjectKB_Class25623
Loaded 83000 instances: essential_baseline_v3.0_ProjectKB_Class25735
Set type on 66000 instances: essential_baseline_v3.0_ProjectKB_Class26716
Loaded 84000 instances: essential_baseline_v3.0_ProjectKB_Class26912
Set type on 67000 instances: essential_baseline_v3.5_ProjectKB_Class10213
Loaded 85000 instances: essential_baseline_v3.5_ProjectKB_Class10457
Set type on 68000 instances: essential_baseline_v3.5_ProjectKB_Class11228
Loaded 86000 instances: essential_baseline_v3.5_ProjectKB_Class11334
Loaded 87000 instances: essential_baseline_v3.5_ProjectKB_Class12159
Set type on 69000 instances: essential_baseline_v3.5_ProjectKB_Class12278
Loaded 88000 instances: essential_baseline_v3.5_ProjectKB_Class12931
Set type on 70000 instances: essential_baseline_v3.5_ProjectKB_Class13302
Loaded 89000 instances: essential_baseline_v3.5_ProjectKB_Class13834
Set type on 71000 instances: essential_baseline_v3.5_ProjectKB_Class14318
Loaded 90000 instances: essential_baseline_v3.5_ProjectKB_Class1892
Set type on 72000 instances: essential_baseline_v3.5_ProjectKB_Class2475
Loaded 91000 instances: essential_baseline_v3.5_ProjectKB_Class2843
Set type on 73000 instances: essential_baseline_v3.5_ProjectKB_Class3528
Loaded 92000 instances: essential_baseline_v3.5_ProjectKB_Class3736
Loaded 93000 instances: essential_baseline_v3.5_ProjectKB_Class4527
Set type on 74000 instances: essential_baseline_v3.5_ProjectKB_Class4575
Loaded 94000 instances: essential_baseline_v3.5_ProjectKB_Class5397
Set type on 75000 instances: essential_baseline_v3.5_ProjectKB_Class5605
Loaded 95000 instances: essential_baseline_v3.5_ProjectKB_Class6300
Set type on 76000 instances: essential_baseline_v3.5_ProjectKB_Class6630
Loaded 96000 instances: essential_baseline_v3.5_ProjectKB_Class7205
Set type on 77000 instances: essential_baseline_v3.5_ProjectKB_Class7645
Loaded 97000 instances: essential_baseline_v3.5_ProjectKB_Class8068
Set type on 78000 instances: essential_baseline_v3.5_ProjectKB_Class8660
Loaded 98000 instances: essential_baseline_v3.5_ProjectKB_Class8921
Set type on 79000 instances: essential_baseline_v3.5_ProjectKB_Class9681
Loaded 99000 instances: essential_baseline_v3.5_ProjectKB_Class9783
Loaded 100000 instances: essential_baseline_v62_ProjectKB_Class16980
Set type on 80000 instances: essential_baseline_v4.0_ProjectKB_Class26040
Loaded 101000 instances: essential_baseline_v4.0_ProjectKB_Class26535
Set type on 81000 instances: essential_baseline_v4.0_ProjectKB_Class27048
Loaded 102000 instances: essential_baseline_v4.0_ProjectKB_Class27061
Loaded 103000 instances: essential_baseline_v4.0_ProjectKB_Class31873
Set type on 82000 instances: essential_baseline_v4.0_ProjectKB_Class32264
Loaded 104000 instances: essential_baseline_v4.0_ProjectKB_Class32954
Set type on 83000 instances: essential_baseline_v4.3.1_ProjectKB_Class1915
Loaded 105000 instances: essential_baseline_v4.3.1_ProjectKB_Class2747
Set type on 84000 instances: essential_baseline_v4.3.1_ProjectKB_Class2952
Loaded 106000 instances: essential_baseline_v4.3.1_ProjectKB_Class4089
Set type on 85000 instances: essential_baseline_v4.3.1_ProjectKB_Class4121
Loaded 107000 instances: essential_baseline_v4.3.1_ProjectKB_Class5061
Set type on 86000 instances: essential_baseline_v4.3.1_ProjectKB_Class5139
Loaded 108000 instances: essential_baseline_v4.3.1_ProjectKB_Class6073
Set type on 87000 instances: essential_baseline_v4.3_ProjectKB_Class1886
Set type on 88000 instances: essential_baseline_v505_ProjectKB_Class11305
Loaded 109000 instances: essential_baseline_v505_ProjectKB_Class11379
Set type on 89000 instances: essential_baseline_v505_ProjectKB_Class12721
Loaded 110000 instances: essential_baseline_v505_ProjectKB_Class13086
Set type on 90000 instances: essential_baseline_v505_ProjectKB_Class13849
