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AllegroGraph: issues with long running queries. (Error: Stack overflow (signal 1000)) #331

Open alexskr opened 1 day ago

alexskr commented 1 day ago

AllegroGraph version 8.0.1

We have noticed a behavior where seemingly simple queries run for exorbitantly long time.

kind: backend
port: 34151
name: bioportal
catalog: false
uuid:
description: SELECT DISTINCT ?id ?attributeProperty ?attributeObject FROM <http://data.bioontology.org/ontologies/CODO/submissions/6> WHERE { ?id a <http://www.w3.org/2002/07/owl#Class> . OPTIONAL { { ?id <http://www.w3.org/2004/02/skos/core#prefLabel> ?attributeObject . BIND( "prefLabel" as ?attributeProperty) } UNION  { ?id <http://data.bioontology.org/metadata/def/prefLabel> ?attributeObject . BIND( "prefLabel" as ?attributeProperty) } UNION  { ?id <http://www.w3.org/2004/02/skos/core#definition> ?attributeObject . BIND( "definition" as ?attributeProperty) } UNION  { ?id <http://purl.obolibrary.org/obo/IAO_0000115> ?attributeObject . BIND( "definition" as ?attributeProperty) } UNION  { ?id <http://www.w3.org/2000/01/rdf-schema#comment> ?attributeObject . BIND( "definition" as ?attributeProperty) } UNION  { ?id <http://purl.obolibrary.org/obo/def> ?attributeObject . BIND( "definition" as ?attributeProperty) } UNION  { ?id <http://www.w3.org/2004/02/skos/core#altLabel> ?attributeObject . BIND( "synonym" as ?attributeProperty) } UNION  { ?id <http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> ?attributeObject . BIND( "synonym" as ?attributeProperty) } UNION  { ?id <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> ?attributeObject . BIND( "synonym" as ?attributeProperty) } UNION  { ?id <http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> ?attributeObject . BIND( "synonym" as ?attributeProperty) } UNION  { ?id <http://purl.obolibrary.org/obo/synonym> ?attributeObject . BIND( "synonym" as ?attributeProperty) } UNION  { ?id <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> ?attributeObject . BIND( "synonym" as ?attributeProperty) } UNION  { ?id <http://www.w3.org/2002/07/owl#deprecated> ?attributeObject . BIND( "obsolete" as ?attributeProperty) } } FILTER(?id = <http://snomed.info/id/404684003>) }
ageInSeconds: 274.931699542d0
status: starting

kind: backend
port: 34151
name: bioportal
catalog: false
uuid:
description: SELECT ?c WHERE {
GRAPH <http://data.bioontology.org/ontologies/EFO/submissions/270> {
  ?c <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://www.ebi.ac.uk/efo/EFO_0001305> .
}
}
LIMIT 1

ageInSeconds: 2494.349124234d0
status: starting

kind: backend
port: 34151
name: bioportal
catalog: false
uuid:
description: SELECT DISTINCT ?id ?attributeProperty ?attributeObject FROM <http://data.bioontology.org/ontologies/CIINTEADO/submissions/2> WHERE { ?id a <http://www.w3.org/2002/07/owl#Class> . OPTIONAL { { ?id <http://www.w3.org/2004/02/skos/core#prefLabel> ?attributeObject . BIND( "prefLabel" as ?attributeProperty) } UNION  { ?id <http://data.bioontology.org/metadata/def/prefLabel> ?attributeObject . BIND( "prefLabel" as ?attributeProperty) } } FILTER(?id = <http://purl.obolibrary.org/obo/CiinteA_0000792> || ?id = <http://purl.obolibrary.org/obo/CiinteA_0000464> || ?id = <http://purl.obolibrary.org/obo/CiinteA_0000411>) }
ageInSeconds: 2648.314144988d0
status: starting

kind: backend
port: 34151
name: bioportal
catalog: false
uuid:
description: SELECT ?c WHERE {
GRAPH <http://data.bioontology.org/ontologies/CCO/submissions/6> {
  ?c <http://data.bioontology.org/metadata/treeView> <http://purl.obolibrary.org/obo/GO_0044785> .
}
}
LIMIT 1

ageInSeconds: 8545.499167287d0
status: starting

kind: backend
port: 34151
name: bioportal
catalog: false
uuid:
description: SELECT ?c WHERE {
GRAPH <http://data.bioontology.org/ontologies/FNS-H/submissions/2> {
  ?c <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.obolibrary.org/obo/UBERON_0036172> .
}
}
LIMIT 1

ageInSeconds: 9677.344251983d0
status: starting

kind: backend
port: 34151
name: bioportal
catalog: false
uuid:
description: SELECT DISTINCT ?id ?attributeProperty ?attributeObject FROM <http://data.bioontology.org/ontologies/BERO/submissions/3> WHERE { ?id a <http://www.w3.org/2002/07/owl#Class> . OPTIONAL { { ?id <http://www.w3.org/2004/02/skos/core#prefLabel> ?attributeObject . BIND( "prefLabel" as ?attributeProperty) } UNION  { ?id <http://data.bioontology.org/metadata/def/prefLabel> ?attributeObject . BIND( "prefLabel" as ?attributeProperty) } } FILTER(?id = <http://purl.obolibrary.org/obo/MESH_D010070>) }
ageInSeconds: 17527.026513174d0
status: starting

kind: backend
port: 34151
name: bioportal
catalog: false
uuid:
description: SELECT DISTINCT ?id ?attributeProperty ?attributeObject FROM <http://data.bioontology.org/ontologies/SCTSPA/submissions/24> WHERE { ?id a <http://www.w3.org/2002/07/owl#Class> . OPTIONAL { { ?attributeObject <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?id . BIND( "children" as ?attributeProperty) } } FILTER(?id = <http://purl.bioontology.org/ontology/SCTSPA/1149522000> || ?id = <http://purl.bioontology.org/ontology/SCTSPA/778303008> || ?id = <http://purl.bioontology.org/ontology/SCTSPA/767879002> || ?id = <http://purl.bioontology.org/ontology/SCTSPA/767934002> || ?id = <http://purl.bioontology.org/ontology/SCTSPA/108572003> || ?id = <http://purl.bioontology.org/ontology/SCTSPA/768607004>) }
ageInSeconds: 17842.703956521d0
status: starting

