We work with Jira/Greenhopper for 6 weeks now without a problem. Suddenly it stopped working. I restarted Jira and now i get HTTP Status 404 - type Status report message description The requested resource () is not available. This is probably related to the fact that de mysql server on this machine has been restarted this morning. Here's the Startup log from catalina.out **************** JIRA starting... **************** 2012-10-01 13:13:49,546 main INFO [atlassian.jira.startup.JiraStartupLogger] ___ Environment _____________________________ JIRA Build : 5.1.3#782-sha1:4389c897ff46ac633147bfa0023fbc37f3cb8ca3 Build Date : Tue Aug 14 00:00:00 CEST 2012 JIRA Installation Type : Standalone Application Server : Apache Tomcat/6.0.32 - Servlet API 2.5 Java Version : 1.6.0_26 - Sun Microsystems Inc. Current Working Directory : /opt/atlassian/jira/bin Maximum Allowable Memory : 682MB Total Memory : 245MB Free Memory : 240MB Used Memory : 5MB Memory Pool: Code Cache : Code Cache: init = 2555904(2496K) used = 1086784(1061K) committed = 2555904(2496K) max = 50331648(49152K) Memory Pool: PS Eden Space : PS Eden Space: init = 67174400(65600K) used = 2696560(2633K) committed = 67174400(65600K) max = 246153216(240384K) Memory Pool: PS Survivor Space : PS Survivor Space: init = 11141120(10880K) used = 3627360(3542K) committed = 11141120(10880K) max = 11141120(10880K) Memory Pool: PS Old Gen : PS Old Gen: init = 178978816(174784K) used = 0(0K) committed = 178978816(174784K) max = 536870912(524288K) Memory Pool: PS Perm Gen : PS Perm Gen: init = 21757952(21248K) used = 16384800(16000K) committed = 21757952(21248K) max = 268435456(262144K) JVM Input Arguments : -Djava.util.logging.config.file=/opt/atlassian/jira/conf/logging.properties -XX:MaxPermSize=256m -Xms256m -Xmx768m -Djava.awt.headless=true -Datlassian.standalone=JIRA -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true -Dmail.mime.decodeparameters=true -XX:+PrintGCDateStamps -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djava.endorsed.dirs=/opt/atlassian/jira/endorsed -Dcatalina.base=/opt/atlassian/jira -Dcatalina.home=/opt/atlassian/jira -Djava.io.tmpdir=/opt/atlassian/jira/temp ___ Java System Properties _________________ atlassian.standalone : JIRA catalina.base : /opt/atlassian/jira catalina.home : /opt/atlassian/jira catalina.useNaming : true common.loader : ${catalina.base}/lib, ${catalina.base}/lib/*.jar, ${catalina.home}/lib, ${catalina.home}/lib/*.jar file.encoding : UTF-8 file.encoding.pkg : sun.io java.awt.graphicsenv : sun.awt.X11GraphicsEnvironment java.awt.headless : true java.awt.printerjob : sun.print.PSPrinterJob java.class.version : 50.0 java.home : /opt/atlassian/jira/jre java.io.tmpdir : /opt/atlassian/jira/temp java.naming.factory.initial : org.apache.naming.java.javaURLContextFactory java.naming.factory.url.pkgs : org.apache.naming java.runtime.name : Java(TM) SE Runtime Environment java.runtime.version : 1.6.0_26-b03 java.specification.name : Java Platform API Specification java.specification.vendor : Sun Microsystems Inc. java.specification.version : 1.6 java.util.logging.config.file : /opt/atlassian/jira/conf/logging.properties java.util.logging.manager : org.apache.juli.ClassLoaderLogManager java.vendor : Sun Microsystems Inc. java.vendor.url : http://java.sun.com/ > java.vendor.url.bug : http://java.sun.com/cgi-bin/bugreport.cgi > java.version : 1.6.0_26 java.vm.info : mixed mode java.vm.name : Java HotSpot(TM) 64-Bit Server VM java.vm.specification.name : Java Virtual Machine Specification java.vm.specification.vendor : Sun Microsystems Inc. java.vm.specification.version : 1.0 java.vm.vendor : Sun Microsystems Inc. java.vm.version : 20.1-b02 mail.mime.decodeparameters : true org.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER : true os.arch : amd64 os.name : Linux os.version : 2.6.32-41-server package.access : sun., org.apache.catalina., org.apache.coyote., org.apache.tomcat., org.apache.jasper., sun.beans. package.definition : sun., java., org.apache.catalina., org.apache.coyote., org.apache.tomcat., org.apache.jasper. server.loader : shared.loader : sun.arch.data.model : 64 sun.boot.library.path : /opt/atlassian/jira/jre/lib/amd64 sun.cpu.endian : little sun.cpu.isalist : sun.io.unicode.encoding : UnicodeLittle sun.java.command : org.apache.catalina.startup.Bootstrap start sun.java.launcher : SUN_STANDARD sun.jnu.encoding : UTF-8 sun.management.compiler : HotSpot 64-Bit Tiered Compilers sun.os.patch.level : unknown tomcat.util.buf.StringCache.byte.enabled : true user.country : US user.dir : /opt/atlassian/jira/bin user.home : /home/jira user.language : en user.name : jira user.timezone : Europe/Berlin 2012-10-01 13:13:49,551 main INFO [atlassian.jira.startup.JiraStartupLogger] Running JIRA startup checks. 2012-10-01 13:13:49,581 main INFO [atlassian.jira.startup.JiraHomeStartupCheck] The jira.home directory '/var/atlassian/application-data/jira' is validated and locked for exclusive use by this instance. 2012-10-01 13:13:49,582 main INFO [atlassian.jira.startup.JiraStartupLogger] JIRA pre-database startup checks completed successfully. 2012-10-01 13:13:49,701 main INFO [jira.config.database.SystemTenantDatabaseConfigurationLoader] Reading database configuration from /var/atlassian/application-data/jira/dbconfig.xml 2012-10-01 13:13:49,759 main INFO [jira.config.database.DatabaseConfigurationManagerImpl] Now running Database Checklist Launcher 2012-10-01 13:13:49,891 main ERROR [NoModule] Error getting datasource via DBCP: JdbcDatasourceInfo{uri='jdbc:mysql://localhost:3306/jira?useUnicode=true&characterEncoding=UTF8&sessionVariables=storage_engine=InnoDB', driverClassName='com.mysql.jdbc.Driver', username='jira', password='********', isolationLevel='null', connectionProperties=null, connectionPoolInfo=ConnectionPoolInfo{maxSize=20, minSize=20, initialSize=null, maxIdle=20, maxWait=30000, sleepTime=300000, lifeTime=600000, deadLockMaxWait=600000, deadLockRetryWait=10000, validationQuery='select 1', minEvictableTimeMillis=60000, timeBetweenEvictionRunsMillis=300000, poolPreparedStatements=null, testOnBorrow=null, testOnReturn=null, testWhileIdle=true, maxOpenPreparedStatements=null, numTestsPerEvictionRun=null, removeAbandonedTimeout=300, validationQueryTimeout=3, defaultCatalog=null}} org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Communications link failure The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.)

