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fusepool / fusepool-sma

This project is an implementation of a dictionary-matching algorithm as an enhancer engine.
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Fatal error on save new dictionary annotator #5

Closed jhercher closed 9 years ago

jhercher commented 9 years ago

Hi,

I got a fatal error on saving a new dictionary. This is how it occured:

1) I started fusepool and created a new graph for persons: urn:x-localinstance:/gndPersons.graph

2) shutdown of fusepool

3) loaded a .ttl into an existing graph ( file has 13332192 triples ) tdbloader --loc=urn%3Ax-localinstance%3A%2FgndPersonsNeu.graph /Data/out/persons.ttl The persons.ttl has 13332192 triples and looks like this:

@prefix :      <http://d-nb.info/gnd/> .
@prefix dc:    <http://purl.org/dc/elements/1.1/> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix foaf:  <http://xmlns.com/foaf/0.1/> .
@prefix dct:   <http://purl.org/dc/terms/> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix owl:   <http://www.w3.org/2002/07/owl#> .
@prefix vann:  <http://purl.org/vocab/vann/> .
@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix gndo:  <http://d-nb.info/standards/elementset/gnd#> .
@prefix fn:    <http://www.w3.org/2005/xpath-functions#> .
@prefix skos:  <http://www.w3.org/2004/02/skos/core#> .
@prefix cc:    <http://creativecommons.org/ns#> .

:123293693  a           gndo:DifferentiatedPerson ;
        skos:altLabel   "Johann Heinrich Crocius" , "Crocius" ;
        skos:prefLabel  "Johann Heinrich Crocius (123293693)" .

4) started fusepool (467) again and I configured the dictionary annotator http://localhost:8080/system/console/configMgr

using the following params:

name: gndPersonsNeu-dict
graph:      urn:x-localinstance:/gndPersonsNeu.graph
label:      skos:prefLabel
alt label:  skos:altLabel
concept:    gndo:DifferentiatedPerson
prefixes:   gndo: <http://d-nb.info/standards/elementset/gnd#> 
            skos: <http://www.w3.org/2004/02/skos/core#>

category:   DifferentiatedPerson;http://d-nb.info/standards/elementset/gnd#DifferentiatedPerson

hit save.

The error.log's last message: 09.01.2015 17:35:01.533 INFO [CM Event Dispatcher (Fire ConfigurationEvent: pid=eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.be25d553-ae8a-444b-95cf-862b80679b2d)] eu.fusepool.enhancer.engines.dictionaryannotator Service [eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.be25d553-ae8a-444b-95cf-862b80679b2d,386] ServiceEvent REGISTERED

in the shell I get:

A fatal error has been detected by the Java Runtime Environment:

#
#  SIGSEGV (0xb) at pc=0x000000010edc50f2, pid=7462, tid=9515
#
# JRE version: Java(TM) SE Runtime Environment (7.0_72-b14) (build 1.7.0_72-b14)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (24.72-b04 mixed mode bsd-amd64 compressed oops)
# Problematic frame:
# V  [libjvm.dylib+0x1c50f2]
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again

The error report:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x000000010edc50f2, pid=7462, tid=9515
#
# JRE version: Java(TM) SE Runtime Environment (7.0_72-b14) (build 1.7.0_72-b14)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (24.72-b04 mixed mode bsd-amd64 compressed oops)
# Problematic frame:
# V  [libjvm.dylib+0x1c50f2]
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.sun.com/bugreport/crash.jsp
#

---------------  T H R E A D  ---------------

Current thread (0x00007f91c380f000):  GCTaskThread [stack: 0x000000011417b000,0x000000011427b000] [id=9515]

siginfo:si_signo=SIGSEGV: si_errno=0, si_code=0 (SEGV0), si_addr=0x0000000000000000

Registers:
RAX=0x000000011488f000, RBX=0x00007f91c2707ac0, RCX=0x03ffffffe9800000, RDX=0x1fffffff4c000000
RSP=0x000000011427ac60, RBP=0x000000011427ac80, RSI=0x000000073a5ca728, RDI=0x00007f91c2707ac0
R8 =0x000000000000234b, R9 =0x000000000000bbee, R10=0x4040004044444444, R11=0x0000000400000000
R12=0x000000073a5ca728, R13=0x000000073a5ca72c, R14=0x0000000080000000, R15=0x000000062249d410
RIP=0x000000010edc50f2, EFLAGS=0x0000000000010206, ERR=0x0000000000000000
  TRAPNO=0x000000000000000d

Top of Stack: (sp=0x000000011427ac60)
0x000000011427ac60:   000000011427acd0 00007f91c2707ac0
0x000000011427ac70:   000000062249d410 000000062249d410
0x000000011427ac80:   000000011427acd0 000000010eea48d5
0x000000011427ac90:   00007f91c2707ac0 000000073a5ca710
0x000000011427aca0:   000000062249d418 00007f91c2707ac0
0x000000011427acb0:   000000073a5ca710 00000000004e6e00
0x000000011427acc0:   00007f91c2707ac8 000000010f37a830
0x000000011427acd0:   000000011427ad50 000000010f050158
0x000000011427ace0:   00007f91c2707b00 00007f91c2707b48
0x000000011427acf0:   00007f91c2707b80 00000007499161f0
0x000000011427ad00:   00000001004e6e00 00005cf30000072e
0x000000011427ad10:   000000011427ad50 000000010f04436b
0x000000011427ad20:   0028e1f900002503 0000000000000001
0x000000011427ad30:   000000011427ad80 000000010f37a830
0x000000011427ad40:   00007f91c2707ac0 000000011427ad6c
0x000000011427ad50:   000000011427adb0 000000010f043b6a
0x000000011427ad60:   00007f91c2b0c470 52ab7f960ee6cb5b
0x000000011427ad70:   00000007499161f0 000000000027ce00
0x000000011427ad80:   0000000000000000 00007f91c380f000
0x000000011427ad90:   0000000000000000 000000010f17b28a
0x000000011427ada0:   00007f91c2b0c470 0000000000000001
0x000000011427adb0:   000000011427ae90 000000010ee6d057
0x000000011427adc0:   000000011427adf0 00007f91c260a030
0x000000011427add0:   00007f91c260a060 00007f91c260a070
0x000000011427ade0:   00007f91c260a448 00000000000003d8
0x000000011427adf0:   00007f91c380f000 00007f91c260a450
0x000000011427ae00:   00007f91c260a480 00007f91c260a490
0x000000011427ae10:   00007f91c260a868 00000000000003d8
0x000000011427ae20:   000000011427ae30 0000000000000000
0x000000011427ae30:   00007f91c380f000 00007f91c260a450
0x000000011427ae40:   00007f91c260a480 00007f91c260a490
0x000000011427ae50:   00007f91c260a868 00000000000003d8 

Instructions: (pc=0x000000010edc50f2)
0x000000010edc50d2:   10 48 c1 ea 03 48 8d 0d 0a f4 59 00 8a 09 48 d3
0x000000010edc50e2:   ea 48 89 d1 48 83 e1 c0 48 c1 e9 03 48 8b 40 30
0x000000010edc50f2:   48 8b 04 08 48 0f a3 d0 72 5d 4c 89 f7 e8 a4 c8
0x000000010edc5102:   02 00 4c 63 f8 48 8d 3d 52 0d 65 00 4c 89 f6 4c 

Register to memory mapping:

RAX=0x000000011488f000 is an unknown value
RBX=0x00007f91c2707ac0 is an unknown value
RCX=0x03ffffffe9800000 is an unknown value
RDX=0x1fffffff4c000000 is an unknown value
RSP=0x000000011427ac60 is an unknown value
RBP=0x000000011427ac80 is an unknown value
RSI=0x000000073a5ca728 is pointing into object: 0x000000073a5ca710
eu.fusepool.enhancer.engines.dictionaryannotator.Concept 
 - klass: 'eu/fusepool/enhancer/engines/dictionaryannotator/Concept'
RDI=0x00007f91c2707ac0 is an unknown value
R8 =0x000000000000234b is an unknown value
R9 =0x000000000000bbee is an unknown value
R10=0x4040004044444444 is an unknown value
R11=0x0000000400000000 is an unknown value
R12=0x000000073a5ca728 is pointing into object: 0x000000073a5ca710
eu.fusepool.enhancer.engines.dictionaryannotator.Concept 
 - klass: 'eu/fusepool/enhancer/engines/dictionaryannotator/Concept'
R13=0x000000073a5ca72c is pointing into object: 0x000000073a5ca710
eu.fusepool.enhancer.engines.dictionaryannotator.Concept 
 - klass: 'eu/fusepool/enhancer/engines/dictionaryannotator/Concept'
R14=0x0000000080000000 is an unknown value
R15=0x000000062249d410 is pointing into object: 0x000000062249d1d8
{instance class} 
 - klass: {other class}

Stack: [0x000000011417b000,0x000000011427b000],  sp=0x000000011427ac60,  free space=1023k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
V  [libjvm.dylib+0x1c50f2]
V  [libjvm.dylib+0x2a48d5]
V  [libjvm.dylib+0x450158]
V  [libjvm.dylib+0x443b6a]
V  [libjvm.dylib+0x26d057]
V  [libjvm.dylib+0x420eb6]
C  [libsystem_pthread.dylib+0x1899]  _pthread_body+0x8a
C  [libsystem_pthread.dylib+0x172a]  _pthread_struct_init+0x0
C  [libsystem_pthread.dylib+0x5fc9]  thread_start+0xd