kind: backend
port: 34151
name: bioportal
catalog: false
uuid:
description: SELECT DISTINCT ?id ?attributeProperty ?attributeObject FROM <http://data.bioontology.org/ontologies/COVID-19/submissions/4> WHERE { ?id a <http://www.w3.org/2002/07/owl#Class> . OPTIONAL { { ?id <http://www.w3.org/2004/02/skos/core#prefLabel> ?attributeObject . BIND( "prefLabel" as ?attributeProperty) } UNION  { ?id <http://data.bioontology.org/metadata/def/prefLabel> ?attributeObject . BIND( "prefLabel" as ?attributeProperty) } } FILTER(?id = <http://purl.obolibrary.org/obo/BFO_0000141> || ?id = <http://purl.obolibrary.org/obo/BFO_0000040> || ?id = <http://purl.obolibrary.org/obo/OGMS_0000032> || ?id = <http://purl.obolibrary.org/obo/OGMS_0000031> || ?id = <http://purl.obolibrary.org/obo/BFO_0000034> || ?id = <http://purl.obolibrary.org/obo/NCIT_C17103> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000570> || ?id = <https://bio.scai.fraunhofer.de/ontology/COVID_0000034> || ?id = <http://purl.obolibrary.org/obo/NCIT_C79748> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000061> || ?id = <http://purl.obolibrary.org/obo/SYMP_0019174> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000692> || ?id = <http://purl.obolibrary.org/obo/BFO_0000004> || ?id = <http://purl.obolibrary.org/obo/BFO_0000031> || ?id = <http://purl.obolibrary.org/obo/BFO_0000020> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000613> || ?id = <http://purl.obolibrary.org/obo/SYMP_0019177> || ?id = <http://purl.obolibrary.org/obo/SYMP_0019176> || ?id = <https://bio.scai.fraunhofer.de/ontology/COVID_0000032> || ?id = <https://bio.scai.fraunhofer.de/ontology/COVID_0000112> || ?id = <http://purl.obolibrary.org/obo/SYMP_0017795> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000459> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000528> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000488> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000480> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000724> || ?id = <https://bio.scai.fraunhofer.de/ontology/COVID_0000059> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000514> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000597> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000567> || ?id = <https://bio.scai.fraunhofer.de/ontology/COVID_0000099> || ?id = <https://bio.scai.fraunhofer.de/ontology/COVID_0000081> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000410> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000473> || ?id = <http://purl.obolibrary.org/obo/BFO_0000017> || ?id = <http://purl.obolibrary.org/obo/BFO_0000019> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000387> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000538> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000107> || ?id = <http://purl.obolibrary.org/obo/OBI_0000097> || ?id = <http://purl.obolibrary.org/obo/BFO_0000023> || ?id = <http://purl.obolibrary.org/obo/BFO_0000016> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000462> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000450> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000041> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000095> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000292> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000287> || ?id = <http://purl.obolibrary.org/obo/OGMS_0000029> || ?id = <http://purl.obolibrary.org/obo/BFO_0000015> || ?id = <http://purl.obolibrary.org/obo/BFO_0000008> || ?id = <http://purl.obolibrary.org/obo/BFO_0000011> || ?id = <http://purl.obolibrary.org/obo/BFO_0000035> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000178> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000892> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000551> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000124> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000734> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000614> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000431> || ?id = <http://purl.obolibrary.org/obo/NCIT_C126929> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000517> || ?id = <https://bio.scai.fraunhofer.de/ontology/COVID_0000100> || ?id = <http://purl.obolibrary.org/obo/NCIT_C85859> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000598> || ?id = <http://purl.obolibrary.org/obo/NCIT_C50747> || ?id = <http://purl.obolibrary.org/obo/SYMP_0000146> || ?id = <http://purl.obolibrary.org/obo/SYMP_0019138> || ?id = <http://purl.obolibrary.org/obo/SYMP_0019139> || ?id = <http://purl.obolibrary.org/obo/PATO_0002146> || ?id = <http://purl.obolibrary.org/obo/HP_0000118> || ?id = <http://purl.obolibrary.org/obo/OGI_0000012> || ?id = <https://bio.scai.fraunhofer.de/ontology/COVID_0000103> || ?id = <http://purl.obolibrary.org/obo/BFO_0000145> || ?id = <http://purl.obolibrary.org/obo/PATO_0002003> || ?id = <http://purl.obolibrary.org/obo/IAO_0000030>) }
ageInSeconds: 21227.144926974d0
status: starting

kind: backend
port: 34151
name: bioportal
catalog: false
uuid:
description: SELECT ?c WHERE {
GRAPH <http://data.bioontology.org/ontologies/NMOBR/submissions/36> {
  ?c <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://neuromorpho.org/ontologies/vertebrateH.owl#NMOBr_577> .
}
}
LIMIT 1

