Define the project for the Essential repository.

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hz6231
Posts: 3
Joined: 11 May 2014, 13:28

Hay Guys,

trying to get the Essential Project to work... I I think I may require a little help.

I'm building the multi-User build.

Web Server seems fine
Protege Server seems fine
MySql seems fine
Client Seems fine...

However, when I try to Define an additional repository for essential_baseline_v4.3.1 I get the following errors when I reload the server using run_protege_server.bat...

any idea what I'm doing wrong?

Thanks

Code: Select all

Protege server is starting...
Protege 3.5 Build 663, JVM 1.6.0_01-b06, memory=466M, Windows Vista, encoding=UT
F-8, language=en, country=US
Server port = 0, registry port = 1099, compressed stream
Using metaproject from: file:/C:/EssentialAM/Repository/metaproject.pprj
Loading project Collaborative Newspaper from file:/C:/Program%20Files/Protege_3.
5/examples/collaborativeNewspaper/collaborativeNewspaper.pprj
Loading project Collaborative Newspaper Annotations from file:/C:/Program%20File
s/Protege_3.5/examples/collaborativeNewspaper/annotation_collaborativeNewspaper.
pprj
Loading project Collaborative Pizza from file:/C:/Program%20Files/Protege_3.5/ex
amples/collaborativePizza/collaborativePizza.owl.pprj
Backwards compatibility fixup for OWL project file (really ancient one)
Loading triples for: file:/C:/Program%20Files/Protege_3.5/examples/collaborative
Pizza/collaborativePizza.owl
    Completed triple loading after 360 ms
Importing http://protege.stanford.edu/plugins/owl/protege from location: C:\Prog
ram Files\Protege_3.5\plugins\edu.stanford.smi.protegex.owl\protege.owl
Loading triples for: http://protege.stanford.edu/plugins/owl/protege
    Completed triple loading after 13 ms
http://protege.stanford.edu/plugins/owl/protege already imported as triple store
 http://protege.stanford.edu/plugins/owl/protege
Postprocess: Process entities with incorrect Java type (0 entities) ... 0 ms
Postprocess: Process metaclasses (3 metaclasses) ... 0 ms
Postprocess: Process subclasses of rdf:List (1 classes) ... 0 ms
Postprocess: Instances with multiple types (122 instances) ... 5 ms
Postprocess: Add inferred superclasses ... 3 ms
Postprocess: Process orphan classes (98 classes) ... 1 ms
Postprocess: Generalized Concept Inclusion (0 axioms) ... 0 ms
Postprocess: Abstract classes... 0 ms
Postprocess: Domain and range of properties... 5 ms
Postprocess: Possibly typed entities (0 resources) ... 0 ms
Updating underlying frames model in 6 ms
Loading project Collaborative Pizza Annotations from file:/C:/Program%20Files/Pr
otege_3.5/examples/collaborativePizza/annotation_collaborativePizza.owl.pprj
Loading project Newspaper from file:/C:/Program%20Files/Protege_3.5/examples/new
spaper/newspaper.pprj
Loading project Pizza from file:/C:/Program%20Files/Protege_3.5/examples/pizza/p
izza.owl.pprj
Backwards compatibility fixup for OWL project file (really ancient one)
Loading triples for: file:/C:/Program%20Files/Protege_3.5/examples/pizza/pizza.o
wl
    Completed triple loading after 307 ms
Importing http://protege.stanford.edu/plugins/owl/protege from location: C:\Prog
ram Files\Protege_3.5\plugins\edu.stanford.smi.protegex.owl\protege.owl
Loading triples for: http://protege.stanford.edu/plugins/owl/protege
    Completed triple loading after 11 ms
http://protege.stanford.edu/plugins/owl/protege already imported as triple store
