-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Hugh,
Yeah, on second thought I was rather ignoring those errors mainly because I didn't want to have to deal with them! Here are the details of the machine on which I am installing: 1. Windows Vista Ultimate 32-bit 2. 2GB physical RAM 3. Intel(R) Core(TM)2 CPU @ 2.13 GHz Now that you say the minimum for Amazon EC2 hosting is a machine with 8GB memory, I'm starting to see that the specs may be a problem. It didn't actually cross my mind initially, since this machine was relatively high-end for 3 years ago when I bought it. Optimism again, perhaps... Finally, here is the version info I got from running `virtuoso-t --help`. Virtuoso Open Source Edition (multi threaded) Version 5.0.11.3039-threads as of Apr 21 2009 Compiled for 32 Bit Windows Operating Environments Copyright (C) 1999-2009 OpenLink Software Anyway, thanks for continued speedy replies and sticking with me on all the issues. It has certainly not been a straightforward matter to troubleshoot, and I'm just hoping there will be some fruits to these labours. If it helps at all, I should probably state that my overall aim is simply to set up a DBpedia SPARQL endpoint that can serve over 1000 results per query (the current restriction on the DBpedia.org endpoint). Regards, Alex Hugh Williams wrote: > Hi Alex, > > I would say the "out of memory" errors in the installer log are a bit > more than minor, as the system would appear not to have the resources > for hosting the datasets being loaded. > > What are the details of the machine you are attempting to host your > DBpedia instance on: > > 1. What is OS name and bit'ness ? You mentioned using cygwin, thus I > presume you are on Windows ? What windows variant and is it 32 or 64 bit ? > 2. What is available memory consumption ? I believe you said 2GB in a > previous post ? > 3. What is type and speed of Processor ? > > For hosting the DBpedia datasets on Amazon EC2 the 3.2 datasets we have > currently recommend a minimum Linux x86_64 machine with 8GB memory. > > I also not a few "Can not set NULL to not nullable column > 'DB.DBA.RDF_QUAD.O" errors in your load log which is an issue that has > been fixed in our latest builds thus you would benefit from an updated > build also, as those datasets have probably failed to load. > > Please confirm the version number of build date of the server you are > using. > > Best Regards > Hugh Williams > Professional Services > OpenLink Software > Web: http://www.openlinksw.com > Support: http://support.openlinksw.com > Forums: http://boards.openlinksw.com/support > > > > On 19 Sep 2009, at 18:31, Alex wrote: > > Hi Hugh, > > I suspected you'd ask for them... no idea how pertinent they are to the > issue though. I've attached the console log and the load log that was > generated. > > Cheers, > Alex > > Hugh Williams wrote: >>>> Hi Alex, >>>> >>>> What are the minor errors you indicate having occurred ? >>>> >>>> The SPARQL query timeout is set to 60 by default, thus you might want to >>>> try increasing the MaxQueryExecutionTime paramter in the [SPARQL] >>>> section of the dbpedia.ini file which controls the timeouts and restart >>>> the server. >>>> >>>> Should the problems persist please try enabling tracing on the server >>>> as detailed at: >>>> >>>> http://docs.openlinksw.com/virtuoso/fn_trace_on.html >>>> >>>> This will write trace info to the dbpedia.log file, please provide this >>>> and the dbpedia.ini file for analysis. >>>> >>>> You should also try running the same query via the Virtuoso isql >>>> problem, preceded with the "sparql" keyword to direct it to the SPARQL >>>> processor ... >>>> >>>> Best Regards >>>> Hugh Williams >>>> Professional Services >>>> OpenLink Software >>>> Web: http://www.openlinksw.com >>>> Support: http://support.openlinksw.com >>>> Forums: http://boards.openlinksw.com/support >>>> >>>> >>>> >>>> On 19 Sep 2009, at 16:19, Alex wrote: >>>> >>>> Hi Hugh, >>>> >>>> The installation seems to have completed fine now (a few minor errors), >>>> and I've just tested the SPARQL endpoint in the browser, but the server >>>> seems to be complaining. >>>> >>>> S1T00 Error SR171: Transaction timed out >>>> >>>> SPARQL