ageInSeconds: 22743.192764358d0
status: starting

kind: backend
port: 34151
name: bioportal
catalog: false
uuid:
description: SELECT DISTINCT ?id ?attributeProperty ?attributeObject FROM <http://data.bioontology.org/metadata/Metrics> FROM <http://data.bioontology.org/metadata/OntologySubmission> WHERE { ?id a <http://data.bioontology.org/metadata/Metrics> . OPTIONAL { { ?id <http://data.bioontology.org/metadata/created> ?attributeObject . BIND( "created" as ?attributeProperty) } UNION  { ?id <http://data.bioontology.org/metadata/classes> ?attributeObject . BIND( "classes" as ?attributeProperty) } UNION  { ?id <http://data.bioontology.org/metadata/individuals> ?attributeObject . BIND( "individuals" as ?attributeProperty) } UNION  { ?id <http://data.bioontology.org/metadata/properties> ?attributeObject . BIND( "properties" as ?attributeProperty) } UNION  { ?id <http://data.bioontology.org/metadata/maxDepth> ?attributeObject . BIND( "maxDepth" as ?attributeProperty) } UNION  { ?id <http://data.bioontology.org/metadata/maxChildCount> ?attributeObject . BIND( "maxChildCount" as ?attributeProperty) } UNION  { ?id <http://data.bioontology.org/metadata/averageChildCount> ?attributeObject . BIND( "averageChildCount" as ?attributeProperty) } UNION  { ?id <http://data.bioontology.org/metadata/classesWithOneChild> ?attributeObject . BIND( "classesWithOneChild" as ?attributeProperty) } UNION  { ?id <http://data.bioontology.org/metadata/classesWithMoreThan25Children> ?attributeObject . BIND( "classesWithMoreThan25Children" as ?attributeProperty) } UNION  { ?id <http://data.bioontology.org/metadata/classesWithNoDefinition> ?attributeObject . BIND( "classesWithNoDefinition" as ?attributeProperty) } UNION  { ?attributeObject <http://data.bioontology.org/metadata/metrics> ?id . BIND( "submission" as ?attributeProperty) } } FILTER(?id = <http://data.bioontology.org/ontologies/EDAMT/submissions/1/metrics>) }
ageInSeconds: 24468.697892252d0
status: starting

kind: backend
port: 34151
name: bioportal
catalog: false
uuid:
description: SELECT ?c WHERE {
GRAPH <http://data.bioontology.org/ontologies/OMIT/submissions/41> {
  ?c <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.obolibrary.org/obo/OMIT_0007291> .
}
}
LIMIT 1

ageInSeconds: 27247.444147465d0
status: starting

kind: backend
port: 34151
name: bioportal
catalog: false
uuid:
description: SELECT ?c WHERE {
GRAPH <http://data.bioontology.org/ontologies/NMOSP/submissions/22> {
  ?c <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://neuromorpho.org/ontologies/NMOSp.owl#NMOSp_1062> .
}
}
LIMIT 1

ageInSeconds: 27369.587565357d0
status: starting

kind: backend
port: 34151
name: bioportal
catalog: false
uuid:
description: SELECT ?c WHERE {
GRAPH <http://data.bioontology.org/ontologies/GO-PLUS/submissions/701> {
  ?c <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.obolibrary.org/obo/CHEBI_55336> .
}
}
LIMIT 1

ageInSeconds: 34877.985947235d0
status: starting

kind: backend
port: 34151
name: bioportal
catalog: false
uuid:
description: SELECT DISTINCT ?id ?attributeProperty ?attributeObject FROM <http://data.bioontology.org/ontologies/MA/submissions/128> WHERE { ?id a <http://www.w3.org/2002/07/owl#Class> . OPTIONAL { { ?id <http://www.w3.org/2004/02/skos/core#prefLabel> ?attributeObject . BIND( "prefLabel" as ?attributeProperty) } UNION  { ?id <http://data.bioontology.org/metadata/def/prefLabel> ?attributeObject . BIND( "prefLabel" as ?attributeProperty) } } FILTER(?id = <http://purl.obolibrary.org/obo/MA_0000218> || ?id = <http://purl.obolibrary.org/obo/MA_0000217> || ?id = <http://purl.obolibrary.org/obo/MA_0000167> || ?id = <http://purl.obolibrary.org/obo/MA_0002406> || ?id = <http://purl.obolibrary.org/obo/MA_0002407> || ?id = <http://purl.obolibrary.org/obo/MA_0002408>) }
ageInSeconds: 35779.33663255d0
status: starting

server logs have: An unexpected error has occurred. If possible, please leave AllegroGraph running and contact support@franz.com for debugging assistance. Error: Stack overflow (signal 1000)

[2024-11-21T03:57:31.157 p7694 transaction-log] Store "bioportal", Begin checkpoint (interval elapsed)
[2024-11-21T03:57:31.157 p7694 transaction-log] Store "bioportal", Transaction log lock acquired
[2024-11-21T03:57:31.157 p7694 transaction-log] Store "bioportal", Generation: 577427
[2024-11-21T03:57:33.282 p7694 checkpoint-bitmap] Store "bioportal", Checkpointing deleted triple bitmap 0 (rec size: 1.5 MiB)
[2024-11-21T03:57:33.290 p7694 checkpoint-mem-chunk] Store "bioportal", Checkpointing mem chunk 0, 95 triples
[2024-11-21T03:57:34.138 p7694 transaction-log] Store "bioportal", End checkpoint.  Total time: 0h0m2s, Wait: 258us, Work: 0h0m2s
[2024-11-21T05:22:34.476 p7694 transaction-log] Store "bioportal", Begin checkpoint (interval elapsed)
[2024-11-21T05:22:34.477 p7694 transaction-log] Store "bioportal", Transaction log lock acquired
[2024-11-21T05:22:34.477 p7694 transaction-log] Store "bioportal", Generation: 577428
[2024-11-21T05:22:36.614 p7694 checkpoint-bitmap] Store "bioportal", Checkpointing deleted triple bitmap 0 (rec size: 1.5 MiB)
[2024-11-21T05:22:36.622 p7694 checkpoint-mem-chunk] Store "bioportal", Checkpointing mem chunk 0, 103 triples
[2024-11-21T05:22:37.649 p7694 transaction-log] Store "bioportal", Done writing to tlog-47f266a7-6068-fac4-1aa8-005056010183-4191
[2024-11-21T05:22:37.664 p7694 transaction-log] Store "bioportal", End checkpoint.  Total time: 0h0m3s, Wait: 283us, Work: 0h0m3s
[2024-11-21T05:37:45.835 p7645 http] The number of free http workers is 2, keep-alive may not be honoured.
[2024-11-21T05:40:08.521 p7645 http] The number of free http workers is 2, keep-alive may not be honoured.
[2024-11-21T05:40:08.535 p7645 http] The number of free http workers is 1, keep-alive may not be honoured.
[2024-11-21T05:51:05.254 p7645 http] The number of free http workers is 2, keep-alive may not be honoured.
[2024-11-21T05:51:05.281 p7645 http] The number of free http workers is 0, keep-alive may not be honoured.
[2024-11-21T05:51:05.295 p7645 http] Creating http worker thread #60
[2024-11-21T05:51:05.295 p7645 http] Creating http worker thread #61
[2024-11-21T05:51:05.636 p7645 http] Creating http worker thread #62
[2024-11-21T05:51:05.659 p7645 http] Creating http worker thread #63
[2024-11-21T05:51:05.673 p7645 http] Creating http worker thread #64
[2024-11-21T05:51:05.677 p7645 http] Creating http worker thread #65
[2024-11-21T05:51:05.677 p7645 http] Creating http worker thread #66
[2024-11-21T05:51:07.321 p7645 http] Creating http worker thread #67
[2024-11-21T05:51:12.051 p7663 error-reporting] An unexpected error has occurred.  If possible, please leave AllegroGraph running and contact support@franz.com for debugging assistance. Error: Stack overflow (signal 1000)
[2024-11-21T05:51:12.052 p7663 error-reporting] Registers at the time of the fault:\n register saving not enabled
[2024-11-21T05:51:12.169 p7663 backtrace] Backtrace:
Version: AllegroGraph Server Edition 8.0.1 (rc4), built on January 16, 2024 19:16:58 GMT-0800
Process: backend 7
Thread: 7-aserve-worker