Loaded 111000 instances: essential_baseline_v505_ProjectKB_Class14269
Set type on 91000 instances: essential_baseline_v505_ProjectKB_Class2335
Loaded 112000 instances: essential_baseline_v505_ProjectKB_Class2712
Set type on 92000 instances: essential_baseline_v505_ProjectKB_Class3445
Loaded 113000 instances: essential_baseline_v505_ProjectKB_Class3807
Set type on 93000 instances: essential_baseline_v505_ProjectKB_Class4550
Loaded 114000 instances: essential_baseline_v505_ProjectKB_Class5017
Set type on 94000 instances: essential_baseline_v505_ProjectKB_Class5830
Loaded 115000 instances: essential_baseline_v505_ProjectKB_Class6767
Set type on 95000 instances: essential_baseline_v505_ProjectKB_Class7070
Loaded 116000 instances: essential_baseline_v505_ProjectKB_Class8150
Set type on 96000 instances: essential_baseline_v505_ProjectKB_Class8313
Set type on 97000 instances: essential_baseline_v505_ProjectKB_Class9518
Loaded 117000 instances: essential_baseline_v505_ProjectKB_Class9569
Loaded 118000 instances: essential_baseline_v5_ProjectKB_Class16801
Set type on 98000 instances: essential_baseline_v5_ProjectKB_Class16844
Loaded 119000 instances: essential_baseline_v5_ProjectKB_Class17829
Set type on 99000 instances: essential_baseline_v5_ProjectKB_Class17858
Set type on 100000 instances: essential_baseline_v5_ProjectKB_Class18854
Loaded 120000 instances: essential_baseline_v5_ProjectKB_Class1910
Set type on 101000 instances: essential_baseline_v5_ProjectKB_Class19787
Loaded 121000 instances: essential_baseline_v5_ProjectKB_Class19871
Loaded 122000 instances: essential_baseline_v5_ProjectKB_Class2602
Set type on 102000 instances: essential_baseline_v5_ProjectKB_Class2757
Loaded 123000 instances: essential_baseline_v5_ProjectKB_Class3787
Set type on 103000 instances: essential_baseline_v5_ProjectKB_Class3775
Loaded 124000 instances: essential_baseline_v5_ProjectKB_Class4828
Set type on 104000 instances: essential_baseline_v5_ProjectKB_Class4797
Set type on 105000 instances: essential_baseline_v5_ProjectKB_Class5810
Loaded 125000 instances: essential_baseline_v5_ProjectKB_Class5873
Set type on 106000 instances: essential_baseline_v62_ProjectKB_Class12486
Loaded 126000 instances: essential_baseline_v62_ProjectKB_Class12815
Set type on 107000 instances: essential_baseline_v62_ProjectKB_Class13497
Loaded 127000 instances: essential_baseline_v62_ProjectKB_Class13735
Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.util.HashMap.resize(HashMap.java:704)
at java.util.HashMap.putVal(HashMap.java:629)
at java.util.HashMap.put(HashMap.java:612)
at java.util.HashSet.add(HashSet.java:220)
at edu.stanford.smi.protege.model.framestore.InMemoryFrameDb.addRecord(Unknown Source)
at edu.stanford.smi.protege.model.framestore.InMemoryFrameDb.addRecord(Unknown Source)
at edu.stanford.smi.protege.model.framestore.InMemoryFrameDb.createRecord(Unknown Source)
at edu.stanford.smi.protege.model.framestore.InMemoryFrameDb.setValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.MergingNarrowFrameStore.setValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.ClosureCachingBasicFrameStore.setValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.ImmutableNamesNarrowFrameStore.setValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.SimpleFrameStore.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.ChangeMonitorFrameStore.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.cleandispatch.DefaultDispatch.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.cleandispatch.CleanDispatchFrameStore.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.DefaultKnowledgeBase.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.DefaultKnowledgeBase.setOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.DefaultFrame.setOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.storage.clips.Parser.slotValue(Unknown Source)
