There are several possible culprits:
- Past non-transactional use of the database
- Multiple JVMs using the database at the same time
- Actual disk corruption (i.e. failing disk, bad sectors etc)
Rob
On 04/07/2019, 11:04, "Mikael Pesonen" <mikael.peso...@lingsoft.fi>
wrote:
Ok. Is it possible to guess what could cause this?
On 04/07/2019 12:18, Rob Vesse wrote:
> Impossibly Large Object means the database has been corrupted
(more specifically the Node Table). This is non-recoverable although
it may not affect the entire database i.e. any query that tries to
access the affected portion of the node table will fail but other
queries may continue to succeed.
>
>
https://jena.apache.org/documentation/tdb/faqs.html#impossibly-large-object
>
> To recover you would need to reload the database from a known
good backup/dump.
>
> Rob
>
> On 04/07/2019, 10:06, "Mikael Pesonen"
<mikael.peso...@lingsoft.fi> wrote:
>
>
> Any idea how to fix this? upgrade from Jena 3.5 to 3.12
didn't help.
>
> On 02/07/2019 15:01, Mikael Pesonen wrote:
> >
> > We have had the service running for few months without
issues but now
> > got this. So there is exception and also weird #011
happening in log...
> > This same error happens now every time with this query.
> >
> > Jul 2 07:59:37 insight-kaupk java[1043]: [2019-07-02
07:59:37]
> > Fuseki INFO [3457647] POST http://localhost:3030/ds
> > Jul 2 07:59:37 insight-kaupk java[1043]: [2019-07-02
07:59:37]
> > Fuseki INFO [3457647] POST /ds :: '' ::
[application/sparql-query] ?
> > Jul 2 07:59:37 insight-kaupk java[1043]: [2019-07-02
07:59:37]
> > Fuseki INFO [3457647] Query = PREFIX
> > xsd:#011#011<http://www.w3.org/2001/XMLSchema#> PREFIX
> > dc:#011#011<http://purl.org/dc/elements/1.1/> PREFIX
> > dcterms:#011<http://purl.org/dc/terms/> PREFIX
> > dctype:#011<http://purl.org/dc/dcmitype/> PREFIX
> > dcat:#011<http://www.w3.org/ns/dcat#> PREFIX
> > skos:#011<http://www.w3.org/2004/02/skos/core#> PREFIX
> > skosxl:#011<http://www.w3.org/2008/05/skos-xl#> PREFIX
> > isothes:#011<http://purl.org/iso25964/skos-thes#> PREFIX
> > rdfs:#011<http://www.w3.org/2000/01/rdf-schema#> PREFIX
> >
rdf:#011#011<http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX
> >
lsrm:#011<https://resource.lingsoft.fi/ns/resource_meta/> PREFIX
> > ls:#011#011<https://resource.lingsoft.fi/ns/search/> PREFIX
> > lsr:#011#011<https://resource.lingsoft.fi/> PREFIX
> > lsext:#011<https://resource.lingsoft.fi/ns/ext/> PREFIX
> > foaf:#011<http://xmlns.com/foaf/0.1/> PREFIX
> >
nfo:#011#011<http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#>
> > PREFIX
> >
nmo:#011#011<http://www.semanticdesktop.org/ontologies/2007/03/22/nmo#>
> > PREFIX
> >
nie:#011#011<http://www.semanticdesktop.org/ontologies/2007/01/19/nie#>
> > PREFIX
> >
nco:#011#011<http://www.semanticdesktop.org/ontologies/2007/03/22/nco#>
> > PREFIX org:#011#011<http://www.w3.org/ns/org#> PREFIX
> >
cp:#011#011<http://schemas.openxmlformats.org/package/2006/metadata/core-properties>
> > PREFIX mime:#011<http://purl.org/NET/mediatypes/> PREFIX
> >
cdm:#011#011<http://publications.europa.eu/ontology/cdm#> PREFIX
> >
cmr:#011#011<http://publications.europa.eu/ontology/cdm/cmr#> PREFIX
> > owl:#011#011<http://www.w3.org/2002/07/owl#> PREFIX
> > frbr:#011<http://purl.org/vocab/frbr/core#> PREFIX jupo:
> > #011<http://www.yso.fi/onto/jupo/> PREFIX jupo-meta:
> > <http://www.yso.fi/onto/jupo-meta/> PREFIX
> > v:#011#011<http://www.w3.org/2006/vcard/ns#> PREFIX
> > vcard:#011<http://www.w3.org/2006/vcard/ns#> PREFIX
> > lvont:#011<http://lexvo.org/ontology#> PREFIX
> > lexvo:#011<http://lexvo.org/id/> PREFIX
> > dcterms:#011<http://purl.org/dc/terms/> PREFIX
> > dctype:#011<http://purl.org/dc/dcmitype/> PREFIX
> > foaf:#011<http://xmlns.com/foaf/0.1/> SELECT * WHERE
{ #011GRAPH
> > <https://resource.lingsoft.fi/rdf/agents/> #011{
#011#011VALUES ?s {
> > <https://resource.li
> > Jul 2 07:59:37 insight-kaupk java[1043]:
> > ngsoft.fi/2b7f1869-b956-47d2-9e9e-455bedb15ba0> }
#011#011?s a
> > foaf:OnlineAccount . #011#011?s ?p ?o . #011} }
> > Jul 2 07:59:37 insight-kaupk java[1043]: [2019-07-02
07:59:37]
> > Fuseki INFO [3457647] 200 OK (5 ms)
> > Jul 2 07:59:37 insight-kaupk java[1043]: [2019-07-02
07:59:37]
> > Fuseki INFO [3457648] POST http://localhost:3030/ds
> > Jul 2 07:59:37 insight-kaupk java[1043]: [2019-07-02
07:59:37]
> > Fuseki INFO [3457648] POST /ds :: '' ::
[application/sparql-query] ?
