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Fedora Startup Error

Posted on 2013-12-31
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Last Modified: 2014-01-08
Can somebody give me a hint of what's going on here?  I've done some searching on some of the terms like "Cannot create PoolableConnectionFactory (Communications link failure due to underlying exception: " and I think Fedora can't connect to MySql.  All was well yesterday, this just started today.  The catalina.out log file is error free, it does have some warnings but they're not related to this problem.  I got this snip out of the syslog file.  I've restarted Tomcat, and Apache2, and when that didn't solve the problem I rebooted the server, and that didn't solve it either.

I'm not sure of what version of Fedora I'm running so the command to determine the version would be helpful.

Debian version 5, Java version 1.6.0, MySql version 5, Apache2, PHP version 5

Dec 31 14:09:30 linuxserver jsvc.exec[18011]: Dec 31, 2013 2:09:30 PM org.apache.catalina.startup.HostConfig deployWAR INFO: Deploying web application archive fedora.war
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: ** FEDORA STARTUP ERROR **
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: **************************
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: Fedora startup failed
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: fedora.server.errors.ModuleInitializationException: Error while attempting to check for and create non-existing table(s): org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Communications link failure due to underlying exception:   ** BEGIN NESTED EXCEPTION **   java.net.ConnectException MESSAGE: Connection refused  STACKTRACE:  java.net.ConnectException: Connection refused at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333) at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195) at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366) at java.net.Socket.connect(Socket.java:529) at java.net.Socket.connect(Socket.java:478) at java.net.Socket.<init>(Socket.java:375) at java.net.Socket.<init>(Socket.java:218) at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFact
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: >(MysqlIO.java:271) at com.mysql.jdbc.Connection.createNewIO(Connection.java:2744) at com.mysql.jdbc.Connection.<init>(Connection.java:1553) at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:285) at org.apache.commons.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:37) at org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:290) at org.apache.commons.dbcp.BasicDataSource.validateConnectionFactory(BasicDataSource.java:877) at org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:851) at org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:540) at fedora.server.storage.ConnectionPool.getConnection(ConnectionPool.java:275) at fedora.server.utilities.SQLUtilityImpl.i_createNonExistingTables(SQLUtilityImpl.java:274) at fedora.server.utilities.SQLUtility.createNonExistingTables(SQLUtility.java:146) at fedora.server.storage
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: r.java:373) at fedora.server.Server.<init>(Server.java:625) at fedora.server.BasicServer.<init>(BasicServer.java:41) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:513) at fedora.server.Server.getInstance(Server.java:1022) at fedora.server.ServerController.init(ServerController.java:207) at javax.servlet.GenericServlet.init(GenericServlet.java:211) at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139) at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966) at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3956) at org.apache.catalina.core.StandardContext.start(StandardContext.java:4230)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: Internal(ContainerBase.java:760) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:740) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544) at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:831) at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:720) at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:490) at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1149) at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:311) at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022) at org.apache.catalina.core.StandardHost.start(StandardHost.java:736) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014) at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443) at org.apache.catalina.core.St
Dec 31 14:09:31 linuxserver jsvc.exec[18011]:  org.apache.catalina.core.StandardServer.start(StandardServer.java:700) at org.apache.catalina.startup.Catalina.start(Catalina.java:552) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.apache.commons.daemon.support.DaemonLoader.start(DaemonLoader.java:177)   ** END NESTED EXCEPTION **    Last packet sent to the server was 1 ms ago.)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at fedora.server.storage.DefaultDOManager.postInitModule(DefaultDOManager.java:375)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at fedora.server.Server.<init>(Server.java:625)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at fedora.server.BasicServer.<init>(BasicServer.java:41)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at fedora.server.Server.getInstance(Server.java:1022)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at fedora.server.ServerController.init(ServerController.java:207)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at javax.servlet.GenericServlet.init(GenericServlet.java:211)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3956)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.core.StandardContext.start(StandardContext.java:4230)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:740)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:831)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:720)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:490)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1149)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:311)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.core.StandardHost.start(StandardHost.java:736)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.core.StandardService.start(StandardService.java:448)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.core.StandardServer.start(StandardServer.java:700)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at java.lang.reflect.Method.invoke(Method.java:597)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at java.lang.reflect.Method.invoke(Method.java:597)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.commons.daemon.support.DaemonLoader.start(DaemonLoader.java:177)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: ERROR 2013-12-31 14:09:31.184 [main] ([/fedora]) Servlet /fedora threw load() exception fedora.server.errors.ModuleInitializationException: Error while attempting to check for and create non-existing table(s): org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Communications link failure due to underlying exception:   ** BEGIN NESTED EXCEPTION **   java.net.ConnectException MESSAGE: Connection refused  STACKTRACE:  java.net.ConnectException: Connection refused at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333) at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195) at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366) at java.net.Socket.connect(Socket.java:529) at java.net.Socket.connect(Socket.java:478) at java.net.Socket.<init>(Socket.java:375) at java.net.Socket.<ini
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: rdSocketFactory.connect(StandardSocketFactory.java:256) at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:271) at com.mysql.jdbc.Connection.createNewIO(Connection.java:2744) at com.mysql.jdbc.Connection.<init>(Connection.java:1553) at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:285) at org.apache.commons.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:37) at org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:290) at org.apache.commons.dbcp.BasicDataSource.validateConnectionFactory(BasicDataSource.java:877) at org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:851) at org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:540) at fedora.server.storage.ConnectionPool.getConnection(ConnectionPool.java:275) at fedora.server.utilities.SQLUtilityImpl.i_createNonExistingTables(SQLUtilityImpl.java:274) at fedora.server.uti
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: lity.java:146) at fedora.server.storage.DefaultDOManager.postInitModule(DefaultDOManager.java:373) at fedora.server.Server.<init>(Server.java:625) at fedora.server.BasicServer.<init>(BasicServer.java:41) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:513) at fedora.server.Server.getInstance(Server.java:1022) at fedora.server.ServerController.init(ServerController.java:207) at javax.servlet.GenericServlet.init(GenericServlet.java:211) at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139) at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966) at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.jav
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: ext.start(StandardContext.java:4230) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:740) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544) at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:831) at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:720) at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:490) at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1149) at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:311) at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022) at org.apache.catalina.core.StandardHost.start(StandardHost.java:736) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014) at org.apache.cat
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: va:443) at org.apache.catalina.core.StandardService.start(StandardService.java:448) at org.apache.catalina.core.StandardServer.start(StandardServer.java:700) at org.apache.catalina.startup.Catalina.start(Catalina.java:552) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.apache.commons.daemon.support.DaemonLoader.start(DaemonLoader.java:177)   ** END NESTED EXCEPT
Dec 31 14:09:31 linuxserver jsvc.exec[18011]:  ago.) at fedora.server.storage.DefaultDOManager.postInitModule(DefaultDOManager.java:375) at fedora.server.Server.<init>(Server.java:625) at fedora.server.BasicServer.<init>(BasicServer.java:41) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:513) at fedora.server.Server.getInstance(Server.java:1022) at fedora.server.ServerController.init(ServerController.java:207) at javax.servlet.GenericServlet.init(GenericServlet.java:211) at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139) at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966) at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3956)
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: t(StandardContext.java:4230) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:740) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544) at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:831) at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:720) at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:490) at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1149) at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:311) at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022) at org.apache.catalina.core.StandardHost.start(StandardHost.java:736) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014) at org.apache.catalina.co
Dec 31 14:09:31 linuxserver jsvc.exec[18011]: at org.apache.catalina.core.StandardService.start(StandardService.java:448) at org.apache.catalina.core.StandardServer.start(StandardServer.java:700) at org.apache.catalina.startup.Catalina.start(Catalina.java:552) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.apache.commons.daemon.support.DaemonLoader.start(DaemonLoader.java:177)
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Question by:mobot
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Accepted Solution