---------------  P R O C E S S  ---------------

Java Threads: ( => current thread )
  0x00007f91c39b2000 JavaThread "qtp1335108214-79" [_thread_blocked, id=39943, stack(0x0000000127b92000,0x0000000127c12000)]
  0x00007f91c3801000 JavaThread "DestroyJavaVM" [_thread_blocked, id=3335, stack(0x000000010daa8000,0x000000010db28000)]
  0x00007f91c434c000 JavaThread "DataFileTrackingDaemon" daemon [_thread_blocked, id=54279, stack(0x0000000129fb0000,0x000000012a030000)]
  0x00007f91c40d8000 JavaThread "CRIS Reindex Thread[74]" daemon [_thread_blocked, id=53763, stack(0x000000012a23b000,0x000000012a2bb000)]
  0x00007f91c5895000 JavaThread "Timer-1" daemon [_thread_blocked, id=53251, stack(0x0000000129f2d000,0x0000000129fad000)]
  0x00007f91c4237000 JavaThread "Event Job Manager Observer Daemon" daemon [_thread_blocked, id=52739, stack(0x0000000129a81000,0x0000000129b01000)]
  0x00007f91c287e800 JavaThread "Thread-53" daemon [_thread_blocked, id=52227, stack(0x00000001299fe000,0x0000000129a7e000)]
  0x00007f91caa98000 JavaThread "searcherExecutor-4-thread-1" [_thread_blocked, id=50695, stack(0x0000000129793000,0x0000000129813000)]
  0x00007f91c70bd000 JavaThread "Thread-52" daemon [_thread_blocked, id=51207, stack(0x0000000129710000,0x0000000129790000)]
  0x00007f91c3c67800 JavaThread "Thread-51" daemon [_thread_blocked, id=51715, stack(0x000000012986c000,0x00000001298ec000)]
  0x00007f91c3c8c800 JavaThread "pool-2-thread-1" [_thread_blocked, id=50179, stack(0x0000000129d49000,0x0000000129dc9000)]
  0x00007f91c2ccd000 JavaThread "ForkJoinPool-1-worker-11" daemon [_thread_blocked, id=49667, stack(0x0000000129cc6000,0x0000000129d46000)]
  0x00007f91c3dc2000 JavaThread "Timer-0" daemon [_thread_blocked, id=49155, stack(0x0000000129c43000,0x0000000129cc3000)]
  0x00007f91c2aef000 JavaThread "ForkJoinPool-1-worker-29" daemon [_thread_blocked, id=48643, stack(0x0000000129918000,0x0000000129998000)]
  0x00007f91c3ca8000 JavaThread "ForkJoinScheduler" daemon [_thread_blocked, id=48131, stack(0x0000000128bb1000,0x0000000128c31000)]
  0x00007f91c331d000 JavaThread "SyncDaemon for Jena TDB /Users/JoH/Documents/codespace/stanbol467/stanbol/felix/bundle138/data/singleTdb/org.apache.clerezza.rdf.jena.tdb.storage.SingleTdbDatasetTcProvider" daemon [_thread_blocked, id=47619, stack(0x0000000128a0c000,0x0000000128a8c000)]
  0x00007f91c2d3d800 JavaThread "Thread-45" daemon [_thread_blocked, id=47107, stack(0x0000000128893000,0x0000000128913000)]
  0x00007f91c42d3800 JavaThread "Event delivery timer" daemon [_thread_blocked, id=46595, stack(0x0000000127da7000,0x0000000127e27000)]
  0x00007f91c4177800 JavaThread "OsgiInstallerImpl" daemon [_thread_blocked, id=36611, stack(0x0000000128810000,0x0000000128890000)]
  0x00007f91c420e800 JavaThread "qtp1335108214-35" [_thread_blocked, id=35587, stack(0x000000012870a000,0x000000012878a000)]
  0x00007f91c3205800 JavaThread "qtp1335108214-34" [_thread_blocked, id=35075, stack(0x0000000128687000,0x0000000128707000)]
  0x00007f91c5008800 JavaThread "qtp1335108214-33" [_thread_blocked, id=34563, stack(0x0000000128604000,0x0000000128684000)]
  0x00007f91c3ba0000 JavaThread "qtp1335108214-32 Selector1" [_thread_blocked, id=34051, stack(0x0000000128581000,0x0000000128601000)]
  0x00007f91c3b9f000 JavaThread "qtp1335108214-31 Acceptor1 SelectChannelConnector@0.0.0.0:8080" [_thread_in_native, id=33539, stack(0x00000001284fe000,0x000000012857e000)]
  0x00007f91c3b9e800 JavaThread "qtp1335108214-30 Acceptor0 SelectChannelConnector@0.0.0.0:8080" [_thread_blocked, id=33027, stack(0x000000012847b000,0x00000001284fb000)]
  0x00007f91c3b92800 JavaThread "qtp1335108214-29 Selector0" [_thread_blocked, id=32515, stack(0x00000001283f8000,0x0000000128478000)]
  0x00007f91c396f000 JavaThread "HashSessionScavenger-0" daemon [_thread_blocked, id=32003, stack(0x0000000128375000,0x00000001283f5000)]
  0x00007f91c420f000 JavaThread "LogEntry Dispatcher" daemon [_thread_blocked, id=31491, stack(0x00000001282f2000,0x0000000128372000)]
  0x00007f91c3174800 JavaThread "SCR Component Actor" daemon [_thread_blocked, id=30467, stack(0x00000001281ec000,0x000000012826c000)]
  0x00007f91c397e000 JavaThread "CM Event Dispatcher (Fire ConfigurationEvent: pid=eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.be25d553-ae8a-444b-95cf-862b80679b2d)" daemon [_thread_blocked, id=25347, stack(0x0000000127a96000,0x0000000127b16000)]
  0x00007f91c3184000 JavaThread "CM Configuration Updater" daemon [_thread_blocked, id=24835, stack(0x000000012728f000,0x000000012730f000)]
  0x00007f91c3183000 JavaThread "FelixStartLevel" daemon [_thread_blocked, id=24323, stack(0x000000012720c000,0x000000012728c000)]
  0x00007f91c3915000 JavaThread "FelixDispatchQueue" [_thread_blocked, id=22275, stack(0x00000001273f3000,0x0000000127473000)]
  0x00007f91c3004000 JavaThread "Service Thread" daemon [_thread_blocked, id=21251, stack(0x0000000126c99000,0x0000000126d19000)]
  0x00007f91c4047800 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=20739, stack(0x0000000126b96000,0x0000000126c96000)]
  0x00007f91c280a800 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=20227, stack(0x0000000126a93000,0x0000000126b93000)]
  0x00007f91c280d800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=19715, stack(0x0000000126a10000,0x0000000126a90000)]
  0x00007f91c300a000 JavaThread "Finalizer" daemon [_thread_blocked, id=14595, stack(0x0000000126841000,0x00000001268c1000)]
  0x00007f91c3009000 JavaThread "Reference Handler" daemon [_thread_blocked, id=14083, stack(0x00000001267be000,0x000000012683e000)]

Other Threads:
  0x00007f91c403f800 VMThread [stack: 0x00000001266bb000,0x00000001267bb000] [id=13571]
  0x00007f91c4050800 WatcherThread [stack: 0x0000000126d1c000,0x0000000126e1c000] [id=21763]

=>0x00007f91c380f000 (exited) GCTaskThread [stack: 0x000000011417b000,0x000000011427b000] [id=9515]

VM state:at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread:  ([mutex/lock_event])
[0x00007f91c25034e0] Threads_lock - owner thread: 0x00007f91c403f800
[0x00007f91c25039e0] Heap_lock - owner thread: 0x00007f91c397e000

Heap
 PSYoungGen      total 1631232K, used 688812K [0x000000076aa80000, 0x0000000800000000, 0x0000000800000000)
  eden space 815616K, 0% used [0x000000076aa80000,0x000000076aa80000,0x000000079c700000)
  from space 815616K, 84% used [0x00000007ce380000,0x00000007f842b020,0x0000000800000000)
  to   space 815616K, 0% used [0x000000079c700000,0x000000079c700000,0x00000007ce380000)
 ParOldGen       total 4889600K, used 4546017K [0x0000000640000000, 0x000000076a700000, 0x000000076aa80000)
  object space 4889600K, 92% used [0x0000000640000000,0x0000000755778630,0x000000076a700000)
 PSPermGen       total 339456K, used 213237K [0x0000000620000000, 0x0000000634b80000, 0x0000000640000000)
  object space 339456K, 62% used [0x0000000620000000,0x000000062d03d4d8,0x0000000634b80000)

Card table byte_map: [0x0000000112720000,0x0000000113621000] byte_map_base: 0x000000010f620000

Polling page: 0x000000010db67000

Code Cache  [0x000000010f660000, 0x00000001100e0000, 0x0000000112660000)
 total_blobs=4078 nmethods=3592 adapters=437 free_code_cache=38728Kb largest_free_block=39370816

Compilation events (10 events):
Event: 477,283 Thread 0x00007f91c4047800 nmethod 4049 0x000000010fd8c2d0 code [0x000000010fd8c540, 0x000000010fd8d2a0]
Event: 477,283 Thread 0x00007f91c4047800 4052             com.hp.hpl.jena.tdb.nodetable.NodeTableCache::cacheLookup (23 bytes)
Event: 477,287 Thread 0x00007f91c4047800 nmethod 4052 0x000000010fd26f10 code [0x000000010fd270a0, 0x000000010fd27498]
Event: 477,291 Thread 0x00007f91c280a800 nmethod 4051 0x000000010fd8a7d0 code [0x000000010fd8a9e0, 0x000000010fd8b630]
Event: 477,410 Thread 0x00007f91c4047800 4053   !         org.apache.clerezza.rdf.jena.facade.JenaGraph::filter (173 bytes)
Event: 477,410 Thread 0x00007f91c280a800 4054             org.apache.clerezza.rdf.jena.storage.JenaGraphAdaptor::performFilter (107 bytes)
Event: 477,415 Thread 0x00007f91c280a800 nmethod 4054 0x000000010fd22b90 code [0x000000010fd22d60, 0x000000010fd23270]
Event: 477,418 Thread 0x00007f91c4047800 nmethod 4053 0x000000010f7f3910 code [0x000000010f7f3b80, 0x000000010f7f44e0]
Event: 477,420 Thread 0x00007f91c280a800 4055             com.hp.hpl.jena.sparql.engine.iterator.QueryIterTriplePattern$TripleMapper::closeIterator (20 bytes)
Event: 477,421 Thread 0x00007f91c280a800 nmethod 4055 0x000000010fd20f90 code [0x000000010fd210e0, 0x000000010fd211f8]

