[Virtuoso-users] Segmentation fault

Wed, 06 Feb 2008 06:20:39 -0800 

Hi,
we're running 5.0.3 on a linux box. So far everything was going perfectly until we tested the following query which is very simple against a huge graph (that could be found here: http://www.cellcycleontology.org/ontology/rdf/cco.rdf): 

PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
PREFIX cco:<http://www.cellcycleontology.org/ontology/rdf/CCO#>

SELECT ?prot
WHERE{
  cco:CCO_B0001243 cco:is_a ?ortholog_cluster .
  ?prot cco:is_a ?ortholog_cluster .
  FILTER(!sameTerm(?prot,cco:CCO_B0001243))
}

the endpoint is: http://crunch.fvms.ugent.be:8890/sparql


It seems that the "sameTerm" is causing this problem. I tried to play 
with the parameters int he INI file by increasing the buffers, etc, etc 
but no success...Any hints would be appreciated.


In the logs, we got:

15:11:52 LTRS_1 0 130.88.195.199 Internal Commit transact 0x354ffcf890 0
15:11:52 LTRS_2 0 130.88.195.199 Internal Restart transact 0x354ffcf890
15:11:52 LTRS_1 0 130.88.195.199 Internal Commit transact 0x354ffcf890 0
15:11:52 LTRS_2 0 130.88.195.199 Internal Restart transact 0x354ffcf890
15:14:38 LTRS_1 0 130.88.195.199 Internal Commit transact 0x354ffcf890 0
15:14:38 LTRS_2 0 130.88.195.199 Internal Restart transact 0x354ffcf890

15:14:38 COMP_2 0 130.88.195.199 Internal Compile text:  isnull 
(sparql_to_sql_text (?))
15:14:38 COMP_2 0 130.88.195.199 Internal Compile text:  sparql define 
output:valmode "LONG" define input:default-graph-uri 
<http://www.cellcycleontology.org/ontology/rdf/CCO> PREFIX 
rdfs:<http://www.w3.org/2000/01/rdf-schema#>

PREFIX cco:<http://www.cellcycleontology.org/ontology/rdf/CCO#>

SELECT ?prot
WHERE{
  cco:CCO_B0001243 cco:is_a ?ortholog_cluster .
  ?prot cco:is_a ?ortholog_cluster .
  FILTER(!sameTerm(?prot,cco:CCO_B0001243))
}

and we also got:

15:11:52 LTRS_1 0 130.88.195.199 Internal Commit transact 0x354ffcf890 0
15:11:52 LTRS_2 0 130.88.195.199 Internal Restart transact 0x354ffcf890
15:11:52 LTRS_1 0 130.88.195.199 Internal Commit transact 0x354ffcf890 0
15:11:52 LTRS_2 0 130.88.195.199 Internal Restart transact 0x354ffcf890
15:14:38 LTRS_1 0 130.88.195.199 Internal Commit transact 0x354ffcf890 0
15:14:38 LTRS_2 0 130.88.195.199 Internal Restart transact 0x354ffcf890

15:14:38 COMP_2 0 130.88.195.199 Internal Compile text:  isnull 
(sparql_to_sql_text (?))
15:14:38 COMP_2 0 130.88.195.199 Internal Compile text:  sparql define 
output:valmode "LONG" define input:default-graph-uri 
<http://www.cellcycleontology.org/ontology/rdf/CCO> PREFIX 
rdfs:<http://www.w3.org/2000/01/rdf-schema#>

PREFIX cco:<http://www.cellcycleontology.org/ontology/rdf/CCO#>

SELECT ?prot
WHERE{
  cco:CCO_B0001243 cco:is_a ?ortholog_cluster .
  ?prot cco:is_a ?ortholog_cluster .
  FILTER(!sameTerm(?prot,cco:CCO_B0001243))
}

thanks,
Erick
p.s. Here it is the HTTP line:

http://crunch.fvms.ugent.be:8890/sparql?default-graph-uri=http%3A%2F%2Fwww.cellcycleontology.org%2Fontology%2Frdf%2FCCO&query=PREFIX+rdfs%3A%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0D%0APREFIX+cco%3A%3Chttp%3A%2F%2Fwww.cellcycleontology.org%2Fontology%2Frdf%2FCCO%23%3E%0D%0A%0D%0ASELECT+%3Fprot%0D%0AWHERE%7B%0D%0A+++cco%3ACCO_B0001243+cco%3Ais_a+%3Fortholog_cluster+.%0D%0A+++%3Fprot+cco%3Ais_a+%3Fortholog_cluster+.%0D%0A+++FILTER%28%21sameTerm%28%3Fprot%2Ccco%3ACCO_B0001243%29%29%0D%0A%7D&format=text%2Fhtml&debug=on 

























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