Hi dear Hugh,
I've been using 7.2.1 version since last year but I will get the latest
version as you said.
I'm running these queries on a much larger triple set (80 GB). Can the size
of the ontology be the reason for "Virtuoso 42000 Error SR483: Stack
Overflow" message?
If not, could you please tell me what is the meaning of this error and what
causes it?
Regards,
Delaram
On Sat, Mar 5, 2016 at 6:47 PM, Hugh Williams <hwilli...@openlinksw.com>
wrote:
> Hi Delaram,
>
> I have loaded your sample dataset into a latest Virtuoso 7.2.2 open source
> database (once missing prefixes haad been added) and both queries run
> successfully, although query_3 returns no results. Is the a reason you are
> running 7.2.1 and can you update to the latest 7.2.2 version available in
> git ?
>
> SQL> DB.DBA.TTLP_MT (file_to_string_output('./delaram.ttl'),
> '','delaram',0);
>
> Done. -- 44 msec.
> SQL> sparql select count(*) from <delaram> where {?s ?p ?o};
> callret-0
> INTEGER
>
> _______________________________________________________________________________
>
> 765
>
> 1 Rows. -- 12 msec.
> SQL>
> SQL> SPARQL PREFIX : <http://gmmo.uga.edu/#>
> Type the rest of statement, end with a semicolon (;)> PREFIX rdf: <
> http://www.w3.org/1999/02/22-rdf-syntax-ns#>
> Type the rest of statement, end with a semicolon (;)> PREFIX owl: <
> http://www.w3.org/2002/07/owl#>
> Type the rest of statement, end with a semicolon (;)> PREFIX rdfs: <
> http://www.w3.org/2000/01/rdf-schema#>
> Type the rest of statement, end with a semicolon (;)> PREFIX xsd: <
> http://www.w3.org/2001/XMLSchema#>
> Type the rest of statement, end with a semicolon (;)> SELECT ?pdb WHERE {
> Type the rest of statement, end with a semicolon (;)>
> ?oligo0:hasRoot?mono0.
> Type the rest of statement, end with a semicolon (;)> ?mono0
> :hasRingAtom?mono0_ring_atom2.
> Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom2
> :ringIndex "2".
> Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom2
> :hasSideAtom ?mono0_side_atom2 .
> Type the rest of statement, end with a semicolon (;)>
> ?mono0_side_atom2:sideIndex "2".
> Type the rest of statement, end with a semicolon (;)>
> ?mono0_side_atom2:orientation"Down".
> Type the rest of statement, end with a semicolon (;)> ?mono0
> :hasRingAtom?mono0_ring_atom3.
> Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom3
> :ringIndex "3".
> Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom3
> :hasSideAtom ?mono0_side_atom3 .
> Type the rest of statement, end with a semicolon (;)>
> ?mono0_side_atom3:sideIndex "3".
> Type the rest of statement, end with a semicolon (;)>
> ?mono0_side_atom3:orientation"Up".
> Type the rest of statement, end with a semicolon (;)> ?mono0
> :hasRingAtom?mono0_ring_atom4.
> Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom4
> :ringIndex "4".
> Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom4
> :hasSideAtom ?mono0_side_atom4 .
> Type the rest of statement, end with a semicolon (;)>
> ?mono0_side_atom4:sideIndex "4".
> Type the rest of statement, end with a semicolon (;)>
> ?mono0_side_atom4:orientation"Down".
> Type the rest of statement, end with a semicolon (;)> ?mono0
> :hasRingAtom?mono0_last_c.
> Type the rest of statement, end with a semicolon (;)> ?mono0_last_c
> :ringIndex "5".
> Type the rest of statement, end with a semicolon (;)> ?mono0_last_c
> :hasSideAtom ?mono0_last_c_side_atom.
> Type the rest of statement, end with a semicolon (;)>
> ?mono0_last_c_side_atom :sideIndex "+1".
> Type the rest of statement, end with a semicolon (;)>
> ?mono0_last_c_side_atom :orientation"Up".
> Type the rest of statement, end with a semicolon (;)>
> ?oligo1:hasRoot?mono1.
> Type the rest of statement, end with a semicolon (;)> ?mono1
> :hasRingAtom?mono1_anomeric.
> Type the rest of statement, end with a semicolon (;)> ?mono1_anomeric
> :ringIndex "1".
> Type the rest of statement, end with a semicolon (;)> ?mono1_anomeric
> :hasSideAtom ?mono1_anomeric_side_atom .
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_anomeric_side_atom:sideIndex "1".
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_anomeric_side_atom:orientation"Up".
> Type the rest of statement, end with a semicolon (;)> ?mono1
> :hasRingAtom?mono1_ring_atom2.
> Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom2
> :ringIndex "2".
> Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom2
> :hasSideAtom ?mono1_side_atom2 .
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_side_atom2:sideIndex "2".
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_side_atom2:orientation"Down".
> Type the rest of statement, end with a semicolon (;)> ?mono1
> :hasRingAtom?mono1_ring_atom3.
> Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom3
> :ringIndex "3".
> Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom3
> :hasSideAtom ?mono1_side_atom3 .
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_side_atom3:sideIndex "3".
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_side_atom3:orientation"Up".
> Type the rest of statement, end with a semicolon (;)> ?mono1
> :hasRingAtom?mono1_ring_atom4.
> Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom4
> :ringIndex "4".
> Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom4
> :hasSideAtom ?mono1_side_atom4 .
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_side_atom4:sideIndex "4".
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_side_atom4:orientation"Down".
> Type the rest of statement, end with a semicolon (;)> ?mono1
> :hasRingAtom?mono1_last_c.
> Type the rest of statement, end with a semicolon (;)> ?mono1_last_c
> :ringIndex "5".
> Type the rest of statement, end with a semicolon (;)> ?mono1_last_c
> :hasSideAtom ?mono1_last_c_side_atom.
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_last_c_side_atom :sideIndex "+1".
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_last_c_side_atom :orientation"Up".
> Type the rest of statement, end with a semicolon (;)> {
> Type the rest of statement, end with a semicolon (;)> ?linkage0 :hasParent
> ?oligo0.
> Type the rest of statement, end with a semicolon (;)> ?linkage0 :hasChild
> ?oligo1.
> Type the rest of statement, end with a semicolon (;)> } UNION {
> Type the rest of statement, end with a semicolon (;)> ?linkage0 :hasParent
> ?oligo1.
> Type the rest of statement, end with a semicolon (;)> ?linkage0 :hasChild
> ?oligo0.
> Type the rest of statement, end with a semicolon (;)> }
> Type the rest of statement, end with a semicolon (;)> ?pdb
> :hasOligo ?oligo0.
> Type the rest of statement, end with a semicolon (;)> ?pdb
> :hasOligo ?oligo1.
> Type the rest of statement, end with a semicolon (;)> }
> Type the rest of statement, end with a semicolon (;)> ;
> pdb
> LONG VARCHAR
>
> _______________________________________________________________________________
>
> http://gmmo.uga.edu/#sample
> http://gmmo.uga.edu/#sample
>
> 2 Rows. -- 6516 msec.
> SQL>
> SQL> SPARQL PREFIX : <http://gmmo.uga.edu/#>
> Type the rest of statement, end with a semicolon (;)> PREFIX rdf: <
> http://www.w3.org/1999/02/22-rdf-syntax-ns#>
> Type the rest of statement, end with a semicolon (;)> PREFIX owl: <
> http://www.w3.org/2002/07/owl#>
> Type the rest of statement, end with a semicolon (;)> PREFIX rdfs: <
> http://www.w3.org/2000/01/rdf-schema#>
> Type the rest of statement, end with a semicolon (;)> PREFIX xsd: <
> http://www.w3.org/2001/XMLSchema#>
> Type the rest of statement, end with a semicolon (;)> SELECT ?pdb WHERE {
> Type the rest of statement, end with a semicolon (;)>
> ?oligo0:hasRoot?mono0.
> Type the rest of statement, end with a semicolon (;)> ?mono0
> :hasRingAtom ?mono0_ring_atom2.
> Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom2
> :ringIndex "2".
> Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom2
> :hasSideAtom ?mono0_side_atom2 .
> Type the rest of statement, end with a semicolon (;)>
> ?mono0_side_atom2:sideIndex "2".
> Type the rest of statement, end with a semicolon (;)>
> ?mono0_side_atom2:orientation"Down".
> Type the rest of statement, end with a semicolon (;)> ?mono0
> :hasRingAtom?mono0_ring_atom3.
> Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom3
> :ringIndex "3".
> Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom3
> :hasSideAtom ?mono0_side_atom3 .
> Type the rest of statement, end with a semicolon (;)>
> ?mono0_side_atom3:sideIndex "3".
> Type the rest of statement, end with a semicolon (;)>
> ?mono0_side_atom3:orientation"Up".
> Type the rest of statement, end with a semicolon (;)> ?mono0
> :hasRingAtom?mono0_ring_atom4.
> Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom4
> :ringIndex "4".
> Type the rest of statement, end with a semicolon (;)> ?mono0_ring_atom4
> :hasSideAtom ?mono0_side_atom4 .
> Type the rest of statement, end with a semicolon (;)>
> ?mono0_side_atom4:sideIndex "4".
