Hi Eliza, The default indexes in place should suffice for most use cases, thus cause of the slow running query needs to be determined.
How long does the query take to execute when cold ie first run and when warmed
up ie on consecutive runs ?
Please provide the output of running the "status();" command run from the isql
command line tool
What is the version of Virtuoso being used "virtuoso-t -?" ?
it would also be useful to obtain the "profile" for the query to see whether
the time is being spent compiling or executing the query, which be done with
the "profile" function as detailed at:
http://virtuoso.openlinksw.com/dataspace/doc/dav/wiki/Main/VirtTipsAndTricksAanalyzingSPARQLQuery
http://docs.openlinksw.com/virtuoso/databaseadmsrv.html#readingqueryprofile
Best Regards
Hugh Williams
Professional Services
OpenLink Software, Inc. // http://www.openlinksw.com/
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Universal Data Access, Integration, and Management Technology Providers
> On 30 Oct 2014, at 17:45, Eliza Chan <elc2...@med.cornell.edu> wrote:
>
> Hi,
>
> I have a SPARQL query that took more than 25 sec to return with some results.
>
> Our database size is 700 MB, with about 2 GB of free memory. Our data are
> stored in multiple graphs. The virtuoso.ini file was configured as follows:
>
> NumberOfBuffers = 170000
> MaxDirtyBuffers = 130000
> MaxCheckpointRemap = 20000
>
> However, the changes in the ini file didn't seem to improve the speed.
>
> Is there a way to improve the performance by changing the index scheme? I saw
> the instructions but not sure about the best index setting for our particular
> query.
>
> Please see below an example of our large query:
>
> PREFIX core: <http://vivoweb.org/ontology/core#>
> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
> PREFIX bibo: <http://purl.org/ontology/bibo/>
> PREFIX foaf: <http://xmlns.com/foaf/0.1/>
>
> CONSTRUCT {
> <http://mydomain.edu/individual/userid>
> <http://vivoweb.org/ontology/core#relatedBy> ?authorship .
> ?authorship a core:Authorship .
> ?authorship ?authorshipProperty ?authorshipValue .
> ?authorship core:relates ?infoResource .
> ?infoResource a <http://purl.obolibrary.org/obo/IAO_0000030> .
> ?infoResource ?infoResourceProperty ?infoResourceValue .
> ?infoResource bibo:reproducedIn ?appearsInObj .
> ?infoResource core:publisher ?publisherObj .
> ?infoResource core:relatedBy ?editorship .
> ?editorship a core:Editorship .
> ?editorship core:relates ?editorObj .
> ?editorObj a foaf:Person .
> ?infoResource <http://purl.obolibrary.org/obo/BFO_0000050> ?partOfObj .
> ?appearsInObj rdfs:label ?appearsIn .
> ?publisherObj rdfs:label ?publisher .
> ?editorObj rdfs:label ?editor .
> ?partOfObj rdfs:label ?partOf
> } WHERE {
> {
> <http://mydomain.edu/individual/userid>
> <http://vivoweb.org/ontology/core#relatedBy> ?authorship .
> ?authorship a core:Authorship
> }
> UNION {
> <http://mydomain.edu/individual/userid>
> <http://vivoweb.org/ontology/core#relatedBy> ?authorship .
> ?authorship a core:Authorship .
> ?authorship ?authorshipProperty ?authorshipValue
> } UNION {
> <http://mydomain.edu/individual/userid>
> <http://vivoweb.org/ontology/core#relatedBy> ?authorship .
> ?authorship a core:Authorship .
> ?authorship core:relates ?infoResource .
> ?infoResource a <http://purl.obolibrary.org/obo/IAO_0000030> .
> } UNION {
> <http://mydomain.edu/individual/userid>
> <http://vivoweb.org/ontology/core#relatedBy> ?authorship .
> ?authorship a core:Authorship .
> ?authorship core:relates ?infoResource .
> ?infoResource a <http://purl.obolibrary.org/obo/IAO_0000030> .
> ?infoResource ?infoResourceProperty ?infoResourceValue
> } UNION {
> <http://mydomain.edu/individual/userid>
> <http://vivoweb.org/ontology/core#relatedBy> ?authorship .
> ?authorship a core:Authorship .
> ?authorship core:relates ?infoResource .
> ?infoResource a <http://purl.obolibrary.org/obo/IAO_0000030> .
> ?infoResource bibo:reproducedIn ?appearsInObj .
> ?appearsInObj rdfs:label ?appearsIn
> } UNION {
> <http://mydomain.edu/individual/userid>
> <http://vivoweb.org/ontology/core#relatedBy> ?authorship .
> ?authorship a core:Authorship .
> ?authorship core:relates ?infoResource .
> ?infoResource a <http://purl.obolibrary.org/obo/IAO_0000030> .
> ?infoResource core:publisher ?publisherObj .
> ?publisherObj rdfs:label ?publisher
> } UNION {
> <http://mydomain.edu/individual/userid>
> <http://vivoweb.org/ontology/core#relatedBy> ?authorship .
> ?authorship a core:Authorship .
> ?authorship core:relates ?infoResource .
> ?infoResource a <http://purl.obolibrary.org/obo/IAO_0000030> .
> ?infoResource core:relatedBy ?editorship .
> ?editorship a core:Editorship .
> ?editorship core:relates ?editorObj .
> ?editorObj a foaf:Person .
> ?editorObj rdfs:label ?editor
> } UNION {
> <http://mydomain.edu/individual/userid>
> <http://vivoweb.org/ontology/core#relatedBy> ?authorship .
> ?authorship a core:Authorship .
> ?authorship core:relates ?infoResource .
> ?infoResource a <http://purl.obolibrary.org/obo/IAO_0000030> .
> ?infoResource <http://purl.obolibrary.org/obo/BFO_0000050> ?partOfObj .
> ?partOfObj rdfs:label ?partOf
> }
> }
>
> Unfortunately I cannot modify the query because it's part of the application.
> So I can only modify any possible settings in Virtuoso to improve the
> performance.
>
> Any suggestion is greatly appreciated.
>
> Thank you so much for your help.
>
> Regards,
> Eliza
>
>
>
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