[Netarchivesuite-devel] FW: [SBForge JIRA] Commented: (NAS-1845) Database Deadlock
Nicolas Giraud
nikokode at gmail.com
Thu Apr 14 10:33:10 CEST 2011
Hi Colin and Mikis,
I have uploaded a patch NAS-1845, that solves the particular avatar of the
issue I had. As I suspected, it would seem that Derby might detect deadlocks
if the same thread opens several connections. However in this example, I
don't understand why a deadlock happens, as we don't access the same tables
in the nested DAO method
(HarvestDefinitionDBDAO#getSparseDomainConfigurations) and the top-level
call (HarvestDefinitionDBDAO#flipActive).
Can you guys have a look at this?
Currently I see two options to fix this:
1) refactor all DAO classes to make sure that only top-level DAO calls (i.e.
called from JSPs) request a connection from the pool, and that all nested
call reuse the same connection. That's probably a tad tedious and painful,
but would enhance the code.
2) modify HarvestDBConnection to ensure that a same thread cannot have more
than one connection opened at a time
What's your opinion?
Cheers,
Nicolas Giraud
2011/4/14 Nicolas Giraud <nikokode at gmail.com>
> Hi Mikis,
>
> I have a similar error when attempting to activate a harvest definition. I
> will continue investigating but so far I don't understand what's happening.
>
> Regards,
>
> Nicolas
>
> 2011/4/14 Mikis Seth Sørensen <mss at statsbiblioteket.dk>
>
>> Hi Nicolas
>>
>> Have you got any idea of the cause for Colins problem is. Could you try to
>> reproduce the error in your environment based on Colins instructions?
>>
>> Note that this is a Blocker.
>>
>> ~Mikis
>>
>> From: "Colin Rosenthal (JIRA)" <jira at sbforge.org>
>> Date: Thu, 14 Apr 2011 09:15:37 +0200
>> To: Mikis Seth Sørensen <mss at statsbiblioteket.dk>
>> Subject: [SBForge JIRA] Commented: (NAS-1845) Database Deadlock
>>
>> *Issue* (*View Online <https://sbforge.org/jira/browse/NAS-1845>*)
>> *Key:* NAS-1845 <https://sbforge.org/jira/browse/NAS-1845> Issue
>> Type: [image: Bug] <https://sbforge.org/jira/browse/NAS-1845> Bug
>> Status: [image: Triage] Triage Priority: [image: Blocker] Blocker
>> Assignee: Unassigned Reporter: Colin Rosenthal<https://sbforge.org/jira/secure/ViewProfile.jspa?name=csr>
>> Operations *View all<https://sbforge.org/jira/browse/NAS-1845?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel>
>> * *View comments<https://sbforge.org/jira/browse/NAS-1845?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel>
>> * *View history<https://sbforge.org/jira/browse/NAS-1845?page=com.atlassian.jira.plugin.system.issuetabpanels:changehistory-tabpanel>
>> * *Database Deadlock <https://sbforge.org/jira/browse/NAS-1845>*
>>
>> Updated: 14/Apr/11 9:14 AM Created: 13/Apr/11 2:53 PM
>> The following comment has been added to this issue: [ Permalink<https://sbforge.org/jira/browse/NAS-1845?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=26252#comment-26252>]
>> *Author:* Colin Rosenthal<https://sbforge.org/jira/secure/ViewProfile.jspa?name=csr>
>> *Date:* 14/Apr/11 9:14 AM
>> *Comment:*
>>
>> The issue appears to be reproducible:
>> i) Create a new install
>> ii) add an alias (netarkivet.dk is an alias for kb.dk)
>> iii) Run a snapshot harvest with byte limit 100000
>> iv) After the harvest is finished, edit sulnudu.dk to make it an alias of
>> kb.dk. This step deadlocks.
>>
>> *Project:* NetarchiveSuite <https://sbforge.org/jira/browse/NAS> *
>> Components:* GUI *Affects Versions:* 3.16.0 *Fix Versions:* 3.16.0
>> Description
>>
>> Received the following deadlock when trying to update alias information
>> (Step 9 of Test 2).
