[Building Sakai] Add Particicpants MySQL table lock
Jon Higham
J.Higham at hull.ac.uk
Tue Feb 16 06:14:41 PST 2010
The only customised code around site-manage is some to prevent
Instructors from deleting their own sites and hiding of the site contact
details, so I don't think that is the issue.
I will check DB load with our DB admin, who is on leave this week, but
would be surprised if he hadn't mentioned high load.
My first thoughts were that it was linked to there being a large number
of users on the site (approx 580), but we can experience the problem on
small member sizes (12) and when adding or removing members
individually.
I have also noticed that the Instructors adding users sometimes have 2
sessions open, and perhaps trying to update membership simultaneously on
both, but again that doesn't appear to be the case.
I've also wondered it could be linked to us using web services to
add/remove site members somehow interfering, but again I don't see why
that would happen.
Could missing something on a conversion script cause the issue?
Jon
-----Original Message-----
From: sakai-dev-bounces at collab.sakaiproject.org
[mailto:sakai-dev-bounces at collab.sakaiproject.org] On Behalf Of Stephen
Marquard
Sent: 16 February 2010 12:10
To: Sakai-Dev; Jon Higham
Subject: Re: [Building Sakai] Add Particicpants MySQL table lock
Lock wait timeouts are very unusual - it basically means other queries
have locked one or more of the tables involved for update for greater
than 50 seconds (unless your mysql settings for this are non-standard).
Is your MySQL server under extreme load, or do you have any other custom
code or processes that is perhaps using these tables and not handling
locking correctly?
Regards
Stephen
>>> "Jon Higham" <J.Higham at hull.ac.uk> 2010/02/16 02:03 PM >>>
We are running sakai 2.6 with MySQL. Occasionally, site instructors
report that they have gone through the procedure (Site Info > Add
Participants) to manually add users to their sites. No errors or
warnings are given to the Instructor, but the users are not added. This
also occasionally occurs for removing users too.
Looking at the sakai_event table I can see a row showing
site.upd.site.mbrshp, but this is not followed by site.upd. Later
attempts, that eventually work for the Instructor, show a
site.upd.site.mbrshp row followed by site.upd.
The logs for this happening are below. Looks like a lock on the table
causing a timeout. Can anyone suggest what might be causing the lock?
Thanks
Jon Higham
IT Systems
University of Hull
2010-02-14 08:50:14,888 [TP-Processor551] WARN
org.sakaiproject.db.impl.BasicSqlService - Sql.dbWrite(): error code:
1205 sql: update SAKAI_REALM set PROVIDER_ID = ?,MAINTAIN_ROLE = (select
MAX(ROLE_KEY) from SAKAI_REALM_ROLE where ROLE_NAME = ?),CREATEDBY =
?,MODIFIEDBY = ?,CREATEDON = ?,MODIFIEDON = ? where ( REALM_ID = ? )
binds: Instructor admin ggshf 20081217141209000 20100214084923732
/site/20239_0910S2
java.sql.SQLException: Lock wait timeout exceeded; try restarting
transaction
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1055)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:956)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3515)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3447)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1951)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2101)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2554)
at
com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:
1761)
at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:20
46)
at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:19
64)
at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:19
49)
at
org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delega
tingPreparedStatement.java:102)
at
org.sakaiproject.db.impl.BasicSqlService.dbWrite(BasicSqlService.java:12
05)
at
org.sakaiproject.db.impl.BasicSqlService.dbWrite(BasicSqlService.java:10
39)
at
org.sakaiproject.util.BaseDbFlatStorage.commitResource(BaseDbFlatStorage
.java:855)
at
org.sakaiproject.authz.impl.DbAuthzGroupService$DbStorage.saveTx(DbAuthz
GroupService.java:1015)
at
org.sakaiproject.authz.impl.DbAuthzGroupService$DbStorage$8.run(DbAuthzG
roupService.java:986)
at
org.sakaiproject.db.impl.BasicSqlService.transact(BasicSqlService.java:3
28)
at
org.sakaiproject.authz.impl.DbAuthzGroupService$DbStorage.save(DbAuthzGr
oupService.java:982)
at