by:
Duncan Roe earned 250 total points
ID: 39749359
You got a connection refused The client (apache) is trying to connect to the server (mysqld) over tcp/ip. You can check whether your mysqld is using a tcp/ip or unix socket as below. On my system, it uses a unix socket (for local access only)(see line 50)
13:59:30# lsof -p $(pgrep mysqld|tail -1)
COMMAND  PID  USER   FD   TYPE     DEVICE SIZE/OFF     NODE NAME
mysqld  1757 mysql  cwd    DIR        8,2     4096  2310198 /var/lib/mysql
mysqld  1757 mysql  rtd    DIR        8,2     4096        2 /
mysqld  1757 mysql  txt    REG        8,2 13725176  5800046 /usr/libexec/mysqld
mysqld  1757 mysql  DEL    REG       0,10              3487 /[aio]
mysqld  1757 mysql  mem    REG        8,2    54519  5129880 /lib/libnss_files-2.17.so
mysqld  1757 mysql  mem    REG        8,2    49301  5129882 /lib/libnss_nis-2.17.so
mysqld  1757 mysql  mem    REG        8,2   112829  5129876 /lib/libnsl-2.17.so
mysqld  1757 mysql  mem    REG        8,2    39608  5129877 /lib/libnss_compat-2.17.so
mysqld  1757 mysql  mem    REG        8,2   109496  5807250 /usr/lib/libgcc_s.so.1
mysqld  1757 mysql  mem    REG        8,2  1816558  5129993 /lib/libc-2.17.so
mysqld  1757 mysql  mem    REG        8,2   297740  5129875 /lib/libm-2.17.so
mysqld  1757 mysql  mem    REG        8,2   917900  5801435 /usr/lib/libstdc++.so.6.0.18
mysqld  1757 mysql  mem    REG        8,2    17505  5129994 /lib/libdl-2.17.so
mysqld  1757 mysql  mem    REG        8,2  1780292  5129912 /lib/libcrypto.so.1.0.0
mysqld  1757 mysql  mem    REG        8,2   406080  5129986 /lib/libssl.so.1.0.0
mysqld  1757 mysql  mem    REG        8,2    46929  5129873 /lib/libcrypt-2.17.so
mysqld  1757 mysql  mem    REG        8,2    85748  5129863 /lib/libz.so.1.2.8
mysqld  1757 mysql  mem    REG        8,2     2512  5129594 /lib/libaio.so.1.0.1
mysqld  1757 mysql  mem    REG        8,2   124153  5129884 /lib/libpthread-2.17.so
mysqld  1757 mysql  DEL    REG       0,10              3488 /[aio]
mysqld  1757 mysql  DEL    REG       0,10              3486 /[aio]
mysqld  1757 mysql  DEL    REG       0,10              3485 /[aio]
mysqld  1757 mysql  DEL    REG       0,10              3484 /[aio]
mysqld  1757 mysql  DEL    REG       0,10              3483 /[aio]
mysqld  1757 mysql  DEL    REG       0,10              3482 /[aio]
mysqld  1757 mysql  DEL    REG       0,10              3481 /[aio]
mysqld  1757 mysql  DEL    REG       0,10              3480 /[aio]
mysqld  1757 mysql  DEL    REG       0,10              3479 /[aio]
mysqld  1757 mysql  DEL    REG       0,10              3478 /[aio]
mysqld  1757 mysql  DEL    REG       0,10              3477 /[aio]
mysqld  1757 mysql  mem    REG        8,2   153528  5130017 /lib/ld-2.17.so
mysqld  1757 mysql    0r   CHR        1,3      0t0     1033 /dev/null
mysqld  1757 mysql    1w   REG        8,2    32023  2310311 /var/lib/mysql/dwarfstar.err
mysqld  1757 mysql    2w   REG        8,2    32023  2310311 /var/lib/mysql/dwarfstar.err
mysqld  1757 mysql    3uW  REG        8,2       52  2310303 /var/lib/mysql/aria_log_control
mysqld  1757 mysql    4r   DIR        8,2     4096  2310198 /var/lib/mysql