at edu.stanford.smi.protege.storage.clips.Parser.instance(Unknown Source)
at edu.stanford.smi.protege.storage.clips.Parser.parseKnowledgeBase(Unknown Source)
at edu.stanford.smi.protege.storage.clips.Parser.loadInstances(Unknown Source)
at edu.stanford.smi.protege.storage.clips.ClipsKnowledgeBaseFactory.loadKnowledgeBase(Unknown Source)
at edu.stanford.smi.protege.model.Project.loadProjectKB(Unknown Source)
at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
at edu.stanford.smi.protege.model.Project.loadProjectFromURI(Unknown Source)
at edu.stanford.smi.protege.util.ProjectChooser.loadProject(Unknown Source)
beerninr@DEV_VM7:/opt/protege$
beerninr@DEV_VM7:/opt/protege$ sh run_protege.sh
DARWIN = false
JAVA_HOME = /usr/lib/jvm/java-8-openjdk-amd64
JAVA_PATH = /usr/lib/jvm/java-8-openjdk-amd64/jre/bin
Protege 3.5 Build 663, JVM 1.8.0_222-8u222-b10-1ubuntu1~16.04.1-b10, memory=466M, Linux, encoding=UTF-8, language=en, country=NZ
Loaded plugin edu.stanford.smi.protegex.owl - OWL Plugin
Loaded plugin edu.stanford.smi.protegex.pal_tabs - PAL Tabs
Loaded plugin se.liu.ida.JessTab - JessTab Plugin
Loaded plugin uk.ac.man.cs.mig.coode.debugger
Loaded plugin uk.ac.man.cs.mig.coode.owldoc
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.standard_extensions - Graph Widget, Table Widget
Loaded plugin edu.stanford.smi.protegex.chatPlugin - Chat
Loaded plugin edu.stanford.smi.protege.collab - Collaborative Protege
Loaded plugin edu.stanford.smi.protegex.changeanalysis - Change Analysis Tab
Loaded plugin edu.stanford.smi.protegex.ezpal - EZPal Tab
Loaded plugin edu.stanford.bmir.protegex.bp.ref - BioPortal Reference Plugin, BioPortal Import Plugin
Loaded plugin edu.stanford.smi.protegex.prompt - PROMPT Tab
Loaded plugin uk.ac.man.cs.mig.coode.manchesterowlsyntaxeditor
Loaded plugin dfki.protege.ontoviz
Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard - Basic Wizards
Loaded plugin com.enterprise_architecture.essential.update - Essential Update Tab
Loaded plugin edu.stanford.smi.protegex.metaanalysis - MetaAnalysis Tab
Loaded plugin uk.ac.iam.soton.akt.tgviztab - TGVizTab
Loaded plugin org.protege.owl.mappingmaster - MappingMaster Plugin
Loaded plugin com.enterprise_architecture.essential.integration.widgets - Essential Integration Tab
Loaded plugin org.protege.owl.axiome - Axiome Plugin
Loaded plugin edu.stanford.smi.protege.stringsearch - String Search Tab
Loaded plugin edu.stanford.smi.protegex.instance_tree
Loaded plugin edu.stanford.smi.protegex.datamaster - DataMaster Tab
Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard.owl - OWL Wizards
Loaded plugin com.enterprise_architecture.essential.snapshot - Essential Snapshot Tab
Loaded plugin uk.ac.man.cs.mig.coode.owlviz
Loaded plugin edu.stanford.smi.protege.script - Script Plugin
Loaded plugin edu.stanford.smi.protegex.query.lucene - LuceneQueryTab
Loaded plugin edu.stanford.smi.protegex.xml_tab - XML Tab
Loaded plugin uk.ac.man.cs.mig.coode.owlindividualstab
Loaded plugin edu.stanford.smi.protegex.facets_tab
Loaded plugin ca.uvic.cs.chisel.jambalaya - Jambalaya
Loaded plugin com.enterprise_architecture.essential.widgets - Essential Viewer Tab
Loaded plugin edu.stanford.smi.protegex.owl.inference.pellet - Protege Pellet Reasoner
Loaded 5000 instances: essential_baseline_6.5.4_ProjectKB_Class14734
Loaded 6000 instances: essential_baseline_6.5.4_ProjectKB_Class15490
Loaded 7000 instances: essential_baseline_6.5.4_ProjectKB_Class16725
Set type on 5000 instances: essential_baseline_6.5.4_ProjectKB_Class17070
Loaded 8000 instances: essential_baseline_6.5.4_ProjectKB_Class17558
Set type on 6000 instances: essential_baseline_6.5.4_ProjectKB_Class18082
Loaded 9000 instances: essential_baseline_6.5.4_ProjectKB_Class18498
