Hi Jerven,
I have run the query many times, but as said I keep getting the "SR325:
Transaction aborted because it's log after image size went above the limit"
first time the query is run and have to increase the
"TransactionAfterImageLimit" param in the INI file. Thus have you encountered
this error yourself or do you even have the "TransactionAfterImageLimit" param
set for your instance as I am wondering if this might be the cause of the crash
you are seeing on your instance and perhaps the param needs to be increased for
your instance ?
Best Regards
Hugh Williams
Professional Services
OpenLink Software, Inc. // http://www.openlinksw.com/
Weblog -- http://www.openlinksw.com/blogs/
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Universal Data Access, Integration, and Management Technology Providers
On 27 Jan 2014, at 13:52, Jerven Bolleman <jerven.bolle...@isb-sib.ch> wrote:
> Hi Hugh,
>
> Sorry I won’t have time to get a memory dump for at least two weeks.
> However, I must have explained something badly you need to run the insert
> query 4 or 5 times in a row to get the crash.
>
> Regards,
> Jerven
> On 26 Jan 2014, at 15:51, Hugh Williams <hwilli...@openlinksw.com> wrote:
>
>> Hi Jerven,
>>
>> I have tried recreating this against the VOS develop/7 branch on Mac OS X
>> but have been unable to do so ...
>>
>> Hughs-MacBook-Pro-478:database hwilliams$ /Applications/Virtuoso\
>> 7.1.app/Contents/virtuoso/bin/isql 1111
>> Connected to OpenLink Virtuoso
>> Driver: 07.10.3207 OpenLink Virtuoso ODBC Driver
>> OpenLink Interactive SQL (Virtuoso), version 0.9849b.
>> Type HELP; for help and EXIT; to exit.
>> SQL> status('');
>> REPORT
>> VARCHAR
>> _______________________________________________________________________________
>>
>> OpenLink Virtuoso Server
>> Version 07.00.3207-pthreads for Darwin as of Dec 10 2013
>> Started on: 2014-01-26 14:16 GMT+0
>>
>> Database Status:
>> File size 614465536, 75008 pages, 51817 free.
>> 170000 buffers, 21735 used, 0 dirty 0 wired down, repl age 0 0 w. io 0
>> w/crsr.
>> Disk Usage: 524 reads avg 1 msec, 0% r 0% w last 0 s, 21387 writes,
>> 13 read ahead, batch = 14. Autocompact 40700 in 18150 out, 55% saved col
>> ac: 4997 in 47% saved.
>> Gate: 44 2nd in reads, 0 gate write waits, 0 in while read 0 busy scrap.
>> Log = /usr/local/vos7/database/virtuoso.trx, 185 bytes
>> 23061 pages have been changed since last backup (in checkpoint state)
>> Current backup timestamp: 0x0000-0x00-0x00
>> Last backup date: unknown
>> Clients: 1 connects, max 1 concurrent
>> RPC: 4 calls, 1 pending, 1 max until now, 0 queued, 0 burst reads (0%), 0
>> second 0M large, 83M max
>> Checkpoint Remap 95 pages, 0 mapped back. 0 s atomic time.
>> DB master 75008 total 51817 free 95 remap 0 mapped back
>> temp 1024 total 1019 free
>>
>> Lock Status: 0 deadlocks of which 0 2r1w, 0 waits,
>> Currently 1 threads running 0 threads waiting 0 threads in vdb.
>> Pending:
>>
>> 23 Rows. -- 8 msec.
>> SQL> DB.DBA.RDF_LOAD_RDFXML_MT (file_to_string_output ('./taxonomy.rdf'),
>> '', 'http://beta.sparql.uniprot.org/taxonomy/');
>>
>> Done. -- 118988 msec.