Evaluation stack:

[2024-11-21T06:15:25.601 p7645 http] The number of free http workers is 2, keep-alive may not be honoured.
[2024-11-21T06:15:25.622 p7645 http] The number of free http workers is 1, keep-alive may not be honoured.
[2024-11-21T06:17:37.823 p7694 transaction-log] Store "bioportal", Begin checkpoint (interval elapsed)
[2024-11-21T06:17:37.824 p7694 transaction-log] Store "bioportal", Transaction log lock acquired
[2024-11-21T06:17:37.824 p7694 transaction-log] Store "bioportal", Generation: 577429
[2024-11-21T06:17:39.996 p7694 checkpoint-bitmap] Store "bioportal", Checkpointing deleted triple bitmap 0 (rec size: 1.5 MiB)
[2024-11-21T06:17:40.004 p7694 checkpoint-mem-chunk] Store "bioportal", Checkpointing mem chunk 0, 112 triples
[2024-11-21T06:17:40.880 p7694 transaction-log] Store "bioportal", End checkpoint.  Total time: 0h0m3s, Wait: 263us, Work: 0h0m3s
[2024-11-21T06:47:58.047 p7645 http] The number of free http workers is 2, keep-alive may not be honoured.
[2024-11-21T06:52:40.983 p7694 transaction-log] Store "bioportal", Begin checkpoint (interval elapsed)
[2024-11-21T06:52:40.983 p7694 transaction-log] Store "bioportal", Transaction log lock acquired
[2024-11-21T06:52:40.983 p7694 transaction-log] Store "bioportal", Generation: 577430
[2024-11-21T06:52:43.129 p7694 checkpoint-bitmap] Store "bioportal", Checkpointing deleted triple bitmap 0 (rec size: 1.5 MiB)
[2024-11-21T06:52:43.137 p7694 checkpoint-mem-chunk] Store "bioportal", Checkpointing mem chunk 0, 121 triples
[2024-11-21T06:52:44.165 p7694 transaction-log] Store "bioportal", Done writing to tlog-47f266a7-6068-fac4-1aa8-005056010183-4192
[2024-11-21T06:52:44.178 p7694 transaction-log] Store "bioportal", End checkpoint.  Total time: 0h0m3s, Wait: 250us, Work: 0h0m3s
[2024-11-21T06:57:44.193 p7694 transaction-log] Store "bioportal", Begin checkpoint (interval elapsed)
[2024-11-21T06:57:44.194 p7694 transaction-log] Store "bioportal", Transaction log lock acquired
[2024-11-21T06:57:44.194 p7694 transaction-log] Store "bioportal", Generation: 577431
[2024-11-21T06:57:46.328 p7694 checkpoint-bitmap] Store "bioportal", Checkpointing deleted triple bitmap 0 (rec size: 1.5 MiB)
[2024-11-21T06:57:46.336 p7694 checkpoint-mem-chunk] Store "bioportal", Checkpointing mem chunk 0, 130 triples
[2024-11-21T06:57:47.426 p7694 transaction-log] Store "bioportal", End checkpoint.  Total time: 0h0m3s, Wait: 284us, Work: 0h0m3s
[2024-11-21T07:02:47.453 p7694 transaction-log] Store "bioportal", Begin checkpoint (interval elapsed)
[2024-11-21T07:02:47.454 p7694 transaction-log] Store "bioportal", Transaction log lock acquired
[2024-11-21T07:02:47.454 p7694 transaction-log] Store "bioportal", Generation: 577432
[2024-11-21T07:02:49.599 p7694 checkpoint-bitmap] Store "bioportal", Checkpointing deleted triple bitmap 0 (rec size: 1.5 MiB)
[2024-11-21T07:02:49.607 p7694 checkpoint-mem-chunk] Store "bioportal", Checkpointing mem chunk 0, 138 triples
[2024-11-21T07:02:50.591 p7694 transaction-log] Store "bioportal", Done writing to tlog-47f266a7-6068-fac4-1aa8-005056010183-4193
[2024-11-21T07:02:50.604 p7694 transaction-log] Store "bioportal", End checkpoint.  Total time: 0h0m3s, Wait: 250us, Work: 0h0m3s
[2024-11-21T07:42:50.750 p7694 transaction-log] Store "bioportal", Begin checkpoint (interval elapsed)
[2024-11-21T07:42:50.750 p7694 transaction-log] Store "bioportal", Transaction log lock acquired
[2024-11-21T07:42:50.750 p7694 transaction-log] Store "bioportal", Generation: 577433
[2024-11-21T07:42:52.877 p7694 checkpoint-bitmap] Store "bioportal", Checkpointing deleted triple bitmap 0 (rec size: 1.5 MiB)
[2024-11-21T07:42:52.884 p7694 checkpoint-mem-chunk] Store "bioportal", Checkpointing mem chunk 0, 146 triples
[2024-11-21T07:42:53.734 p7694 transaction-log] Store "bioportal", End checkpoint.  Total time: 0h0m2s, Wait: 256us, Work: 0h0m2s
[2024-11-21T08:52:54.008 p7694 transaction-log] Store "bioportal", Begin checkpoint (interval elapsed)
[2024-11-21T08:52:54.008 p7694 transaction-log] Store "bioportal", Transaction log lock acquired