query: >>>> ... >>>> >>>> I received this message for the recommended sample query in README.txt, >>>> as well as several others. Any suggestions please? >>>> >>>> Regards, >>>> Alex Started. Checking files load_nt.sh : present dbpedia_dav.vad : present dbpedia_post.sql : present dbpedia-ontology.owl : present umbel_class_hierarchy_v071.n3 : present umbel_abstract_concepts.n3 : present umbel_external_ontologies_linkage.n3 : present yago-class-hierarchy_en.nt : present umbel_subject_concepts.n3 : present opencyc-2008-06-10.owl : present opencyc-2008-06-10-readable.owl : present Installing dbpedia_dav.vad Starting... Logging into: load_nt.sh.log ======================================= Loading started. ======================================= Loading data/externallinks_en.nt (3653630 lines) 13:25:50 Retryng from line 1235724 Loaded. Loading data/geo_en.nt (1110708 lines) 13:41:43 Loaded. Loading data/homepage_en.nt (65178 lines) 13:47:38 Loaded. Loading data/image_en.nt (2775360 lines) 13:49:16 Loaded. Loading data/infobox-mappingbased-loose.nt (8238555 lines) 14:11:35 Loaded. Loading data/infoboxproperties_en.nt (98244 lines) 15:07:53 Loaded. Loading data/infobox_en.nt (39855823 lines) 15:12:25 Loaded. Loading data/instancetype_en.nt (3790668 lines) 16:04:50 Loaded. Loading data/longabstract_en.nt (2788812 lines) 16:31:05 Loaded. Loading data/pagelinks_en.nt (77092350 lines) 19:11:57 Retryng from line 16209818 Loaded. Loading data/persondata_en.nt (118002 lines) 14:44:55 Loaded. Loading data/redirect_en.nt (3494567 lines) 15:14:27 Loaded. Loading data/shortabstract_en.nt (2787499 lines) 16:36:46 Loaded. Loading data/skoscategories_en.nt (1844055 lines) 23:28:05 Loaded. Loading data/wikipage_en.nt (3201391 lines) 00:35:10 Loaded. Loading data/yagolink_en.nt (1889985 lines) 02:44:03 Loaded. Loading data/yago_en.nt (4645108 lines) 08:32:36 Loaded. ======================================= Final checkpoint. ======================================= Check bad.nt file for skipped triples. ======================================= Running post-install scripts PASSED: RDF_OBJ_FT_RULE_ADD : STATE=OK MESSAGE=OK PASSED: VT_INC_INDEX_DB_DBA_RDF_OBJ : STATE=OK MESSAGE=OK PASSED: RDF_QUAD_POGS : STATE=OK MESSAGE=OK PASSED: RDF_QUAD_PSOG : STATE=OK MESSAGE=OK PASSED: RDF_QUAD_SOPG : STATE=OK MESSAGE=OK PASSED: Load 2008-10-31_dbpedia.owl : STATE=OK MESSAGE=OK PASSED: Load 2008-10-31_dbpedia.owl : STATE=OK MESSAGE=OK PASSED: DBpedia inference : STATE=OK MESSAGE=OK ***FAILED: Load umbel_class_hierarchy_v071 : STATE=23000 MESSAGE=[OpenLink][Virt uoso ODBC Driver][Virtuoso Server]SR133: Can not set NULL to not nullable column 'DB.DBA.RDF_QUAD.O' PASSED: Load umbel_subject_concepts : STATE=OK MESSAGE=OK PASSED: Load umbel_abstract_concepts : STATE=OK MESSAGE=OK PASSED: Load umbel_external_ontologies_linkage : STATE=OK MESSAGE=OK PASSED: UMBEL inference : STATE=OK MESSAGE=OK PASSED: Load yago-class-hierarchy_en : STATE=OK MESSAGE=OK PASSED: Yago inference : STATE=OK MESSAGE=OK PASSED: Load opencyc_class_hierarchy : STATE=OK MESSAGE=OK ***FAILED: Opencyc inference : STATE=40006 MESSAGE=[OpenLink][Virtuoso ODBC Driv er][Virtuoso Server]SR337: Transaction aborted because the server is out of memo ry ***FAILED: opencyc-2008-06-10-readable : STATE=40006 MESSAGE=[OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SR337: Transaction aborted because the server is o ut of memory ***FAILED: DBpedia property inference : STATE=40006 MESSAGE=[OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SR337: Transaction aborted because the server is ou t of memory =============================== Install finished. Sat Sep 19 06:39:55 GMTDT 2009 =============================== The MAIL_SERVER environment variable is not set, e.g. export MAIL_SERVER=mail.do main:25 =============================== Install started Tue Sep 15 13:25:15 GMTDT 2009 =============================== Checking for VOS setup Starting Virtuoso server, please wait ... Cannot start Virtuoso server, please consult dbpedia.log file Started. Checking files load_nt.sh : present dbpedia_dav.vad : present dbpedia_post.sql : present dbpedia-ontology.owl : present umbel_class_hierarchy_v071.n3 : present umbel_abstract_concepts.n3 : present umbel_external_ontologies_linkage.n3 : present yago-class-hierarchy_en.nt : present umbel_subject_concepts.n3 : present opencyc-2008-06-10.owl : present opencyc-2008-06-10-readable.owl : present Installing dbpedia_dav.vad 00000 No errors detected 00000 Installation of "DBpedia" is complete. 