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Error connecting to database

Thomas D

Trying to set up JIRA 7.9 with mysql 5.7.22 on ubuntu 16.04

When trying to test the connection with the setup wizard, getting the "Error connecting to database, communication link failure" message.

Mysql is up and running, jiradb and jiradbuser have been created following manual instructions.

bind-address is set to 0.0.0.0 in my.cnf

No firewall set up as far as I can tell.

Can't find helpful messages in either JIRA or mysql logs

Any idea what else could be causing this issue?

Accepted answers

All comments

Adrián Plaza [DEISER]

Hi @Thomas D,

You need to change your my.cnf and comment this lines:

#skip-networking
#bind-address                   = 0.0.0.0

for more information, you can see this post: https://serverfault.com/questions/139323/how-to-bind-mysql-server-to-more-than-one-ip-address

Cheers,
Adrián.

Thomas D

Thanks Adrian but there is no skip-networking line in my.cnf and it makes no difference whether bind-address is commented or not, still can't connect.

Adrián Plaza [DEISER]

Hi @Thomas D,

When you comment the line

<span>#</span><span>bind-address</span>

execute this command:

service mysql restart

And try to connect do you get the same message?

Cheers,

Adrián.

Thomas D

Sure, I did restart mysql, no changes.

Andy Heinzer

Jira does not ship with the mysql database driver needed to connect to that kind of database. I would want to make sure first that you have downloaded the jdbc file from mysql's site and then extract the .jar from that .zip file into the $JIRAINSTALL/lib/ folder. If you have not done this yet, there is no way Jira is going to be able to use that database type. This is explained in the documentation Connecting Jira to MySQL.

It is possible that you would have to restart Jira after copying that .jar file in place.

If that is not the solution here, then I would be interested to learn more about Jira's own logging on this. The $JIRAHOME/log/atlassian-jira.log might have some info, but in this case the $JIRAINSTALL/logs/catalina.out might be better since it tends to have some more verbose information in this setup phase of Jira.

Thomas D

Hi Andrew,

Thanks for the reply, mysql-connector-java-5.1.10.jar is in the lib dir and although I am not sure if this is the correct version, I think it is working as I've seen a different error message when the connector was missing.

The message in catalina.out looks like a generic db connection failure report, here it is, let me know if you can get anything from it:

2018-05-07 00:30:57,831 http-nio-8080-exec-13 ERROR anonymous 30x521x1 zv474o 10.50.1.205 /secure/SetupDatabase!connectionCheck.jspa [c.a.config.bootstrap.DefaultAtlassianBootstrapManager] Could not successfully test your database:
com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: 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.
   at sun.reflect.GeneratedConstructorAccessor56.newInstance(Unknown Source)
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
   at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
   at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
   at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
   at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2214)
   at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:781)
   at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
   ... 2 filtered
   at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
   at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
   at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:352)
   at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:284)
   at java.sql.DriverManager.getConnection(DriverManager.java:664)
   at java.sql.DriverManager.getConnection(DriverManager.java:247)
   at com.atlassian.config.bootstrap.DefaultAtlassianBootstrapManager.getTestDatabaseConnection(DefaultAtlassianBootstrapManager.java:347)
   at com.atlassian.jira.config.database.JdbcDatasource.getConnection(JdbcDatasource.java:211)
   at com.atlassian.jira.config.database.DatabaseConfig.testConnection(DatabaseConfig.java:88)
   at com.atlassian.jira.web.action.setup.SetupDatabase.testConnection(SetupDatabase.java:225)
   at com.atlassian.jira.web.action.setup.SetupDatabase.doValidation(SetupDatabase.java:189)
   at com.atlassian.jira.web.action.setup.SetupDatabase.doConnectionCheck(SetupDatabase.java:121)
   ... 2 filtered
   at java.lang.reflect.Method.invoke(Method.java:498)
   at webwork.util.InjectionUtils$DefaultInjectionImpl.invoke(InjectionUtils.java:70)
   at webwork.util.InjectionUtils.invoke(InjectionUtils.java:56)
   ... 2 filtered
   at com.atlassian.jira.action.JiraActionSupport.execute(JiraActionSupport.java:63)
   ... 7 filtered
   at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
   ... 45 filtered
   at com.atlassian.jira.security.JiraSecurityFilter.lambda$doFilter$0(JiraSecurityFilter.java:66)
   ... 1 filtered
   at com.atlassian.jira.security.JiraSecurityFilter.doFilter(JiraSecurityFilter.java:64)
   ... 28 filtered
   at com.atlassian.jira.servermetrics.CorrelationIdPopulatorFilter.doFilter(CorrelationIdPopulatorFilter.java:30)
   ... 24 filtered
   at com.atlassian.jira.servermetrics.MetricsCollectorFilter.doFilter(MetricsCollectorFilter.java:25)
   ... 23 filtered
   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
   at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
   at java.lang.Thread.run(Thread.java:745)
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: 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.
   at sun.reflect.GeneratedConstructorAccessor56.newInstance(Unknown Source)
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
   at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
   at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
   at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:343)
   at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2137)
   ... 161 more
Caused by: java.net.UnknownHostException: address=(protocol=tcp)(host=10.50.1.9)(port=3306)
   at java.net.InetAddress.getAllByName0(InetAddress.java:1280)
   at java.net.InetAddress.getAllByName(InetAddress.java:1192)
   at java.net.InetAddress.getAllByName(InetAddress.java:1126)
   at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:243)
   at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:292)

Andy Heinzer

I recommend downloading the 5.1.46 version instead: https://dev.mysql.com/get/Downloads/Connector-J/mysql-connector-java-5.1.46.zip

There have been lots of performance improvements and known bugs that could be avoided just by using this updated version. To do this you would need to:

Download that file
Stop Jira
Go to the $JIRAINSTALL/lib/ folder
remove the existing mysql-xxx.jar file
Extract the 5.1.46 archive to find the updated .jar file and copy this to that same directory
Start Jira again

Try that first. My next concern is over the error you see in the stacktrace of

Caused by: java.net.UnknownHostException: address=(protocol=tcp)(host=10.50.1.9)(port=3306)

This indicates that the connection string Jira is trying to use could be incorrect. Instead of trying to connect to the database while Jira is running, I think it might help to try to manually configure the $JIRAHOME/dbconfig.xml file before Jira starts. There are a couple of ways to do this, you could create this file manually, or you can use the jira config tool to help set this up for you. I suggest that tool because it can be a good starting point to help get the file created correctly. From there, we ultimately want to see your dbconfig.xml file look very much like the sample on that exists in Connecting Jira to MySQL.

Try these two things. If you still cannot connect, please share with us both your dbconfig.xml and any new exceptions you might find in the logs.

Thomas D

Hi Andrew,

Thanks, updating the connector did it, the communication is now working.

I am now trying to import some datas from v6.4 but am getting the message that the xml is too old to be imported.

Could you let me know what is the most recent version that will accept the xml generated by v6.4 ?

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