Connections timing out even with validation query??

[Ken Bowen]

Hi All,

I get the feeling this was lost over the weekend when I sent it last  
Saturday.
Does anyone have any thoughts on this?

Using: Tomcat 5.5.26 ; Java 1.5 ; MySQL 5.0.51 running on CentOs 5.0  
hosted in a Virtuozzo container.

The problem: With MySQL connect_timeout = 5, I'm getting timeout  
exceptions (below)  even though I have a
validation query set; Here's my app's META-INF/context-xml:

<Context path="" debug="5" reloadable="true" crossContext="true">
   <Resource name="jdbc/sb_data" auth="Container"  
type="javax.sql.DataSource"
             maxActive="100" maxIdle="30" maxWait="10000"
             username="xxxxxx" password="xxxxxx"
             driverClassName="com.mysql.jdbc.Driver"
             url="jdbc:mysql://localhost:3306/sb_data"
             validationQuery="select 1"/>
   <Resource name="jdbc/sb_users" auth="Container"  
type="javax.sql.DataSource"
             maxActive="100" maxIdle="30" maxWait="10000"
             username="xxxxxx" password="xxxxxx"
             driverClassName="com.mysql.jdbc.Driver"
             url="jdbc:mysql://localhost:3306/sb_users"
             validationQuery="select 1"/>
</Context>

My understanding is that if a closed connection is detected, it should  
automatically be replaced by a new connection??

The exception trace is below.  Any guidance would be greatly  
appreciated.
Thanks in advance,
Ken Bowen

-------------------------
javax.servlet.ServletException: No operations allowed after connection  
closed.Connection was implicitly closed due to underlying exception/
error:


** BEGIN NESTED EXCEPTION **

com.mysql.jdbc.CommunicationsException
MESSAGE: Communications link failure due to underlying exception:

** BEGIN NESTED EXCEPTION **

java.io.EOFException

STACKTRACE:
java.io.EOFException
        at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1934)
        at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2380)
        at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909)
        at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695)
        at com.mysql.jdbc.Connection.execSQL(Connection.java:3020)
        at com.mysql.jdbc.Connection.execSQL(Connection.java:2949)
        at com.mysql.jdbc.Statement.executeQuery(Statement.java:959)
        at  
com.mysql.jdbc.DatabaseMetaData.getUserName(DatabaseMetaData.java:5986)
        at  
org
.apache
.tomcat
.dbcp.dbcp.DelegatingConnection.toString(DelegatingConnection.java:104)
        at org.apache.tomcat.dbcp.dbcp.PoolingDataSource
$PoolGuardConnectionWrapper.toString(PoolingDataSourc
e.java:344)
        at java.lang.String.valueOf(String.java:2615)
        at java.lang.StringBuilder.append(StringBuilder.java:116)
        at  
com.strongbrain.database.DAOBaseUsers.getConnection(DAOBaseUsers.java:
38)
        at  
com.strongbrain.database.UserManager.getUserFromLogin(UserManager.java:
276)
        at  
com.strongbrain.auth.LoggedInUser.loggedInFromCookie(LoggedInUser.java:
59)
        at com.strongbrain.actions.BaseAction.execute(BaseAction.java:
105)
        at  
org
.apache
.struts
.action.RequestProcessor.processActionPerform(RequestProcessor.java:419)
        at  
org
.apache.struts.action.RequestProcessor.process(RequestProcessor.java:
224)
        at  
org.apache.struts.action.ActionServlet.process(ActionServlet.java:1194)
        at  
org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:414)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
        at  
org
.apache
.catalina
.core
.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
269)
        at  
org
.apache
.catalina
.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at  
org
.tuckey
.web
.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:738)
        at  
org
.apache
.catalina
.core
.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
215)
        at  
org
.apache
.catalina
.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at  
org
.apache
.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:
679)
        at  
org
.apache
.catalina
.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:
461)
        at  
org
.apache
.catalina
.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399)
        at  
org
.apache
.catalina
.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
        at  
org
.tuckey
.web.filters.urlrewrite.RewrittenUrl.doRewrite(RewrittenUrl.java:176)
        at  
org
.tuckey
.web
.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:728)
        at  
org
.apache
.catalina
.core
.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
215)
        at  
org
.apache
.catalina
.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at  
com
.strongbrain
.DisableUrlSessionFilter.doFilter(DisableUrlSessionFilter.java:42)
        at  
org
.apache
.catalina
.core
.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
215)
        at  
org
.apache
.catalina
.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at  
org
.apache
.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:
213)
        at  
org
.apache
.catalina.core.StandardContextValve.invoke(StandardContextValve.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:
174)
        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)


** END NESTED EXCEPTION **



Last packet sent to the server was 1 ms ago.