Sorry, I wasn't clear - Jira only tries to log into the database when it (re)starts. Once it's been rejected, it does not try again. Establishing the connection with the database is a start-up process - once completed, it's not triggered again by simple refreshes. You'll need to restart Jira to provoke it into attempting the connection again. In the past, I've used http://dev.mysql.com/doc/refman/5.5/en/query-log.html to enable login logging on the database side - I am NOT a DBA though, and certainly not a MySQL guru, so I really don't know if that's the best way to do it (And your SQL people may have more better ideas)

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Jira stopt working after restarting MySQL

Fré de Vries

We work with Jira/Greenhopper for 6 weeks now without a problem. Suddenly it stopped working.

I restarted Jira and now i get

HTTP Status 404 -

type Status report

message

description The requested resource () is not available.

This is probably related to the fact that de mysql server on this machine has been restarted this morning.

Here's the Startup log from catalina.out

****************

JIRA starting...

****************

2012-10-01 13:13:49,546 main INFO [atlassian.jira.startup.JiraStartupLogger]

___ Environment _____________________________

JIRA Build : 5.1.3#782-sha1:4389c897ff46ac633147bfa0023fbc37f3cb8ca3

Build Date : Tue Aug 14 00:00:00 CEST 2012

JIRA Installation Type : Standalone

Application Server : Apache Tomcat/6.0.32 - Servlet API 2.5

Java Version : 1.6.0_26 - Sun Microsystems Inc.

Current Working Directory : /opt/atlassian/jira/bin

Maximum Allowable Memory : 682MB

Total Memory : 245MB

Free Memory : 240MB

Used Memory : 5MB

Memory Pool: Code Cache : Code Cache: init = 2555904(2496K) used = 1086784(1061K) committed = 2555904(2496K) max = 50331648(49152K)

Memory Pool: PS Eden Space : PS Eden Space: init = 67174400(65600K) used = 2696560(2633K) committed = 67174400(65600K) max = 246153216(240384K)

Memory Pool: PS Survivor Space : PS Survivor Space: init = 11141120(10880K) used = 3627360(3542K) committed = 11141120(10880K) max = 11141120(10880K)

Memory Pool: PS Old Gen : PS Old Gen: init = 178978816(174784K) used = 0(0K) committed = 178978816(174784K) max = 536870912(524288K)