Set type on 7000 instances: essential_baseline_6.5.4_ProjectKB_Class19110
Loaded 10000 instances: essential_baseline_6.5.4_ProjectKB_Class19577
Set type on 8000 instances: essential_baseline_6.5.4_ProjectKB_Class20126
Loaded 11000 instances: essential_baseline_6.5.4_ProjectKB_Class20614
Set type on 9000 instances: essential_baseline_6.5.4_ProjectKB_Class21338
Loaded 12000 instances: essential_baseline_6.5.4_ProjectKB_Class21613
Set type on 10000 instances: essential_baseline_6.5.4_ProjectKB_Class22361
Loaded 13000 instances: essential_baseline_6.5.4_ProjectKB_Class22689
Set type on 11000 instances: essential_baseline_6.5.4_ProjectKB_Class23418
Loaded 14000 instances: essential_baseline_6.5.4_ProjectKB_Class23612
Set type on 12000 instances: essential_baseline_6.5.4_ProjectKB_Class24434
Loaded 15000 instances: essential_baseline_6.5.4_ProjectKB_Class24820
Set type on 13000 instances: essential_baseline_6.5.4_ProjectKB_Class25445
Loaded 16000 instances: essential_baseline_6.5.4_ProjectKB_Class25621
Set type on 14000 instances: essential_baseline_6.5.4_ProjectKB_Class26477
Loaded 17000 instances: essential_baseline_6.5.4_ProjectKB_Class26651
Set type on 15000 instances: essential_baseline_6.5.4_ProjectKB_Class27493
Loaded 18000 instances: essential_baseline_6.5.4_ProjectKB_Class27566
Loaded 19000 instances: essential_baseline_v1.1_ProjectKB_Class3936
Set type on 16000 instances: essential_baseline_v1.2_ProjectKB_Class16170
Loaded 20000 instances: essential_baseline_v1.2_ProjectKB_Class16648
Set type on 17000 instances: essential_baseline_v1.2_ProjectKB_Class17330
Loaded 21000 instances: essential_baseline_v1.2_ProjectKB_Class17685
Set type on 18000 instances: essential_baseline_v1.2_ProjectKB_Class18577
Loaded 22000 instances: essential_baseline_v1.2_ProjectKB_Class18629
Loaded 23000 instances: essential_baseline_v1.2_ProjectKB_Class19630
Set type on 19000 instances: essential_baseline_v1.2_ProjectKB_Class19687
Loaded 24000 instances: essential_baseline_v3.0.4_ProjectKB_Class15365
Set type on 20000 instances: essential_baseline_v1_ProjectKB_Instance_122
Loaded 25000 instances: essential_baseline_v1_ProjectKB_Instance_2124
Loaded 26000 instances: essential_baseline_v1_ProjectKB_Instance_24010
Set type on 21000 instances: essential_baseline_v1_ProjectKB_Instance_24041
Loaded 27000 instances: viewer3_dev_12032012_ProjectKB_Class12906
Set type on 22000 instances: essential_baseline_v1_ProjectKB_Instance_30472
Loaded 28000 instances: essential_baseline_v4.0_ProjectKB_Class25644
Set type on 23000 instances: essential_baseline_v1_ProjectKB_Instance_31922
Loaded 29000 instances: essential_baseline_v1_ProjectKB_Instance_33013
Loaded 30000 instances: essential_baseline_v1_ProjectKB_Instance_35615
Set type on 24000 instances: essential_baseline_v1_ProjectKB_Instance_36854
Loaded 31000 instances: essential_baseline_v1_ProjectKB_Instance_43358
Set type on 25000 instances: essential_baseline_v1_ProjectKB_Instance_4552
Loaded 32000 instances: essential_baseline_v3.0_ProjectKB_Class25232
Set type on 26000 instances: essential_baseline_v1_ProjectKB_Instance_49829
Loaded 33000 instances: store_1_ProjectKB_Class7103
Loaded 34000 instances: essential_baseline_v1_ProjectKB_Instance_5578
Set type on 27000 instances: essential_baseline_v1_ProjectKB_Instance_56372
Loaded 35000 instances: essential_baseline_v1_ProjectKB_Instance_57970
Set type on 28000 instances: essential_baseline_v1_ProjectKB_Instance_58401
Loaded 36000 instances: essential_baseline_v1_ProjectKB_Instance_61716
Set type on 29000 instances: essential_baseline_v1_ProjectKB_Instance_66060
Loaded 37000 instances: essential_baseline_v2.0_ProjectKB_Class114104
Loaded 38000 instances: essential_baseline_v1_ProjectKB_Instance_70100
Set type on 30000 instances: essential_baseline_v1_ProjectKB_Instance_70236
