Egon,
On 14 Dec 2013, at 13:06, Egon Willighagen <egon.willigha...@gmail.com> wrote:
> On Sun, Dec 8, 2013 at 10:57 PM, Hugh Williams <hwilli...@openlinksw.com>
> wrote:
>> No problem, looking back through the thread I presume the query you are
>> running is:
>>
>> SELECT DISTINCT ?property
>> WHERE { [] ?property [] }
>> ORDER BY ?property
>>
>> I believe ?
>
> Yeah, but I am starting to believe the crashes have nothing to do with
> the configuration, but that someone or something is just sending nasty
> things...
>
>> Can you provide the output of running the profile('<query>') function which
>> will provide the query execution plan and compiler and execution times:
>>
>> profile('SPARQL SELECT DISTINCT ?property WHERE { [] ?property [] } ORDER BY
>> ?property')
>
> ----------------------------------------------------------------------------------------------------------------------
> result
> LONG VARCHAR
> _______________________________________________________________________________
>
> http://purl.obolibrary.org/obo#has_role
> http://purl.org/dc/elements/1.1/date
> http://purl.org/dc/elements/1.1/identifier
> http://purl.org/dc/elements/1.1/isPartOf
> http://purl.org/dc/elements/1.1/title
> http://purl.org/dc/terms/created
> http://purl.org/dc/terms/modified
> http://purl.org/ontology/bibo/doi
> http://purl.org/ontology/bibo/issue
> http://purl.org/ontology/bibo/pageEnd
> http://purl.org/ontology/bibo/pageStart
> http://purl.org/ontology/bibo/pmid
> http://purl.org/ontology/bibo/volume
> http://purl.org/spar/cito/citesAsDataSource
> http://rdf.farmbio.uu.se/chembl/onto/#activeCompound
> http://rdf.farmbio.uu.se/chembl/onto/#classL1
> http://rdf.farmbio.uu.se/chembl/onto/#classL2
> http://rdf.farmbio.uu.se/chembl/onto/#classL3
> http://rdf.farmbio.uu.se/chembl/onto/#classL4
> http://rdf.farmbio.uu.se/chembl/onto/#classL5
>
> {
> time -nan% fanout 1 input 1 rows
> Subquery 27
> {
> time -nan% fanout 1 input 1 rows
> { fork
> time -nan% fanout 1.3e+08 input 1 rows
> RDF_QUAD 1.2e+08 rows(s_1_4_t0.P)
>
>
> After code:
> 0: __id2in := Call __id2in (s_1_4_t0.P)
> 5: BReturn 0
> time -nan% fanout 1.1e-06 input 1.3e+08 rows
> Distinct (__id2in)
> time -nan% fanout 0 input 1.5e+02 rows
> Sort (__id2in)
> }
> time -nan% fanout 1.5e+02 input 1 rows
> Key from temp (__id2in)
>
>
> After code:
> 0: property := := artm __id2in
> 4: BReturn 0
> time -nan% fanout 0 input 1.5e+02 rows
> Subquery Select(property)
> }
>
> After code:
> 0: property := Call __ro2sq (property)
> 5: BReturn 0
> time -nan% fanout 0 input 1.5e+02 rows
> Select (property)
> }
>
>
> *** Error 22012: [Virtuoso Driver][Virtuoso Server]SR083: Division by zero
> in lines 1-2 of Top-Level:
> #line 1 "(console)"
> profile('SPARQL SELECT DISTINCT ?property WHERE { [] ?property [] }
> ORDER BY ?property')
> ----------------------------------------------------------------------------------------------------------------------
>
>> and also the query without the "ORDER BY" for comparison:
>>
>> profile('SPARQL SELECT DISTINCT ?property WHERE { [] ?property [] } ')
>
> ----------------------------------------------------------------------------------------------------------------------
> LONG VARCHAR
> _______________________________________________________________________________
>
> BLOB 1169 chars
> {
> time -nan% fanout 1 input 1 rows
> Subquery 27
> {
> time -nan% fanout 2.6e+07 input 1 rows
> RDF_QUAD 1.2e+08 rows(s_1_4_t0.P)
>
> time -nan% fanout 3.5e-06 input 2.6e+07 rows
> Distinct (s_1_4_t0.P)
>
> After code:
> 0: property := := artm s_1_4_t0.P
> 4: BReturn 0
> time -nan% fanout 0 input 93 rows
> Subquery Select(property)
> }
>
> After code:
> 0: property := Call __ro2sq (property)
> 5: BReturn 0
> time -nan% fanout 0 input 93 rows
> Select (property)
> }
>
>
> *** Error 22012: [Virtuoso Driver][Virtuoso Server]SR083: Division by zero
> at line 3 of Top-Level:
> profile('SPARQL SELECT DISTINCT ?property WHERE { [] ?property [] } ')
> ----------------------------------------------------------------------------------------------------------------------
>
>> Looking at the status('') output only "137785 " of the "680000" buffers are
>> in use so there in plenty of memory available so the "129857455" triples
>> should be hosted in memory.
>
> OK. That doesn't surprise me, as with VOS6 it worked well...
>
>> I am wondering if this maybe due to a bad query plan. Note there have been
>> some major query optimizer fixes that have been pushed to the git Virtuoso
>> open source develop/7 branch at:
>>
>> http://github.com/openlink/virtuoso-opensource
>>
>> thus I would recommend performing an updated build from the branch to see if
>> the problem persists ...
>
> OK, I will ask the server administrator to update the version. I will
> then rerun the profile() call then too...
[Hugh] Note that the "SR083: Division by zero" error occurs with the latest git
develop/7 build also, thus we are working on a fix for this, I shall let you
know when it is completed and available on git.
Regards
Hugh
>
> Thanks,
>
> Egon
>
>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
> ORCID: 0000-0001-7542-0286
>
> ------------------------------------------------------------------------------
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