> > Jul 2 07:59:37 insight-kaupk java[1043]: [2019-07-02
07:59:37]
> > Fuseki INFO [3457648] Query = PREFIX
> > xsd:#011#011<http://www.w3.org/2001/XMLSchema#> PREFIX
> > dc:#011#011<http://purl.org/dc/elements/1.1/> PREFIX
> > dcterms:#011<http://purl.org/dc/terms/> PREFIX
> > dctype:#011<http://purl.org/dc/dcmitype/> PREFIX
> > dcat:#011<http://www.w3.org/ns/dcat#> PREFIX
> > skos:#011<http://www.w3.org/2004/02/skos/core#> PREFIX
> > skosxl:#011<http://www.w3.org/2008/05/skos-xl#> PREFIX
> > isothes:#011<http://purl.org/iso25964/skos-thes#> PREFIX
> > rdfs:#011<http://www.w3.org/2000/01/rdf-schema#> PREFIX
> >
rdf:#011#011<http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX
> >
lsrm:#011<https://resource.lingsoft.fi/ns/resource_meta/> PREFIX
> > ls:#011#011<https://resource.lingsoft.fi/ns/search/> PREFIX
> > lsr:#011#011<https://resource.lingsoft.fi/> PREFIX
> > lsext:#011<https://resource.lingsoft.fi/ns/ext/> PREFIX
> > foaf:#011<http://xmlns.com/foaf/0.1/> PREFIX
> >
nfo:#011#011<http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#>
> > PREFIX
> >
nmo:#011#011<http://www.semanticdesktop.org/ontologies/2007/03/22/nmo#>
> > PREFIX
> >
nie:#011#011<http://www.semanticdesktop.org/ontologies/2007/01/19/nie#>
> > PREFIX
> >
nco:#011#011<http://www.semanticdesktop.org/ontologies/2007/03/22/nco#>
> > PREFIX org:#011#011<http://www.w3.org/ns/org#> PREFIX
> >
cp:#011#011<http://schemas.openxmlformats.org/package/2006/metadata/core-properties>
> > PREFIX mime:#011<http://purl.org/NET/mediatypes/> PREFIX
> >
cdm:#011#011<http://publications.europa.eu/ontology/cdm#> PREFIX
> >
cmr:#011#011<http://publications.europa.eu/ontology/cdm/cmr#> PREFIX
> > owl:#011#011<http://www.w3.org/2002/07/owl#> PREFIX
> > frbr:#011<http://purl.org/vocab/frbr/core#> PREFIX jupo:
> > #011<http://www.yso.fi/onto/jupo/> PREFIX jupo-meta:
> > <http://www.yso.fi/onto/jupo-meta/> PREFIX
> > v:#011#011<http://www.w3.org/2006/vcard/ns#> PREFIX
> > vcard:#011<http://www.w3.org/2006/vcard/ns#> PREFIX
> > lvont:#011<http://lexvo.org/ontology#> PREFIX
> > lexvo:#011<http://lexvo.org/id/> CONSTRUCT { ?s ?p ?o
} WHERE {
> > #011GRAPH <http://www.lingsoft.fi/resource-meta/> #011{
#011#011{
> > #011#011#011SELECT ?s WHERE #011#011#011{ #011#011#011#011
> >
#011#011#011#011<https://resource.lingsoft.fi/97f1bf15-3fff-4a3d-a439-bc02f702dbc2>
> > dcterms:hasPart ?s . #011#011VALUES ?s
{lsr:1a88fb07-76af-43f8-bac
> > Jul 2 07:59:37 insight-kaupk java[1043]: 5-f136caaa7b02
> > lsr:c490bb36-a7fb-4e68-9a0d-055f75f7d265
> > lsr:a2105a66-c2cf-46c3-bd76-5f7e0650e055
> > lsr:4c3adcc8-371e-4803-8eb6-c4201b9f9c58
> > lsr:a28daae8-96e3-409d-bdf7-9f3ba2a0b0bd
> > lsr:98cb3190-ccbb-4fd2-acd6-2dc8614e0b62
> > lsr:446775fd-f6fd-4270-bcf0-e8b31240c7cc
> > lsr:bd523d3d-2302-4dc1-a056-4ae26e05beb5
> > lsr:e289db0f-e285-4465-9ec3-53ec5aab2ec8
> > lsr:7f829ce7-ba6d-4572-b400-d1e9401bd3e0} #011#011#011#011
> > #011#011#011#011 #011#011#011#011 #011#011#011}
#011#011#011
> > #011#011#011OFFSET 0 LIMIT 10000 #011#011} #011#011?s ?p
?o #011} }
> > Jul 2 07:59:37 insight-kaupk java[1043]: [2019-07-02
07:59:37]
> > TDB ERROR
> >
ObjectFileStorage.read[nodes](219334170)[filesize=220380875][file.size()=220380871]:
> > Impossibly large object : 577075530 bytes >
> > filesize-(loc+SizeOfInt)=1046701
> > Jul 2 07:59:37 insight-kaupk java[1043]: [2019-07-02
07:59:37]
> > BindingTDB ERROR get1(?o)
> > Jul 2 07:59:37 insight-kaupk java[1043]:
> > org.apache.jena.tdb.base.file.FileException:
> >
ObjectFileStorage.read[nodes](219334170)[filesize=220380875][file.size()=220380871]:
> > Impossibly large object : 577075530 bytes >
> > filesize-(loc+SizeOfInt)=1046701
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.tdb.base.objectfile.ObjectFileStorage.read(ObjectFileStorage.java:348)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.tdb.base.objectfile.ObjectFileWrapper.read(ObjectFileWrapper.java:57)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:78)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.tdb.store.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:186)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.tdb.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:111)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.tdb.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:70)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.tdb.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:128)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.tdb.