Loaded 39000 instances: essential_baseline_v2.0_ProjectKB_Class10011
Set type on 31000 instances: essential_baseline_v2.0_ProjectKB_Class10788
Loaded 40000 instances: viewer3_dev_12032012_ProjectKB_Class16872
Set type on 32000 instances: essential_baseline_v2.0_ProjectKB_Class12186
Loaded 41000 instances: store_1_ProjectKB_Class2666
Set type on 33000 instances: essential_baseline_v2.0_ProjectKB_Class136090
Loaded 42000 instances: essential_baseline_v2.0_ProjectKB_Class136140
Loaded 43000 instances: essential_baseline_v2.0_ProjectKB_Class145412
Set type on 34000 instances: essential_baseline_v2.0_ProjectKB_Class145432
Loaded 44000 instances: store_1_ProjectKB_Class710
Set type on 35000 instances: essential_baseline_v2.0_ProjectKB_Class22242
Loaded 45000 instances: essential_baseline_v64_ProjectKB_Class16171
Set type on 36000 instances: essential_baseline_v2.0_ProjectKB_Class2332
Loaded 46000 instances: essential_baseline_v2.0_ProjectKB_Class27128
Set type on 37000 instances: essential_baseline_v2.0_ProjectKB_Class27528
Loaded 47000 instances: essential_baseline_v2.0_ProjectKB_Class28125
Set type on 38000 instances: essential_baseline_v2.0_ProjectKB_Class28752
Loaded 48000 instances: essential_baseline_v2.0_ProjectKB_Class29288
Set type on 39000 instances: essential_baseline_v2.0_ProjectKB_Class29832
Loaded 49000 instances: essential_baseline_v2.0_ProjectKB_Class3222
Set type on 40000 instances: essential_baseline_v2.0_ProjectKB_Class41993
Loaded 50000 instances: essential_baseline_v2.0_ProjectKB_Class42241
Set type on 41000 instances: essential_baseline_v2.0_ProjectKB_Class45639
Loaded 51000 instances: essential_baseline_v2.0_ProjectKB_Class45716
Loaded 52000 instances: essential_baseline_v2.0_ProjectKB_Class46645
Set type on 42000 instances: essential_baseline_v2.0_ProjectKB_Class46707
Loaded 53000 instances: essential_baseline_v2.0_ProjectKB_Class4918
Set type on 43000 instances: essential_baseline_v2.0_ProjectKB_Class5081
Loaded 54000 instances: essential_baseline_v2.0_ProjectKB_Class5415
Set type on 44000 instances: essential_baseline_v2.0_ProjectKB_Class5636
Loaded 55000 instances: store_1_ProjectKB_Class3709
Set type on 45000 instances: essential_baseline_v2.0_ProjectKB_Class6239
Loaded 56000 instances: essential_baseline_v2.0_ProjectKB_Class71892
Set type on 46000 instances: essential_baseline_v2.0_ProjectKB_Class71960
Loaded 57000 instances: essential_baseline_v2.0_ProjectKB_Class8108
Set type on 47000 instances: essential_baseline_v2.0_ProjectKB_Class81878
Set type on 48000 instances: essential_baseline_v2.0_ProjectKB_Class9079
Loaded 58000 instances: essential_baseline_v2.0_ProjectKB_Class9125
Set type on 49000 instances: essential_baseline_v2.0_ProjectKB_Class9841
Loaded 59000 instances: essential_baseline_v2.0_ProjectKB_Class9934
Loaded 60000 instances: store_1_ProjectKB_Class6649
Set type on 50000 instances: essential_baseline_v3.0.3_ProjectKB_Class14085
Loaded 61000 instances: essential_baseline_v3.0.4_ProjectKB_Class10894
Set type on 51000 instances: essential_baseline_v3.0.3_ProjectKB_Class72200
Loaded 62000 instances: essential_baseline_v3.0.3_ProjectKB_Class79440
Loaded 63000 instances: essential_baseline_v3.0.4_ProjectKB_Class11931
Set type on 52000 instances: essential_baseline_v3.0.4_ProjectKB_Class12283
Loaded 64000 instances: store_1_ProjectKB_Class5403
Set type on 53000 instances: essential_baseline_v3.0.4_ProjectKB_Class13304
Loaded 65000 instances: essential_baseline_v5_ProjectKB_Class20050
Loaded 66000 instances: essential_baseline_v3.0.4_ProjectKB_Class16416
Loaded 67000 instances: essential_baseline_v64_ProjectKB_Class23398
Loaded 68000 instances: essential_baseline_v3.0.4_ProjectKB_Class14138
Set type on 54000 instances: essential_baseline_v3.0.4_ProjectKB_Class14341