>>
>> SQL error updating domain Domain:sulnudu.dk;
>> Comment:;
>> Configurations:
>> defaultconfig;
>> Seedlists:
>> defaultseeds;
>> Passwords:
>> ---------------
>> in database
>> SQLException trace:
>> SQL State:40XL2
>> Error Code:-1
>> java.sql.SQLTransactionRollbackException: A lock could not be obtained
>> within the time requested. The lockTable dump is:
>> 2011-04-13 12:50:14.632 GMT
>> XID |TYPE |MODE|LOCKCOUNT|LOCKNAME |STATE|TABLETYPE / LOCKOBJ |INDEXNAME /
>> CONTAINER_ID / (MODE for LATCH only) |TABLENAME / CONGLOM_ID |
>>
>> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>
>> -
>> -
>> - The following row is the victim ***
>> 6641 |ROW |S |0 |(2,15) |WAIT |T |NULL |DOMAINS |
>> - The above row is the victim ***
>> 6630 |ROW |X |4 |(2,15) |GRANT|T |NULL |DOMAINS |
>> 6630 |TABLE |IX |4 |Tablelock |GRANT|T |NULL |DOMAINS |
>> 6641 |TABLE |IS |1 |Tablelock |GRANT|T |NULL |DOMAINS |
>>
>> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>
>> at
>> org.apache.derby.client.am.SQLExceptionFactory40.getSQLException(Unknown
>> Source)
>> at org.apache.derby.client.am.SqlException.getSQLException(Unknown Source)
>> at org.apache.derby.client.am.PreparedStatement.executeUpdate(Unknown
>> Source)
>> at
>> com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProxyPreparedStatement.java:105)
>> at
>> dk.netarkivet.harvester.datamodel.DomainDBDAO.updateHarvestInfo(DomainDBDAO.java:646)
>> at
>> dk.netarkivet.harvester.datamodel.DomainDBDAO.update(DomainDBDAO.java:292)
>> at
>> dk.netarkivet.harvester.webinterface.DomainDefinition.updateDomain(DomainDefinition.java:195)
>> at
>> dk.netarkivet.harvester.webinterface.DomainDefinition.processRequest(DomainDefinition.java:138)
>> at
>> org.apache.jsp.Definitions_002dedit_002ddomain_jsp._jspService(org.apache.jsp.Definitions_002dedit_002ddomain_jsp:125)
>> at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:109)
>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
>> at
>> org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:389)
>> at
>> org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:486)
>> at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:380)
>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
>> at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511)
>> at
>> org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:401)
>> at
>> org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
>> at
>> org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
>> at
>> org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:766)
>> at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:450)
>> at
>> org.mortbay.jetty.handler.HandlerCollection.handle(HandlerCollection.java:114)
>> at
>> org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152)
>> at org.mortbay.jetty.Server.handle(Server.java:322)
>> at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542)
>> at
>> org.mortbay.jetty.HttpConnection$RequestHandler.content(HttpConnection.java:945)
>> at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:756)
>> at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:218)
>> at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
>> at
>> org.mortbay.jetty.bio.SocketConnector$Connection.run(SocketConnector.java:228)
>> at
>> org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582)
>> Caused by: org.apache.derby.client.am.SqlException: A lock could not be
>> obtained within the time requested. The lockTable dump is:
>> 2011-04-13 12:50:14.632 GMT
>> XID |TYPE |MODE|LOCKCOUNT|LOCKNAME |STATE|TABLETYPE / LOCKOBJ |INDEXNAME /
>> CONTAINER_ID / (MODE for LATCH only) |TABLENAME / CONGLOM_ID |
>>
>> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>
>> -
>> -
>> - The following row is the victim ***
>> 6641 |ROW |S |0 |(2,15) |WAIT |T |NULL |DOMAINS |
>> - The above row is the victim ***
>> 6630 |ROW |X |4 |(2,15) |GRANT|T |NULL |DOMAINS |
>> 6630 |TABLE |IX |4 |Tablelock |GRANT|T |NULL |DOMAINS |
>> 6641 |TABLE |IS |1 |Tablelock |GRANT|T |NULL |DOMAINS |
>>
>> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>
>> at org.apache.derby.client.am.Statement.completeExecute(Unknown Source)
>> at
>> org.apache.derby.client.net.NetStatementReply.parseEXCSQLSTTreply(Unknown
>> Source)
>> at org.apache.derby.client.net.NetStatementReply.readExecute(Unknown
>> Source)
>> at org.apache.derby.client.net.StatementReply.readExecute(Unknown Source)
>> at org.apache.derby.client.net.NetPreparedStatement.readExecute_(Unknown
>> Source)
>> at org.apache.derby.client.am.PreparedStatement.readExecute(Unknown
>> Source)
>> at org.apache.derby.client.am.PreparedStatement.flowExecute(Unknown
>> Source)
>> at org.apache.derby.client.am.PreparedStatement.executeUpdateX(Unknown
>> Source)
>> ... 29 more
>> End of SQLException trace
>>
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>>
>
>
> --
> Nicolas Giraud
>
> ---------------------------------------------------------------------------------------------
> Développeur Archives du Web - Bibliothèque Nationale de France
> Web Archiving Developper - National Library of France
>
> ---------------------------------------------------------------------------------------------
>
--
Nicolas Giraud
---------------------------------------------------------------------------------------------
Développeur Archives du Web - Bibliothèque Nationale de France
Web Archiving Developper - National Library of France
---------------------------------------------------------------------------------------------
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