STACKTRACE:

com.mysql.jdbc.CommunicationsException: Communications link failure  
due to underlying exception:

** BEGIN NESTED EXCEPTION **

java.io.EOFException

STACKTRACE:

java.io.EOFException
        at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1934)
        at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2380)
        at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909)
        at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695)
        at com.mysql.jdbc.Connection.execSQL(Connection.java:3020)
        at com.mysql.jdbc.Connection.execSQL(Connection.java:2949)
        at com.mysql.jdbc.Statement.executeQuery(Statement.java:959)
        at  
com.mysql.jdbc.DatabaseMetaData.getUserName(DatabaseMetaData.java:5986)
        at  
org
.apache
.tomcat
.dbcp.dbcp.DelegatingConnection.toString(DelegatingConnection.java:104)
        at org.apache.tomcat.dbcp.dbcp.PoolingDataSource
$PoolGuardConnectionWrapper.toString(PoolingDataSource.java:344)
        at java.lang.String.valueOf(String.java:2615)
        at java.lang.StringBuilder.append(StringBuilder.java:116)
        at  
com.strongbrain.database.DAOBaseUsers.getConnection(DAOBaseUsers.java:
38)
        at  
com.strongbrain.database.UserManager.getUserFromLogin(UserManager.java:
276)
        at  
com.strongbrain.auth.LoggedInUser.loggedInFromCookie(LoggedInUser.java:
59)
        at com.strongbrain.actions.BaseAction.execute(BaseAction.java:
105)
        at  
org
.apache
.struts
.action.RequestProcessor.processActionPerform(RequestProcessor.java:419)
        at  
org
.apache.struts.action.RequestProcessor.process(RequestProcessor.java:
224)
        at  
org.apache.struts.action.ActionServlet.process(ActionServlet.java:1194)
        at  
org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:414)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
        at  
org
.apache
.catalina
.core
.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
269)
        at  
org
.apache
.catalina
.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at  
org
.tuckey
.web
.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:738)
        at  
org
.apache
.catalina
.core
.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
215)
        at  
org
.apache
.catalina
.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at  
org
.apache
.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:
679)
        at  
org
.apache
.catalina
.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:
461)
        at  
org
.apache
.catalina
.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399)
        at  
org
.apache
.catalina
.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
        at  
org
.tuckey
.web.filters.urlrewrite.RewrittenUrl.doRewrite(RewrittenUrl.java:176)
        at  
org
.tuckey
.web
.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:728)
        at  
org
.apache
.catalina
.core
.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
215)
        at  
org
.apache
.catalina
.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at  
com
.strongbrain
.DisableUrlSessionFilter.doFilter(DisableUrlSessionFilter.java:42)
        at  
org
.apache
.catalina
.core
.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
215)
        at  
org
.apache
.catalina
.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at  
org
.apache
.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:
213)
        at  
org
.apache
.catalina.core.StandardContextValve.invoke(StandardContextValve.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:
174)
        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)


** END NESTED EXCEPTION **



Last packet sent to the server was 1 ms ago.
        at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2592)
        at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909)
        at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695)
        at com.mysql.jdbc.Connection.execSQL(Connection.java:3020)
        at com.mysql.jdbc.Connection.execSQL(Connection.java:2949)
        at com.mysql.jdbc.Statement.executeQuery(Statement.java:959)
        at  
com.mysql.jdbc.DatabaseMetaData.getUserName(DatabaseMetaData.java:5986)
        at  
org
.apache
.tomcat
.dbcp.dbcp.DelegatingConnection.toString(DelegatingConnection.java:104)
        at org.apache.tomcat.dbcp.dbcp.PoolingDataSource
$PoolGuardConnectionWrapper.toString(PoolingDataSource.java:344)
        at java.lang.String.valueOf(String.java:2615)
        at java.lang.StringBuilder.append(StringBuilder.java:116)
        at  
com.strongbrain.database.DAOBaseUsers.getConnection(DAOBaseUsers.java:
38)
        at  
com.strongbrain.database.UserManager.getUserFromLogin(UserManager.java:
276)
        at  
com.strongbrain.auth.LoggedInUser.loggedInFromCookie(LoggedInUser.java:
59)
        at com.strongbrain.actions.BaseAction.execute(BaseAction.java:
105)
        at  
org
.apache
.struts
.action.RequestProcessor.processActionPerform(RequestProcessor.java:419)
        at  
org
.apache.struts.action.RequestProcessor.process(RequestProcessor.java:
224)
        at  
org.apache.struts.action.ActionServlet.process(ActionServlet.java:1194)
        at  
org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:414)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
at  
org
.apache
.catalina
.core
.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
269)
        at  
org
.apache
.catalina
.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at  
org
.tuckey
.web
.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:738)
        at  
org
.apache
.catalina
.core
.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
215)
        at  
org
.apache
.catalina
.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at  
org
.apache
.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:
679)
        at  
org
.apache
.catalina
.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:
461)
        at  
org
.apache
.catalina
.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399)
        at  
org
.apache
.catalina
.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
        at  
org
.tuckey
.web.filters.urlrewrite.RewrittenUrl.doRewrite(RewrittenUrl.java:176)
        at  
org
.tuckey
.web
.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:728)
        at  
org
.apache
.catalina
.core
.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
215)
        at  
org
.apache
.catalina
.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at  
com
.strongbrain
.DisableUrlSessionFilter.doFilter(DisableUrlSessionFilter.java:
42)        at  
org
.apache
.catalina
.core
.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
215)
        at  
org
.apache
.catalina
.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at  
org
.apache
.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:
213)
        at  
org
.apache
.catalina.core.StandardContextValve.invoke(StandardContextValve.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:
174)
        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)