> Type the rest of statement, end with a semicolon (;)>
> ?mono0_side_atom4:orientation"Down".
> Type the rest of statement, end with a semicolon (;)> ?mono0
> :hasRingAtom?mono0_last_c.
> Type the rest of statement, end with a semicolon (;)> ?mono0_last_c
> :ringIndex "5".
> Type the rest of statement, end with a semicolon (;)> ?mono0_last_c
> :hasSideAtom ?mono0_last_c_side_atom.
> Type the rest of statement, end with a semicolon (;)>
> ?mono0_last_c_side_atom :sideIndex "+1".
> Type the rest of statement, end with a semicolon (;)>
> ?mono0_last_c_side_atom :orientation"Up".
> Type the rest of statement, end with a semicolon (;)>
> ?oligo1:hasRoot?mono1.
> Type the rest of statement, end with a semicolon (;)> ?mono1
> :hasRingAtom?mono1_anomeric.
> Type the rest of statement, end with a semicolon (;)> ?mono1_anomeric
> :ringIndex "1".
> Type the rest of statement, end with a semicolon (;)> ?mono1_anomeric
> :hasSideAtom ?mono1_anomeric_side_atom .
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_anomeric_side_atom:sideIndex "1".
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_anomeric_side_atom:orientation"Up".
> Type the rest of statement, end with a semicolon (;)> ?mono1
> :hasRingAtom?mono1_ring_atom2.
> Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom2
> :ringIndex "2".
> Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom2
> :hasSideAtom ?mono1_side_atom2 .
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_side_atom2:sideIndex "2".
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_side_atom2:orientation"Down".
> Type the rest of statement, end with a semicolon (;)> ?mono1
> :hasRingAtom?mono1_ring_atom3.
> Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom3
> :ringIndex "3".
> Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom3
> :hasSideAtom ?mono1_side_atom3 .
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_side_atom3:sideIndex "3".
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_side_atom3:orientation"Up".
> Type the rest of statement, end with a semicolon (;)> ?mono1
> :hasRingAtom?mono1_ring_atom4.
> Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom4
> :ringIndex "4".
> Type the rest of statement, end with a semicolon (;)> ?mono1_ring_atom4
> :hasSideAtom ?mono1_side_atom4 .
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_side_atom4:sideIndex "4".
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_side_atom4:orientation"Down".
> Type the rest of statement, end with a semicolon (;)> ?mono1
> :hasRingAtom?mono1_last_c.
> Type the rest of statement, end with a semicolon (;)> ?mono1_last_c
> :ringIndex "5".
> Type the rest of statement, end with a semicolon (;)> ?mono1_last_c
> :hasSideAtom ?mono1_last_c_side_atom.
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_last_c_side_atom :sideIndex "+1".
> Type the rest of statement, end with a semicolon (;)>
> ?mono1_last_c_side_atom :orientation"Up".
> Type the rest of statement, end with a semicolon (;)>
> ?oligo2:hasRoot?mono2.
> Type the rest of statement, end with a semicolon (;)> ?mono2
> :hasRingAtom?mono2_anomeric.
> Type the rest of statement, end with a semicolon (;)> ?mono2_anomeric
> :ringIndex "1".
> Type the rest of statement, end with a semicolon (;)> ?mono2_anomeric
> :hasSideAtom ?mono2_anomeric_side_atom .
> Type the rest of statement, end with a semicolon (;)>
> ?mono2_anomeric_side_atom:sideIndex "1".
> Type the rest of statement, end with a semicolon (;)>
> ?mono2_anomeric_side_atom:orientation"Up".
> Type the rest of statement, end with a semicolon (;)> ?mono2
> :hasRingAtom?mono2_ring_atom2.
> Type the rest of statement, end with a semicolon (;)> ?mono2_ring_atom2
> :ringIndex "2".
> Type the rest of statement, end with a semicolon (;)> ?mono2_ring_atom2
> :hasSideAtom ?mono2_side_atom2 .
> Type the rest of statement, end with a semicolon (;)>
> ?mono2_side_atom2:sideIndex "2".
> Type the rest of statement, end with a semicolon (;)>
> ?mono2_side_atom2:orientation"Up".
> Type the rest of statement, end with a semicolon (;)> ?mono2
> :hasRingAtom?mono2_ring_atom3.
> Type the rest of statement, end with a semicolon (;)> ?mono2_ring_atom3
> :ringIndex "3".
> Type the rest of statement, end with a semicolon (;)> ?mono2_ring_atom3
> :hasSideAtom ?mono2_side_atom3 .
> Type the rest of statement, end with a semicolon (;)>
> ?mono2_side_atom3:sideIndex "3".
> Type the rest of statement, end with a semicolon (;)>
> ?mono2_side_atom3:orientation"Up".