>>
>> SQL> SPARQL PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> INSERT {
>> GRAPH <http://beta.sparql.uniprot.org/taxonomy/> { ?sub rdfs:subClassOf
>> ?super}} WHERE { GRAPH <http://beta.sparql.uniprot.org/taxonomy/> { ?sub
>> rdfs:subClassOf/rdfs:subClassOf ?super . MINUS { ?sub rdfs:subClassOf ?super
>> .}}};
>>
>> *** Error 40005: VD [Virtuoso Server]SR325: Transaction aborted because it's
>> log after image size went above the limit
>> at line 4 of Top-Level:
>> SPARQL PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> INSERT { GRAPH
>> <http://beta.sparql.uniprot.org/taxonomy/> { ?sub rdfs:subClassOf ?super}}
>> WHERE { GRAPH <http://beta.sparql.uniprot.org/taxonomy/> { ?sub
>> rdfs:subClassOf/rdfs:subClassOf ?super . MINUS { ?sub rdfs:subClassOf ?super
>> .}}}
>> SQL>
>>
>> I got around the SR325 erro by doubling the "TransactionAfterImageLimit"
>> param in the INI file from the default of 50000000 to 100000000 and
>> restarted Virtuoso as indicated in the documentation at:
>>
>> http://docs.openlinksw.com/virtuoso/databaseadmsrv.html#dbadm
>>
>> Then the insertion was successful:
>>
>> Hughs-MacBook-Pro-478:database hwilliams$ /Applications/Virtuoso\
>> 7.1.app/Contents/virtuoso/bin/isql 1111
>> Connected to OpenLink Virtuoso
>> Driver: 07.10.3207 OpenLink Virtuoso ODBC Driver
>> OpenLink Interactive SQL (Virtuoso), version 0.9849b.
>> Type HELP; for help and EXIT; to exit.
>> SQL> SPARQL PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> INSERT {
>> GRAPH <http://beta.sparql.uniprot.org/taxonomy/> { ?sub rdfs:subClassOf
>> ?super}} WHERE { GRAPH <http://beta.sparql.uniprot.org/taxonomy/> { ?sub
>> rdfs:subClassOf/rdfs:subClassOf ?super . MINUS { ?sub rdfs:subClassOf ?super
>> .}}};
>>
>> Done. -- 41081 msec.
>> SQL> sparql select count(*) from <http://beta.sparql.uniprot.org/taxonomy/>
>> where {?s ?p ?o};
>> callret-0
>> INTEGER
>> _______________________________________________________________________________
>>
>> 9549986
>>
>> 1 Rows. -- 150 msec.
>> SQL>
>>
>> In your case Is a core file being created when the server crashes ( note
>> core size for user account should be set to be unlimited with command
>> “ulimit -c unlimited” first), as if so you can create a debug unstripped
>> Virtuoso binary, recreate the core with it and use gdb to debug it as
>> follows:
>>
>> 1. Edit ~//Makefile
>>
>> 2. To CONFIGURE_ARGS add --with-debug
>>
>> 3. To CONFIGURE_ENV prepend CC='cc -g’
>>
>> 4. Then do "make clean all deinstall reinstall” to build a new debug
>> unstripped binary (virtuoso-t)
>>
>> 5. Start database with this new binary and force the crash condition again
>> to generate a new core file
>>
>> 6. Use gdb to load core file
>>
>> gdb virtuoso-t core
>>
>> 7. At the prompt, type "bt" or “backtrace” to backtrace through stack and
>> provide the output when top of stack is reached.
>>
>> 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 22 Jan 2014, at 11:08, Jerven Bolleman <jerven.bolle...@isb-sib.ch> wrote:
>>
>>> Dear Virtuoso devs,
>>>
>>> On commit 2701d3f242a630562302471d168d20fec5ed2805 of the develop/7 branch.
>>>
>>> I load the file
>>> ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/taxonomy.rdf.gz
>>> into the graph named
>>> http://beta.sparql.uniprot.org/taxonomy/.
>>>
>>> Then checkpoint. Then I the run the SPARUL query
>>>
>>> PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
>>> INSERT { GRAPH <http://beta.sparql.uniprot.org/taxonomy/> {
>>> ?sub rdfs:subClassOf ?super}}
>>> WHERE { GRAPH <http://beta.sparql.uniprot.org/taxonomy/> {
>>> ?sub rdfs:subClassOf/rdfs:subClassOf
>>> ?super .