mysqld  1757 mysql    5u   REG        8,2    16384  2310307 /var/lib/mysql/aria_log.00000001
mysqld  1757 mysql    6uW  REG        8,2 18874368  2310377 /var/lib/mysql/ibdata1
mysqld  1757 mysql    7u   REG        8,2        0 14180416 /tmp/ibXwSRLJ (deleted)
mysqld  1757 mysql    8u   REG        8,2        0 14180417 /tmp/ibYSGEnp (deleted)
mysqld  1757 mysql    9u   REG        8,2        0 14180423 /tmp/ibdUqKa5 (deleted)
mysqld  1757 mysql   10u   REG        8,2        0 14180428 /tmp/ibHiW4jB (deleted)
mysqld  1757 mysql   11uW  REG        8,2 50331648  2310309 /var/lib/mysql/ib_logfile0
mysqld  1757 mysql   12uW  REG        8,2 50331648  2310378 /var/lib/mysql/ib_logfile1
mysqld  1757 mysql   13u   REG        8,2     1024  2310259 /var/lib/mysql/mysql/servers.MYI
mysqld  1757 mysql   14u   REG        8,2        0 14180430 /tmp/ibN1EnIX (deleted)
mysqld  1757 mysql   15u   REG        8,2        0  2310287 /var/lib/mysql/mysql/servers.MYD
mysqld  1757 mysql   16u  unix 0xf260d200      0t0     2480 /var/run/mysql/mysql.sock
mysqld  1757 mysql   17u   REG        8,2     2048  2310242 /var/lib/mysql/mysql/host.MYI
mysqld  1757 mysql   18u   REG        8,2        0  2310277 /var/lib/mysql/mysql/host.MYD
mysqld  1757 mysql   19u   REG        8,2     4096  2310260 /var/lib/mysql/mysql/user.MYI
mysqld  1757 mysql   20u   REG        8,2      464  2310294 /var/lib/mysql/mysql/user.MYD
mysqld  1757 mysql   21u   REG        8,2     9216  2310248 /var/lib/mysql/mysql/db.MYI
mysqld  1757 mysql   22u   REG        8,2     1896  2310257 /var/lib/mysql/mysql/db.MYD
mysqld  1757 mysql   23u   REG        8,2    10240  2310218 /var/lib/mysql/mysql/proxies_priv.MYI
mysqld  1757 mysql   24u   REG        8,2     2538  2310263 /var/lib/mysql/mysql/proxies_priv.MYD
mysqld  1757 mysql   25u   REG        8,2     4096  2310382 /var/lib/mysql/mysql/roles_mapping.MYI
mysqld  1757 mysql   26u   REG        8,2        0  2310383 /var/lib/mysql/mysql/roles_mapping.MYD
mysqld  1757 mysql   27u   REG        8,2     4096  2310234 /var/lib/mysql/mysql/tables_priv.MYI
mysqld  1757 mysql   28u   REG        8,2        0  2310293 /var/lib/mysql/mysql/tables_priv.MYD
mysqld  1757 mysql   29u   REG        8,2     4096  2310270 /var/lib/mysql/mysql/columns_priv.MYI
mysqld  1757 mysql   30u   REG        8,2        0  2310295 /var/lib/mysql/mysql/columns_priv.MYD
mysqld  1757 mysql   31u   REG        8,2     4096  2310275 /var/lib/mysql/mysql/procs_priv.MYI
mysqld  1757 mysql   32u   REG        8,2        0  2310281 /var/lib/mysql/mysql/procs_priv.MYD
mysqld  1757 mysql   33u   REG        8,2     2048  2310244 /var/lib/mysql/mysql/event.MYI
mysqld  1757 mysql   34u   REG        8,2        0  2310299 /var/lib/mysql/mysql/event.MYD
mysqld  1757 mysql   35uW  REG        8,2    98304  2310217 /var/lib/mysql/mysql/innodb_table_stats.ibd
mysqld  1757 mysql   36uW  REG        8,2    98304  2310240 /var/lib/mysql/mysql/innodb_index_stats.ibd
mysqld  1757 mysql   37uW  REG        8,2    98304  2310206 /var/lib/mysql/mysql/gtid_slave_pos.ibd
mysqld  1757 mysql   38u   REG        8,2        0  2310310 /var/lib/mysql/multi-master.info
13:59:53# 