GC Heap History (10 events):
Event: 477,262 GC heap after
Heap after GC invocations=71 (full 9):
 PSYoungGen      total 1605120K, used 365920K [0x000000076aa80000, 0x00000007fa700000, 0x0000000800000000)
  eden space 861696K, 0% used [0x000000076aa80000,0x000000076aa80000,0x000000079f400000)
  from space 743424K, 49% used [0x00000007cd100000,0x00000007e3658020,0x00000007fa700000)
  to   space 747008K, 0% used [0x000000079f400000,0x000000079f400000,0x00000007ccd80000)
 ParOldGen       total 4889600K, used 3950270K [0x0000000640000000, 0x000000076a700000, 0x000000076aa80000)
  object space 4889600K, 80% used [0x0000000640000000,0x00000007311afb90,0x000000076a700000)
 PSPermGen       total 339456K, used 213237K [0x0000000620000000, 0x0000000634b80000, 0x0000000640000000)
  object space 339456K, 62% used [0x0000000620000000,0x000000062d03d400,0x0000000634b80000)
}
Event: 478,768 GC heap before
{Heap before GC invocations=72 (full 9):
 PSYoungGen      total 1605120K, used 1227616K [0x000000076aa80000, 0x00000007fa700000, 0x0000000800000000)
  eden space 861696K, 100% used [0x000000076aa80000,0x000000079f400000,0x000000079f400000)
  from space 743424K, 49% used [0x00000007cd100000,0x00000007e3658020,0x00000007fa700000)
  to   space 747008K, 0% used [0x000000079f400000,0x000000079f400000,0x00000007ccd80000)
 ParOldGen       total 4889600K, used 3950270K [0x0000000640000000, 0x000000076a700000, 0x000000076aa80000)
  object space 4889600K, 80% used [0x0000000640000000,0x00000007311afb90,0x000000076a700000)
 PSPermGen       total 339456K, used 213237K [0x0000000620000000, 0x0000000634b80000, 0x0000000640000000)
  object space 339456K, 62% used [0x0000000620000000,0x000000062d03d4d8,0x0000000634b80000)
Event: 479,055 GC heap after
Heap after GC invocations=72 (full 9):
 PSYoungGen      total 1608704K, used 602377K [0x000000076aa80000, 0x0000000800000000, 0x0000000800000000)
  eden space 861696K, 0% used [0x000000076aa80000,0x000000076aa80000,0x000000079f400000)
  from space 747008K, 80% used [0x000000079f400000,0x00000007c40427c8,0x00000007ccd80000)
  to   space 810496K, 0% used [0x00000007ce880000,0x00000007ce880000,0x0000000800000000)
 ParOldGen       total 4889600K, used 3950270K [0x0000000640000000, 0x000000076a700000, 0x000000076aa80000)
  object space 4889600K, 80% used [0x0000000640000000,0x00000007311afb90,0x000000076a700000)
 PSPermGen       total 339456K, used 213237K [0x0000000620000000, 0x0000000634b80000, 0x0000000640000000)
  object space 339456K, 62% used [0x0000000620000000,0x000000062d03d4d8,0x0000000634b80000)
}
Event: 480,507 GC heap before
{Heap before GC invocations=73 (full 9):
 PSYoungGen      total 1608704K, used 1464073K [0x000000076aa80000, 0x0000000800000000, 0x0000000800000000)
  eden space 861696K, 100% used [0x000000076aa80000,0x000000079f400000,0x000000079f400000)
  from space 747008K, 80% used [0x000000079f400000,0x00000007c40427c8,0x00000007ccd80000)
  to   space 810496K, 0% used [0x00000007ce880000,0x00000007ce880000,0x0000000800000000)
 ParOldGen       total 4889600K, used 3950270K [0x0000000640000000, 0x000000076a700000, 0x000000076aa80000)
  object space 4889600K, 80% used [0x0000000640000000,0x00000007311afb90,0x000000076a700000)
 PSPermGen       total 339456K, used 213237K [0x0000000620000000, 0x0000000634b80000, 0x0000000640000000)
  object space 339456K, 62% used [0x0000000620000000,0x000000062d03d4d8,0x0000000634b80000)
Event: 480,894 GC heap after
Heap after GC invocations=73 (full 9):
 PSYoungGen      total 1626112K, used 810494K [0x000000076aa80000, 0x0000000800000000, 0x0000000800000000)
  eden space 815616K, 0% used [0x000000076aa80000,0x000000076aa80000,0x000000079c700000)
  from space 810496K, 99% used [0x00000007ce880000,0x00000007fffff928,0x0000000800000000)
  to   space 815616K, 0% used [0x000000079c700000,0x000000079c700000,0x00000007ce380000)
 ParOldGen       total 4889600K, used 3979918K [0x0000000640000000, 0x000000076a700000, 0x000000076aa80000)
  object space 4889600K, 81% used [0x0000000640000000,0x0000000732ea3b90,0x000000076a700000)
 PSPermGen       total 339456K, used 213237K [0x0000000620000000, 0x0000000634b80000, 0x0000000640000000)
  object space 339456K, 62% used [0x0000000620000000,0x000000062d03d4d8,0x0000000634b80000)
}
Event: 482,249 GC heap before
{Heap before GC invocations=74 (full 9):
 PSYoungGen      total 1626112K, used 1626110K [0x000000076aa80000, 0x0000000800000000, 0x0000000800000000)
  eden space 815616K, 100% used [0x000000076aa80000,0x000000079c700000,0x000000079c700000)
  from space 810496K, 99% used [0x00000007ce880000,0x00000007fffff928,0x0000000800000000)
  to   space 815616K, 0% used [0x000000079c700000,0x000000079c700000,0x00000007ce380000)
 ParOldGen       total 4889600K, used 3979918K [0x0000000640000000, 0x000000076a700000, 0x000000076aa80000)
  object space 4889600K, 81% used [0x0000000640000000,0x0000000732ea3b90,0x000000076a700000)
 PSPermGen       total 339456K, used 213237K [0x0000000620000000, 0x0000000634b80000, 0x0000000640000000)
  object space 339456K, 62% used [0x0000000620000000,0x000000062d03d4d8,0x0000000634b80000)
Event: 482,761 GC heap after
Heap after GC invocations=74 (full 9):
 PSYoungGen      total 1631232K, used 815613K [0x000000076aa80000, 0x0000000800000000, 0x0000000800000000)
  eden space 815616K, 0% used [0x000000076aa80000,0x000000076aa80000,0x000000079c700000)
  from space 815616K, 99% used [0x000000079c700000,0x00000007ce37f598,0x00000007ce380000)
  to   space 815616K, 0% used [0x00000007ce380000,0x00000007ce380000,0x0000000800000000)
 ParOldGen       total 4889600K, used 4199942K [0x0000000640000000, 0x000000076a700000, 0x000000076aa80000)
  object space 4889600K, 85% used [0x0000000640000000,0x0000000740581b90,0x000000076a700000)
 PSPermGen       total 339456K, used 213237K [0x0000000620000000, 0x0000000634b80000, 0x0000000640000000)
  object space 339456K, 62% used [0x0000000620000000,0x000000062d03d4d8,0x0000000634b80000)
}
Event: 484,266 GC heap before
{Heap before GC invocations=75 (full 9):
 PSYoungGen      total 1631232K, used 1631229K [0x000000076aa80000, 0x0000000800000000, 0x0000000800000000)
  eden space 815616K, 100% used [0x000000076aa80000,0x000000079c700000,0x000000079c700000)
  from space 815616K, 99% used [0x000000079c700000,0x00000007ce37f598,0x00000007ce380000)
  to   space 815616K, 0% used [0x00000007ce380000,0x00000007ce380000,0x0000000800000000)
 ParOldGen       total 4889600K, used 4199942K [0x0000000640000000, 0x000000076a700000, 0x000000076aa80000)
  object space 4889600K, 85% used [0x0000000640000000,0x0000000740581b90,0x000000076a700000)
 PSPermGen       total 339456K, used 213237K [0x0000000620000000, 0x0000000634b80000, 0x0000000640000000)
  object space 339456K, 62% used [0x0000000620000000,0x000000062d03d4d8,0x0000000634b80000)
Event: 484,873 GC heap after
Heap after GC invocations=75 (full 9):
 PSYoungGen      total 1631232K, used 688812K [0x000000076aa80000, 0x0000000800000000, 0x0000000800000000)
  eden space 815616K, 0% used [0x000000076aa80000,0x000000076aa80000,0x000000079c700000)
  from space 815616K, 84% used [0x00000007ce380000,0x00000007f842b020,0x0000000800000000)
  to   space 815616K, 0% used [0x000000079c700000,0x000000079c700000,0x00000007ce380000)
 ParOldGen       total 4889600K, used 4546017K [0x0000000640000000, 0x000000076a700000, 0x000000076aa80000)
  object space 4889600K, 92% used [0x0000000640000000,0x0000000755778630,0x000000076a700000)
 PSPermGen       total 339456K, used 213237K [0x0000000620000000, 0x0000000634b80000, 0x0000000640000000)
  object space 339456K, 62% used [0x0000000620000000,0x000000062d03d4d8,0x0000000634b80000)
}
Event: 484,873 GC heap before
{Heap before GC invocations=76 (full 10):
 PSYoungGen      total 1631232K, used 688812K [0x000000076aa80000, 0x0000000800000000, 0x0000000800000000)
  eden space 815616K, 0% used [0x000000076aa80000,0x000000076aa80000,0x000000079c700000)
  from space 815616K, 84% used [0x00000007ce380000,0x00000007f842b020,0x0000000800000000)
  to   space 815616K, 0% used [0x000000079c700000,0x000000079c700000,0x00000007ce380000)
 ParOldGen       total 4889600K, used 4546017K [0x0000000640000000, 0x000000076a700000, 0x000000076aa80000)
  object space 4889600K, 92% used [0x0000000640000000,0x0000000755778630,0x000000076a700000)
 PSPermGen       total 339456K, used 213237K [0x0000000620000000, 0x0000000634b80000, 0x0000000640000000)
  object space 339456K, 62% used [0x0000000620000000,0x000000062d03d4d8,0x0000000634b80000)

Deoptimization events (10 events):
Event: 477,029 Thread 0x00007f91c397e000 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000010fb7ffec method=com.hp.hpl.jena.sparql.engine.iterator.QueryIterTriplePattern$TripleMapper.substitute(Lcom/hp/hpl/jena/graph/Node;Lcom/hp/hpl/jena/sparql/engine/binding/Binding;)Lcom/hp
Event: 477,029 Thread 0x00007f91c397e000 Uncommon trap: reason=unreached action=reinterpret pc=0x000000010ff17104 method=org.apache.clerezza.rdf.jena.facade.JenaGraph.filter(Lcom/hp/hpl/jena/graph/TripleMatch;)Ljava/util/Iterator; @ 13
Event: 477,030 Thread 0x00007f91c397e000 Uncommon trap: reason=unreached action=reinterpret pc=0x000000010f7b5078 method=org.apache.clerezza.rdf.jena.storage.JenaGraphAdaptor.performFilter(Lorg/apache/clerezza/rdf/core/NonLiteral;Lorg/apache/clerezza/rdf/core/UriRef;Lorg/apache/clerezza/rdf/core
Event: 477,032 Thread 0x00007f91c397e000 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000010fb25888 method=com.hp.hpl.jena.tdb.nodetable.NodeTableCache.cacheLookup(Lcom/hp/hpl/jena/tdb/store/NodeId;)Lcom/hp/hpl/jena/graph/Node; @ 19
Event: 477,032 Thread 0x00007f91c397e000 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000010fb25888 method=com.hp.hpl.jena.tdb.nodetable.NodeTableCache.cacheLookup(Lcom/hp/hpl/jena/tdb/store/NodeId;)Lcom/hp/hpl/jena/graph/Node; @ 19
Event: 477,034 Thread 0x00007f91c397e000 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000010fb25888 method=com.hp.hpl.jena.tdb.nodetable.NodeTableCache.cacheLookup(Lcom/hp/hpl/jena/tdb/store/NodeId;)Lcom/hp/hpl/jena/graph/Node; @ 19
Event: 477,035 Thread 0x00007f91c397e000 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000010fb25888 method=com.hp.hpl.jena.tdb.nodetable.NodeTableCache.cacheLookup(Lcom/hp/hpl/jena/tdb/store/NodeId;)Lcom/hp/hpl/jena/graph/Node; @ 19
Event: 477,036 Thread 0x00007f91c397e000 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000010fee8c80 method=com.hp.hpl.jena.tdb.nodetable.NodeTableCache.cacheLookup(Lcom/hp/hpl/jena/tdb/store/NodeId;)Lcom/hp/hpl/jena/graph/Node; @ 19
Event: 477,037 Thread 0x00007f91c397e000 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000010ff9c740 method=com.hp.hpl.jena.tdb.nodetable.NodeTableCache.cacheLookup(Lcom/hp/hpl/jena/tdb/store/NodeId;)Lcom/hp/hpl/jena/graph/Node; @ 19
Event: 477,038 Thread 0x00007f91c397e000 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000010fb96598 method=com.hp.hpl.jena.tdb.nodetable.NodeTableCache.cacheLookup(Lcom/hp/hpl/jena/tdb/store/NodeId;)Lcom/hp/hpl/jena/graph/Node; @ 19