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:82)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.tdb.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:50)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.tdb.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.tdb.solver.BindingTDB.get1(BindingTDB.java:122)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.sparql.engine.binding.BindingBase.get(BindingBase.java:121)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.sparql.engine.binding.BindingFactory.materialize(BindingFactory.java:60)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.tdb.solver.QueryEngineTDB$QueryIteratorMaterializeBinding.moveToNextBinding(QueryEngineTDB.java:131)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.sparql.engine.iterator.QueryIteratorBase.nextBinding(QueryIteratorBase.java:156)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.moveToNextBinding(QueryIteratorWrapper.java:42)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.sparql.engine.iterator.QueryIteratorBase.nextBinding(QueryIteratorBase.java:156)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.sparql.engine.iterator.QueryIteratorBase.next(QueryIteratorBase.java:131)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.sparql.engine.iterator.QueryIteratorBase.next(QueryIteratorBase.java:40)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> > org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:270)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.ext.com.google.common.collect.MultitransformedIterator.hasNext(MultitransformedIterator.java:52)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.ext.com.google.common.collect.MultitransformedIterator.hasNext(MultitransformedIterator.java:50)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> > java.util.Iterator.forEachRemaining(Iterator.java:115)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.sparql.engine.QueryExecutionBase.execConstructDataset(QueryExecutionBase.java:243)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.sparql.engine.QueryExecutionBase.execConstructDataset(QueryExecutionBase.java:236)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.fuseki.servlets.SPARQL_Query.executeQuery(SPARQL_Query.java:331)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.java:270)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.fuseki.servlets.SPARQL_Query.executeBody(SPARQL_Query.java:239)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.java:219)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.fuseki.servlets.ActionSPARQL.executeLifecycle(ActionSPARQL.java:132)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.fuseki.servlets.SPARQL_UberServlet.executeRequest(SPARQL_UberServlet.java:356)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.fuseki.servlets.SPARQL_UberServlet.executeAction(SPARQL_UberServlet.java:220)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.fuseki.servlets.ActionSPARQL.execCommonWorker(ActionSPARQL.java:83)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:82)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:73)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1637)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1637)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.fuseki.servlets.CrossOriginFilter.handle(CrossOriginFilter.java:285)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.apache.jena.fuseki.servlets.CrossOriginFilter.doFilter(CrossOriginFilter.java:248)
> > Jul 2 07:59:37 insight-kaupk java[1043]: #011at
> >
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1629)
> >
>
> --
> Lingsoft - 30 years of Leading Language Management
>
> www.lingsoft.fi
>
> Speech Applications - Language Management - Translation -
Reader's and Writer's Tools - Text Tools - E-books and M-books
>
> Mikael Pesonen
> System Engineer
>
> e-mail: mikael.peso...@lingsoft.fi
> Tel. +358 2 279 3300
>
> Time zone: GMT+2
>
> Helsinki Office
> Eteläranta 10
> FI-00130 Helsinki
> FINLAND
>
> Turku Office
> Kauppiaskatu 5 A
> FI-20100 Turku
> FINLAND
>
>
>
>
>
>
--
Lingsoft - 30 years of Leading Language Management
www.lingsoft.fi
Speech Applications - Language Management - Translation -
Reader's and Writer's Tools - Text Tools - E-books and M-books
Mikael Pesonen
System Engineer
e-mail: mikael.peso...@lingsoft.fi
Tel. +358 2 279 3300
Time zone: GMT+2
Helsinki Office
Eteläranta 10
FI-00130 Helsinki
FINLAND
Turku Office
Kauppiaskatu 5 A
FI-20100 Turku
FINLAND