Memory Pool: PS Perm Gen : PS Perm Gen: init = 21757952(21248K) used = 16384800(16000K) committed = 21757952(21248K) max = 268435456(262144K)

JVM Input Arguments : -Djava.util.logging.config.file=/opt/atlassian/jira/conf/logging.properties -XX:MaxPermSize=256m -Xms256m -Xmx768m -Djava.awt.headless=true -Datlassian.standalone=JIRA -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true -Dmail.mime.decodeparameters=true -XX:+PrintGCDateStamps -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djava.endorsed.dirs=/opt/atlassian/jira/endorsed -Dcatalina.base=/opt/atlassian/jira -Dcatalina.home=/opt/atlassian/jira -Djava.io.tmpdir=/opt/atlassian/jira/temp

___ Java System Properties _________________

atlassian.standalone : JIRA

catalina.base : /opt/atlassian/jira

catalina.home : /opt/atlassian/jira

catalina.useNaming : true

common.loader : ${catalina.base}/lib,

${catalina.base}/lib/*.jar,

${catalina.home}/lib,

${catalina.home}/lib/*.jar

file.encoding : UTF-8

file.encoding.pkg : sun.io

java.awt.graphicsenv : sun.awt.X11GraphicsEnvironment

java.awt.headless : true

java.awt.printerjob : sun.print.PSPrinterJob

java.class.version : 50.0

java.home : /opt/atlassian/jira/jre

java.io.tmpdir : /opt/atlassian/jira/temp

java.naming.factory.initial : org.apache.naming.java.javaURLContextFactory

java.naming.factory.url.pkgs : org.apache.naming

java.runtime.name : Java(TM) SE Runtime Environment

java.runtime.version : 1.6.0_26-b03

java.specification.name : Java Platform API Specification

java.specification.vendor : Sun Microsystems Inc.

java.specification.version : 1.6

java.util.logging.config.file : /opt/atlassian/jira/conf/logging.properties

java.util.logging.manager : org.apache.juli.ClassLoaderLogManager

java.vendor : Sun Microsystems Inc.

java.vendor.url : http://java.sun.com/</span<>>

java.vendor.url.bug : http://java.sun.com/cgi-bin/bugreport.cgi</span<>>

java.version : 1.6.0_26

java.vm.info : mixed mode

java.vm.name : Java HotSpot(TM) 64-Bit Server VM

java.vm.specification.name : Java Virtual Machine Specification

java.vm.specification.vendor : Sun Microsystems Inc.

java.vm.specification.version : 1.0

java.vm.vendor : Sun Microsystems Inc.

java.vm.version : 20.1-b02

mail.mime.decodeparameters : true

org.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER : true

os.arch : amd64

os.name : Linux

os.version : 2.6.32-41-server

package.access : sun.,

org.apache.catalina.,

org.apache.coyote.,

org.apache.tomcat.,

org.apache.jasper.,

sun.beans.

package.definition : sun.,

java.,

org.apache.catalina.,

org.apache.coyote.,

org.apache.tomcat.,

org.apache.jasper.

server.loader :

shared.loader :

sun.arch.data.model : 64

sun.boot.library.path : /opt/atlassian/jira/jre/lib/amd64

sun.cpu.endian : little

sun.cpu.isalist :

sun.io.unicode.encoding : UnicodeLittle

sun.java.command : org.apache.catalina.startup.Bootstrap start

sun.java.launcher : SUN_STANDARD

sun.jnu.encoding : UTF-8

sun.management.compiler : HotSpot 64-Bit Tiered Compilers

sun.os.patch.level : unknown

tomcat.util.buf.StringCache.byte.enabled : true

user.country : US

user.dir : /opt/atlassian/jira/bin

user.home : /home/jira

user.language : en

user.name : jira

user.timezone : Europe/Berlin

2012-10-01 13:13:49,551 main INFO [atlassian.jira.startup.JiraStartupLogger] Running JIRA startup checks.

2012-10-01 13:13:49,581 main INFO [atlassian.jira.startup.JiraHomeStartupCheck] The jira.home directory '/var/atlassian/application-data/jira' is validated and locked for exclusive use by this instance.

2012-10-01 13:13:49,582 main INFO [atlassian.jira.startup.JiraStartupLogger] JIRA pre-database startup checks completed successfully.

