The SPARQL update approach does not immediately crash if I change the
following settings.
TransactionAfterImageLimit = 500000000 <!-- 10x as big (does not crash
if smaller but won't do the update)
ColumnStore = 1
MaxQueryMem = 2000K <!-- increased
VectorSize = 10000 <!-- increased
MaxVectorSize = 1000000 <!-- increased
AdjustVectorSize = 1 <!-- enabled
It instead disappears without trace in executing 4 of this query.
If I change the SPARQL insert query a bit.
We get to loop 8
INSERT {GRAPH <http://beta.sparql.uniprot.org/taxonomy/> {?sub
rdfs:subClassOf ?super} }
WHERE { GRAPH <http://beta.sparql.uniprot.org/taxonomy/> {
?sub rdfs:subClassOf ?midle . ?midle rdfs:subClassOf ?super .
MINUS { ?sub rdfs:subClassOf ?super .}} }
This get a bit slower every loop (currently about 14 minutes for per
query), but that is natural.
Regards,
Jerven
On 14/10/13 11:15, Jerven Bolleman wrote:
> Hi Virtuoso devs,
>
> The following queries crash the virtuoso server.
> Version 07.00.3203-pthreads for Linux as of Oct 11 2013
> This is a build from the develop/7 branch commit
> 0bc9bc2dbd846a58d47bacee60b3a236a56abd4a
>
> In each of these cases I first turn do log_enable(0);
> With the aim turn this back on afterwards log_enable(3);
> Also autocheckpointing is turned off with checkpoint_interval (0);
>
> The data is
> ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/taxonomy.rdf.gz.
> Put into a graph.
>
> I attached the config/ini file.
>
> This first query (below) is the UNION 25 path query levels deep for
> materializing rdfs:subClassOf relationships.
>
> The server also crashes the same way if running the following
> a few times (each time adding the result file to the server). Again with
> the aim of materializing the rdfs:subClassOf relationships/
>
> CONSTRUCT {?sub rdfs:subClassOf ?super}
> FROM <http://beta.sparql.uniprot.org/taxonomy/>
> WHERE {
> { ?sub rdfs:subClassOf/rdfs:subClassOf ?super}
>
>
> If I try to use SPARQL update directly with this query
>
> PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
> INSERT {GRAPH <http://beta.sparql.uniprot.org/taxonomy/> {?sub
> rdfs:subClassOf ?super} }
> FROM <http://beta.sparql.uniprot.org/taxonomy/>
> WHERE {
> ?sub rdfs:subClassOf ?midle . ?midle rdfs:subClassOf ?super .}
>
> I see this in the logs
>
> 11:00:13 virtuoso-t() [0x8f0bf8]
> 11:00:13 virtuoso-t() [0x8f0c66]
> 11:00:13 virtuoso-t() [0x659840]
> 11:00:13 virtuoso-t() [0x65df30]
> 11:00:13 virtuoso-t() [0x6893ee]
> 11:00:13 virtuoso-t(bif_rl_dp_ids+0x7c) [0x68a1ec]
> 11:00:13 virtuoso-t() [0x5ce525]
> 11:00:13 virtuoso-t() [0x5d5ca1]
> 11:00:13 virtuoso-t() [0x5fe49a]
> 11:00:13 virtuoso-t() [0x602b7c]
> 11:00:13 virtuoso-t() [0x5d1b46]
> 11:00:13 virtuoso-t() [0x5d6413]
> 11:00:13 virtuoso-t() [0x5fe49a]
> 11:00:13 virtuoso-t() [0x602b7c]
> 11:00:13 virtuoso-t() [0x5d1b46]
> 11:00:13 virtuoso-t() [0x5d6413]
> 11:00:13 virtuoso-t() [0x5fe49a]
> 11:00:13 virtuoso-t() [0x602b7c]
> 11:00:13 virtuoso-t() [0x5d1b46]
> 11:00:13 virtuoso-t() [0x5d2662]
> 11:00:13 virtuoso-t() [0x5d310c]
> 11:00:13 virtuoso-t() [0x5faca6]
> 11:00:13 virtuoso-t() [0x5fe85c]
> 11:00:13 virtuoso-t(skip_node_input+0x20b) [0x5fff6b]
> 11:00:13 virtuoso-t() [0x5fe3a8]
> 11:00:13 virtuoso-t() [0x5fe903]
> 11:00:13 virtuoso-t() [0x5fe3a8]
> 11:00:13 virtuoso-t() [0x5fe903]
> 11:00:13 virtuoso-t() [0x6329d9]
> 11:00:13 virtuoso-t() [0x5fe3a8]
> 11:00:13 virtuoso-t() [0x5d0353]
> 11:00:13 virtuoso-t() [0x5d0808]
> 11:00:13 virtuoso-t() [0x5d6022]
> 11:00:13 virtuoso-t() [0x5fe49a]
> 11:00:13 virtuoso-t() [0x604048]
> 11:00:13 virtuoso-t() [0x60bce7]
> 11:00:13 virtuoso-t(sf_sql_execute_w+0x7f) [0x60c30f]
> 11:00:13 virtuoso-t() [0x8f72de]
> 11:00:13 virtuoso-t() [0x8f7f3f]
> 11:00:13 /lib64/libpthread.so.0() [0x35e3407851]
> 11:00:13 /lib64/libc.so.6(clone+0x6d) [0x35e2ce890d]
> 11:00:13 GPF: vec.c:1181 extending dc past max batch size
> GPF: vec.c:1181 extending dc past max batch size
>
> And again virtuoso-t crashes without a trace.
>
>
> Regards,
> Jerven
>
> PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
> CONSTRUCT {?sub rdfs:subClassOf ?super}
> FROM <http://beta.sparql.uniprot.org/taxonomy/>
> WHERE {
> { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf
> ?super}
> UNION { ?sub
> rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf ?super}
> UNION { ?sub rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf ?super}
> UNION { ?sub rdfs:subClassOf/rdfs:subClassOf ?super}}
>
--
-------------------------------------------------------------------
Jerven Bolleman jerven.bolle...@isb-sib.ch
SIB Swiss Institute of Bioinformatics Tel: +41 (0)22 379 58 85
CMU, rue Michel Servet 1 Fax: +41 (0)22 379 58 58
1211 Geneve 4,
Switzerland www.isb-sib.ch - www.uniprot.org
Follow us at https://twitter.com/#!/uniprot
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