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Apache has gotten out of step with what mysqld is doing. Problems like that don't happen by themselves - there must have been some configuration change somewhere.
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Assisted Solution

by:Gerwin Jansen
Gerwin Jansen earned 250 total points
ID: 39750971
Is mysqld running on the same server? If mysql has an (configuration) issue or is not running properly, your application will give a connection error like you're seeing.

Can you verify that mysql is running properly (restart if necessary) and then restart Tomcat and Apache?
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LVL 34

Expert Comment

by:Duncan Roe
ID: 39751025
If mysqld is running on another system, could the IP address of that system have changed? I did wonder if it might have been on another system, but inferred from the tenor of your question that it probably wasn't.
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Author Comment

by:mobot
ID: 39752417
Everything is running on one box.  I was having a problem with Tomcat that turns out to be unrelated to this one.  And that's been resolved.  I stumbled across this one digging through log files for clues to the other problem.  I need another day so syslog rolls over and I can check it for this error message now that I have the other one solved.
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LVL 37

Expert Comment

by:Gerwin Jansen
ID: 39753219
Ok, but is mysql running properly?
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Author Comment

by:mobot
ID: 39766320
Sorry for the delayed reply.  MySQL is running properly.  There are no errors in the .err log.  The Fedora error is not listed in syslog today.  I consider the matter closed for now.

Thank you both for taking the time to reply.
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