Hi Nuria,
How much memory is available on your server machine as the buffers seem to be
set to the default of "20000" , thus has any performance tuning be made on
this instance as detailed at:
http://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/VirtRDFPerformanceTuning
In particular you should set the "NumberOfBuffers" param to match the size of
available memory for use by Virtuoso and restart the database for the settings
to take effect ...
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
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Facebook -- http://www.facebook.com/OpenLinkSoftware
Universal Data Access, Integration, and Management Technology Providers
On 17 Feb 2014, at 19:25, "QUERALT ROSINACH, NÚRIA" <nuria.quer...@upf.edu>
wrote:
> Hi Hugh,
>
>
> 2014-01-27 11:18 GMT+01:00 Hugh Williams <hwilli...@openlinksw.com>:
> Hi Núria,
>
> Can you please provide the output of running the following command to check
> the status() of the Virtuoso Server instance from the isql command line
> prompt:
>
> status();
>
> I am particularly interested is seeing the Server "buffers" allocated and
> used to confirm the server has been tuned.
>
> The retrieved info from the status(); command:
>
> SQL> status();
> REPORT
> VARCHAR
> _______________________________________________________________________________
>
> OpenLink Virtuoso Server
> Version 07.00.3207-pthreads for Linux as of Jan 9 2014
> Started on: 2014-01-10 09:13 GMT+1
>
> Database Status:
> File size 419430400, 51200 pages, 27550 free.
> 20000 buffers, 16962 used, 3 dirty 0 wired down, repl age 71085 0 w. io 0
> w/crsr.
> Disk Usage: 14552 reads avg 1 msec, 0% r 0% w last 23 s, 85707 writes,
> 67 read ahead, batch = 20. Autocompact 20184 in 14931 out, 26% saved col
> ac: 4117 in 18% saved.
> Gate: 183 2nd in reads, 0 gate write waits, 0 in while read 0 busy scrap.
> Log = /usr/local/virtuoso-opensource-7.0.1/var/lib/virtuoso/db/virtuoso.trx,
> 6912 bytes
> 23609 pages have been changed since last backup (in checkpoint state)
> Current backup timestamp: 0x0000-0x00-0x00
> Last backup date: unknown
> Clients: 7 connects, max 1 concurrent
> RPC: 70 calls, -4 pending, 1 max until now, 0 queued, 0 burst reads (0%), 0
> second 1M large, 286M max
> Checkpoint Remap 0 pages, 0 mapped back. 4010 s atomic time.
> DB master 51200 total 27550 free 0 remap 0 mapped back
> temp 3072 total 3067 free
>
> Lock Status: 1 deadlocks of which 0 2r1w, 2241 waits,
> Currently 1 threads running 0 threads waiting 0 threads in vdb.
> Pending:
>
> Client 1111:12:-13: Account: dba, 485 bytes in, 2638 bytes out, 1 stmts.
> PID: 19446, OS: unix, Application: unknown, IP#: 127.0.0.1
> Transaction status: PENDING, 1 threads.
> Locks:
>
>
> Running Statements:
> Time (msec) Text
> 28 status()
>
>
> Hash indexes
>
>
> 37 Rows. -- 43 msec.
>
>
>
>
> Also, what is the total number of triples in your virtuoso server instance
> "sparql select count(*) where {?s ?p ?o}" ;
>
>
>
> Answer: 1.301.738 triples
>
>
>
>
> what is the triple count of the <http://source.cat> graph
>
>
>
> Answer: 1.246.495 triples
>
>
>
> and the expected number to be inserted into the other graphs in the query ?
>
>
>
> Graph 1: 289.560 triples
>
> Graph 2: 231.648 triples
>
> Graph 3: 405.384 triples
>
> Thanks!
>
> Best,
> n
>
>
>
> 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 21 Jan 2014, at 14:28, "QUERALT ROSINACH, NÚRIA" <nuria.quer...@upf.edu>
> wrote:
>
> > Hi Hugh,
> >
> > I suspected that the solution was to grant execute for this function, but
> > just in case...I granted this privilege to 'SPARQL' user and now i have the
> > typical message:
> >
> > Virtuoso S1T00 Error SR171: Transaction timed out
> >
> > basically, the query i am trying to perform is something like:
> >
> > PREFIX foaf: <http://xmlns.com/foaf/0.1/>
> > PREFIX ...
> >
> > INSERT
> > {
> > GRAPH <http://example.cat>
> > {
> > ?s a vocab:sth .
> > ?sth foaf:name ?name .
> > }
> > GRAPH ?anotherGraph
> > {
> > _:bn foaf:name "case" .
> > }
> > }
> > USING <http://source.cat>
> > WHERE
> > {
> > ?s foaf:name ?name .