> Type the rest of statement, end with a semicolon (;)> ?mono2
> :hasRingAtom?mono2_ring_atom4.
> Type the rest of statement, end with a semicolon (;)> ?mono2_ring_atom4
> :ringIndex "4".
> Type the rest of statement, end with a semicolon (;)> ?mono2_ring_atom4
> :hasSideAtom ?mono2_side_atom4 .
> Type the rest of statement, end with a semicolon (;)>
> ?mono2_side_atom4:sideIndex "4".
> Type the rest of statement, end with a semicolon (;)>
> ?mono2_side_atom4:orientation"Down".
> Type the rest of statement, end with a semicolon (;)> ?mono2
> :hasRingAtom?mono2_last_c.
> Type the rest of statement, end with a semicolon (;)> ?mono2_last_c
> :ringIndex "5".
> Type the rest of statement, end with a semicolon (;)> ?mono2_last_c
> :hasSideAtom ?mono2_last_c_side_atom.
> Type the rest of statement, end with a semicolon (;)>
> ?mono2_last_c_side_atom :sideIndex "+1".
> Type the rest of statement, end with a semicolon (;)>
> ?mono2_last_c_side_atom :orientation"Up".
> Type the rest of statement, end with a semicolon (;)> {
> Type the rest of statement, end with a semicolon (;)> ?linkage0 :hasParent
> ?oligo0.
> Type the rest of statement, end with a semicolon (;)> ?linkage0 :hasChild
> ?oligo1.
> Type the rest of statement, end with a semicolon (;)> } UNION {
> Type the rest of statement, end with a semicolon (;)> ?linkage0 :hasParent
> ?oligo1.
> Type the rest of statement, end with a semicolon (;)> ?linkage0 :hasChild
> ?oligo0.
> Type the rest of statement, end with a semicolon (;)> }
> Type the rest of statement, end with a semicolon (;)> {
> Type the rest of statement, end with a semicolon (;)> ?linkage1 :hasParent
> ?oligo1.
> Type the rest of statement, end with a semicolon (;)> ?linkage1 :hasChild
> ?oligo2.
> Type the rest of statement, end with a semicolon (;)> } UNION {
> Type the rest of statement, end with a semicolon (;)> ?linkage1 :hasParent
> ?oligo2.
> Type the rest of statement, end with a semicolon (;)> ?linkage1 :hasChild
> ?oligo1.
> Type the rest of statement, end with a semicolon (;)> }
> Type the rest of statement, end with a semicolon (;)> ?pdb
> :hasOligo ?oligo0.
> Type the rest of statement, end with a semicolon (;)> ?pdb
> :hasOligo ?oligo1.
> Type the rest of statement, end with a semicolon (;)> ?pdb
> :hasOligo ?oligo2.
> Type the rest of statement, end with a semicolon (;)> }
> Type the rest of statement, end with a semicolon (;)> ;
> pdb
> LONG VARCHAR
>
> _______________________________________________________________________________
>
>
> 0 Rows. -- 35524 msec.
> SQL>
>
> SQL> status('');
> REPORT
> VARCHAR
>
> _______________________________________________________________________________
>
> OpenLink Virtuoso Server
> Version 07.20.3216-pthreads for Darwin as of Mar 2 2016
> Started on: 2016-03-04 02:14 GMT+0
>
> Best Regards
> Hugh Williams
> Professional Services
> OpenLink Software, Inc. // http://www.openlinksw.com/
> Weblog -- http://www.openlinksw.com/blogs/
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> Google+ -- http://plus.google.com/100570109519069333827/
> Facebook -- http://www.facebook.com/OpenLinkSoftware
> Universal Data Access, Integration, and Management Technology Providers
>
>
>
> On 4 Mar 2016, at 15:44, Delaram Ra <delaram...@gmail.com> wrote:
>
> Hi all,
>
> I ran into this problem recently, my program generates queries that
> sometimes are too long. When I try to execute these queries on virtuoso
> (7.2.1) it gives me the following error:
> Virtuoso 42000 Error SR483: Stack Overflow
> I have attached the sample RDF graph that I'm trying to query and the
> sample queries as well. One of them tries to find 2 attached structures
> (works fine) and the other tries to find 3 attached structures (this is
> when error happens).
> I have checked the semantics of the queries and they seem fine to me.
> So I'm wondering if the error is related to length of the query? or it is
> something else?
>
> Any suggestion/help is appreciated.
>
> Best,
> Delaram
> <query_2structures.txt><test.ttl><query_3structures.txt>
> ------------------------------------------------------------------------------
> _______________________________________________
> Virtuoso-users mailing list
> Virtuoso-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/virtuoso-users
>
>
>
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