 http://protege.stanford.edu/plugins/owl/protege
Postprocess: Process entities with incorrect Java type (0 entities) ... 0 ms
Postprocess: Process metaclasses (3 metaclasses) ... 0 ms
Postprocess: Process subclasses of rdf:List (1 classes) ... 0 ms
Postprocess: Instances with multiple types (122 instances) ... 4 ms
Postprocess: Add inferred superclasses ... 1 ms
Postprocess: Process orphan classes (97 classes) ... 1 ms
Postprocess: Generalized Concept Inclusion (0 axioms) ... 0 ms
Postprocess: Abstract classes... 0 ms
Postprocess: Domain and range of properties... 2 ms
Postprocess: Possibly typed entities (0 resources) ... 0 ms
Updating underlying frames model in 5 ms
Loading project Wines from file:/C:/Program%20Files/Protege_3.5/examples/wines/w
ines.pprj
Loaded 5000 instances: essential_baseline_v1.2_ProjectKB_Class18492
Loaded 6000 instances: essential_baseline_v1.2_ProjectKB_Class19557
Loaded 7000 instances: essential_baseline_v3.0.4_ProjectKB_Class15364
Loaded 8000 instances: essential_baseline_v1_ProjectKB_Instance_21308
Set type on 5000 instances: essential_baseline_v1_ProjectKB_Instance_21368
Loaded 9000 instances: essential_baseline_v1_ProjectKB_Instance_24304
Set type on 6000 instances: essential_baseline_v1_ProjectKB_Instance_24566
Loaded 10000 instances: essential_baseline_v1_ProjectKB_Instance_30520
Set type on 7000 instances: essential_baseline_v1_ProjectKB_Instance_31201
Loaded 11000 instances: essential_baseline_v1_ProjectKB_Instance_31725
Set type on 8000 instances: essential_baseline_v1_ProjectKB_Instance_35082
Loaded 12000 instances: essential_baseline_v1_ProjectKB_Instance_35223
Loaded 13000 instances: essential_baseline_v1_ProjectKB_Instance_42298
Set type on 9000 instances: essential_baseline_v1_ProjectKB_Instance_42428
Loaded 14000 instances: essential_baseline_v1_ProjectKB_Instance_46800
Set type on 10000 instances: essential_baseline_v1_ProjectKB_Instance_4710
Loaded 15000 instances: essential_baseline_v1_ProjectKB_Instance_49880
Set type on 11000 instances: essential_baseline_v1_ProjectKB_Instance_53906
Loaded 16000 instances: essential_baseline_v3.0.3_ProjectKB_Class4500
Set type on 12000 instances: essential_baseline_v1_ProjectKB_Instance_5714
Loaded 17000 instances: essential_baseline_v1_ProjectKB_Instance_58237
Set type on 13000 instances: essential_baseline_v1_ProjectKB_Instance_59894
Loaded 18000 instances: essential_baseline_v2.0_ProjectKB_Class2530
Set type on 14000 instances: essential_baseline_v1_ProjectKB_Instance_68117
Loaded 19000 instances: essential_baseline_v1_ProjectKB_Instance_6889
Set type on 15000 instances: essential_baseline_v1_ProjectKB_Instance_8342
Loaded 20000 instances: essential_baseline_v1_ProjectKB_Instance_8363
Loaded 21000 instances: essential_baseline_v2.0_ProjectKB_Class11029
Set type on 16000 instances: essential_baseline_v2.0_ProjectKB_Class115038
Loaded 22000 instances: essential_baseline_v2.0_ProjectKB_Class12129
Set type on 17000 instances: essential_baseline_v2.0_ProjectKB_Class12592
Loaded 23000 instances: essential_baseline_v2.0_ProjectKB_Class135943
Set type on 18000 instances: essential_baseline_v2.0_ProjectKB_Class136446
Loaded 24000 instances: essential_baseline_v2.0_ProjectKB_Class143134
Set type on 19000 instances: essential_baseline_v2.0_ProjectKB_Class16072
Loaded 25000 instances: essential_baseline_v2.0_ProjectKB_Class21908