Loaded 69000 instances: essential_baseline_v3.0.4_ProjectKB_Class15056
Set type on 55000 instances: essential_baseline_v3.0.4_ProjectKB_Class15369
Set type on 56000 instances: essential_baseline_v3.0.4_ProjectKB_Class16394
Loaded 70000 instances: essential_baseline_v3.0.4_ProjectKB_Class2387
Set type on 57000 instances: essential_baseline_v3.0.4_ProjectKB_Class2423
Loaded 71000 instances: essential_baseline_v3.0.4_ProjectKB_Class3627
Loaded 72000 instances: essential_baseline_v3.0.4_ProjectKB_Class4699
Loaded 73000 instances: essential_baseline_v3.0.4_ProjectKB_Class5795
Loaded 74000 instances: essential_baseline_v3.0.4_ProjectKB_Class6833
Set type on 58000 instances: essential_baseline_v3.0.4_ProjectKB_Class7452
Loaded 75000 instances: essential_baseline_v3.0.4_ProjectKB_Class8497
Loaded 76000 instances: essential_baseline_v3.0.4_ProjectKB_Class9486
Set type on 59000 instances: essential_baseline_v3.0.6_ProjectKB_Class19527
Loaded 77000 instances: essential_baseline_v3.0.6_ProjectKB_Class19957
Set type on 60000 instances: essential_baseline_v3.0.6_ProjectKB_Class20549
Loaded 78000 instances: essential_baseline_v3.0.6_ProjectKB_Class20875
Set type on 61000 instances: essential_baseline_v3.0_ProjectKB_Class17288
Loaded 79000 instances: essential_baseline_v3.0_ProjectKB_Class17466
Set type on 62000 instances: essential_baseline_v3.0_ProjectKB_Class22080
Loaded 80000 instances: essential_baseline_v3.0_ProjectKB_Class2283
Set type on 63000 instances: essential_baseline_v3.0_ProjectKB_Class23405
Loaded 81000 instances: essential_baseline_v3.0_ProjectKB_Class23534
Set type on 64000 instances: essential_baseline_v3.0_ProjectKB_Class24553
Loaded 82000 instances: essential_baseline_v3.0_ProjectKB_Class24638
Set type on 65000 instances: essential_baseline_v3.0_ProjectKB_Class25623
Loaded 83000 instances: essential_baseline_v3.0_ProjectKB_Class25735
Set type on 66000 instances: essential_baseline_v3.0_ProjectKB_Class26716
Loaded 84000 instances: essential_baseline_v3.0_ProjectKB_Class26912
Set type on 67000 instances: essential_baseline_v3.5_ProjectKB_Class10213
Loaded 85000 instances: essential_baseline_v3.5_ProjectKB_Class10457
Set type on 68000 instances: essential_baseline_v3.5_ProjectKB_Class11228
Loaded 86000 instances: essential_baseline_v3.5_ProjectKB_Class11334
Loaded 87000 instances: essential_baseline_v3.5_ProjectKB_Class12159
Set type on 69000 instances: essential_baseline_v3.5_ProjectKB_Class12278
Loaded 88000 instances: essential_baseline_v3.5_ProjectKB_Class12931
Set type on 70000 instances: essential_baseline_v3.5_ProjectKB_Class13302
Loaded 89000 instances: essential_baseline_v3.5_ProjectKB_Class13834
Set type on 71000 instances: essential_baseline_v3.5_ProjectKB_Class14318
Loaded 90000 instances: essential_baseline_v3.5_ProjectKB_Class1892
Set type on 72000 instances: essential_baseline_v3.5_ProjectKB_Class2475
Loaded 91000 instances: essential_baseline_v3.5_ProjectKB_Class2843
Set type on 73000 instances: essential_baseline_v3.5_ProjectKB_Class3528
Loaded 92000 instances: essential_baseline_v3.5_ProjectKB_Class3736
Loaded 93000 instances: essential_baseline_v3.5_ProjectKB_Class4527
Set type on 74000 instances: essential_baseline_v3.5_ProjectKB_Class4575
Loaded 94000 instances: essential_baseline_v3.5_ProjectKB_Class5397
Set type on 75000 instances: essential_baseline_v3.5_ProjectKB_Class5605
Loaded 95000 instances: essential_baseline_v3.5_ProjectKB_Class6300
Set type on 76000 instances: essential_baseline_v3.5_ProjectKB_Class6630
Loaded 96000 instances: essential_baseline_v3.5_ProjectKB_Class7205
Set type on 77000 instances: essential_baseline_v3.5_ProjectKB_Class7645
Loaded 97000 instances: essential_baseline_v3.5_ProjectKB_Class8068
Set type on 78000 instances: essential_baseline_v3.5_ProjectKB_Class8660
