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
-------------------------------------------------------------------
------------------------------------------------------------------------------
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Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
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