Set type on 20000 instances: essential_baseline_v2.0_ProjectKB_Class22571
Loaded 26000 instances: essential_baseline_v2.0_ProjectKB_Class22973
Set type on 21000 instances: essential_baseline_v2.0_ProjectKB_Class26579
Loaded 27000 instances: essential_baseline_v2.0_ProjectKB_Class27299
Set type on 22000 instances: essential_baseline_v2.0_ProjectKB_Class2789
Loaded 28000 instances: essential_baseline_v2.0_ProjectKB_Class28446
Set type on 23000 instances: essential_baseline_v2.0_ProjectKB_Class29119
Loaded 29000 instances: essential_baseline_v2.0_ProjectKB_Class2974
Set type on 24000 instances: essential_baseline_v2.0_ProjectKB_Class32011
Loaded 30000 instances: essential_baseline_v2.0_ProjectKB_Class3905
Set type on 25000 instances: essential_baseline_v2.0_ProjectKB_Class42346
Loaded 31000 instances: essential_baseline_v2.0_ProjectKB_Class4455
Set type on 26000 instances: essential_baseline_v2.0_ProjectKB_Class46023
Loaded 32000 instances: essential_baseline_v2.0_ProjectKB_Class46191
Set type on 27000 instances: essential_baseline_v2.0_ProjectKB_Class47043
Loaded 33000 instances: essential_baseline_v2.0_ProjectKB_Class47154
Set type on 28000 instances: essential_baseline_v2.0_ProjectKB_Class52226
Loaded 34000 instances: essential_baseline_v2.0_ProjectKB_Class52339
Set type on 29000 instances: essential_baseline_v2.0_ProjectKB_Class5980
Loaded 35000 instances: essential_baseline_v2.0_ProjectKB_Class60678
Set type on 30000 instances: essential_baseline_v2.0_ProjectKB_Class6585
Loaded 36000 instances: essential_baseline_v2.0_ProjectKB_Class6818
Set type on 31000 instances: essential_baseline_v2.0_ProjectKB_Class7375
Loaded 37000 instances: essential_baseline_v2.0_ProjectKB_Class7664
Set type on 32000 instances: essential_baseline_v2.0_ProjectKB_Class8355
Loaded 38000 instances: essential_baseline_v2.0_ProjectKB_Class8783
Set type on 33000 instances: essential_baseline_v2.0_ProjectKB_Class9401
Loaded 39000 instances: essential_baseline_v2.0_ProjectKB_Class96271
Set type on 34000 instances: essential_baseline_v3.0.2_ProjectKB_Class4041
Loaded 40000 instances: essential_baseline_v3.0.3_ProjectKB_Class11070
Loaded 41000 instances: essential_baseline_v3.0.3_ProjectKB_Class2051
Set type on 35000 instances: essential_baseline_v3.0.3_ProjectKB_Class2093
Loaded 42000 instances: essential_baseline_v3.0.3_ProjectKB_Class72048
Set type on 36000 instances: essential_baseline_v3.0.4_ProjectKB_Class10166
Loaded 43000 instances: essential_baseline_v3.0.4_ProjectKB_Class10704
Set type on 37000 instances: essential_baseline_v3.0.4_ProjectKB_Class12601
Loaded 44000 instances: essential_baseline_v3.0.4_ProjectKB_Class12713
Set type on 38000 instances: essential_baseline_v3.0.4_ProjectKB_Class13624
Loaded 45000 instances: essential_baseline_v3.0.4_ProjectKB_Class13751
Loaded 46000 instances: essential_baseline_v3.0.4_ProjectKB_Class16351
Loaded 47000 instances: essential_baseline_v3.0.4_ProjectKB_Class13931
Set type on 39000 instances: essential_baseline_v3.0.4_ProjectKB_Class14653
Loaded 48000 instances: essential_baseline_v3.0.4_ProjectKB_Class15014
Set type on 40000 instances: essential_baseline_v3.0.4_ProjectKB_Class15698
Set type on 41000 instances: essential_baseline_v3.0.4_ProjectKB_Class16698
Loaded 49000 instances: essential_baseline_v3.0.4_ProjectKB_Class2361
Loaded 50000 instances: essential_baseline_v3.0.4_ProjectKB_Class3601
Loaded 51000 instances: essential_baseline_v3.0.4_ProjectKB_Class4673