Loaded 98000 instances: essential_baseline_v3.5_ProjectKB_Class8921
Set type on 79000 instances: essential_baseline_v3.5_ProjectKB_Class9681
Loaded 99000 instances: essential_baseline_v3.5_ProjectKB_Class9783
Loaded 100000 instances: essential_baseline_v62_ProjectKB_Class16980
Set type on 80000 instances: essential_baseline_v4.0_ProjectKB_Class26040
Loaded 101000 instances: essential_baseline_v4.0_ProjectKB_Class26535
Set type on 81000 instances: essential_baseline_v4.0_ProjectKB_Class27048
Loaded 102000 instances: essential_baseline_v4.0_ProjectKB_Class27061
Loaded 103000 instances: essential_baseline_v4.0_ProjectKB_Class31873
Set type on 82000 instances: essential_baseline_v4.0_ProjectKB_Class32264
Loaded 104000 instances: essential_baseline_v4.0_ProjectKB_Class32954
Set type on 83000 instances: essential_baseline_v4.3.1_ProjectKB_Class1915
Loaded 105000 instances: essential_baseline_v4.3.1_ProjectKB_Class2747
Set type on 84000 instances: essential_baseline_v4.3.1_ProjectKB_Class2952
Loaded 106000 instances: essential_baseline_v4.3.1_ProjectKB_Class4089
Set type on 85000 instances: essential_baseline_v4.3.1_ProjectKB_Class4121
Loaded 107000 instances: essential_baseline_v4.3.1_ProjectKB_Class5061
Set type on 86000 instances: essential_baseline_v4.3.1_ProjectKB_Class5139
Loaded 108000 instances: essential_baseline_v4.3.1_ProjectKB_Class6073
Set type on 87000 instances: essential_baseline_v4.3_ProjectKB_Class1886
Set type on 88000 instances: essential_baseline_v505_ProjectKB_Class11305
Loaded 109000 instances: essential_baseline_v505_ProjectKB_Class11379
Set type on 89000 instances: essential_baseline_v505_ProjectKB_Class12721
Loaded 110000 instances: essential_baseline_v505_ProjectKB_Class13086
Set type on 90000 instances: essential_baseline_v505_ProjectKB_Class13849
Loaded 111000 instances: essential_baseline_v505_ProjectKB_Class14269
Set type on 91000 instances: essential_baseline_v505_ProjectKB_Class2335
Loaded 112000 instances: essential_baseline_v505_ProjectKB_Class2712
Set type on 92000 instances: essential_baseline_v505_ProjectKB_Class3445
Loaded 113000 instances: essential_baseline_v505_ProjectKB_Class3807
Set type on 93000 instances: essential_baseline_v505_ProjectKB_Class4550
Loaded 114000 instances: essential_baseline_v505_ProjectKB_Class5017
Set type on 94000 instances: essential_baseline_v505_ProjectKB_Class5830
Loaded 115000 instances: essential_baseline_v505_ProjectKB_Class6767
Set type on 95000 instances: essential_baseline_v505_ProjectKB_Class7070
Loaded 116000 instances: essential_baseline_v505_ProjectKB_Class8150
Set type on 96000 instances: essential_baseline_v505_ProjectKB_Class8313
Set type on 97000 instances: essential_baseline_v505_ProjectKB_Class9518
Loaded 117000 instances: essential_baseline_v505_ProjectKB_Class9569
Loaded 118000 instances: essential_baseline_v5_ProjectKB_Class16801
Set type on 98000 instances: essential_baseline_v5_ProjectKB_Class16844
Loaded 119000 instances: essential_baseline_v5_ProjectKB_Class17829
Set type on 99000 instances: essential_baseline_v5_ProjectKB_Class17858
Set type on 100000 instances: essential_baseline_v5_ProjectKB_Class18854
Loaded 120000 instances: essential_baseline_v5_ProjectKB_Class1910
Set type on 101000 instances: essential_baseline_v5_ProjectKB_Class19787
Loaded 121000 instances: essential_baseline_v5_ProjectKB_Class19871
Loaded 122000 instances: essential_baseline_v5_ProjectKB_Class2602
Set type on 102000 instances: essential_baseline_v5_ProjectKB_Class2757
Loaded 123000 instances: essential_baseline_v5_ProjectKB_Class3787
Set type on 103000 instances: essential_baseline_v5_ProjectKB_Class3775
Loaded 124000 instances: essential_baseline_v5_ProjectKB_Class4828
Set type on 104000 instances: essential_baseline_v5_ProjectKB_Class4797