Internal exceptions (10 events):
Event: 168,738 Thread 0x00007f91c5008800 Implicit null exception at 0x000000010fd89546 to 0x000000010fd8c1d9
Event: 168,739 Thread 0x00007f91c5008800 Implicit null exception at 0x000000010fd21c64 to 0x000000010fd26ec5
Event: 168,754 Thread 0x00007f91c420e800 Implicit null exception at 0x000000010fc7824e to 0x000000010fc78ae1
Event: 168,765 Thread 0x00007f91c5008800 Implicit null exception at 0x000000010fc2b710 to 0x000000010fc2b799
Event: 168,765 Thread 0x00007f91c3205800 Implicit null exception at 0x000000010fc2b710 to 0x000000010fc2b799
Event: 181,922 Thread 0x00007f91c5008800 Implicit null exception at 0x000000010fe4fe62 to 0x000000010fe502b9
Event: 186,362 Thread 0x00007f91c39b2000 Implicit null exception at 0x000000010fe50a24 to 0x000000010fe50d5d
Event: 407,040 Thread 0x00007f91c5008800 Implicit null exception at 0x000000010fe4a275 to 0x000000010fe4a7f9
Event: 407,130 Thread 0x00007f91c397e000 Implicit null exception at 0x000000010f950189 to 0x000000010f950555
Event: 477,030 Thread 0x00007f91c397e000 Implicit null exception at 0x000000010f7b4cda to 0x000000010f7b5065

Events (10 events):
Event: 477,262 Executing VM operation: ParallelGCFailedAllocation done
Event: 477,282 Thread 0x00007f91c280a800 flushing nmethod 0x000000010f94ff90
Event: 477,419 Thread 0x00007f91c4047800 flushing nmethod 0x000000010fc60350
Event: 478,767 Executing VM operation: ParallelGCFailedAllocation
Event: 479,055 Executing VM operation: ParallelGCFailedAllocation done
Event: 480,506 Executing VM operation: ParallelGCFailedAllocation
Event: 480,895 Executing VM operation: ParallelGCFailedAllocation done
Event: 482,249 Executing VM operation: ParallelGCFailedAllocation
Event: 482,761 Executing VM operation: ParallelGCFailedAllocation done
Event: 484,266 Executing VM operation: ParallelGCFailedAllocation

Dynamic libraries:
0x000000000a418000  /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa
0x000000000a418000  /System/Library/Frameworks/Security.framework/Versions/A/Security
0x000000000a418000  /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
0x000000000a418000  /usr/lib/libz.1.dylib
0x000000000a418000  /usr/lib/libSystem.B.dylib
0x000000000a418000  /usr/lib/libobjc.A.dylib
0x000000000a418000  /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
0x000000000a418000  /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation
0x000000000a418000  /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
0x000000000a418000  /System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
0x000000000a418000  /System/Library/PrivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServices
0x000000000a418000  /System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox
0x000000000a418000  /System/Library/Frameworks/AudioUnit.framework/Versions/A/AudioUnit
0x000000000a418000  /System/Library/PrivateFrameworks/DataDetectorsCore.framework/Versions/A/DataDetectorsCore
0x000000000a418000  /System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv
0x000000000a418000  /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/HIToolbox
0x000000000a418000  /System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore
0x000000000a418000  /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SpeechRecognition.framework/Versions/A/SpeechRecognition
0x000000000a418000  /usr/lib/libauto.dylib
0x000000000a418000  /usr/lib/libicucore.A.dylib
0x000000000a418000  /usr/lib/libxml2.2.dylib
0x000000000a418000  /System/Library/PrivateFrameworks/CoreUI.framework/Versions/A/CoreUI
0x000000000a418000  /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio
0x000000000a418000  /System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration
0x000000000a418000  /usr/lib/liblangid.dylib
0x000000000a418000  /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport
0x000000000a418000  /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit
0x000000000a418000  /usr/lib/libDiagnosticMessagesClient.dylib
0x000000000a418000  /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices
0x000000000a418000  /System/Library/PrivateFrameworks/PerformanceAnalysis.framework/Versions/A/PerformanceAnalysis
0x000000000a418000  /System/Library/PrivateFrameworks/GenerationalStorage.framework/Versions/A/GenerationalStorage
0x000000000a418000  /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
0x000000000a418000  /System/Library/PrivateFrameworks/Sharing.framework/Versions/A/Sharing
0x000000000a418000  /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
0x000000000a418000  /System/Library/Frameworks/CoreText.framework/Versions/A/CoreText
0x000000000a418000  /System/Library/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
0x000000000a418000  /System/Library/PrivateFrameworks/Backup.framework/Versions/A/Backup
0x000000000a418000  /System/Library/Frameworks/CFNetwork.framework/Versions/A/CFNetwork
0x000000000a418000  /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration
0x000000000a418000  /usr/lib/libCRFSuite.dylib
0x000000000a418000  /usr/lib/libc++.1.dylib
0x000000000a418000  /usr/lib/libc++abi.dylib
0x000000000a418000  /usr/lib/system/libcache.dylib
0x000000000a418000  /usr/lib/system/libcommonCrypto.dylib
0x000000000a418000  /usr/lib/system/libcompiler_rt.dylib
0x000000000a418000  /usr/lib/system/libcopyfile.dylib
0x000000000a418000  /usr/lib/system/libcorecrypto.dylib
0x000000000a418000  /usr/lib/system/libdispatch.dylib
0x000000000a418000  /usr/lib/system/libdyld.dylib
0x000000000a418000  /usr/lib/system/libkeymgr.dylib
0x000000000a418000  /usr/lib/system/liblaunch.dylib
0x000000000a418000  /usr/lib/system/libmacho.dylib
0x000000000a418000  /usr/lib/system/libquarantine.dylib
0x000000000a418000  /usr/lib/system/libremovefile.dylib
0x000000000a418000  /usr/lib/system/libsystem_asl.dylib
0x000000000a418000  /usr/lib/system/libsystem_blocks.dylib
0x000000000a418000  /usr/lib/system/libsystem_c.dylib
0x000000000a418000  /usr/lib/system/libsystem_configuration.dylib
0x000000000a418000  /usr/lib/system/libsystem_dnssd.dylib
0x000000000a418000  /usr/lib/system/libsystem_info.dylib
0x000000000a418000  /usr/lib/system/libsystem_kernel.dylib
0x000000000a418000  /usr/lib/system/libsystem_m.dylib
0x000000000a418000  /usr/lib/system/libsystem_malloc.dylib
0x000000000a418000  /usr/lib/system/libsystem_network.dylib
0x000000000a418000  /usr/lib/system/libsystem_notify.dylib
0x000000000a418000  /usr/lib/system/libsystem_platform.dylib
0x000000000a418000  /usr/lib/system/libsystem_pthread.dylib
0x000000000a418000  /usr/lib/system/libsystem_sandbox.dylib
0x000000000a418000  /usr/lib/system/libsystem_stats.dylib
0x000000000a418000  /usr/lib/system/libunc.dylib
0x000000000a418000  /usr/lib/system/libunwind.dylib
0x000000000a418000  /usr/lib/system/libxpc.dylib
0x000000000a418000  /usr/lib/libbsm.0.dylib
0x000000000a418000  /usr/lib/libsqlite3.dylib
0x000000000a418000  /usr/lib/libxar.1.dylib
0x000000000a418000  /usr/lib/libpam.2.dylib
0x000000000a418000  /usr/lib/libOpenScriptingUtil.dylib
0x000000000a418000  /usr/lib/libbz2.1.0.dylib
0x000000000a418000  /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore
0x000000000a418000  /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Metadata
0x000000000a418000  /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices
0x000000000a418000  /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/Versions/A/SearchKit
0x000000000a418000  /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE
0x000000000a418000  /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices
0x000000000a418000  /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServices.framework/Versions/A/DictionaryServices
0x000000000a418000  /System/Library/Frameworks/NetFS.framework/Versions/A/NetFS
0x000000000a418000  /usr/lib/system/libkxld.dylib
0x000000000a418000  /System/Library/PrivateFrameworks/NetAuth.framework/Versions/A/NetAuth
0x000000000a418000  /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC
0x000000000a418000  /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory
0x000000000a418000  /System/Library/Frameworks/ServiceManagement.framework/Versions/A/ServiceManagement
0x000000000a418000  /usr/lib/libxslt.1.dylib
0x000000000a418000  /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink
0x000000000a418000  /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS
0x000000000a418000  /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync
0x000000000a418000  /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
0x000000000a418000  /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis
0x000000000a418000  /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore
0x000000000a418000  /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD
0x000000000a418000  /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis
0x000000000a418000  /System/Library/Frameworks/IOSurface.framework/Versions/A/IOSurface
0x000000000a418000  /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
0x000000000a418000  /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
0x000000000a418000  /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
0x000000000a418000  /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
0x000000000a418000  /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
0x000000000a418000  /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
0x000000000a418000  /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
0x000000000a418000  /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib
0x000000000a418000  /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib
0x000000000a418000  /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib
0x000000000a418000  /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib
0x000000000a418000  /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib
0x000000000a418000  /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib
0x000000000a418000  /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib
0x000000000a418000  /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib
0x000000000a418000  /usr/lib/libcups.2.dylib
0x000000000a418000  /System/Library/Frameworks/Kerberos.framework/Versions/A/Kerberos
0x000000000a418000  /System/Library/Frameworks/GSS.framework/Versions/A/GSS
0x000000000a418000  /usr/lib/libresolv.9.dylib
0x000000000a418000  /usr/lib/libiconv.2.dylib
0x000000000a418000  /System/Library/PrivateFrameworks/Heimdal.framework/Versions/A/Heimdal
0x000000000a418000  /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
0x000000000a418000  /usr/lib/libheimdal-asn1.dylib
0x000000000a418000  /System/Library/Frameworks/OpenDirectory.framework/Versions/A/OpenDirectory
0x000000000a418000  /System/Library/PrivateFrameworks/CommonAuth.framework/Versions/A/CommonAuth
0x000000000a418000  /System/Library/Frameworks/SecurityFoundation.framework/Versions/A/SecurityFoundation
0x000000000a418000  /System/Library/PrivateFrameworks/Bom.framework/Versions/A/Bom
0x000000000a418000  /System/Library/Frameworks/CoreVideo.framework/Versions/A/CoreVideo
0x000000000a418000  /System/Library/Frameworks/QuartzCore.framework/Versions/A/Frameworks/CoreImage.framework/Versions/A/CoreImage
0x000000000a418000  /System/Library/Frameworks/QuartzCore.framework/Versions/A/Frameworks/ScalableUserInterface.framework/Versions/A/ScalableUserInterface
0x000000000a418000  /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
0x000000000a418000  /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
0x000000000a418000  /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
0x000000000a418000  /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
0x000000000a418000  /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
0x000000000a418000  /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
0x000000000a418000  /System/Library/PrivateFrameworks/FaceCore.framework/Versions/A/FaceCore
0x000000000a418000  /System/Library/PrivateFrameworks/CrashReporterSupport.framework/Versions/A/CrashReporterSupport
0x000000000a418000  /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x000000000a418000  /System/Library/PrivateFrameworks/AppleFSCompression.framework/Versions/A/AppleFSCompression
0x000000000a418000  /System/Library/PrivateFrameworks/Ubiquity.framework/Versions/A/Ubiquity
0x000000000a418000  /System/Library/PrivateFrameworks/IconServices.framework/Versions/A/IconServices
0x000000000a418000  /System/Library/PrivateFrameworks/ChunkingLibrary.framework/Versions/A/ChunkingLibrary
0x000000000a418000  /System/Library/PrivateFrameworks/CoreSymbolication.framework/Versions/A/CoreSymbolication
0x000000000a418000  /System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication
0x000000000a418000  /System/Library/PrivateFrameworks/DebugSymbols.framework/Versions/A/DebugSymbols
0x000000010ec00000  /Library/Java/JavaVirtualMachines/jdk1.7.0_72.jdk/Contents/Home/jre/lib/server/libjvm.dylib
0x000000000a418000  /usr/lib/libstdc++.6.dylib
0x000000010db2a000  /Library/Java/JavaVirtualMachines/jdk1.7.0_72.jdk/Contents/Home/jre/lib/libverify.dylib
0x000000010db37000  /Library/Java/JavaVirtualMachines/jdk1.7.0_72.jdk/Contents/Home/jre/lib/libjava.dylib
0x000000010db71000  /Library/Java/JavaVirtualMachines/jdk1.7.0_72.jdk/Contents/Home/jre/lib/libzip.dylib
0x00000001268c3000  /System/Library/Frameworks/JavaVM.framework/Frameworks/JavaRuntimeSupport.framework/JavaRuntimeSupport
0x00000001268db000  /System/Library/Frameworks/JavaVM.framework/Versions/A/Frameworks/JavaNativeFoundation.framework/Versions/A/JavaNativeFoundation
0x00000001268f0000  /System/Library/Frameworks/JavaVM.framework/Versions/A/JavaVM
0x000000000a418000  /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon
0x00000001268fd000  /System/Library/PrivateFrameworks/JavaLaunching.framework/Versions/A/JavaLaunching
0x000000000a418000  /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/A/CommonPanels
0x000000000a418000  /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Help.framework/Versions/A/Help
0x000000000a418000  /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ImageCapture.framework/Versions/A/ImageCapture
0x000000000a418000  /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/Versions/A/OpenScripting
0x000000000a418000  /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/Print
0x000000000a418000  /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/SecurityHI
0x0000000126e6c000  /Library/Java/JavaVirtualMachines/jdk1.7.0_72.jdk/Contents/Home/jre/lib/libnet.dylib
0x0000000126eca000  /Library/Java/JavaVirtualMachines/jdk1.7.0_72.jdk/Contents/Home/jre/lib/libnio.dylib
0x0000000126efd000  /Library/Java/JavaVirtualMachines/jdk1.7.0_72.jdk/Contents/Home/jre/lib/libmanagement.dylib
0x00000001298ee000  /Library/Java/JavaVirtualMachines/jdk1.7.0_72.jdk/Contents/Home/jre/lib/libsunec.dylib