00000 Now making a final checkpoint. 00000 Final checkpoint is made. 00000 SUCCESS >> ======================================= Loading started. ======================================= Loading data/externallinks_en.nt (3653630 lines) 13:25:50 Retryng from line 1235724 Loading data/geo_en.nt (1110708 lines) 13:41:43 Loading data/homepage_en.nt (65178 lines) 13:47:38 Loading data/image_en.nt (2775360 lines) 13:49:16 Loading data/infobox-mappingbased-loose.nt (8238555 lines) 14:11:35 Loading data/infoboxproperties_en.nt (98244 lines) 15:07:53 Loading data/infobox_en.nt (39855823 lines) 15:12:25 Loading data/instancetype_en.nt (3790668 lines) 16:04:50 Loading data/longabstract_en.nt (2788812 lines) 16:31:05 Loading data/pagelinks_en.nt (77092350 lines) 19:11:57 Retryng from line 16209818 Loading data/persondata_en.nt (118002 lines) 14:44:55 Loading data/redirect_en.nt (3494567 lines) 15:14:27 Loading data/shortabstract_en.nt (2787499 lines) 16:36:46 Loading data/skoscategories_en.nt (1844055 lines) 23:28:05 Loading data/wikipage_en.nt (3201391 lines) 00:35:10 Loading data/yagolink_en.nt (1889985 lines) 02:44:03 Loading data/yago_en.nt (4645108 lines) 08:32:36 Final checkpoint. ======================================= Check bad.nt file for skipped triples. ======================================= Running post-install scripts PASSED: RDF_OBJ_FT_RULE_ADD : STATE=OK MESSAGE=OK PASSED: VT_INC_INDEX_DB_DBA_RDF_OBJ : STATE=OK MESSAGE=OK PASSED: RDF_QUAD_POGS : STATE=OK MESSAGE=OK PASSED: RDF_QUAD_PSOG : STATE=OK MESSAGE=OK PASSED: RDF_QUAD_SOPG : STATE=OK MESSAGE=OK PASSED: Load 2008-10-31_dbpedia.owl : STATE=OK MESSAGE=OK PASSED: Load 2008-10-31_dbpedia.owl : STATE=OK MESSAGE=OK PASSED: DBpedia inference : STATE=OK MESSAGE=OK >> *** Error 23000: [OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SR133: Can not set NULL to not nullable column 'DB.DBA.RDF_QUAD.O' at line 36 of Top-Level: ttlp_mt (file_to_string_output ('umbel_class_hierarchy_v071.n3'), '', 'http://dbpedia.org/resource/classes/umbel#') ***FAILED: Load umbel_class_hierarchy_v071 : STATE=23000 MESSAGE=[OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SR133: Can not set NULL to not nullable column 'DB.DBA.RDF_QUAD.O' PASSED: Load umbel_subject_concepts : STATE=OK MESSAGE=OK PASSED: Load umbel_abstract_concepts : STATE=OK MESSAGE=OK PASSED: Load umbel_external_ontologies_linkage : STATE=OK MESSAGE=OK PASSED: UMBEL inference : STATE=OK MESSAGE=OK PASSED: Load yago-class-hierarchy_en : STATE=OK MESSAGE=OK PASSED: Yago inference : STATE=OK MESSAGE=OK PASSED: Load opencyc_class_hierarchy : STATE=OK MESSAGE=OK >> *** Error 40006: [OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SR337: Transaction aborted because the server is out of memory at line 80 of Top-Level: rdfs_rule_set ('http://dbpedia.org/resource/inference/rules/opencyc#', 'http://dbpedia.org/resource/classes/opencyc#') >> *** Error 40006: [OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SR337: Transaction aborted because the server is out of memory at line 80 of Top-Level: rdfs_rule_set ('http://dbpedia.org/resource/inference/rules/opencyc#', 'http://dbpedia.org/resource/classes/opencyc#') ***FAILED: Opencyc inference : STATE=40006 MESSAGE=[OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SR337: Transaction aborted because the server is out of memory >> *** Error .....: [OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SQ200: Out of memory at line 84 of Top-Level: checkpoint >> *** Error 40006: [OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SR337: Transaction aborted because the server is out of memory at line 84 of Top-Level: checkpoint >> *** Error .....: [OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SQ200: Out of memory at line 85 of Top-Level: DB..RDF_LOAD_RDFXML_MT (file_to_string_output ('opencyc-2008-06-10-readable.owl'), 'http://sw.opencyc.org/2008/06/10/concept/', 