org.sakaiproject.authz.impl.BaseAuthzGroupService.completeSave(BaseAuthz
GroupService.java:592)
at
org.sakaiproject.authz.impl.BaseAuthzGroupService.save(BaseAuthzGroupSer
vice.java:578)
at
org.sakaiproject.site.tool.helper.participant.impl.SiteAddParticipantHan
dler.addUsersRealm(SiteAddParticipantHandler.java:503)
at
org.sakaiproject.site.tool.helper.participant.impl.SiteAddParticipantHan
dler.processConfirmContinue(SiteAddParticipantHandler.java:591)
at sun.reflect.GeneratedMethodAccessor11940.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at
uk.org.ponder.reflect.JDKReflectiveCache.invokeMethod(JDKReflectiveCache
.java:23)
at
uk.org.ponder.reflect.JDKReflectiveCache.invokeMethod(JDKReflectiveCache
.java:17)
at
uk.org.ponder.reflect.JDKReflectiveCache.invokeMethod(JDKReflectiveCache
.java:77)
at
uk.org.ponder.reflect.ReflectiveCache.invokeMethod(ReflectiveCache.java:
141)
at
uk.org.ponder.mapping.support.DARApplier.invokeBeanMethod(DARApplier.jav
a:179)
at
uk.org.ponder.rsf.state.support.RSVCApplier.invokeAction(RSVCApplier.jav
a:218)
at
uk.org.ponder.rsf.processor.support.RSFActionHandler$1.run(RSFActionHand
ler.java:189)
at
uk.org.ponder.util.CollectingRunnableInvoker$1.run(CollectingRunnableInv
oker.java:25)
at
uk.org.ponder.rsf.flow.support.BasicScopedAlterationWrapper.lockUUPP(Bas
icScopedAlterationWrapper.java:73)
at
uk.org.ponder.rsf.flow.support.BasicScopedAlterationWrapper.lockUUPP(Bas
icScopedAlterationWrapper.java:80)
at
uk.org.ponder.rsf.flow.support.BasicScopedAlterationWrapper.invokeRunnab
le(BasicScopedAlterationWrapper.java:64)
at
uk.org.ponder.rsf.flow.support.BasicScopedAlterationWrapper$$FastClassBy
CGLIB$$84f89202.invoke(<generated>)
at net.sf.cglib.proxy.MethodProxy.invoke(MethodProxy.java:149)
at
org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedIntercept
or.intercept(Cglib2AopProxy.java:623)
at
uk.org.ponder.rsf.flow.support.BasicScopedAlterationWrapper$$EnhancerByC
GLIB$$9392038c.invokeRunnable(<generated>)
at
uk.org.ponder.rsf.flow.support.BasicScopedAlterationWrapper$$FastClassBy
CGLIB$$84f89202.invoke(<generated>)
at net.sf.cglib.proxy.MethodProxy.invoke(MethodProxy.java:149)
at
org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedIntercept
or.intercept(Cglib2AopProxy.java:623)
at
uk.org.ponder.rsf.flow.support.BasicScopedAlterationWrapper$$EnhancerByC
GLIB$$9392038c.invokeRunnable(<generated>)
at
uk.org.ponder.util.CollectingRunnableInvoker$1.run(CollectingRunnableInv
oker.java:29)
at
uk.org.ponder.util.CollectingRunnableInvoker.invokeWrappers(CollectingRu
nnableInvoker.java:22)
at
uk.org.ponder.util.CollectingRunnableInvoker.invokeRunnable(CollectingRu
nnableInvoker.java:14)
at
uk.org.ponder.rsf.processor.support.RSFActionHandler.handle(RSFActionHan
dler.java:165)
at
uk.org.ponder.rsf.processor.support.RSFActionHandler$$FastClassByCGLIB$$
e3b6899d.invoke(<generated>)
at net.sf.cglib.proxy.MethodProxy.invoke(MethodProxy.java:149)
at
org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedIntercept
or.intercept(Cglib2AopProxy.java:623)
at
uk.org.ponder.rsf.processor.support.RSFActionHandler$$EnhancerByCGLIB$$6
3cbf9f5.handle(<generated>)
at
uk.org.ponder.rsf.processor.support.RootHandlerBeanBase.handlePost(RootH
andlerBeanBase.java:125)
at
uk.org.ponder.rsf.processor.support.RootHandlerBeanBase.handle(RootHandl
erBeanBase.java:82)
at sun.reflect.GeneratedMethodAccessor5806.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at
uk.org.ponder.reflect.JDKReflectiveCache.invokeMethod(JDKReflectiveCache
.java:23)
at
uk.org.ponder.reflect.JDKReflectiveCache.invokeMethod(JDKReflectiveCache
.java:17)
at
uk.org.ponder.reflect.JDKReflectiveCache.invokeMethod(JDKReflectiveCache
.java:77)
at
uk.org.ponder.rsac.support.RSACBeanLocatorImpl.createBean(RSACBeanLocato
rImpl.java:553)
at
uk.org.ponder.rsac.support.RSACBeanLocatorImpl.access$000(RSACBeanLocato
rImpl.java:75)
at
uk.org.ponder.rsac.support.RSACBeanLocatorImpl$1.run(RSACBeanLocatorImpl
.java:449)
at
uk.org.ponder.rsac.RSACErrorBridge.invokeRunnable(RSACErrorBridge.java:3
8)
at
uk.org.ponder.rsac.support.RSACBeanLocatorImpl.createBean(RSACBeanLocato
rImpl.java:447)
at
uk.org.ponder.rsac.support.RSACBeanLocatorImpl.getLocalBean(RSACBeanLoca
torImpl.java:348)
at
uk.org.ponder.rsac.support.RSACBeanLocatorImpl.getBean(RSACBeanLocatorIm
pl.java:379)
at
uk.org.ponder.rsac.support.PerRequestInfo$1.locateBean(PerRequestInfo.ja
va:49)
at