** END NESTED EXCEPTION **


         
org
.apache
.struts.action.RequestProcessor.processException(RequestProcessor.java:
523)
         
org
.apache
.struts
.action.RequestProcessor.processActionPerform(RequestProcessor.java:421)
         
org
.apache.struts.action.RequestProcessor.process(RequestProcessor.java:
224)
         
org.apache.struts.action.ActionServlet.process(ActionServlet.java:1194)
         
org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:414)
        javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
        javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
         
org
.tuckey
.web
.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:738)
         
org
.tuckey
.web.filters.urlrewrite.RewrittenUrl.doRewrite(RewrittenUrl.java:176)
         
org
.tuckey
.web
.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:728)
         
com
.strongbrain
.DisableUrlSessionFilter.doFilter(DisableUrlSessionFilter.java:42)

[David Smith-2]

Looks like for some reason your mysql db is closing the connection in
the middle of your query reads.  This isn't normal behavior in a
tomcat/mysql setup.  Setting connect_timeout only impacts the initial
handshake and validationQuery just tests the connection before you
borrow it.  I wouldn't expect either to make a difference in this problem.

If you use the command line client, can you hold a connection open long
enough to query the database?  Also have you made any non-standard
changes in the config of your mysql server?

--David

Ken Bowen wrote:

> Hi All,
>
> I get the feeling this was lost over the weekend when I sent it last
> Saturday.
> Does anyone have any thoughts on this?
>
> Using: Tomcat 5.5.26 ; Java 1.5 ; MySQL 5.0.51 running on CentOs 5.0
> hosted in a Virtuozzo container.
>
> The problem: With MySQL connect_timeout = 5, I'm getting timeout
> exceptions (below)  even though I have a
> validation query set; Here's my app's META-INF/context-xml:
>
> <Context path="" debug="5" reloadable="true" crossContext="true">
>   <Resource name="jdbc/sb_data" auth="Container"
> type="javax.sql.DataSource"
>             maxActive="100" maxIdle="30" maxWait="10000"
>             username="xxxxxx" password="xxxxxx"
>             driverClassName="com.mysql.jdbc.Driver"
>             url="jdbc:mysql://localhost:3306/sb_data"
>             validationQuery="select 1"/>
>   <Resource name="jdbc/sb_users" auth="Container"
> type="javax.sql.DataSource"
>             maxActive="100" maxIdle="30" maxWait="10000"
>             username="xxxxxx" password="xxxxxx"
>             driverClassName="com.mysql.jdbc.Driver"
>             url="jdbc:mysql://localhost:3306/sb_users"
>             validationQuery="select 1"/>
> </Context>
>
> My understanding is that if a closed connection is detected, it should
> automatically be replaced by a new connection??
>
> The exception trace is below.  Any guidance would be greatly appreciated.
> Thanks in advance,
> Ken Bowen
>
> -------------------------
> javax.servlet.ServletException: No operations allowed after connection
> closed.Connection was implicitly closed due to underlying
> exception/error:
>
>
> ** BEGIN NESTED EXCEPTION **
>
> com.mysql.jdbc.CommunicationsException
> MESSAGE: Communications link failure due to underlying exception:
>
> ** BEGIN NESTED EXCEPTION **
>
> java.io.EOFException
>
> STACKTRACE:
> java.io.EOFException
>        at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1934)
>        at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2380)
>        at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909)
>        at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
>        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695)
>        at com.mysql.jdbc.Connection.execSQL(Connection.java:3020)
>        at com.mysql.jdbc.Connection.execSQL(Connection.java:2949)
>        at com.mysql.jdbc.Statement.executeQuery(Statement.java:959)
>        at
> com.mysql.jdbc.DatabaseMetaData.getUserName(DatabaseMetaData.java:5986)
>        at
> org.apache.tomcat.dbcp.dbcp.DelegatingConnection.toString(DelegatingConnection.java:104)
>
>        at
> org.apache.tomcat.dbcp.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.toString(PoolingDataSourc
>
> e.java:344)
>        at java.lang.String.valueOf(String.java:2615)
>        at java.lang.StringBuilder.append(StringBuilder.java:116)
>        at
> com.strongbrain.database.DAOBaseUsers.getConnection(DAOBaseUsers.java:38)
>        at
> com.strongbrain.database.UserManager.getUserFromLogin(UserManager.java:276)
>
>        at
> com.strongbrain.auth.LoggedInUser.loggedInFromCookie(LoggedInUser.java:59)
>
>        at com.strongbrain.actions.BaseAction.execute(BaseAction.java:105)
>        at
> org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:419)
>
>        at
> org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:224)
>
>        at
> org.apache.struts.action.ActionServlet.process(ActionServlet.java:1194)
>        at
> org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:414)
>        at javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
>        at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
>        at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>
>        at
> org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:738)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>
>        at
> org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679)
>
>        at
> org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461)
>
>        at
> org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399)
>
>        at
> org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
>
>        at
> org.tuckey.web.filters.urlrewrite.RewrittenUrl.doRewrite(RewrittenUrl.java:176)
>
>        at
> org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:728)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>
>        at
> com.strongbrain.DisableUrlSessionFilter.doFilter(DisableUrlSessionFilter.java:42)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>
>        at
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
>
>        at
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.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:174)
>
>        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$ControlRunnable.run(ThreadPool.java:689)
>
>        at java.lang.Thread.run(Thread.java:595)
>
>
> ** END NESTED EXCEPTION **
>
>
>
> Last packet sent to the server was 1 ms ago.
>
> STACKTRACE:
>
> com.mysql.jdbc.CommunicationsException: Communications link failure
> due to underlying exception:
>
> ** BEGIN NESTED EXCEPTION **
>
> java.io.EOFException
>
> STACKTRACE:
>
> java.io.EOFException
>        at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1934)
>        at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2380)
>        at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909)
>        at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
>        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695)
>        at com.mysql.jdbc.Connection.execSQL(Connection.java:3020)
>        at com.mysql.jdbc.Connection.execSQL(Connection.java:2949)
>        at com.mysql.jdbc.Statement.executeQuery(Statement.java:959)
>        at
> com.mysql.jdbc.DatabaseMetaData.getUserName(DatabaseMetaData.java:5986)
>        at
> org.apache.tomcat.dbcp.dbcp.DelegatingConnection.toString(DelegatingConnection.java:104)
>
>        at
> org.apache.tomcat.dbcp.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.toString(PoolingDataSource.java:344)
>
>        at java.lang.String.valueOf(String.java:2615)
>        at java.lang.StringBuilder.append(StringBuilder.java:116)
>        at
> com.strongbrain.database.DAOBaseUsers.getConnection(DAOBaseUsers.java:38)
>        at
> com.strongbrain.database.UserManager.getUserFromLogin(UserManager.java:276)
>
>        at
> com.strongbrain.auth.LoggedInUser.loggedInFromCookie(LoggedInUser.java:59)
>
>        at com.strongbrain.actions.BaseAction.execute(BaseAction.java:105)
>        at
> org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:419)
>
>        at
> org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:224)
>
>        at
> org.apache.struts.action.ActionServlet.process(ActionServlet.java:1194)
>        at
> org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:414)
>        at javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
>        at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
>        at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>
>        at
> org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:738)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>
>        at
> org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679)
>
>        at
> org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461)
>
>        at
> org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399)
>
>        at
> org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
>
>        at
> org.tuckey.web.filters.urlrewrite.RewrittenUrl.doRewrite(RewrittenUrl.java:176)
>
>        at
> org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:728)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>
>        at
> com.strongbrain.DisableUrlSessionFilter.doFilter(DisableUrlSessionFilter.java:42)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>
>        at
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
>
>        at
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.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:174)
>
>        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)
>
>
> ** END NESTED EXCEPTION **
>
>
>
> Last packet sent to the server was 1 ms ago.
>        at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2592)
>        at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909)
>        at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
>        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695)
>        at com.mysql.jdbc.Connection.execSQL(Connection.java:3020)
>        at com.mysql.jdbc.Connection.execSQL(Connection.java:2949)
>        at com.mysql.jdbc.Statement.executeQuery(Statement.java:959)
>        at
> com.mysql.jdbc.DatabaseMetaData.getUserName(DatabaseMetaData.java:5986)
>        at
> org.apache.tomcat.dbcp.dbcp.DelegatingConnection.toString(DelegatingConnection.java:104)
>
>        at
> org.apache.tomcat.dbcp.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.toString(PoolingDataSource.java:344)
>
>        at java.lang.String.valueOf(String.java:2615)
>        at java.lang.StringBuilder.append(StringBuilder.java:116)
>        at
> com.strongbrain.database.DAOBaseUsers.getConnection(DAOBaseUsers.java:38)
>        at
> com.strongbrain.database.UserManager.getUserFromLogin(UserManager.java:276)
>
>        at
> com.strongbrain.auth.LoggedInUser.loggedInFromCookie(LoggedInUser.java:59)
>
>        at com.strongbrain.actions.BaseAction.execute(BaseAction.java:105)
>        at
> org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:419)
>
>        at
> org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:224)
>
>        at
> org.apache.struts.action.ActionServlet.process(ActionServlet.java:1194)
>        at
> org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:414)
>        at javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
>        at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
> at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>
>        at
> org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:738)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>
>        at
> org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679)
>
>        at
> org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461)
>
>        at
> org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399)
>
>        at
> org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
>
>        at
> org.tuckey.web.filters.urlrewrite.RewrittenUrl.doRewrite(RewrittenUrl.java:176)
>
>        at
> org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:728)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>
>        at
> com.strongbrain.DisableUrlSessionFilter.doFilter(DisableUrlSessionFilter.java:42)        
> at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
>
>        at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>
>        at
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
>
>        at
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.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:174)
>
>        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)
>
>
> ** END NESTED EXCEPTION **
>
>
>        
> org.apache.struts.action.RequestProcessor.processException(RequestProcessor.java:523)
>
>        
> org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:421)
>
>        
> org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:224)
>
>        
> org.apache.struts.action.ActionServlet.process(ActionServlet.java:1194)
>        
> org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:414)
>        javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
>        javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
>        
> org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:738)
>
>        
> org.tuckey.web.filters.urlrewrite.RewrittenUrl.doRewrite(RewrittenUrl.java:176)
>
>        
> org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:728)
>
>        
> com.strongbrain.DisableUrlSessionFilter.doFilter(DisableUrlSessionFilter.java:42)
>
>
>
>
>