> > BIND(iri(concat(str(?sth),"_",str(?name))) as ?s)
> > BIND(iri(concat(str(?s),"_data")) as ?anotherGraph)
> > }
> >
> > 2014/1/21 Hugh Williams <hwilli...@openlinksw.com>
> > Hi Núria,
> >
> > As for the other function you should be able to grant execute ... to get
> > around this:
> >
> > GRANT EXECUTE ON DB.DBA.L_O_LOOK TO "SPARQL"
> >
> > We have had a report of this error before and is should have been fixed,
> > thus can you please confirm the steps, you performed to get this error and
> > confirm the version and build date of the Virtuoso server being used
> > (virtuoso-t -? ) ...
> >
> >
> > The steps were:
> >
> > 1. Installation of Virtuoso server from develop/7 branch in github
> > 2. Loading our rdf data into the triple store without problems
> > 3. Query the prior query in the Virtuoso sparql endpoint
> > 4. An the following error message come up:
> > Virtuoso 42000 Error SR186: No permission to execute procedure
> > DB.DBA.SPARQL_INSERT_QUAD_DICT_CONTENT with user ID 106, group ID 106
> > Solved granting the function with execute privilege.
> >
> >
> > and the version and the build date of the server is:
> >
> > Virtuoso Open Source Edition (Column Store) (multi threaded)
> > Version 7.0.1-dev.3207-pthreads as of Jan 9 2014
> > Compiled for Linux (x86_64-unknown-linux-gnu)
> > Copyright (C) 1998-2013 OpenLink Software
> >
> > thanks!
> > nuria
> >
> > 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 21 Jan 2014, at 11:37, "QUERALT ROSINACH, NÚRIA" <nuria.quer...@upf.edu>
> > wrote:
> >
> > > Hi all,
> > >
> > > I am trying to do an Insert of data in a Virtuoso server v7.0.1, but the
> > > following error appeared:
> > >
> > > Virtuoso 42000 Error SR186: No permission to execute dpipe
> > > DB.DBA.L_O_LOOK with user ID 106, group ID 106
> > >
> > > Any idea on how to overcome this? Any help it'll be very welcome!
> > >
> > > Many thanks in advance!
> > >
> > > Kind regards,
> > > núria
> > >
> > > --
> > > ********************************************************************
> > > Núria Queralt Rosinach
> > > Research Programme on Biomedical Informatics (GRIB)
> > > Department of Experimental and Health Sciences
> > > Universitat Pompeu Fabra
> > > IMIM (Hospital del Mar Medical Research Institute)
> > > C/Dr. Aiguader 88, 08003
> > > Barcelona, Spain
> > > Tel.: +34 93 316 0536
> > > E-mail: nuria.quer...@upf.edu
> > > http://ibi.imim.es/
> > > ********************************************************************
> > > ------------------------------------------------------------------------------
> > > CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> > > Learn Why More Businesses Are Choosing CenturyLink Cloud For
> > > Critical Workloads, Development Environments & Everything In Between.
> > > Get a Quote or Start a Free Trial Today.
> > > http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk_______________________________________________
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> > > Virtuoso-users@lists.sourceforge.net
> > > https://lists.sourceforge.net/lists/listinfo/virtuoso-users
> >
> >
> >
> >
> > --
> > ********************************************************************
> > Núria Queralt Rosinach
> > Research Programme on Biomedical Informatics (GRIB)
> > Department of Experimental and Health Sciences
> > Universitat Pompeu Fabra
> > IMIM (Hospital del Mar Medical Research Institute)
> > C/Dr. Aiguader 88, 08003
> > Barcelona, Spain
> > Tel.: +34 93 316 0536
> > E-mail: nuria.quer...@upf.edu
> > http://ibi.imim.es/
> > ********************************************************************
> > ------------------------------------------------------------------------------
> > CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> > Learn Why More Businesses Are Choosing CenturyLink Cloud For
> > Critical Workloads, Development Environments & Everything In Between.
> > Get a Quote or Start a Free Trial Today.
> > http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk_______________________________________________
> > Virtuoso-users mailing list
> > Virtuoso-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/virtuoso-users
>
>
>
>
> --
> ********************************************************************
> Núria Queralt Rosinach
> Research Programme on Biomedical Informatics (GRIB)
> Department of Experimental and Health Sciences
> Universitat Pompeu Fabra
> IMIM (Hospital del Mar Medical Research Institute)
> C/Dr. Aiguader 88, 08003
> Barcelona, Spain
> Tel.: +34 93 316 0536
> E-mail: nuria.quer...@upf.edu
> http://ibi.imim.es/
> ********************************************************************
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