2012-10-01 13:13:49,701 main INFO [jira.config.database.SystemTenantDatabaseConfigurationLoader] Reading database configuration from /var/atlassian/application-data/jira/dbconfig.xml

2012-10-01 13:13:49,759 main INFO [jira.config.database.DatabaseConfigurationManagerImpl] Now running Database Checklist Launcher

2012-10-01 13:13:49,891 main ERROR [NoModule] Error getting datasource via DBCP: JdbcDatasourceInfo{uri='jdbc:mysql://localhost:3306/jira?useUnicode=true&characterEncoding=UTF8&sessionVariables=storage_engine=InnoDB', driverClassName='com.mysql.jdbc.Driver', username='jira', password='********', isolationLevel='null', connectionProperties=null, connectionPoolInfo=ConnectionPoolInfo{maxSize=20, minSize=20, initialSize=null, maxIdle=20, maxWait=30000, sleepTime=300000, lifeTime=600000, deadLockMaxWait=600000, deadLockRetryWait=10000, validationQuery='select 1', minEvictableTimeMillis=60000, timeBetweenEvictionRunsMillis=300000, poolPreparedStatements=null, testOnBorrow=null, testOnReturn=null, testWhileIdle=true, maxOpenPreparedStatements=null, numTestsPerEvictionRun=null, removeAbandonedTimeout=300, validationQueryTimeout=3, defaultCatalog=null}}

org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Communications link failure

The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.)

Accepted answers

All comments

Nic Brough -Adaptavist-

Ok, Jira doesn't handle the database disappearing very well, and you've done exactly the right thing and restarted Jira - this makes it reread the configuration and reconnect to the database cleanly.

The problem now is that the database is not responding to the connection attempt. The usual culprits of the error message you've got are incorrect settings in the connection string, network problems or a change in the database locking your user out.

For debugging all of these though, you start by checking the settings - can you connect locally with the mysql command line? As root? As the Jira user? The attempts to connect would give you a lot more information about what's wrong.

Fré de Vries

I can also connect locally with the msyql command line with the jira credentials and then do 'use jira' and then 'show tables'

PauloP

Hi All

As default behavior, JIRA is not able to properly handle database conection pool after a server failure (networking or GDB system failure). However, you may try to use validation queries in order to ask JIRA to try to restablish the connection before fail.

For further details, please use the following link as your guideline:

https://confluence.atlassian.com/display/JIRA/Surviving+Connection+Closures

Cheers,

Paulo Renato

Fré de Vries

Thanks Nic,

Other sites/apps using the same Mysql server still work so I assumed that its still running on port 3306.

The Jira installation is on the same server as where MySQL runs

I can login to PHPMyAdmin with the credentials from /var/atlassian/application-data/jira/dbconfig.xml

What else can i test?

Fré de Vries

I haven't changed anything anywhere, so that cannot be the problem.

There's nothing about a user not able to log in in the mysql log

I assume that tomcat is running because its tomcat that puts the error on the screen i think

type Status report

message

description The requested resource () is not available.

Apache Tomcat/6.0.32

Fré de Vries

Validation query is already in the config file by default is guess...

<jira-database-config>

<name>defaultDS</name>

<delegator-name>default</delegator-name>

<database-type>mysql</database-type>

<jdbc-datasource>

<url>jdbc:mysql://localhost:3306/jira?useUnicode=true&characterEncoding=UTF8&sessionVariables=storage_engine=InnoDB</url>

<driver-class>com.mysql.jdbc.Driver</driver-class>

<pool-min-size>20</pool-min-size>

<pool-max-size>20</pool-max-size>

<pool-max-wait>30000</pool-max-wait>

<validation-query>select 1</validation-query>

<min-evictable-idle-time-millis>60000</min-evictable-idle-time-millis>

<time-between-eviction-runs-millis>300000</time-between-eviction-runs-millis>

<pool-max-idle>20</pool-max-idle>

<pool-remove-abandoned>true</pool-remove-abandoned>

<pool-remove-abandoned-timeout>300</pool-remove-abandoned-timeout>

<pool-test-while-idle>true</pool-test-while-idle>

<validation-query-timeout>3</validation-query-timeout>

</jdbc-datasource>

</jira-database-config>

unknown

I asked JIRA support about the validation query after having the same issue. Database pool connections were not being restored even when the validation query was in the config file. Atlassian's documentation would have you believe that the validation query will fix communication hiccups:

When a database server reboots or a network failure has occurred, all connections in the database connection pool are broken. To overcome this issue, JIRA would normally need restarting (or for JIRA WAR distributions, the application server running JIRA would need restarting).

However, database connections in the database connection pool can be validated by running a simple SQL query. If a broken database connection is detected in the pool, a new one is created to replace it.

[...]

You should now be able to recover from a complete loss of all connections in the database connection pool without the need to restart JIRA or the application server running JIRA.

However, Atlassian support told me that the validation query doesn't always restore database connections after a loss of communication with the database. I asked them to update the wiki article to reflect this, but I don't see any changes on the article.

Fré de Vries

I created an issue at Atlassian support. The helped me out. I took half an hour to find out that mysql wasn't bound to the localhost, only to the server ip. We changed the config with config.sh and things work again.