uk.ac.cam.caret.sakai.rsf.servlet.ReasonableSakaiServlet.service(Reasona
bleSakaiServlet.java:65)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:269)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
at
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatc
her.java:679)
at
org.apache.catalina.core.ApplicationDispatcher.processRequest(Applicatio
nDispatcher.java:461)
at
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDisp
atcher.java:364)
at
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispat
cher.java:301)
at
org.sakaiproject.tool.impl.ActiveToolComponent$MyActiveTool.help(ActiveT
oolComponent.java:545)
at
org.sakaiproject.cheftool.ToolServlet.sendToHelper(ToolServlet.java:652)
at
org.sakaiproject.cheftool.ToolServlet.doGet(ToolServlet.java:212)
at
org.sakaiproject.cheftool.VelocityPortletPaneledAction.doGet(VelocityPor
tletPaneledAction.java:1014)
at
org.sakaiproject.cheftool.ToolServlet.doPost(ToolServlet.java:151)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:710)
at
org.sakaiproject.vm.ComponentServlet.service(ComponentServlet.java:56)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:269)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
at
org.sakaiproject.util.RequestFilter.doFilter(RequestFilter.java:565)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
at
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatc
her.java:679)
at
org.apache.catalina.core.ApplicationDispatcher.processRequest(Applicatio
nDispatcher.java:461)
at
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDisp
atcher.java:364)
at
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispat
cher.java:301)
at
org.sakaiproject.tool.impl.ActiveToolComponent$MyActiveTool.forward(Acti
veToolComponent.java:475)
at
org.sakaiproject.portal.charon.SkinnableCharonPortal.forwardTool(Skinnab
leCharonPortal.java:1216)
at
org.sakaiproject.portal.charon.handlers.ToolHandler.doTool(ToolHandler.j
ava:188)
at
org.sakaiproject.portal.charon.handlers.ToolHandler.doGet(ToolHandler.ja
va:93)
at
org.sakaiproject.portal.charon.handlers.ToolHandler.doPost(ToolHandler.j
ava:70)
at
org.sakaiproject.portal.charon.SkinnableCharonPortal.doPost(SkinnableCha
ronPortal.java:1059)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:710)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:269)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
at
org.sakaiproject.util.RequestFilter.doFilter(RequestFilter.java:616)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:215)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv
e.java:213)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv
e.java:174)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java
:127)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java
:117)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.
java:108)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:1
74)
at
org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:200)
at
org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:283)
at
org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:773)
at
org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:
703)
at
org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.
java:895)
at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool
.java:689)
at java.lang.Thread.run(Thread.java:595)
2010-02-14 08:50:14,911 [TP-Processor551] WARN
org.sakaiproject.db.impl.BasicSqlService - transact: rolling back:
azg:/site/20239_0910S2
2010-02-14 08:50:14,911 [TP-Processor551] WARN
org.sakaiproject.db.impl.BasicSqlService - transact: failure:
java.lang.RuntimeException: SqlService.dbWrite failure
2010-02-14 08:50:14,912 [TP-Processor551] WARN
org.sakaiproject.site.tool.helper.participant.impl.SiteAddParticipantHan
dler -
org.sakaiproject.site.tool.helper.participant.impl.SiteAddParticipantHan
dler at 507d337b.addUsersRealm: SqlService.dbWrite failure
realmId=/site/20239_0910S2
2010-02-14 08:50:14,912 [TP-Processor551] INFO PonderUtilCore -
BeanCopy preserved to path siteAddParticipantHandler:
org.sakaiproject.site.tool.helper.participant.impl.SiteAddParticipantHan
dler at 507d337b
2010-02-14 08:50:14,913 [TP-Processor551] INFO PonderUtilCore -
BeanCopy saved 1 beans to token resultScope
2010-02-14 08:50:14,913 [TP-Processor551] INFO PonderUtilCore -
Redirecting to
/portal/tool/849b094d-629c-474b-00ca-3acb5766d961?sakai.tool.helper.idMa
in=done&panel=Main
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