VM Arguments:
jvm_args: -Xmx7G -XX:MaxPermSize=512M -Xss512k -XX:+UseCompressedOops 
java_command: launcher-0.1-SNAPSHOT.jar
Launcher Type: SUN_STANDARD

Environment Variables:
PATH=/usr/local/git/bin:/sw/bin/:/usr/local/bin:/usr/local/:/usr/local/sbin:/usr/local/mysql/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/bin/:/usr/local/apache-jena/apache-jena-2.12.1/bin
SHELL=/bin/bash

Signal Handlers:
SIGSEGV: [libjvm.dylib+0x52c465], sa_mask[0]=0xfffefeff, sa_flags=0x00000043
SIGBUS: [libjvm.dylib+0x52c465], sa_mask[0]=0xfffefeff, sa_flags=0x00000042
SIGFPE: [libjvm.dylib+0x41e5ce], sa_mask[0]=0xfffefeff, sa_flags=0x00000042
SIGPIPE: [libjvm.dylib+0x41e5ce], sa_mask[0]=0xfffefeff, sa_flags=0x00000042
SIGXFSZ: [libjvm.dylib+0x41e5ce], sa_mask[0]=0xfffefeff, sa_flags=0x00000042
SIGILL: [libjvm.dylib+0x41e5ce], sa_mask[0]=0xfffefeff, sa_flags=0x00000042
SIGUSR1: SIG_DFL, sa_mask[0]=0x63807efb, sa_flags=0x00000000
SIGUSR2: [libjvm.dylib+0x41e0c0], sa_mask[0]=0x00000000, sa_flags=0x00000042
SIGHUP: [libjvm.dylib+0x41c351], sa_mask[0]=0xfffefeff, sa_flags=0x00000042
SIGINT: [libjvm.dylib+0x41c351], sa_mask[0]=0xfffefeff, sa_flags=0x00000042
SIGTERM: [libjvm.dylib+0x41c351], sa_mask[0]=0xfffefeff, sa_flags=0x00000042
SIGQUIT: [libjvm.dylib+0x41c351], sa_mask[0]=0xfffefeff, sa_flags=0x00000042

---------------  S Y S T E M  ---------------

OS:Bsduname:Darwin 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun  3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64
rlimit: STACK 8192k, CORE 0k, NPROC 709, NOFILE 10240, AS infinity
load average:3,67 2,12 1,60

CPU:total 8 (4 cores per cpu, 2 threads per core) family 6 model 70 stepping 1, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, erms, ht, tsc, tscinvbit

Memory: 4k page, physical 16777216k(4194304k free)

/proc/meminfo:

vm_info: Java HotSpot(TM) 64-Bit Server VM (24.72-b04) for bsd-amd64 JRE (1.7.0_72-b14), built on Sep 26 2014 18:48:06 by "java_re" with gcc 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)

time: Fri Jan  9 17:36:20 2015
elapsed time: 486 seconds

After restart of Fusepool I saved the dictionary again and get:

"Error happened while creating the dictionary!"

Any ideas?

Cheers, Johannes

akuckartz commented 9 years ago

What happens when you use OpenJDK 8 ?

gaborremenyi commented 9 years ago

Hi, I'm not yet sure what goes wrong. Could you please check the error.log after you get this: "Error happened while creating the dictionary!" Because I checked the code and there should be log entry when such thing happens: log.error("Error happened while creating the dictionary!",e); If so, please attach the body of the exception. Thanks, Gabor

jhercher commented 9 years ago

Hi Gabor and Andreas,

thank you for your quick reply. I'm a few days away from my office, but will be able to check this next monday.

Johannes

jhercher commented 9 years ago

Hi Gabor,

sorry there is no exeception written to the error.log. The next messages are from starting up again:

09.01.2015 17:35:01.533 *INFO* [CM Event Dispatcher (Fire ConfigurationEvent: pid=eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.be25d553-ae8a-444b-95cf-862b80679b2d)] eu.fusepool.enhancer.engines.dictionaryannotator Service [eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.be25d553-ae8a-444b-95cf-862b80679b2d,386] ServiceEvent REGISTERED
???
09.01.2015 17:57:54.243 *INFO* [FelixStartLevel] org.apache.sling.commons.log.internal.LogManager LogManager: Logging set up from context
09.01.2015 17:57:54.259 *INFO* [FelixStartLevel] org.apache.sling.commons.logservice Service [org.apache.sling.commons.logservice.internal.LogServiceFactory,42] ServiceEvent REGISTERED
09.01.2015 17:57:54.262 *INFO* [FelixStartLevel] org.apache.sling.commons.logservice Service [org.apache.sling.commons.logservice.internal.LogReaderServiceFactory,43] ServiceEvent REGISTERED

Btw. I'm using the precompiled jars from jenkins (release 467) maybe there is a difference?

However, I found some other exceptions regarding the dictionary annotator, see below. 1.) "16:10:37" On starting up for the first time that day 2.) 17:28:41 On starting up for the 2nd time (after loading the .ttl into an existing graph ( file had 13332192 triples ) tdbloader --loc=urn%3Ax-localinstance%3A%2FgndPersonsNeu.graph /Data/out/persons.ttl Shortly before the crash. 3.) 17:58:21 On starting the system again

Could it be problematic that I loaded turtle into the ../mgraph/urn:x-localinstance:/gndPersons.graph ?

The logs: (1)