>>> MINUS { ?sub rdfs:subClassOf ?super .}}}
>>>
>>> I get a message
>>> 17:27:41 * Monitor: Low query memory limit, try to increase MaxQueryMem
>>> Then I again run the same query
>>> PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
>>> INSERT { GRAPH <http://beta.sparql.uniprot.org/taxonomy/> {
>>> ?sub rdfs:subClassOf ?super}}
>>> WHERE { GRAPH <http://beta.sparql.uniprot.org/taxonomy/> {
>>> ?sub rdfs:subClassOf/rdfs:subClassOf
>>> ?super .
>>> MINUS { ?sub rdfs:subClassOf ?super .}}}
>>>
>>> And virtuoso crashes without leaving a trace in the logs.
>>>
>>> The query log shows the first execution but not the second.
>>> And that looks like this
>>>
>>> Precode:
>>> 0: { FOR UPDATE
>>> time -nan% fanout 1 input 1 rows
>>> time -nan% fanout 1 input 1 rows
>>>
>>> Precode:
>>> 0: vector := Call vector ( 1 , 0 , 3 , ##subClassOf , 1 , 1 )
>>> 5: vector := Call vector (vector)
>>> 10: vector := Call vector ()
>>> 15: __bft := Call __bft (<c http://beta.sparql.uniprot.org/taxonomy/>,
>>> 1 )
>>> 20: BReturn 0
>>> { fork
>>> time -nan% fanout 1.09875e+06 input 1 rows
>>> RDF_QUAD_POGS 2.4e+03 rows(s_6_4_t1.O, s_6_4_t1.S)
>>> inlined P = ##subClassOf G = #/
>>> time -nan% fanout 0.999965 input 1.09875e+06 rows
>>> RDF_QUAD 1 rows(s_6_7_t2.O)
>>> inlined P = ##subClassOf , S = k_s_6_4_t1.O G = #/
>>> time -nan% fanout 0 input 1.09871e+06 rows
>>> END Node
>>> After test:
>>> 0: if ({
>>> time -nan% fanout 1 input 1.09871e+06 rows
>>> time -nan% fanout 0 input 1.09871e+06 rows
>>> RDF_QUAD_POGS unq 0.0011 rows ()
>>> P = ##subClassOf , O = k_s_6_7_t2.O , S = k_s_6_4_t1.S , G = #/
>>> time -nan% fanout 0 input 0 rows
>>> Subquery Select( <none> )
>>> }
>>> ) then 5 else 4 unkn 5
>>> 4: BReturn 1
>>> 5: BReturn 0
>>>
>>> After code:
>>> 0: __ro2lo := Call __ro2lo (s_6_7_t2.O)
>>> 5: vector := Call vector (s_6_4_t1.S, __ro2lo)
>>> 10: if ($63 "user_aggr_notfirst" = 1 ) then 25 else 14 unkn 14
>>> 14: $63 "user_aggr_notfirst" := := artm 1
>>> 18: user_aggr_ret := Call DB.DBA.SPARQL_CONSTRUCT_INIT ($64
>>> "user_aggr_env")
>>> 25: user_aggr_ret := Call DB.DBA.SPARQL_CONSTRUCT_ACC ($64
>>> "user_aggr_env", vector, vector, vector, 0 )
>>> 32: BReturn 0
>>> }
>>> time -nan% fanout 1 input 1 rows
>>> skip node 1 <none> set_ctr
>>>
>>> After code:
>>> 0: DB.DBA.SPARQL_CONSTRUCT_FIN := Call DB.DBA.SPARQL_CONSTRUCT_FIN ($64
>>> "user_aggr_env")
>>> 7: callret-0 := Call DB.DBA.SPARQL_INSERT_DICT_CONTENT (__bft,
>>> DB.DBA.SPARQL_CONSTRUCT_FIN, 0 , <DB_NULL>, 0 )
>>> 14: BReturn 0
>>> time -nan% fanout 0 input 1 rows
>>> skip node 1 <none> set_ctr
>>>
>>> After code:
>>> 0: DB.DBA.SPARQL_CONSTRUCT_FIN := Call DB.DBA.SPARQL_CONSTRUCT_FIN ($64
>>> "user_aggr_env")
>>> 7: callret-0 := Call DB.DBA.SPARQL_INSERT_DICT_CONTENT (__bft,
>>> DB.DBA.SPARQL_CONSTRUCT_FIN, 0 , <DB_NULL>, 0 )
>>> 14: BReturn 0
>>> time -nan% fanout 0 input 1 rows
>>> Subquery Select(callret-0)
>>> }
>>>
>>> 8: $184 "vector" := Call vector ($185 "scalar")
>>> 13: $183 "DB.DBA.SPARUL_RUN" := Call DB.DBA.SPARUL_RUN ($184 "vector")