--
David Smith
Programmer/Analyst
College of Agriculture and Life Sciences
Cornell University
B32 Morrison Hall
Ithaca, NY 14853
Phone: [phone]


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[Ken Bowen]

David...see below...

On Jul 15, 2008, at 8:28 AM, David Smith wrote:

> Looks like for some reason your mysql db is closing the connection  
> in the middle of your query reads.  This isn't normal behavior in a  
> tomcat/mysql setup.  Setting connect_timeout only impacts the  
> initial handshake and validationQuery just tests the connection  
> before you borrow it.  I wouldn't expect either to make a difference  
> in this problem.
>
> If you use the command line client, can you hold a connection open  
> long enough to query the database?
Yes:
mysql> select * from user;
+---------+----------------------+---------------------+----------+
| userNum | lastName             | firstName           | acctType |
+---------+----------------------+---------------------+----------+
|       1 | User                 | Anonymous           |        0 |
|       2 | User                 | Test                |        0 |
....etc....

> Also have you made any non-standard changes in the config of your  
> mysql server?

The only change I've made at all is to change the timeout (several  
days ago) to 12 hrs.
BUT, thls is a mysql provided by the ISP as a package under the CentOS/
Virtuozzo combination.
The entries in both /etc/my.cnf and /root/.my.cnf are completely  
vanilla:

[mysqld]
datadir=/var/lib/mysql
socket=/var/lib/mysql/mysql.sock
user=mysql
# Default to using old password format for compatibility with mysql 3.x
# clients (those using the mysqlclient10 compatibility package).
old_passwords=1
connect_timeout=43200

[mysqld_safe]
log-error=/var/log/mysqld.log
pid-file=/var/run/mysqld/mysqld.pid


and


[client]
  password=xxxxxxxxxxxxxxx

The system works fine except when I let it go over 12 hrs (night  
before last), and then I got the same exception.