09.01.2015 16:10:36.736 *ERROR* [FelixStartLevel] eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine There is no registered graph with given uri: urn:fusepool-disease-ontology
09.01.2015 16:10:36.737 *INFO* [FelixStartLevel] eu.fusepool.enhancer.engines.dictionaryannotator Service [eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.163902c6-408c-44a4-8eef-9662fb8e631e,255] ServiceEvent REGISTERED
09.01.2015 16:10:37.006 *ERROR* [FelixStartLevel] TDB ObjectFileStorage.read[nodes](13314)[filesize=14414][file.size()=14414]: Impossibly large object : 1751461479 bytes > filesize-(loc+SizeOfInt)=1096
09.01.2015 16:10:37.006 *ERROR* [FelixStartLevel] eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine Error happened while creating the dictionary! com.hp.hpl.jena.tdb.base.file.FileException: ObjectFileStorage.read[nodes](13314)[filesize=14414][file.size()=14414]: Impossibly large object : 1751461479 bytes > filesize-(loc+SizeOfInt)=1096
    at com.hp.hpl.jena.tdb.base.objectfile.ObjectFileStorage.read(ObjectFileStorage.java:346)
    at com.hp.hpl.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:79)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:178)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:103)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:74)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:103)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:74)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:55)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67)
    at com.hp.hpl.jena.tdb.lib.TupleLib.triple(TupleLib.java:137)
    at com.hp.hpl.jena.tdb.lib.TupleLib.triple(TupleLib.java:114)
    at com.hp.hpl.jena.tdb.lib.TupleLib.access$000(TupleLib.java:45)
    at com.hp.hpl.jena.tdb.lib.TupleLib$3.convert(TupleLib.java:76)
    at com.hp.hpl.jena.tdb.lib.TupleLib$3.convert(TupleLib.java:72)
    at org.apache.jena.atlas.iterator.Iter$4.next(Iter.java:322)
    at org.apache.jena.atlas.iterator.Iter$4.next(Iter.java:322)
    at org.apache.jena.atlas.iterator.Iter$4.next(Iter.java:322)
    at org.apache.jena.atlas.iterator.Iter.next(Iter.java:920)
    at com.hp.hpl.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94)
    at org.apache.clerezza.rdf.jena.storage.JenaGraphAdaptor$1.next(JenaGraphAdaptor.java:115)
    at org.apache.clerezza.rdf.jena.storage.JenaGraphAdaptor$1.next(JenaGraphAdaptor.java:96)
    at org.apache.clerezza.rdf.core.impl.AbstractTripleCollection$1.next(AbstractTripleCollection.java:83)
    at org.apache.clerezza.rdf.core.impl.AbstractTripleCollection$1.next(AbstractTripleCollection.java:72)
    at org.apache.clerezza.rdf.core.access.LockingIterator.next(LockingIterator.java:57)
    at org.apache.clerezza.rdf.core.access.LockingIterator.next(LockingIterator.java:31)
    at org.apache.clerezza.rdf.core.access.security.TcAccessController.removeExistingRequiredReadPermissions(TcAccessController.java:278)
    at org.apache.clerezza.rdf.core.access.security.TcAccessController.setRequiredReadPermissionStrings(TcAccessController.java:153)
    at org.apache.clerezza.rdf.core.access.security.TcAccessController.setRequiredReadPermissions(TcAccessController.java:175)
    at eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.activate(DictionaryAnnotatorEnhancerEngine.java:384)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.apache.felix.scr.impl.helper.BaseMethod.invokeMethod(BaseMethod.java:231)
    at org.apache.felix.scr.impl.helper.BaseMethod.access$500(BaseMethod.java:39)
    at org.apache.felix.scr.impl.helper.BaseMethod$Resolved.invoke(BaseMethod.java:624)
    at org.apache.felix.scr.impl.helper.BaseMethod.invoke(BaseMethod.java:508)
    at org.apache.felix.scr.impl.helper.ActivateMethod.invoke(ActivateMethod.java:149)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.createImplementationObject(SingleComponentManager.java:315)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.createComponent(SingleComponentManager.java:127)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.getService(SingleComponentManager.java:871)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.getServiceInternal(SingleComponentManager.java:838)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:850)
    at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:931)
    at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:895)
    at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1480)
    at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1401)
    at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.trackAdding(ServiceTracker.java:1210)
    at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.track(ServiceTracker.java:1148)
    at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:1432)
    at org.apache.felix.framework.util.EventDispatcher$4.run(EventDispatcher.java:925)
    at java.security.AccessController.doPrivileged(Native Method)
    at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:921)
    at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:793)
    at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:543)
    at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4401)
    at org.apache.felix.framework.Felix.registerService(Felix.java:3411)
    at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:346)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:1003)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:992)
    at org.apache.felix.scr.impl.manager.RegistrationManager.changeRegistration(RegistrationManager.java:134)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.registerService(AbstractComponentManager.java:1044)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:841)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.enable(AbstractComponentManager.java:419)
    at org.apache.felix.scr.impl.config.ConfigurableComponentHolder.enableComponents(ConfigurableComponentHolder.java:376)
    at org.apache.felix.scr.impl.BundleComponentActivator.initialize(BundleComponentActivator.java:172)
    at org.apache.felix.scr.impl.BundleComponentActivator.<init>(BundleComponentActivator.java:120)
    at org.apache.felix.scr.impl.Activator.loadComponents(Activator.java:258)
    at org.apache.felix.scr.impl.Activator.access$000(Activator.java:45)
    at org.apache.felix.scr.impl.Activator$ScrExtension.start(Activator.java:185)
    at org.apache.felix.utils.extender.AbstractExtender.createExtension(AbstractExtender.java:259)
    at org.apache.felix.utils.extender.AbstractExtender.modifiedBundle(AbstractExtender.java:232)
    at org.osgi.util.tracker.BundleTracker$Tracked.customizerModified(BundleTracker.java:479)
    at org.osgi.util.tracker.BundleTracker$Tracked.customizerModified(BundleTracker.java:414)
    at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:232)
    at org.osgi.util.tracker.BundleTracker$Tracked.bundleChanged(BundleTracker.java:443)
    at org.apache.felix.framework.util.EventDispatcher$3.run(EventDispatcher.java:861)
    at java.security.AccessController.doPrivileged(Native Method)
    at org.apache.felix.framework.util.EventDispatcher.invokeBundleListenerCallback(EventDispatcher.java:858)
    at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:789)
    at org.apache.felix.framework.util.EventDispatcher.fireBundleEvent(EventDispatcher.java:514)
    at org.apache.felix.framework.Felix.fireBundleEvent(Felix.java:4385)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:2080)
    at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1279)
    at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)
    at java.lang.Thread.run(Thread.java:745)

(2)

09.01.2015 17:28:41.344 *ERROR* [FelixStartLevel] eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine There is no registered graph with given uri: urn:fusepool-disease-ontology
09.01.2015 17:28:41.344 *INFO* [FelixStartLevel] eu.fusepool.enhancer.engines.dictionaryannotator Service [eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.163902c6-408c-44a4-8eef-9662fb8e631e,256] ServiceEvent REGISTERED
09.01.2015 17:28:41.902 *ERROR* [FelixStartLevel] TDB ObjectFileStorage.read[nodes](13314)[filesize=17191][file.size()=17191]: Impossibly large object : 1751461479 bytes > filesize-(loc+SizeOfInt)=3873
09.01.2015 17:28:41.902 *ERROR* [FelixStartLevel] eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine Error happened while creating the dictionary! com.hp.hpl.jena.tdb.base.file.FileException: ObjectFileStorage.read[nodes](13314)[filesize=17191][file.size()=17191]: Impossibly large object : 1751461479 bytes > filesize-(loc+SizeOfInt)=3873
    at com.hp.hpl.jena.tdb.base.objectfile.ObjectFileStorage.read(ObjectFileStorage.java:346)
    at com.hp.hpl.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:79)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:178)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:103)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:74)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:103)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:74)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:55)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67)
    at com.hp.hpl.jena.tdb.lib.TupleLib.triple(TupleLib.java:137)
    at com.hp.hpl.jena.tdb.lib.TupleLib.triple(TupleLib.java:114)
    at com.hp.hpl.jena.tdb.lib.TupleLib.access$000(TupleLib.java:45)
    at com.hp.hpl.jena.tdb.lib.TupleLib$3.convert(TupleLib.java:76)
    at com.hp.hpl.jena.tdb.lib.TupleLib$3.convert(TupleLib.java:72)
    at org.apache.jena.atlas.iterator.Iter$4.next(Iter.java:322)
    at org.apache.jena.atlas.iterator.Iter$4.next(Iter.java:322)
    at org.apache.jena.atlas.iterator.Iter$4.next(Iter.java:322)
    at org.apache.jena.atlas.iterator.Iter.next(Iter.java:920)
    at com.hp.hpl.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94)
    at org.apache.clerezza.rdf.jena.storage.JenaGraphAdaptor$1.next(JenaGraphAdaptor.java:115)
    at org.apache.clerezza.rdf.jena.storage.JenaGraphAdaptor$1.next(JenaGraphAdaptor.java:96)
    at org.apache.clerezza.rdf.core.impl.AbstractTripleCollection$1.next(AbstractTripleCollection.java:83)
    at org.apache.clerezza.rdf.core.impl.AbstractTripleCollection$1.next(AbstractTripleCollection.java:72)
    at org.apache.clerezza.rdf.core.access.LockingIterator.next(LockingIterator.java:57)
    at org.apache.clerezza.rdf.core.access.LockingIterator.next(LockingIterator.java:31)
    at org.apache.clerezza.rdf.core.access.security.TcAccessController.removeExistingRequiredReadPermissions(TcAccessController.java:278)
    at org.apache.clerezza.rdf.core.access.security.TcAccessController.setRequiredReadPermissionStrings(TcAccessController.java:153)
    at org.apache.clerezza.rdf.core.access.security.TcAccessController.setRequiredReadPermissions(TcAccessController.java:175)
    at eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.activate(DictionaryAnnotatorEnhancerEngine.java:384)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.apache.felix.scr.impl.helper.BaseMethod.invokeMethod(BaseMethod.java:231)
    at org.apache.felix.scr.impl.helper.BaseMethod.access$500(BaseMethod.java:39)
    at org.apache.felix.scr.impl.helper.BaseMethod$Resolved.invoke(BaseMethod.java:624)
    at org.apache.felix.scr.impl.helper.BaseMethod.invoke(BaseMethod.java:508)
    at org.apache.felix.scr.impl.helper.ActivateMethod.invoke(ActivateMethod.java:149)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.createImplementationObject(SingleComponentManager.java:315)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.createComponent(SingleComponentManager.java:127)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.getService(SingleComponentManager.java:871)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.getServiceInternal(SingleComponentManager.java:838)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:850)
    at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:931)
    at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:895)
    at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1480)
    at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1401)
    at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.trackAdding(ServiceTracker.java:1210)
    at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.track(ServiceTracker.java:1148)
    at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:1432)
    at org.apache.felix.framework.util.EventDispatcher$4.run(EventDispatcher.java:925)
    at java.security.AccessController.doPrivileged(Native Method)
    at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:921)
    at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:793)
    at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:543)
    at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4401)
    at org.apache.felix.framework.Felix.registerService(Felix.java:3411)
    at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:346)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:1003)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:992)
    at org.apache.felix.scr.impl.manager.RegistrationManager.changeRegistration(RegistrationManager.java:134)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.registerService(AbstractComponentManager.java:1044)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:841)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.enable(AbstractComponentManager.java:419)
    at org.apache.felix.scr.impl.config.ConfigurableComponentHolder.enableComponents(ConfigurableComponentHolder.java:376)
    at org.apache.felix.scr.impl.BundleComponentActivator.initialize(BundleComponentActivator.java:172)
    at org.apache.felix.scr.impl.BundleComponentActivator.<init>(BundleComponentActivator.java:120)
    at org.apache.felix.scr.impl.Activator.loadComponents(Activator.java:258)
    at org.apache.felix.scr.impl.Activator.access$000(Activator.java:45)
    at org.apache.felix.scr.impl.Activator$ScrExtension.start(Activator.java:185)
    at org.apache.felix.utils.extender.AbstractExtender.createExtension(AbstractExtender.java:259)
    at org.apache.felix.utils.extender.AbstractExtender.modifiedBundle(AbstractExtender.java:232)
    at org.osgi.util.tracker.BundleTracker$Tracked.customizerModified(BundleTracker.java:479)
    at org.osgi.util.tracker.BundleTracker$Tracked.customizerModified(BundleTracker.java:414)
    at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:232)
    at org.osgi.util.tracker.BundleTracker$Tracked.bundleChanged(BundleTracker.java:443)
    at org.apache.felix.framework.util.EventDispatcher$3.run(EventDispatcher.java:861)
    at java.security.AccessController.doPrivileged(Native Method)
    at org.apache.felix.framework.util.EventDispatcher.invokeBundleListenerCallback(EventDispatcher.java:858)
    at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:789)
    at org.apache.felix.framework.util.EventDispatcher.fireBundleEvent(EventDispatcher.java:514)
    at org.apache.felix.framework.Felix.fireBundleEvent(Felix.java:4385)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:2080)
    at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1279)
    at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)
    at java.lang.Thread.run(Thread.java:745)
09.01.2015 17:28:41.903 *INFO* [FelixStartLevel] org.apache.clerezza.platform.cris Service [org.apache.clerezza.platform.cris.IndexService,257] ServiceEvent REGISTERED

(3)