[2024-11-21T08:52:54.008 p7694 transaction-log] Store "bioportal", Generation: 577434
[2024-11-21T08:52:56.151 p7694 checkpoint-bitmap] Store "bioportal", Checkpointing deleted triple bitmap 0 (rec size: 1.5 MiB)
[2024-11-21T08:52:56.159 p7694 checkpoint-mem-chunk] Store "bioportal", Checkpointing mem chunk 0, 155 triples
[2024-11-21T08:52:57.164 p7694 transaction-log] Store "bioportal", Done writing to tlog-47f266a7-6068-fac4-1aa8-005056010183-4194
[2024-11-21T08:52:57.176 p7694 transaction-log] Store "bioportal", End checkpoint.  Total time: 0h0m3s, Wait: 267us, Work: 0h0m3s
[2024-11-21T09:17:57.251 p7694 transaction-log] Store "bioportal", Begin checkpoint (interval elapsed)
[2024-11-21T09:17:57.252 p7694 transaction-log] Store "bioportal", Transaction log lock acquired
[2024-11-21T09:17:57.252 p7694 transaction-log] Store "bioportal", Generation: 577435
[2024-11-21T09:17:59.463 p7694 checkpoint-bitmap] Store "bioportal", Checkpointing deleted triple bitmap 0 (rec size: 1.5 MiB)
[2024-11-21T09:17:59.471 p7694 checkpoint-mem-chunk] Store "bioportal", Checkpointing mem chunk 0, 162 triples
[2024-11-21T09:18:00.567 p7694 transaction-log] Store "bioportal", End checkpoint.  Total time: 0h0m3s, Wait: 269us, Work: 0h0m3s
[2024-11-21T09:43:00.649 p7694 transaction-log] Store "bioportal", Begin checkpoint (interval elapsed)
[2024-11-21T09:43:00.649 p7694 transaction-log] Store "bioportal", Transaction log lock acquired
[2024-11-21T09:43:00.649 p7694 transaction-log] Store "bioportal", Generation: 577440
[2024-11-21T09:43:02.815 p7694 checkpoint-bitmap] Store "bioportal", Checkpointing deleted triple bitmap 0 (rec size: 1.5 MiB)
[2024-11-21T09:43:02.823 p7694 checkpoint-mem-chunk] Store "bioportal", Checkpointing mem chunk 0, 186 triples
[2024-11-21T09:43:03.835 p7694 transaction-log] Store "bioportal", Done writing to tlog-47f266a7-6068-fac4-1aa8-005056010183-4195
[2024-11-21T09:43:03.852 p7694 transaction-log] Store "bioportal", End checkpoint.  Total time: 0h0m3s, Wait: 267us, Work: 0h0m3s
[2024-11-21T09:48:03.862 p7694 transaction-log] Store "bioportal", Begin checkpoint (interval elapsed)
[2024-11-21T09:48:03.863 p7694 transaction-log] Store "bioportal", Transaction log lock acquired
[2024-11-21T09:48:03.863 p7694 transaction-log] Store "bioportal", Generation: 577443
[2024-11-21T09:48:05.993 p7694 checkpoint-bitmap] Store "bioportal", Checkpointing deleted triple bitmap 0 (rec size: 1.5 MiB)
[2024-11-21T09:48:06.000 p7694 checkpoint-mem-chunk] Store "bioportal", Checkpointing mem chunk 0, 207 triples
[2024-11-21T09:48:06.900 p7694 transaction-log] Store "bioportal", End checkpoint.  Total time: 0h0m3s, Wait: 265us, Work: 0h0m3s
[2024-11-21T09:53:06.907 p7694 transaction-log] Store "bioportal", Begin checkpoint (interval elapsed)
[2024-11-21T09:53:06.908 p7694 transaction-log] Store "bioportal", Transaction log lock acquired
[2024-11-21T09:53:06.908 p7694 transaction-log] Store "bioportal", Generation: 577445
[2024-11-21T09:53:09.032 p7694 checkpoint-bitmap] Store "bioportal", Checkpointing deleted triple bitmap 0 (rec size: 1.5 MiB)
[2024-11-21T09:53:09.039 p7694 checkpoint-mem-chunk] Store "bioportal", Checkpointing mem chunk 0, 210 triples
[2024-11-21T09:53:10.041 p7694 transaction-log] Store "bioportal", Done writing to tlog-47f266a7-6068-fac4-1aa8-005056010183-4196
[2024-11-21T09:53:10.054 p7694 transaction-log] Store "bioportal", End checkpoint.  Total time: 0h0m3s, Wait: 270us, Work: 0h0m3s
[2024-11-21T10:30:37.331 p7664 error-reporting] An unexpected error has occurred.  If possible, please leave AllegroGraph running and contact support@franz.com for debugging assistance. Error: Stack overflow (signal 1000)
[2024-11-21T10:30:37.331 p7664 error-reporting] Registers at the time of the fault:\n register saving not enabled
[2024-11-21T10:30:37.364 p7664 backtrace] Backtrace:
Version: AllegroGraph Server Edition 8.0.1 (rc4), built on January 16, 2024 19:16:58 GMT-0800
Process: backend 8
Thread: 5-aserve-worker

Evaluation stack:

