protege desktop periodically stops starting

[grandrew]

On ubuntu 14.10, java 1.8 Periodically protege does not start. Here is the start log:

$ ./run.sh
Starting Protege Desktop (Version 5.0.0, Build = beta-17)
Platform:
    Java: JVM 1.8.0_40-b26 Memory: 466M
    Language: ru, Country: RU
    Framework: Apache Software Foundation (1.7)
    OS: linux (3.16.0-23-generic)
    Processor: x86-64
Plugin: Explanation Workbench (2.0.0)
Plugin: null (0.0.0)
Plugin: Annotation Template View (2.1.1)
Plugin: DL Query (2.0.2)
Plugin: OWL Code Generation Plug-in (1.0.2)
Plugin: OWL Difference Engine (2.0.0)
Plugin: Protege HermiT Integration (1.0.0)
Plugin: Cajun Visualization Library (1.0.2)
Plugin: Factplusplus Plug-in (1.6.4)
Plugin: null (0.0.0)
Plugin: Protege Editor OWL (5.0.0.beta-17)
Plugin: OWLViz (4.1.4)
Plugin: Protege SPARQL Plugin (1.0.0)
Plugin: Guava: Google Core Libraries for Java (18.0.0)
Plugin: OWL Difference (5.0.0)
Plugin: OntoGraf (1.0.3)
Plugin: owlapi-osgidistribution (3.5.1)
Plugin: OWLAPI RDF Library (1.0.2)
Plugin: Matrix Views (1.1.2)
    null Plugin has no plugin.xml resource
    OWL Difference Engine Plugin has no plugin.xml resource
    Cajun Visualization Library Plugin has no plugin.xml resource
    null Plugin has no plugin.xml resource
    Guava: Google Core Libraries for Java Plugin has no plugin.xml resource
    owlapi-osgidistribution Plugin has no plugin.xml resource
    OWLAPI RDF Library Plugin has no plugin.xml resource
Using OWL API version 3.5.1
Rebuilding entity indices...
... rebuilt in 6 ms
Setting active ontology to OntologyID(OntologyIRI(<http://www.semanticweb.org/andrew/ontologies/2015/9/untitled-ontology-28>))
Rebuilding entity indices...
... rebuilt in 3 ms
... active ontology changed
Cannot generate ontology catalog for ontology at http://www.semanticweb.org/andrew/ontologies/2015/9/untitled-ontology-28
Setting active ontology to OntologyID(OntologyIRI(<http://www.semanticweb.org/andrew/ontologies/2015/9/untitled-ontology-28>))
Rebuilding entity indices...
... rebuilt in 2 ms
... active ontology changed
Auto-update last performed: Fri Oct 09 14:32:22 MSK 2015
Auto-update has been run today.  Not running it again.

sometimes the main gui window appears but when I select the document to open it disappears and halts again

$ ps aux | grep -i java
andrew   14253 13.4  1.4 3863816 243996 pts/43 Sl+  14:44   0:12 jre/bin/java -Xmx500M -Xms250M -Dlog4j.configuration=file:log4j.xml -DentityExpansionLimit=100000000 -Dfile.encoding=UTF-8 -classpath bin/org.apache.felix.main.jar:bin/ProtegeLauncher.jar org.protege.osgi.framework.Launcher
$ sudo strace -p 14253
Process 14253 attached
futex(0x7f21573369d0, FUTEX_WAIT, 14254, NULL

this happens on latest protege-parent-5.0.0-beta-17-42-g55cbbdc as well as on beta-17 "official" package

[csnyulas]

Is it possible that the window appears on a different screen that you can't see? This happens sometimes to me after I disconnect my laptop from the docking station, where I have 2+1 screens. A way to get to the invisible window in Linux and Windows is to press ALT+Space that gives you access to the menu of the active window, even if it is not visible, and then select Move, and move it to the visible area of your workspace.

[grandrew]

Usually when the window is created I can see the icon at the launcher bar. The window is definitely not created.

I upgraded to ubuntu 15.10 - will see if the problem persists.

[mspix]

I have a similar problem on Win 7 64Bit with Protege-5.0.0-Beta-23. I can see the icon on the taskbar, but I get no GUI by clicking on it. At the beginning, everything was fine. Then I tried to open a very large ttl-file (1.23GB). Protege crashed and since then I can't see a GUI anymore. The only thing that appears is a window for selecting updates and plug-ins. Java 1.8 is also installed.