Set type on 42000 instances: essential_baseline_v3.0.4_ProjectKB_Class4910
Loaded 52000 instances: essential_baseline_v3.0.4_ProjectKB_Class5769
Loaded 53000 instances: essential_baseline_v3.0.4_ProjectKB_Class6822
Loaded 54000 instances: essential_baseline_v3.0.4_ProjectKB_Class8521
Set type on 43000 instances: essential_baseline_v3.0.4_ProjectKB_Class8956
Loaded 55000 instances: essential_baseline_v3.0.4_ProjectKB_Class9562
Set type on 44000 instances: essential_baseline_v3.0.6_ProjectKB_Class19843
Loaded 56000 instances: essential_baseline_v3.0.6_ProjectKB_Class20127
Set type on 45000 instances: essential_baseline_v3.0.6_ProjectKB_Class20858
Loaded 57000 instances: essential_baseline_v3.0_ProjectKB_Class16791
Set type on 46000 instances: essential_baseline_v3.0_ProjectKB_Class17636
Loaded 58000 instances: essential_baseline_v3.0_ProjectKB_Class1884
Set type on 47000 instances: essential_baseline_v3.0_ProjectKB_Class2269
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
        at java.util.ArrayList.<init>(Unknown Source)
        at java.util.ArrayList.<init>(Unknown Source)
        at edu.stanford.smi.protege.storage.clips.Parser.slotValueFields(Unknown
 Source)
        at edu.stanford.smi.protege.storage.clips.Parser.slotValue(Unknown Sourc
e)
        at edu.stanford.smi.protege.storage.clips.Parser.instance(Unknown Source
)
        at edu.stanford.smi.protege.storage.clips.Parser.parseKnowledgeBase(Unkn
own Source)
        at edu.stanford.smi.protege.storage.clips.Parser.loadInstances(Unknown S
ource)
        at edu.stanford.smi.protege.storage.clips.ClipsKnowledgeBaseFactory.load
KnowledgeBase(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.loadProjectFromURI(Unknown Sou
rce)
        at edu.stanford.smi.protege.server.Server.createProject(Unknown Source)
        at edu.stanford.smi.protege.server.Server.initializeProjects(Unknown Sou
rce)
        at edu.stanford.smi.protege.server.Server.initialize(Unknown Source)
        at edu.stanford.smi.protege.server.Server.<init>(Unknown Source)
        at edu.stanford.smi.protege.server.Server.startServer(Unknown Source)
        at edu.stanford.smi.protege.server.Server.main(Unknown Source)
User avatar
jonathan.carter
Posts: 1087
Joined: 04 Feb 2009, 15:44

You're almost there. All looks good until you hit the Out Of Memory exception.

Make sure that you've got at least 1.5-2GB memory allocated for Protege. You'll need this both on the Protege Server and the Protege client.

For Protege server, go to your Protege installation directory and edit run_protege_server.bat (Windows) or run_protege_server.sh (Unix/Mac)

In here, update the parameter MAX_MEMORY to be as follows:

MAX_MEMORY=-Xmx2048M

(for 64-bit platforms and 64-bit JVMs). Note that if you're using a 32-bit JVM on Windows, you'll have to limit this to -Xmx1536M

For Protege client, this article from the Protege team describes how to set the maximum memory for Windows, Linux and Mac.

Once you've made these changes, restart Protege server and it should startup successfully. Everything else from the logs you have sent looks to be in good order.

Jonathan
Essential Project Team
hz6231
Posts: 3
Joined: 11 May 2014, 13:28

Genius!

That seems to have fixed the Badger!

Thanks
hz6231
Posts: 3
Joined: 11 May 2014, 13:28

Genius !

That fixed the badger. thanks for the solution!
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