[2024-11-21T10:57:19.545 p7645 aserve] While reading http request from xxx.xxx.xxx.xx:\n "Connection reset by peer" (errno 104) occurred while\n reading buffer for\n #<multivalent hiper socket connected from xxxxxxxx:/10035\n   to xxxxxxx/38250 @ #x1000a024132>.
[2024-11-21T11:01:51.282 p7663 error-reporting] An unexpected error has occurred.  If possible, please leave AllegroGraph running and contact support@franz.com for debugging assistance. Error: Stack overflow (signal 1000)
[2024-11-21T11:01:51.282 p7663 error-reporting] Registers at the time of the fault:\n register saving not enabled
[2024-11-21T11:01:51.287 p7663 backtrace] Backtrace:
Version: AllegroGraph Server Edition 8.0.1 (rc4), built on January 16, 2024 19:16:58 GMT-0800
Process: backend 7
Thread: 4-aserve-worker

Evaluation stack:

[2024-11-21T11:05:05.823 p7663 error-reporting] An unexpected error has occurred.  If possible, please leave AllegroGraph running and contact support@franz.com for debugging assistance. Error: Stack overflow (signal 1000)
[2024-11-21T11:05:05.823 p7663 error-reporting] Registers at the time of the fault:\n register saving not enabled
[2024-11-21T11:05:05.829 p7663 backtrace] Backtrace:
Version: AllegroGraph Server Edition 8.0.1 (rc4), built on January 16, 2024 19:16:58 GMT-0800
Process: backend 7
Thread: 3-aserve-worker

Evaluation stack:

[2024-11-21T11:25:10.556 p7663 backtrace] Backtrace:
Version: AllegroGraph Server Edition 8.0.1 (rc4), built on January 16, 2024 19:16:58 GMT-0800
Process: backend 7
Thread: 7-aserve-worker

Evaluation stack:

