Hi Jerven, Can you please confirm if this issue has been resolved by upgrading your Virtuoso Server binary and INI file settings ?
Best Regards Hugh Williams Professional Services OpenLink Software, Inc. // http://www.openlinksw.com/ Weblog -- http://www.openlinksw.com/blogs/ LinkedIn -- http://www.linkedin.com/company/openlink-software/ Twitter -- http://twitter.com/OpenLink Google+ -- http://plus.google.com/100570109519069333827/ Facebook -- http://www.facebook.com/OpenLinkSoftware Universal Data Access, Integration, and Management Technology Providers On 15 Oct 2013, at 16:47, Jerven Bolleman <jerven.bolle...@isb-sib.ch> wrote: > Hi Hugh, > > Thanks for your time spent looking into this. > On 15/10/13 04:35, Hugh Williams wrote: >> 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. > git status confirms develop/7 > However, I might have ended up with a build with a little bit of both due to > switching from one branch to the other without make clean. >> >> 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 > I took these settings from a recent mail to this list by kingsley. > But will use the defaults instead (will restart from the virtuoso 7 defaults > from git) >> >> 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 ... > I am now rebuilding after a make clean. > Will let you know if I can rebuild. > > Regards, > Jerven >> >> Best Regards >> Hugh Williams >> Professional Services >> OpenLink Software, Inc. // http://www.openlinksw.com/ >> Weblog -- http://www.openlinksw.com/blogs/ >> LinkedIn -- http://www.linkedin.com/company/openlink-software/ >> Twitter -- http://twitter.com/OpenLink >> Google+ -- http://plus.google.com/100570109519069333827/ >> Facebook -- http://www.facebook.com/OpenLinkSoftware >> Universal Data Access, Integration, and Management Technology Providers >> >> On 14 Oct 2013, at 12:34, Jerven Bolleman <jerven.bolle...@isb-sib.ch >> <mailto: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 >>> <mailto: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 <http://www.isb-sib.ch> - www.uniprot.org >>> <http://www.uniprot.org> >>> Follow us at https://twitter.com/#!/uniprot >>> ------------------------------------------------------------------- >>> >>> ------------------------------------------------------------------------------ >>> October Webinars: Code for Performance >>> Free Intel webinars can help you accelerate application performance. >>> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the >>> most from >>> the latest Intel processors and coprocessors. See abstracts and register > >>> http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk >>> _______________________________________________ >>> Virtuoso-users mailing list >>> Virtuoso-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/virtuoso-users >> > > > -- > ------------------------------------------------------------------- > 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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