09.01.2015 17:58:21.026 *ERROR* [FelixStartLevel] eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine There is no registered graph with given uri: urn:fusepool-disease-ontology
09.01.2015 17:58:21.027 *INFO* [FelixStartLevel] eu.fusepool.enhancer.engines.dictionaryannotator Service [eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.163902c6-408c-44a4-8eef-9662fb8e631e,274] ServiceEvent REGISTERED
09.01.2015 17:58:21.123 *INFO* [Thread-49] org.apache.clerezza.platform.BootMonitor The Apache Clerezza Platform is now operational.
09.01.2015 17:58:21.216 *ERROR* [FelixStartLevel] TDB ObjectFileStorage.read[nodes](13314)[filesize=17191][file.size()=17191]: Impossibly large object : 1751461479 bytes > filesize-(loc+SizeOfInt)=3873
09.01.2015 17:58:21.216 *ERROR* [FelixStartLevel] eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine Error happened while creating the dictionary! com.hp.hpl.jena.tdb.base.file.FileException: ObjectFileStorage.read[nodes](13314)[filesize=17191][file.size()=17191]: Impossibly large object : 1751461479 bytes > filesize-(loc+SizeOfInt)=3873
    at com.hp.hpl.jena.tdb.base.objectfile.ObjectFileStorage.read(ObjectFileStorage.java:346)
    at com.hp.hpl.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:79)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:178)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:103)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:74)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:103)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:74)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:55)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67)
    at com.hp.hpl.jena.tdb.lib.TupleLib.triple(TupleLib.java:137)
    at com.hp.hpl.jena.tdb.lib.TupleLib.triple(TupleLib.java:114)
    at com.hp.hpl.jena.tdb.lib.TupleLib.access$000(TupleLib.java:45)
    at com.hp.hpl.jena.tdb.lib.TupleLib$3.convert(TupleLib.java:76)
    at com.hp.hpl.jena.tdb.lib.TupleLib$3.convert(TupleLib.java:72)
    at org.apache.jena.atlas.iterator.Iter$4.next(Iter.java:322)
    at org.apache.jena.atlas.iterator.Iter$4.next(Iter.java:322)
    at org.apache.jena.atlas.iterator.Iter$4.next(Iter.java:322)
    at org.apache.jena.atlas.iterator.Iter.next(Iter.java:920)
    at com.hp.hpl.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94)
    at org.apache.clerezza.rdf.jena.storage.JenaGraphAdaptor$1.next(JenaGraphAdaptor.java:115)
    at org.apache.clerezza.rdf.jena.storage.JenaGraphAdaptor$1.next(JenaGraphAdaptor.java:96)
    at org.apache.clerezza.rdf.core.impl.AbstractTripleCollection$1.next(AbstractTripleCollection.java:83)
    at org.apache.clerezza.rdf.core.impl.AbstractTripleCollection$1.next(AbstractTripleCollection.java:72)
    at org.apache.clerezza.rdf.core.access.LockingIterator.next(LockingIterator.java:57)
    at org.apache.clerezza.rdf.core.access.LockingIterator.next(LockingIterator.java:31)
    at org.apache.clerezza.rdf.core.access.security.TcAccessController.removeExistingRequiredReadPermissions(TcAccessController.java:278)
    at org.apache.clerezza.rdf.core.access.security.TcAccessController.setRequiredReadPermissionStrings(TcAccessController.java:153)
    at org.apache.clerezza.rdf.core.access.security.TcAccessController.setRequiredReadPermissions(TcAccessController.java:175)
    at eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.activate(DictionaryAnnotatorEnhancerEngine.java:384)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.apache.felix.scr.impl.helper.BaseMethod.invokeMethod(BaseMethod.java:231)
    at org.apache.felix.scr.impl.helper.BaseMethod.access$500(BaseMethod.java:39)
    at org.apache.felix.scr.impl.helper.BaseMethod$Resolved.invoke(BaseMethod.java:624)
    at org.apache.felix.scr.impl.helper.BaseMethod.invoke(BaseMethod.java:508)
    at org.apache.felix.scr.impl.helper.ActivateMethod.invoke(ActivateMethod.java:149)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.createImplementationObject(SingleComponentManager.java:315)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.createComponent(SingleComponentManager.java:127)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.getService(SingleComponentManager.java:871)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.getServiceInternal(SingleComponentManager.java:838)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:850)
    at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:931)
    at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:895)
    at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1480)
    at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1401)
    at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.trackAdding(ServiceTracker.java:1210)
    at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.track(ServiceTracker.java:1148)
    at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:1432)
    at org.apache.felix.framework.util.EventDispatcher$4.run(EventDispatcher.java:925)
    at java.security.AccessController.doPrivileged(Native Method)
    at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:921)
    at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:793)
    at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:543)
    at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4401)
    at org.apache.felix.framework.Felix.registerService(Felix.java:3411)
    at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:346)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:1003)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:992)
    at org.apache.felix.scr.impl.manager.RegistrationManager.changeRegistration(RegistrationManager.java:134)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.registerService(AbstractComponentManager.java:1044)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:841)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.enable(AbstractComponentManager.java:419)
    at org.apache.felix.scr.impl.config.ConfigurableComponentHolder.enableComponents(ConfigurableComponentHolder.java:376)
    at org.apache.felix.scr.impl.BundleComponentActivator.initialize(BundleComponentActivator.java:172)
    at org.apache.felix.scr.impl.BundleComponentActivator.<init>(BundleComponentActivator.java:120)
    at org.apache.felix.scr.impl.Activator.loadComponents(Activator.java:258)
    at org.apache.felix.scr.impl.Activator.access$000(Activator.java:45)
    at org.apache.felix.scr.impl.Activator$ScrExtension.start(Activator.java:185)
    at org.apache.felix.utils.extender.AbstractExtender.createExtension(AbstractExtender.java:259)
    at org.apache.felix.utils.extender.AbstractExtender.modifiedBundle(AbstractExtender.java:232)
    at org.osgi.util.tracker.BundleTracker$Tracked.customizerModified(BundleTracker.java:479)
    at org.osgi.util.tracker.BundleTracker$Tracked.customizerModified(BundleTracker.java:414)
    at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:232)
    at org.osgi.util.tracker.BundleTracker$Tracked.bundleChanged(BundleTracker.java:443)
    at org.apache.felix.framework.util.EventDispatcher$3.run(EventDispatcher.java:861)
    at java.security.AccessController.doPrivileged(Native Method)
    at org.apache.felix.framework.util.EventDispatcher.invokeBundleListenerCallback(EventDispatcher.java:858)
    at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:789)
    at org.apache.felix.framework.util.EventDispatcher.fireBundleEvent(EventDispatcher.java:514)
    at org.apache.felix.framework.Felix.fireBundleEvent(Felix.java:4385)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:2080)
    at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1279)
    at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)
    at java.lang.Thread.run(Thread.java:745)
09.01.2015 17:58:21.217 *INFO* [FelixStartLevel] eu.fusepool.enhancer.engines.dictionaryannotator Service [eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.be25d553-ae8a-444b-95cf-862b80679b2d,275] ServiceEvent REGISTERED
09.01.2015 17:58:21.293 *ERROR* [FelixStartLevel] eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine Error happened while creating the dictionary! org.apache.jena.atlas.lib.InternalErrorException: Invalid id node for object (null node): ([0000000000004A4D], [0000000000000193], [0000000000004A2C])
    at com.hp.hpl.jena.tdb.lib.TupleLib.triple(TupleLib.java:139)
    at com.hp.hpl.jena.tdb.lib.TupleLib.triple(TupleLib.java:114)
    at com.hp.hpl.jena.tdb.lib.TupleLib.access$000(TupleLib.java:45)
    at com.hp.hpl.jena.tdb.lib.TupleLib$3.convert(TupleLib.java:76)
    at com.hp.hpl.jena.tdb.lib.TupleLib$3.convert(TupleLib.java:72)
    at org.apache.jena.atlas.iterator.Iter$4.next(Iter.java:322)
    at org.apache.jena.atlas.iterator.Iter$4.next(Iter.java:322)
    at org.apache.jena.atlas.iterator.Iter$4.next(Iter.java:322)
    at org.apache.jena.atlas.iterator.Iter.next(Iter.java:920)
    at com.hp.hpl.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94)
    at org.apache.clerezza.rdf.jena.storage.JenaGraphAdaptor$1.next(JenaGraphAdaptor.java:115)
    at org.apache.clerezza.rdf.jena.storage.JenaGraphAdaptor$1.next(JenaGraphAdaptor.java:96)
    at org.apache.clerezza.rdf.core.impl.AbstractTripleCollection$1.next(AbstractTripleCollection.java:83)
    at org.apache.clerezza.rdf.core.impl.AbstractTripleCollection$1.next(AbstractTripleCollection.java:72)
    at org.apache.clerezza.rdf.core.access.LockingIterator.next(LockingIterator.java:57)
    at org.apache.clerezza.rdf.core.access.LockingIterator.next(LockingIterator.java:31)
    at org.apache.clerezza.rdf.core.access.security.TcAccessController.removeExistingRequiredReadPermissions(TcAccessController.java:278)
    at org.apache.clerezza.rdf.core.access.security.TcAccessController.setRequiredReadPermissionStrings(TcAccessController.java:153)
    at org.apache.clerezza.rdf.core.access.security.TcAccessController.setRequiredReadPermissions(TcAccessController.java:175)
    at eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.activate(DictionaryAnnotatorEnhancerEngine.java:384)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.apache.felix.scr.impl.helper.BaseMethod.invokeMethod(BaseMethod.java:231)
    at org.apache.felix.scr.impl.helper.BaseMethod.access$500(BaseMethod.java:39)
    at org.apache.felix.scr.impl.helper.BaseMethod$Resolved.invoke(BaseMethod.java:624)
    at org.apache.felix.scr.impl.helper.BaseMethod.invoke(BaseMethod.java:508)
    at org.apache.felix.scr.impl.helper.ActivateMethod.invoke(ActivateMethod.java:149)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.createImplementationObject(SingleComponentManager.java:315)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.createComponent(SingleComponentManager.java:127)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.getService(SingleComponentManager.java:871)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.getServiceInternal(SingleComponentManager.java:838)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:850)
    at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:931)
    at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:895)
    at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1480)
    at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1401)
    at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.trackAdding(ServiceTracker.java:1210)
    at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.track(ServiceTracker.java:1148)
    at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:1432)
    at org.apache.felix.framework.util.EventDispatcher$4.run(EventDispatcher.java:925)
    at java.security.AccessController.doPrivileged(Native Method)
    at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:921)
    at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:793)
    at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:543)
    at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4401)
    at org.apache.felix.framework.Felix.registerService(Felix.java:3411)
    at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:346)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:1003)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:992)
    at org.apache.felix.scr.impl.manager.RegistrationManager.changeRegistration(RegistrationManager.java:134)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.registerService(AbstractComponentManager.java:1044)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:841)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.enable(AbstractComponentManager.java:419)
    at org.apache.felix.scr.impl.config.ConfigurableComponentHolder.enableComponents(ConfigurableComponentHolder.java:376)
    at org.apache.felix.scr.impl.BundleComponentActivator.initialize(BundleComponentActivator.java:172)
    at org.apache.felix.scr.impl.BundleComponentActivator.<init>(BundleComponentActivator.java:120)
    at org.apache.felix.scr.impl.Activator.loadComponents(Activator.java:258)
    at org.apache.felix.scr.impl.Activator.access$000(Activator.java:45)
    at org.apache.felix.scr.impl.Activator$ScrExtension.start(Activator.java:185)
    at org.apache.felix.utils.extender.AbstractExtender.createExtension(AbstractExtender.java:259)
    at org.apache.felix.utils.extender.AbstractExtender.modifiedBundle(AbstractExtender.java:232)
    at org.osgi.util.tracker.BundleTracker$Tracked.customizerModified(BundleTracker.java:479)
    at org.osgi.util.tracker.BundleTracker$Tracked.customizerModified(BundleTracker.java:414)
    at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:232)
    at org.osgi.util.tracker.BundleTracker$Tracked.bundleChanged(BundleTracker.java:443)
    at org.apache.felix.framework.util.EventDispatcher$3.run(EventDispatcher.java:861)
    at java.security.AccessController.doPrivileged(Native Method)
    at org.apache.felix.framework.util.EventDispatcher.invokeBundleListenerCallback(EventDispatcher.java:858)
    at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:789)
    at org.apache.felix.framework.util.EventDispatcher.fireBundleEvent(EventDispatcher.java:514)
    at org.apache.felix.framework.Felix.fireBundleEvent(Felix.java:4385)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:2080)
    at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1279)
    at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)
    at java.lang.Thread.run(Thread.java:745)
09.01.2015 17:58:21.295 *INFO* [FelixStartLevel] org.apache.clerezza.platform.graphprovider.content Service [org.apache.clerezza.platform.graphprovider.content.TcPermissionDescriptionsProvider,276] ServiceEvent REGISTERED
09.01.2015 17:58:21.295 *INFO* [FelixStartLevel] org.apache.clerezza.platform.graphprovider.content BundleEvent STARTED
09.01.2015 17:58:21.296 *INFO* [FelixStartLevel] org.apache.clerezza.rdf.file.storage BundleEvent STARTING