Set type on 105000 instances: essential_baseline_v5_ProjectKB_Class5810
Loaded 125000 instances: essential_baseline_v5_ProjectKB_Class5873
Set type on 106000 instances: essential_baseline_v62_ProjectKB_Class12486
Loaded 126000 instances: essential_baseline_v62_ProjectKB_Class12815
Set type on 107000 instances: essential_baseline_v62_ProjectKB_Class13497
Loaded 127000 instances: essential_baseline_v62_ProjectKB_Class13735
Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.util.HashMap.resize(HashMap.java:704)
at java.util.HashMap.putVal(HashMap.java:629)
at java.util.HashMap.put(HashMap.java:612)
at java.util.HashSet.add(HashSet.java:220)
at edu.stanford.smi.protege.model.framestore.InMemoryFrameDb.addRecord(Unknown Source)
at edu.stanford.smi.protege.model.framestore.InMemoryFrameDb.addRecord(Unknown Source)
at edu.stanford.smi.protege.model.framestore.InMemoryFrameDb.createRecord(Unknown Source)
at edu.stanford.smi.protege.model.framestore.InMemoryFrameDb.setValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.MergingNarrowFrameStore.setValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.ClosureCachingBasicFrameStore.setValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.ImmutableNamesNarrowFrameStore.setValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.SimpleFrameStore.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.ChangeMonitorFrameStore.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.cleandispatch.DefaultDispatch.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.cleandispatch.CleanDispatchFrameStore.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.DefaultKnowledgeBase.setDirectOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.DefaultKnowledgeBase.setOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.model.DefaultFrame.setOwnSlotValues(Unknown Source)
at edu.stanford.smi.protege.storage.clips.Parser.slotValue(Unknown Source)
at edu.stanford.smi.protege.storage.clips.Parser.instance(Unknown Source)
at edu.stanford.smi.protege.storage.clips.Parser.parseKnowledgeBase(Unknown Source)
at edu.stanford.smi.protege.storage.clips.Parser.loadInstances(Unknown Source)
at edu.stanford.smi.protege.storage.clips.ClipsKnowledgeBaseFactory.loadKnowledgeBase(Unknown Source)
at edu.stanford.smi.protege.model.Project.loadProjectKB(Unknown Source)
at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
at edu.stanford.smi.protege.model.Project.loadProjectFromURI(Unknown Source)
at edu.stanford.smi.protege.util.ProjectChooser.loadProject(Unknown Source)
beerninr@DEV_VM7:/opt/protege$
-
neil.walsh
- Posts: 445
- Joined: 16 Feb 2009, 13:45
- Contact:
The error shows you’ve run out of memory whilst opening the project or applying the update. Protege will need at least 1.5 GB or ideally 2 GB or more to run correctly.
You can find out more about setting the correct memory values for Essential here…
https://www.enterprise-architecture.org ... re_memory/
Cheers
Neil
You can find out more about setting the correct memory values for Essential here…
https://www.enterprise-architecture.org ... re_memory/
Cheers
Neil
I should have clarified in my post that I had already configured Protege to set the initial and max java heap size to 700000000, using File->Preferences->Property Files->Protege.lax. I fixed the problem however by editing run_protege.sh and changing the JVM option to MAX_MEMORY=-Xmx2048M. The memory configuration web page does not explain this well for a standalone OS install on Linux unfortunately.
Last edited by Beernink on 06 Nov 2019, 19:44, edited 1 time in total.
-
neil.walsh
- Posts: 445
- Joined: 16 Feb 2009, 13:45
- Contact:
Hi,
700000000 is too small. That's 700mb. We'd suggest a value of 2048000000 (2GB)
Thanks
Neil
700000000 is too small. That's 700mb. We'd suggest a value of 2048000000 (2GB)
Thanks
Neil