>>> 20: <none> := Call set_row_count ($183 "DB.DBA.SPARUL_RUN")
>>> 25: BReturn 0
>>> END Node
>>> }
>>> ^@^B<80>^@<BD>^@^P<C3><D7><C1><BC>+<BD>^@^@8Z<D3>^K8^X^PqP^@ESC
>>> <<BC>^@<BC>^@<B5> 127.0.0.1<B5>^Cdba<CC>^S<BD>^@#k<A2><BD>^@^@G
>>> <B5>^Nlog_enable (3)^A<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@
>>> <BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<B6>^@^@^@W{
>>>
>>> Precode:
>>> 0: <none> := Call log_enable ( 3 )
>>> 5: BReturn 0
>>> END Node
>>> }
>>> ^@^A@^@<BC>^@<C1><BC>+<BD>^@^@8[<D3>^K8^X^PqP^@^\ <<BC>^@<BC>^@<B5>
>>> 127.0.0.1<B5>^Cdba<CC>^S<BD>^@#k<A3><BD>^@^@G <B5>^Xcheckpoint_interval
>>> (60)^A<BC>^@<BC>^A<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@
>>> <BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<B6>^@^@^@a{
>>>
>>> Precode:
>>> 0: <none> := Call checkpoint_interval ( 60 )
>>> 5: BReturn 0
>>> END Node
>>> }
>>> ^@^A@^@<BC>^@<C1><BC>+<BD>^@^@8\<D3>^K8^X^PqP^@^^ <<BC>^@<BC>^@<B5>
>>> 127.0.0.1<B5>^Cdba<CC>^S<BD>^@#k<B6><BD>^@^@G <B5>^Wcheckpoint_interval
>>> (0)^A<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@
>>> <BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<B6>^@^@^@`{
>>>
>>> Precode:
>>> 0: <none> := Call checkpoint_interval ( 0 )
>>> 5: BReturn 0
>>> END Node
>>> }
>>> ^@^A@^@<BC>^@<C1><BC>+<BD>^@^@8]<D3>^K8^X^PqP^@^_ <<BC>^@<BC>^@<B5>
>>> 127.0.0.1<B5>^Cdba<CC>^S<BD>^@#k<B6><BD>^@^@G <B5>^Nlog_enable
>>> (0)^A<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>
>>> ^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<BC>^@<B6>^@^@^@W{
>>>
>>> Precode:
>>> 0: <none> := Call log_enable ( 0 )
>>> 5: BReturn 0
>>> END Node
>>> }
>>> I would expect the next query to show up here but it did not. The change to
>>> the checkpoint interval and logging status show that the two statements
>>> before the SPARUL succeeded.
>>>
>>> The exception caught from the java side is
>>> Exception:virtuoso.jdbc4.VirtuosoException: Virtuoso Communications Link
>>> Failure (timeout) : Connection to the server lost
>>> at
>>> virtuoso.sesame2.driver.VirtuosoRepositoryConnection.executeSPARUL(Unknown
>>> Source)
>>> at
>>> virtuoso.sesame2.driver.VirtuosoRepositoryConnection$4.execute(Unknown
>>> Source)
>>>
>>> Is there a way I can change the error log level to be more
>>> verbose/helpfull?
>>>
>>> Regards,
>>> Jerven
>>>
>>> --
>>> -------------------------------------------------------------------
>>> 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
>>> -------------------------------------------------------------------
>>> <virtuoso-config-expasy4j-sparql702803043962519654.ini><virtuoso.log>------------------------------------------------------------------------------
>>> 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
>>
>
> -------------------------------------------------------------------
> 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
> -------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------------
> 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
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