...

09.01.2015 17:58:29.913 *INFO* [Thread-51] org.apache.clerezza.rdf.core Service [388] ServiceEvent UNREGISTERING
09.01.2015 18:08:52.357 *INFO* [CM Event Dispatcher (Fire ConfigurationEvent: pid=eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.be25d553-ae8a-444b-95cf-862b80679b2d)] eu.fusepool.enhancer.engines.dictionaryannotator Service [eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.be25d553-ae8a-444b-95cf-862b80679b2d,275] ServiceEvent UNREGISTERING
09.01.2015 18:08:52.438 *ERROR* [CM Event Dispatcher (Fire ConfigurationEvent: pid=eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.be25d553-ae8a-444b-95cf-862b80679b2d)] eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine Error happened while creating the dictionary! java.lang.IllegalArgumentException
    at java.nio.Buffer.limit(Buffer.java:267)
    at com.hp.hpl.jena.tdb.base.objectfile.ObjectFileStorage.read(ObjectFileStorage.java:328)
    at com.hp.hpl.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:79)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:178)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:103)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:74)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:103)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:74)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:55)
    at com.hp.hpl.jena.tdb.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67)
    at com.hp.hpl.jena.tdb.lib.TupleLib.triple(TupleLib.java:137)
    at com.hp.hpl.jena.tdb.lib.TupleLib.triple(TupleLib.java:114)
    at com.hp.hpl.jena.tdb.lib.TupleLib.access$000(TupleLib.java:45)
    at com.hp.hpl.jena.tdb.lib.TupleLib$3.convert(TupleLib.java:76)
    at com.hp.hpl.jena.tdb.lib.TupleLib$3.convert(TupleLib.java:72)
    at org.apache.jena.atlas.iterator.Iter$4.next(Iter.java:322)
    at org.apache.jena.atlas.iterator.Iter$4.next(Iter.java:322)
    at org.apache.jena.atlas.iterator.Iter$4.next(Iter.java:322)
    at org.apache.jena.atlas.iterator.Iter.next(Iter.java:920)
    at com.hp.hpl.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94)
    at org.apache.clerezza.rdf.jena.storage.JenaGraphAdaptor$1.next(JenaGraphAdaptor.java:115)
    at org.apache.clerezza.rdf.jena.storage.JenaGraphAdaptor$1.next(JenaGraphAdaptor.java:96)
    at org.apache.clerezza.rdf.core.impl.AbstractTripleCollection$1.next(AbstractTripleCollection.java:83)
    at org.apache.clerezza.rdf.core.impl.AbstractTripleCollection$1.next(AbstractTripleCollection.java:72)
    at org.apache.clerezza.rdf.core.access.LockingIterator.next(LockingIterator.java:57)
    at org.apache.clerezza.rdf.core.access.LockingIterator.next(LockingIterator.java:31)
    at org.apache.clerezza.rdf.core.access.security.TcAccessController.removeExistingRequiredReadPermissions(TcAccessController.java:278)
    at org.apache.clerezza.rdf.core.access.security.TcAccessController.setRequiredReadPermissionStrings(TcAccessController.java:153)
    at org.apache.clerezza.rdf.core.access.security.TcAccessController.setRequiredReadPermissions(TcAccessController.java:175)
    at eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.activate(DictionaryAnnotatorEnhancerEngine.java:384)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.apache.felix.scr.impl.helper.BaseMethod.invokeMethod(BaseMethod.java:231)
    at org.apache.felix.scr.impl.helper.BaseMethod.access$500(BaseMethod.java:39)
    at org.apache.felix.scr.impl.helper.BaseMethod$Resolved.invoke(BaseMethod.java:624)
    at org.apache.felix.scr.impl.helper.BaseMethod.invoke(BaseMethod.java:508)
    at org.apache.felix.scr.impl.helper.ActivateMethod.invoke(ActivateMethod.java:149)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.createImplementationObject(SingleComponentManager.java:315)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.createComponent(SingleComponentManager.java:127)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.getService(SingleComponentManager.java:871)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.getServiceInternal(SingleComponentManager.java:838)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.getService(SingleComponentManager.java:777)
    at org.apache.felix.framework.ServiceRegistrationImpl.getFactoryUnchecked(ServiceRegistrationImpl.java:308)
    at org.apache.felix.framework.ServiceRegistrationImpl.access$100(ServiceRegistrationImpl.java:35)
    at org.apache.felix.framework.ServiceRegistrationImpl$ServiceFactoryPrivileged.run(ServiceRegistrationImpl.java:372)
    at java.security.AccessController.doPrivileged(Native Method)
    at org.apache.felix.framework.ServiceRegistrationImpl.getService(ServiceRegistrationImpl.java:214)
    at org.apache.felix.framework.ServiceRegistry.getService(ServiceRegistry.java:320)
    at org.apache.felix.framework.Felix.getService(Felix.java:3556)
    at org.apache.felix.framework.BundleContextImpl.getService(BundleContextImpl.java:468)
    at org.apache.stanbol.enhancer.jersey.resource.EnhancementEnginesRootResource$1.addingService(EnhancementEnginesRootResource.java:113)
    at org.apache.stanbol.enhancer.servicesapi.impl.NameBasedServiceTrackingState.addingService(NameBasedServiceTrackingState.java:161)
    at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:932)
    at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:864)
    at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.java:256)
    at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:229)
    at org.osgi.util.tracker.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:894)
    at org.apache.felix.framework.util.EventDispatcher$4.run(EventDispatcher.java:925)
    at java.security.AccessController.doPrivileged(Native Method)
    at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:921)
    at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:793)
    at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:543)
    at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4401)
    at org.apache.felix.framework.Felix.registerService(Felix.java:3411)
    at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:346)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:1003)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:992)
    at org.apache.felix.scr.impl.manager.RegistrationManager.changeRegistration(RegistrationManager.java:134)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.registerService(AbstractComponentManager.java:1044)
    at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:841)
    at org.apache.felix.scr.impl.manager.SingleComponentManager.reconfigure(SingleComponentManager.java:648)
    at org.apache.felix.scr.impl.config.ConfigurableComponentHolder.configurationUpdated(ConfigurableComponentHolder.java:328)
    at org.apache.felix.scr.impl.config.ConfigurationSupport.configurationEvent(ConfigurationSupport.java:290)
    at org.apache.felix.cm.impl.ConfigurationManager$FireConfigurationEvent.sendEvent(ConfigurationManager.java:2032)
    at org.apache.felix.cm.impl.ConfigurationManager$FireConfigurationEvent.run(ConfigurationManager.java:2002)
    at org.apache.felix.cm.impl.UpdateThread.run(UpdateThread.java:103)
    at java.lang.Thread.run(Thread.java:745)
09.01.2015 18:08:52.439 *INFO* [CM Event Dispatcher (Fire ConfigurationEvent: pid=eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.be25d553-ae8a-444b-95cf-862b80679b2d)] eu.fusepool.enhancer.engines.dictionaryannotator Service [eu.fusepool.enhancer.engines.dictionaryannotator.DictionaryAnnotatorEnhancerEngine.be25d553-ae8a-444b-95cf-862b80679b2d,390] ServiceEvent REGISTERED
09.01.2015 18:58:10.595 *INFO* [pool-2-thread-1] org.apache.stanbol.commons.namespaceprefix.provider.prefixcc.PrefixccProvider Load Namespace Prefix Mappings form http://prefix.cc/popular/all.file.txt
gaborremenyi commented 9 years ago

Hi Johannes,

I was on vacation for the better part of this week, but I had time this morning to check out the exceptions you had sent.

The cause of the exceptions seem to be the same, and all three are originally thrown by Jena. com.hp.hpl.jena.tdb.base.file.FileException: ObjectFileStorage.read[nodes](13314)[filesize=14414][file.size()=14414]: Impossibly large object : 1751461479 bytes > filesize-(loc+SizeOfInt)=1096

So I did some google-ing and it turns out that, the Impossibly large object message means that your TDB database is (partially) corrupted. Specifically part of the node table that maps between database internal identifiers and the original RDF terms is corrupted. Any query that touches that part of the node table will see this error, other queries may still run without issue.

So the reason that you see this exception as a Dictionary Matcher error is probably because it queries the graph while initializing, but Jena throws this error back, which then terminates the initialization process.

I also found this in one of the exceptions: org.apache.jena.atlas.lib.InternalErrorException: Invalid id node for object (null node): ([0000000000004A4D], [0000000000000193], [0000000000004A2C])

I google-ed this too, it also refers to TDB corruption.

Is there a way you could test your dataset by manually querying it in the platform? The dictionary matcher uses a simple SPARQL query to retrieve the labels and the URI-s. PREFIX ...; SELECT distinct ?uri ?label WHERE { ?uri a <URI Field> . ?uri <Label Field> ?label . } The URI and Label Field comes from the settings in the configuration page.

I hope this information helps you somewhat. If not we may have to contact the person who integrated Jena into the platform.

Cheers, Gabor

ktk commented 9 years ago

Hi everyone,

Gabors explanation makes sense unfortunately. This usually happens when the platform is crashing. The bad news is that there are no tools of recovering from such an error, which means the current database is broken beyond repair :-(

If you do not have a backup you can do a tdbdump but it will fail at the moment it runs into the first corrupt entry. Let me know if you need help on that.

jhercher commented 9 years ago

Hi all,

thanks for the explanations. It looks as if I corrupted the TDB by killing the platform ungently, or shut down during some important tasks :( I have a backup and will try it again.

Cheers Johannes