 ->(tpl::zoom-command :from-read-eval-print-loop nil :count nil :all t :brief nil)
   (sys::..runtime-operation "applyn" :unknown-args)
   (tpl:do-command "zoom" :from-read-eval-print-loop nil :count nil :all t :brief nil)
   (zoom-to-stream #<string-output-simple-stream "" pos 0 @ #x10043390352> :brief nil)
   (maybe-log-backtrace #<asynchronous-operating-system-signal @ #x1004338de32>)
   ((:internal ags.backend::find-or-create-query-package 2) #<asynchronous-operating-system-signal @ #x1004338de32>)
   (signal #<asynchronous-operating-system-signal @ #x1004338de32>)
   (cerror "continue computation" asynchronous-operating-system-signal :name
           "function call stack overflow (delayed response)" :number -3 :format-control
           "Received signal number ~s ~@[(~a)~]" :format-arguments
           (-3 "function call stack overflow (delayed response)"))
   (excl::break-for-signal -3)
   (excl::delegate-break-for-signal -3)
   (excl::handle-pending-signal)
   (excl::run-interruptions)
   (sys::..runtime-operation "process_sig_2" :unknown-args)
   (sys::..runtime-operation "process_sig" :unknown-args)
   (sys::..context-saving-runtime-operation "process_sig1")
   (cerror "continue computation" asynchronous-operating-system-signal :name
           "function call stack overflow (delayed response)" :number -3 :format-control
           "Received signal number ~s ~@[(~a)~]" :format-arguments
           (-3 "function call stack overflow (delayed response)"))
   (excl::break-for-signal -3)
   (excl::delegate-break-for-signal -3)
   (excl::handle-pending-signal)
   (excl::run-interruptions)
   (sys::..runtime-operation "process_sig_2" :unknown-args)
   (sys::..runtime-operation "process_sig" :unknown-args)
   (sys::..context-saving-runtime-operation "process_sig1")
   (cerror "continue computation" asynchronous-operating-system-signal :name
           "function call stack overflow (delayed response)" :number -3 :format-control
           "Received signal number ~s ~@[(~a)~]" :format-arguments
           (-3 "function call stack overflow (delayed response)"))
   (excl::break-for-signal -3)
   (excl::delegate-break-for-signal -3)
   (excl::handle-pending-signal)
   (excl::run-interruptions)
   (sys::..runtime-operation "process_sig_2" :unknown-args)
   (sys::..runtime-operation "process_sig" :unknown-args)
   (sys::..context-saving-runtime-operation "process_sig1")
   (cerror "continue computation" asynchronous-operating-system-signal :name
           "function call stack overflow (delayed response)" :number -3 :format-control
           "Received signal number ~s ~@[(~a)~]" :format-arguments
           (-3 "function call stack overflow (delayed response)"))
   (excl::break-for-signal -3)
   (excl::delegate-break-for-signal -3)
   (excl::handle-pending-signal)
   (excl::run-interruptions)
   (sys::..runtime-operation "process_sig_2" :unknown-args)
   (sys::..runtime-operation "process_sig" :unknown-args)
   (sys::..context-saving-runtime-operation "process_sig1")
   (cerror "continue computation" asynchronous-operating-system-signal :name
           "function call stack overflow (delayed response)" :number -3 :format-control
           "Received signal number ~s ~@[(~a)~]" :format-arguments
           (-3 "function call stack overflow (delayed response)"))
   (excl::break-for-signal -3)
   (excl::delegate-break-for-signal -3)
   (excl::handle-pending-signal)
   (excl::run-interruptions)
   (sys::..runtime-operation "process_sig_2" :unknown-args)
   (sys::..runtime-operation "process_sig" :unknown-args)
   (sys::..context-saving-runtime-operation "process_sig1")
   (cerror "continue computation" asynchronous-operating-system-signal :name
           "function call stack overflow (delayed response)" :number -3 :format-control
           "Received signal number ~s ~@[(~a)~]" :format-arguments
           (-3 "function call stack overflow (delayed response)"))
   (excl::break-for-signal -3)
   (excl::delegate-break-for-signal -3)
   (excl::handle-pending-signal)
   (excl::run-interruptions)
   (sys::..runtime-operation "process_sig_2" :unknown-args)
   (sys::..runtime-operation "process_sig" :unknown-args)
   (sys::..context-saving-runtime-operation "process_sig1")
   ((method selected-metatilities::make-stream-from-specifier (stream symbol))
      #<string-output-simple-stream "(:parsed-spa..." pos 2196467 @ #x100422af942> :output)
   [... selected-metatilities::make-stream-from-specifier ]
   (print-part-to-stream-1 #<string-output-simple-stream "(:parsed-spa..." pos 2196467 @ #x100422af942> 0
                           "http://purl.bioontology.org/ontology/LNC/7740-4" nil t :long t t)
   (print-future-part !<http://purl.bioontology.org/ontology/LNC/7740-4>
                      #<string-output-simple-stream "(:parsed-spa..." pos 2196467 @ #x100422af942>)
   [... print-object ]
   (excl::output-object !<http://purl.bioontology.org/ontology/LNC/7740-4>
                        #<string-output-simple-stream "(:parsed-spa..." pos 2196467 @ #x100422af942> 19108)
   (excl::output-list (= _v::?id !<http://purl.bioontology.org/ontology/LNC/7740-4>)
                      #<string-output-simple-stream "(:parsed-spa..." pos 2196467 @ #x100422af942> t 19107)
   (excl::output-object (= _v::?id !<http://purl.bioontology.org/ontology/LNC/7740-4>)
                        #<string-output-simple-stream "(:parsed-spa..." pos 2196467 @ #x100422af942> 19107)
   (excl::output-list
      (or (= _v::?id !<http://purl.bioontology.org/ontology/LNC/7740-4>)
          (or (= _v::?id !<http://purl.bioontology.org/ontology/LNC/73216-4>)
              (or (= _v::?id !<http://purl.bioontology.org/ontology/LNC/23820-4>)
                  (or (= _v::?id !<http://purl.bioontology.org/ontology/LNC/43074-4>)
                      (or (= _v::?id !<http://purl.bioontology.org/ontology/LNC/90259-3>)
                          (or (= _v::?id !<http://purl.bioontology.org/ontology/LNC/30993-0>)
                              (or (= _v::?id !<http://purl.bioontology.org/ontology/LNC/102640-0>)
                                  (or (= _v::?id !<http://purl.bioontology.org/ontology/LNC/102563-4>)
                                      (or (= _v::?id !<http://purl.bioontology.org/ontology/LNC/15395-7>)
[2024-11-21T11:27:07.284 p9977 storage] Store "system:system", instance starting (open)...
[2024-11-21T11:27:07.288 p9977 storage-fs-check] Store "system:system", /srv/ontoportal/data/agraph/systemcatalog/system/ (FS type xfs).
[2024-11-21T11:27:07.288 p9977 config] Store "system:system", effective database parameters
[2024-11-21T11:27:07.288 p9977 config] Store "system:system", parameter: DesiredTlogFiles     2
[2024-11-21T11:27:07.288 p9977 config] Store "system:system", parameter: DistributedTransactionTimeout 60
[2024-11-21T11:27:07.289 p9977 config] Store "system:system", parameter: Durability           min
[2024-11-21T11:27:07.289 p9977 config] Store "system:system", parameter: InstanceTimeout      10s
[2024-11-21T11:27:07.289 p9977 config] Store "system:system", parameter: Main                 /srv/ontoportal/data/agraph/systemcatalog/
[2024-11-21T11:27:07.289 p9977 config] Store "system:system", parameter: MaximumBackupAge     1h
[2024-11-21T11:27:07.289 p9977 config] Store "system:system", parameter: MaxRecoveryTime      0s
