Hi Jerven, I have downloaded the /taxonomy.rdf.gz dataset and installed, but have not been able to recreate this problem using a commercial or open source Virtuoso build:
$ ./bin/virtuoso-t -?
-bash: ./bin/virtuoso-t: No such file or directory
Hughs-MacBook-Pro-355:database hwilliams$ ../bin/virtuoso-t -?
Virtuoso Open Source Edition (Column Store) (multi threaded)
Version 7.0.1-dev.3203-pthreads as of Oct 13 2013
Compiled for Darwin (x86_64-apple-darwin12.3.0)
Copyright (C) 1998-2013 OpenLink Software
Two points:
1. Your build is labelled as version 07.00.3203 , whereas mine above is
7.0.1-dev.3203 , which is what I would expect from a develop/7 build. So it
seems to me you have a stable/7 build, which can be confirmed by running the
"git status" command on your build tree.
2. Why is you set those Column Store INI file params to such low values as the
defaults recommended are:
MaxQueryMem = 2G ; memory allocated to query processor
VectorSize = 1000 ; initial parallel query vector (array
of query operations) size
MaxVectorSize = 1000000 ; query vector size threshold.
AdjustVectorSize = 0
ThreadsPerQuery = 8
AsyncQueueMaxThreads = 10
Although the only issue I encountered with your low setting was a warning
indicating:
Virtuoso 42000 Error FRVEC: array in for vectored over max vector
length 10001 > 10000
as your MaxVectorSize was set to 10000.
Anyway, I think the key is to confirm which build you are running to ensure it
is a develop/7 build ...
Best Regards
Hugh Williams
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On 14 Oct 2013, at 12:34, Jerven Bolleman <jerven.bolle...@isb-sib.ch> wrote:
> 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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