>
> --David
>
> Ken Bowen wrote:
>> Hi All,
>>
>> I get the feeling this was lost over the weekend when I sent it  
>> last Saturday.
>> Does anyone have any thoughts on this?
>>
>> Using: Tomcat 5.5.26 ; Java 1.5 ; MySQL 5.0.51 running on CentOs  
>> 5.0 hosted in a Virtuozzo container.
>>
>> The problem: With MySQL connect_timeout = 5, I'm getting timeout  
>> exceptions (below)  even though I have a
>> validation query set; Here's my app's META-INF/context-xml:
>>
>> <Context path="" debug="5" reloadable="true" crossContext="true">
>>  <Resource name="jdbc/sb_data" auth="Container"  
>> type="javax.sql.DataSource"
>>            maxActive="100" maxIdle="30" maxWait="10000"
>>            username="xxxxxx" password="xxxxxx"
>>            driverClassName="com.mysql.jdbc.Driver"
>>            url="jdbc:mysql://localhost:3306/sb_data"
>>            validationQuery="select 1"/>
>>  <Resource name="jdbc/sb_users" auth="Container"  
>> type="javax.sql.DataSource"
>>            maxActive="100" maxIdle="30" maxWait="10000"
>>            username="xxxxxx" password="xxxxxx"
>>            driverClassName="com.mysql.jdbc.Driver"
>>            url="jdbc:mysql://localhost:3306/sb_users"
>>            validationQuery="select 1"/>
>> </Context>
>>
>> My understanding is that if a closed connection is detected, it  
>> should automatically be replaced by a new connection??
>>
>> The exception trace is below.  Any guidance would be greatly  
>> appreciated.
>> Thanks in advance,
>> Ken Bowen
>>
>> -------------------------
>> javax.servlet.ServletException: No operations allowed after  
>> connection closed.Connection was implicitly closed due to  
>> underlying exception/error:
>>
>>
>> ** BEGIN NESTED EXCEPTION **
>>
>> com.mysql.jdbc.CommunicationsException
>> MESSAGE: Communications link failure due to underlying exception:
>>
>> ** BEGIN NESTED EXCEPTION **
>>
>> java.io.EOFException
>>
>> STACKTRACE:
>> java.io.EOFException
>>       at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1934)
>>       at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2380)
>>       at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909)
>>       at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
>>       at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695)
>>       at com.mysql.jdbc.Connection.execSQL(Connection.java:3020)
>>       at com.mysql.jdbc.Connection.execSQL(Connection.java:2949)
>>       at com.mysql.jdbc.Statement.executeQuery(Statement.java:959)
>>       at  
>> com.mysql.jdbc.DatabaseMetaData.getUserName(DatabaseMetaData.java:
>> 5986)
>>       at  
>> org
>> .apache
>> .tomcat
>> .dbcp.dbcp.DelegatingConnection.toString(DelegatingConnection.java:
>> 104)
>>       at org.apache.tomcat.dbcp.dbcp.PoolingDataSource
>> $PoolGuardConnectionWrapper.toString(PoolingDataSourc
>> e.java:344)
>>       at java.lang.String.valueOf(String.java:2615)
>>       at java.lang.StringBuilder.append(StringBuilder.java:116)
>>       at  
>> com
>> .strongbrain.database.DAOBaseUsers.getConnection(DAOBaseUsers.java:
>> 38)
>>       at  
>> com
>> .strongbrain.database.UserManager.getUserFromLogin(UserManager.java:
>> 276)
>>       at  
>> com
>> .strongbrain.auth.LoggedInUser.loggedInFromCookie(LoggedInUser.java:
>> 59)
>>       at com.strongbrain.actions.BaseAction.execute(BaseAction.java:
>> 105)
>>       at  
>> org
>> .apache
>> .struts
>> .action.RequestProcessor.processActionPerform(RequestProcessor.java:
>> 419)
>>       at  
>> org
>> .apache
>> .struts.action.RequestProcessor.process(RequestProcessor.java:224)
>>       at  
>> org.apache.struts.action.ActionServlet.process(ActionServlet.java:
>> 1194)
>>       at  
>> org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:414)
>>       at javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
>>       at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
>>       at  
>> org
>> .apache
>> .catalina
>> .core
>> .ApplicationFilterChain
>> .internalDoFilter(ApplicationFilterChain.java:269)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
>> 188)
>>       at  
>> org
>> .tuckey
>> .web
>> .filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:
>> 738)
>>       at  
>> org
>> .apache
>> .catalina
>> .core
>> .ApplicationFilterChain
>> .internalDoFilter(ApplicationFilterChain.java:215)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
>> 188)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679)
>>       at  
>> org
>> .apache
>> .catalina
>> .core
>> .ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
>>       at  
>> org
>> .tuckey
>> .web.filters.urlrewrite.RewrittenUrl.doRewrite(RewrittenUrl.java:176)
>>       at  
>> org
>> .tuckey
>> .web
>> .filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:
>> 728)
>>       at  
>> org
>> .apache
>> .catalina
>> .core
>> .ApplicationFilterChain
>> .internalDoFilter(ApplicationFilterChain.java:215)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
>> 188)
>>       at  
>> com
>> .strongbrain
>> .DisableUrlSessionFilter.doFilter(DisableUrlSessionFilter.java:42)
>>       at  
>> org
>> .apache
>> .catalina
>> .core
>> .ApplicationFilterChain
>> .internalDoFilter(ApplicationFilterChain.java:215)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
>> 188)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.StandardContextValve.invoke(StandardContextValve.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:
>> 174)
>>       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)
>>
>>
>> ** END NESTED EXCEPTION **
>>
>>
>>
>> Last packet sent to the server was 1 ms ago.
>>
>> STACKTRACE:
>>
>> com.mysql.jdbc.CommunicationsException: Communications link failure  
>> due to underlying exception:
>>
>> ** BEGIN NESTED EXCEPTION **
>>
>> java.io.EOFException
>>
>> STACKTRACE:
>>
>> java.io.EOFException
>>       at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1934)
>>       at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2380)
>>       at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909)
>>       at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
>>       at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695)
>>       at com.mysql.jdbc.Connection.execSQL(Connection.java:3020)
>>       at com.mysql.jdbc.Connection.execSQL(Connection.java:2949)
>>       at com.mysql.jdbc.Statement.executeQuery(Statement.java:959)
>>       at  
>> com.mysql.jdbc.DatabaseMetaData.getUserName(DatabaseMetaData.java:
>> 5986)
>>       at  
>> org
>> .apache
>> .tomcat
>> .dbcp.dbcp.DelegatingConnection.toString(DelegatingConnection.java:
>> 104)
>>       at org.apache.tomcat.dbcp.dbcp.PoolingDataSource
>> $PoolGuardConnectionWrapper.toString(PoolingDataSource.java:344)
>>       at java.lang.String.valueOf(String.java:2615)
>>       at java.lang.StringBuilder.append(StringBuilder.java:116)
>>       at  
>> com
>> .strongbrain.database.DAOBaseUsers.getConnection(DAOBaseUsers.java:
>> 38)
>>       at  
>> com
>> .strongbrain.database.UserManager.getUserFromLogin(UserManager.java:
>> 276)
>>       at  
>> com
>> .strongbrain.auth.LoggedInUser.loggedInFromCookie(LoggedInUser.java:
>> 59)
>>       at com.strongbrain.actions.BaseAction.execute(BaseAction.java:
>> 105)
>>       at  
>> org