[2024-11-21T11:27:07.290 p9977 config] Store "system:system", parameter: Name                 system
[2024-11-21T11:27:07.290 p9977 config] Store "system:system", parameter: SharedMemSize        120M
[2024-11-21T11:27:07.290 p9977 config] Store "system:system", parameter: StringTableCompression none
[2024-11-21T11:27:07.290 p9977 config] Store "system:system", parameter: StringTableSize      256K
[2024-11-21T11:27:07.290 p9977 config] Store "system:system", parameter: TransactionLatencyCount 3
[2024-11-21T11:27:07.290 p9977 config] Store "system:system", parameter: TransactionLogRetain recovery
[2024-11-21T11:27:07.291 p9977 config] Store "system:system", expected-triples set to 1000000 (defaulted)
[2024-11-21T11:27:07.292 p9977 config] Store "system:system", triples-per-chunk set to 100000 (defaulted, adjusted)
[2024-11-21T11:27:07.292 p9977 config] Store "system:system", max-recovery-time set to 0s (parameter MaxRecoveryTime)
[2024-11-21T11:27:07.292 p9977 config] Store "system:system", checkpoint-interval set to 5m (defaulted, adjusted)
[2024-11-21T11:27:07.292 p9977 config] Store "system:system", minimum-checkpoint-interval set to 5m (defaulted, adjusted)
[2024-11-21T11:27:07.292 p9977 config] Store "system:system", checkpoint-data-threshold set to 1G (defaulted)
[2024-11-21T11:27:07.292 p9977 config] Store "system:system", tlog-size set to 256M (defaulted)
[2024-11-21T11:27:07.293 p9977 config] Store "system:system", desired-tlog-files set to 2 (parameter DesiredTlogFiles)
[2024-11-21T11:27:07.293 p9977 config] Store "system:system", max-outstanding-deletes set to 1000000 (defaulted)
[2024-11-21T11:27:07.293 p9977 config] Store "system:system", num-chunk-writers set to 4 (defaulted)
[2024-11-21T11:27:07.293 p9977 config] Store "system:system", num-index-optimizers set to 4 (defaulted)
[2024-11-21T11:27:07.293 p9977 config] Store "system:system", index-opt-min-op-size set to nil (defaulted)
[2024-11-21T11:27:07.294 p9977 config] Store "system:system", index-opt-max-op-size set to nil (defaulted)
[2024-11-21T11:27:07.294 p9977 config] Store "system:system", purge-rate-limit set to 0 (defaulted)
[2024-11-21T11:27:07.294 p9977 config] Store "system:system", index-opt-finalize set to 25 (defaulted, adjusted)
[2024-11-21T11:27:07.294 p9977 config] Store "system:system", tlog-sync-method set to nil (defaulted)
[2024-11-21T11:27:07.294 p9977 config] Store "system:system", mlock-indexes set to false (defaulted)
[2024-11-21T11:27:07.295 p9977 config] Store "system:system", string-table-size set to 1M (parameter StringTableSize, adjusted)
[2024-11-21T11:27:07.295 p9977 config] Store "system:system", string-table-compression set to none (parameter StringTableCompression)
[2024-11-21T11:27:07.295 p9977 config] Store "system:system", style-2-indices set to  (defaulted)
[2024-11-21T11:27:07.295 p9977 storage] Store "system:system", Database version: 43  Software DB version: 43
[2024-11-21T11:27:07.296 p9977 storage] Store "system:system", Shared memory segment size: 307,963,432 bytes
[2024-11-21T11:27:07.880 p9977 process-control-info] Store "system:system", Setting generation to 21
[2024-11-21T11:27:07.884 p9977 recover-mem-chunk] Store "system:system", Recovering mem chunk id 0 with 62 triples
[2024-11-21T11:27:07.884 p9977 recover-flavor] Store "system:system", Recovering spogi. Memchunks: 1, diskchunks: 0
[2024-11-21T11:27:07.885 p9977 recover-flavor] Store "system:system", Recovering psogi. Memchunks: 1, diskchunks: 0
[2024-11-21T11:27:07.885 p9977 recover-flavor] Store "system:system", Recovering posgi. Memchunks: 1, diskchunks: 0
[2024-11-21T11:27:07.885 p9977 recover-flavor] Store "system:system", Recovering ospgi. Memchunks: 1, diskchunks: 0
[2024-11-21T11:27:07.885 p9977 recover-flavor] Store "system:system", Recovering gspoi. Memchunks: 1, diskchunks: 0
[2024-11-21T11:27:07.885 p9977 recover-flavor] Store "system:system", Recovering gposi. Memchunks: 1, diskchunks: 0
[2024-11-21T11:27:07.886 p9977 recover-flavor] Store "system:system", Recovering i. Memchunks: 1, diskchunks: 0
[2024-11-21T11:27:07.890 p9977 strings] Store "system:system", Recovered 206 pages of slots
[2024-11-21T11:27:07.941 p9977 storage] Store "system:system", Max triple id: 1,178
[2024-11-21T11:27:07.941 p9977 storage] Store "system:system", sstab number of entries: 218, number of slots used: 218, max chain length: 1
[2024-11-21T11:27:07.942 p9977 storage] Store "system:system", sstab small strings used: 1016.0 bytes, large strings used: 1 byte
[2024-11-21T11:27:07.944 p9977 storage] Store "system:system", instance started
[2024-11-21T11:27:07.952 p9989 transaction-log] Store "system:system", Checkpointer started, interval 300 seconds
[2024-11-21T11:27:07.953 p9989 transaction-log] Store "system:system", Begin checkpoint (requested)
[2024-11-21T11:27:07.953 p9989 transaction-log] Store "system:system", Transaction log lock acquired
[2024-11-21T11:27:07.953 p9989 transaction-log] Store "system:system", Generation: 21[2024-11-21T11:27:07.957 p9989 checkpoint-mem-chunk] Store "system:system", Checkpointing mem chunk 0, 62 triples
[2024-11-21T11:27:08.032 p9989 transaction-log] Store "system:system", End checkpoint.  Total time: 79ms, Wait: 209us, Work: 78ms
[2024-11-21T11:27:28.065 p7645 service-daemon] Linger timeout of 10 seconds reached. Shutting down instance system:system
[2024-11-21T11:27:28.066 p9977 storage] Store "system:system", instance terminating... Uptime: 0h0m21s
[2024-11-21T11:27:30.021 p9977 storage] Store "system:system", instance terminated[2024-11-21T11:27:07.957 p9989 checkpoint-mem-chunk] Store "system:system", Checkpointing mem chunk 0, 62 triples
[2024-11-21T11:27:08.032 p9989 transaction-log] Store "system:system", End checkpoint.  Total time: 79ms, Wait: 209us, Work: 78ms
[2024-11-21T11:27:28.065 p7645 service-daemon] Linger timeout of 10 seconds reached. Shutting down instance system:system
[2024-11-21T11:27:28.066 p9977 storage] Store "system:system", instance terminating... Uptime: 0h0m21s
[2024-11-21T11:27:30.021 p9977 storage] Store "system:system", instance terminated[2024-11-21T11:27:07.957 p9989 checkpoint-mem-chunk] Store "system:system", Checkpointing mem chunk 0, 62 triples
[2024-11-21T11:27:08.032 p9989 transaction-log] Store "system:system", End checkpoint.  Total time: 79ms, Wait: 209us, Work: 78ms
[2024-11-21T11:27:28.065 p7645 service-daemon] Linger timeout of 10 seconds reached. Shutting down instance system:system
[2024-11-21T11:27:28.066 p9977 storage] Store "system:system", instance terminating... Uptime: 0h0m21s
[2024-11-21T11:27:30.021 p9977 storage] Store "system:system", instance terminated[2024-11-21T11:27:07.957 p9989 checkpoint-mem-chunk] Store "system:system", Checkpointing mem chunk 0, 62 triples
[2024-11-21T11:27:08.032 p9989 transaction-log] Store "system:system", End checkpoint.  Total time: 79ms, Wait: 209us, Work: 78ms
[2024-11-21T11:27:28.065 p7645 service-daemon] Linger timeout of 10 seconds reached. Shutting down instance system:system
[2024-11-21T11:27:28.066 p9977 storage] Store "system:system", instance terminating... Uptime: 0h0m21s
[2024-11-21T11:27:30.021 p997
alexskr commented 1 day ago

I am also unable to cancel those jobs/queries using AG admin interface. image clicking on X next to the query does nothing

alexskr commented 1 day ago

First step is to upgrade AG from v8.0.1 -> v8.2.1