Re: [Virtuoso-users] Installing DBpedia datasets

Sat, 19 Sep 2009 21:09:38 +0000 

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:


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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

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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

























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