>> .apache
>> .struts
>> .action.RequestProcessor.processActionPerform(RequestProcessor.java:
>> 419)
>>       at  
>> org
>> .apache
>> .struts.action.RequestProcessor.process(RequestProcessor.java:224)
>>       at  
>> org.apache.struts.action.ActionServlet.process(ActionServlet.java:
>> 1194)
>>       at  
>> org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:414)
>>       at javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
>>       at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
>>       at  
>> org
>> .apache
>> .catalina
>> .core
>> .ApplicationFilterChain
>> .internalDoFilter(ApplicationFilterChain.java:269)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
>> 188)
>>       at  
>> org
>> .tuckey
>> .web
>> .filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:
>> 738)
>>       at  
>> org
>> .apache
>> .catalina
>> .core
>> .ApplicationFilterChain
>> .internalDoFilter(ApplicationFilterChain.java:215)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
>> 188)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679)
>>       at  
>> org
>> .apache
>> .catalina
>> .core
>> .ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
>>       at  
>> org
>> .tuckey
>> .web.filters.urlrewrite.RewrittenUrl.doRewrite(RewrittenUrl.java:176)
>>       at  
>> org
>> .tuckey
>> .web
>> .filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:
>> 728)
>>       at  
>> org
>> .apache
>> .catalina
>> .core
>> .ApplicationFilterChain
>> .internalDoFilter(ApplicationFilterChain.java:215)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
>> 188)
>>       at  
>> com
>> .strongbrain
>> .DisableUrlSessionFilter.doFilter(DisableUrlSessionFilter.java:42)
>>       at  
>> org
>> .apache
>> .catalina
>> .core
>> .ApplicationFilterChain
>> .internalDoFilter(ApplicationFilterChain.java:215)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
>> 188)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.StandardContextValve.invoke(StandardContextValve.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:
>> 174)
>>       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)
>>
>>
>> ** END NESTED EXCEPTION **
>>
>>
>>
>> Last packet sent to the server was 1 ms ago.
>>       at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2592)
>>       at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909)
>>       at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
>>       at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695)
>>       at com.mysql.jdbc.Connection.execSQL(Connection.java:3020)
>>       at com.mysql.jdbc.Connection.execSQL(Connection.java:2949)
>>       at com.mysql.jdbc.Statement.executeQuery(Statement.java:959)
>>       at  
>> com.mysql.jdbc.DatabaseMetaData.getUserName(DatabaseMetaData.java:
>> 5986)
>>       at  
>> org
>> .apache
>> .tomcat
>> .dbcp.dbcp.DelegatingConnection.toString(DelegatingConnection.java:
>> 104)
>>       at org.apache.tomcat.dbcp.dbcp.PoolingDataSource
>> $PoolGuardConnectionWrapper.toString(PoolingDataSource.java:344)
>>       at java.lang.String.valueOf(String.java:2615)
>>       at java.lang.StringBuilder.append(StringBuilder.java:116)
>>       at  
>> com
>> .strongbrain.database.DAOBaseUsers.getConnection(DAOBaseUsers.java:
>> 38)
>>       at  
>> com
>> .strongbrain.database.UserManager.getUserFromLogin(UserManager.java:
>> 276)
>>       at  
>> com
>> .strongbrain.auth.LoggedInUser.loggedInFromCookie(LoggedInUser.java:
>> 59)
>>       at com.strongbrain.actions.BaseAction.execute(BaseAction.java:
>> 105)
>>       at  
>> org
>> .apache
>> .struts
>> .action.RequestProcessor.processActionPerform(RequestProcessor.java:
>> 419)
>>       at  
>> org
>> .apache
>> .struts.action.RequestProcessor.process(RequestProcessor.java:224)
>>       at  
>> org.apache.struts.action.ActionServlet.process(ActionServlet.java:
>> 1194)
>>       at  
>> org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:414)
>>       at javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
>>       at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
>> at  
>> org
>> .apache
>> .catalina
>> .core
>> .ApplicationFilterChain
>> .internalDoFilter(ApplicationFilterChain.java:269)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
>> 188)
>>       at  
>> org
>> .tuckey
>> .web
>> .filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:
>> 738)
>>       at  
>> org
>> .apache
>> .catalina
>> .core
>> .ApplicationFilterChain
>> .internalDoFilter(ApplicationFilterChain.java:215)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
>> 188)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679)
>>       at  
>> org
>> .apache
>> .catalina
>> .core
>> .ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
>>       at  
>> org
>> .tuckey
>> .web.filters.urlrewrite.RewrittenUrl.doRewrite(RewrittenUrl.java:176)
>>       at  
>> org
>> .tuckey
>> .web
>> .filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:
>> 728)
>>       at  
>> org
>> .apache
>> .catalina
>> .core
>> .ApplicationFilterChain
>> .internalDoFilter(ApplicationFilterChain.java:215)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
>> 188)
>>       at  
>> com
>> .strongbrain
>> .DisableUrlSessionFilter.doFilter(DisableUrlSessionFilter.java:
>> 42)        at  
>> org
>> .apache
>> .catalina
>> .core
>> .ApplicationFilterChain
>> .internalDoFilter(ApplicationFilterChain.java:215)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
>> 188)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
>>       at  
>> org
>> .apache
>> .catalina
>> .core.StandardContextValve.invoke(StandardContextValve.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:
>> 174)
>>       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)
>>
>>
>> ** END NESTED EXCEPTION **
>>
>>
>>        
>> org
>> .apache
>> .struts
>> .action.RequestProcessor.processException(RequestProcessor.java:523)
>>        
>> org
>> .apache
>> .struts
>> .action.RequestProcessor.processActionPerform(RequestProcessor.java:
>> 421)
>>        
>> org
>> .apache
>> .struts.action.RequestProcessor.process(RequestProcessor.java:224)
>>        
>> org.apache.struts.action.ActionServlet.process(ActionServlet.java:
>> 1194)
>>        
>> org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:414)
>>       javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
>>       javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
>>        
>> org
>> .tuckey
>> .web
>> .filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:
>> 738)
>>        
>> org
>> .tuckey
>> .web.filters.urlrewrite.RewrittenUrl.doRewrite(RewrittenUrl.java:176)
>>        
>> org
>> .tuckey
>> .web
>> .filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:
>> 728)
>>        
>> com
>> .strongbrain
>> .DisableUrlSessionFilter.doFilter(DisableUrlSessionFilter.java:42)
>>
>>
>>
>>
>
>
> --
> David Smith
> Programmer/Analyst
> College of Agriculture and Life Sciences
> Cornell University
> B32 Morrison Hall
> Ithaca, NY 14853
> Phone: [phone]
>
>
> ---------------------------------------------------------------------
> To start a new topic, e-mail: users@...
> To unsubscribe, e-mail: users-unsubscribe@...
> For additional commands, e-mail: users-help@...
>