'opencyc-2008-06-10-readable') >> *** Error 40006: [OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SR337: Transaction aborted because the server is out of memory at line 85 of Top-Level: DB..RDF_LOAD_RDFXML_MT (file_to_string_output ('opencyc-2008-06-10-readable.owl'), 'http://sw.opencyc.org/2008/06/10/concept/', 'opencyc-2008-06-10-readable') ***FAILED: opencyc-2008-06-10-readable : STATE=40006 MESSAGE=[OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SR337: Transaction aborted because the server is out of memory >> *** Error .....: [OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SQ200: Out of memory in lines 89-98 of Top-Level: #line 89 "(console)" ttlp ( '@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . <http://dbpedia.org/property/birthcity> rdfs:subPropertyOf <http://dbpedia.org/property/birthPlace> . <http://dbpedia.org/property/birthcountry> rdfs:subPropertyOf <http://dbpedia.org/property/birthPlace> . <http://dbpedia.org/property/cityofbirth> rdfs:subPropertyOf <http://dbpedia.org/property/birthPlace> . <http://dbpedia.org/property/countryofbirth> rdfs:subPropertyOf <http://dbpedia.org/property/birthPlace> . <http://dbpedia.org/property/countyofbirth> rdfs:subPropertyOf <http://dbpedia.org/property/birthPlace>. <http://dbpedia.org/property/cityofdeath> rdfs:subPropertyOf <http://dbpedia.org/property/deathPlace> . <http://dbpedia.org/property/countryofdeath> rdfs:subPropertyOf <http://dbpedia.org/property/deathPlace> .', '','http://dbpedia.org/schema/property_rules#') >> *** Error 40006: [OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SR337: Transaction aborted because the server is out of memory in lines 89-98 of Top-Level: #line 89 "(console)" ttlp ( '@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . <http://dbpedia.org/property/birthcity> rdfs:subPropertyOf <http://dbpedia.org/property/birthPlace> . <http://dbpedia.org/property/birthcountry> rdfs:subPropertyOf <http://dbpedia.org/property/birthPlace> . <http://dbpedia.org/property/cityofbirth> rdfs:subPropertyOf <http://dbpedia.org/property/birthPlace> . <http://dbpedia.org/property/countryofbirth> rdfs:subPropertyOf <http://dbpedia.org/property/birthPlace> . <http://dbpedia.org/property/countyofbirth> rdfs:subPropertyOf <http://dbpedia.org/property/birthPlace>. <http://dbpedia.org/property/cityofdeath> rdfs:subPropertyOf <http://dbpedia.org/property/deathPlace> . <http://dbpedia.org/property/countryofdeath> rdfs:subPropertyOf <http://dbpedia.org/property/deathPlace> .', '','http://dbpedia.org/schema/property_rules#') >> *** Error .....: [OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SQ200: Out of memory at line 100 of Top-Level: rdfs_rule_set ('http://dbpedia.org/schema/property_rules#', 'http://dbpedia.org/schema/property_rules#') >> *** Error 40006: [OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SR337: Transaction aborted because the server is out of memory at line 100 of Top-Level: rdfs_rule_set ('http://dbpedia.org/schema/property_rules#', 'http://dbpedia.org/schema/property_rules#') ***FAILED: DBpedia property inference : STATE=40006 MESSAGE=[OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SR337: Transaction aborted because the server is out of memory >> *** Error .....: [OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SQ200: Out of memory at line 104 of Top-Level: checkpoint >> *** Error 40006: [OpenLink][Virtuoso ODBC Driver][Virtuoso Server]SR337: Transaction aborted because the server is out of memory at line 104 of Top-Level: checkpoint =============================== Install finished. Sat Sep 19 06:39:55 GMTDT 2009 =============================== The MAIL_SERVER environment variable is not set, e.g. export MAIL_SERVER=mail.domain:25 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iQEcBAEBAgAGBQJKtXnfAAoJEOqaT4w4/280IAsH/Ahgl70R6UxR7FfvwjKjNnhM bjp0rZpDTnBanPG+hdtNHebb7aNxWYaXr2G3L3ylWS6hwV/px9vFT5IR2WUHLq15 CiNp4u78D09C+eWs34nWgMhfea8X+DxtD/ERj1ii6/G+jMj/BhEzrvoBRlJ3nwDa cwvRcYWzWf+1IyH7RPWwFr1XEvL2iULidLiuQhIhZEy3AnW2iTHvrOldHOD4/JTs anKs00DdbrYU3gJy12/1AZDtUIGY6KTVoelnvBeesLvMHEmJYYXNgSZHIIXzlV2y zgfosKJ/+51uLM5DSgmZVpaG48JAENQ7/jR/gruw4jJnh7cwX2+ClE2+UQtTYsI= =oVVc -----END PGP SIGNATURE-----