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[Hassan Schroeder-2]

On Tue, Jul 15, 2008 at 4:04 AM, Ken Bowen <kbowen@...> wrote:

> The problem: With MySQL connect_timeout = 5, I'm getting timeout exceptions
> (below)  even though I have a
> validation query set; Here's my app's META-INF/context-xml:
>
> <Context path="" debug="5" reloadable="true" crossContext="true">
>  <Resource name="jdbc/sb_data" auth="Container" type="javax.sql.DataSource"
>            maxActive="100" maxIdle="30" maxWait="10000"
>            username="xxxxxx" password="xxxxxx"
>            driverClassName="com.mysql.jdbc.Driver"
>            url="jdbc:mysql://localhost:3306/sb_data"
>            validationQuery="select 1"/>

<http://commons.apache.org/dbcp/configuration.html>

You might try setting testWhileIdle to true (with a reasonable value
for  timeBetweenEvictionRunsMillis) and removeAbandoned to true.

Just to see if that changes/eliminates the symptom...

FWIW,
--
Hassan Schroeder ------------------------ hassan.schroeder@...

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[Ken Bowen]

Definitely a plan.  I put the following in my context.xml:

            validationQuery="select 1"
             testWhileIdle="true"
             timeBetweenEvictionRunsMillis="1000*60"
             removeAbandoned="true"

I set connect_timeout=5 in /etc/my.cnf,  and restarted both mysql and  
tomcat.
After 30min, everything's fine, but that's not much of test.  I'll see  
what it looks like tomorrow morning.

Thanks,
Ken


On Jul 15, 2008, at 10:23 AM, Hassan Schroeder wrote:

> On Tue, Jul 15, 2008 at 4:04 AM, Ken Bowen <kbowen@...> wrote:
>
>> The problem: With MySQL connect_timeout = 5, I'm getting timeout  
>> exceptions
>> (below)  even though I have a
>> validation query set; Here's my app's META-INF/context-xml:
>>
>> <Context path="" debug="5" reloadable="true" crossContext="true">
>> <Resource name="jdbc/sb_data" auth="Container"  
>> type="javax.sql.DataSource"
>>           maxActive="100" maxIdle="30" maxWait="10000"
>>           username="xxxxxx" password="xxxxxx"
>>           driverClassName="com.mysql.jdbc.Driver"
>>           url="jdbc:mysql://localhost:3306/sb_data"
>>           validationQuery="select 1"/>
>
> <http://commons.apache.org/dbcp/configuration.html>
>
> You might try setting testWhileIdle to true (with a reasonable value
> for  timeBetweenEvictionRunsMillis) and removeAbandoned to true.
>
> Just to see if that changes/eliminates the symptom...
>
> FWIW,
> --
> Hassan Schroeder ------------------------ hassan.schroeder@...
>
> ---------------------------------------------------------------------
> To start a new topic, e-mail: users@...
> To unsubscribe, e-mail: users-unsubscribe@...
> For additional commands, e-mail: users-help@...
>

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