Communication failure during Jira installation with MySQL database

[Ananta Ram das]

Hi Team,

During installation of Jira software I'm experiencing following issue:

    Caused by: java.sql.SQLException: Could not retrieve transation read-only status server
        at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:998) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:937) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:926) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:872) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:904) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:894) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.ConnectionImpl.isReadOnly(ConnectionImpl.java:3613) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.ConnectionImpl.isReadOnly(ConnectionImpl.java:3582) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2111) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2081) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2066) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at org.apache.commons.dbcp2.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:98) [commons-dbcp2-2.1.jar:2.1]
        at org.apache.commons.dbcp2.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:98) [commons-dbcp2-2.1.jar:2.1]
        at org.ofbiz.core.entity.jdbc.SQLProcessor.executeUpdate(SQLProcessor.java:562) [entityengine-1.3.10.jar:?]
        ... 249 more
    Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure

        The last packet successfully received from the server was 20,007 milliseconds ago.  The last packet sent successfully to the server was 0 milliseconds ago.
        at sun.reflect.GeneratedConstructorAccessor210.newInstance(Unknown Source) [?:?]
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) [?:1.8.0_102]
        at java.lang.reflect.Constructor.newInstance(Constructor.java:423) [?:1.8.0_102]
        at com.mysql.jdbc.Util.handleNewInstance(Util.java:389) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1038) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3422) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3322) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3762) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2435) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2582) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2531) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2489) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.StatementImpl.executeQuery(StatementImpl.java:1446) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.ConnectionImpl.isReadOnly(ConnectionImpl.java:3607) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        ... 256 more
    Caused by: java.io.EOFException: Can not read response from server. Expected to read 4 bytes, read 0 bytes before connection was unexpectedly lost.
        at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:2914) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3332) [mysql-connector-java-5.1.35-bin.jar:5.1.35]
        ... 264 more
    , referer=http://jira.raxkor.com.ua:8090/secure/SetupLicense!default.jspa, servletErrorMessage=}

I have already find following article https://confluence.atlassian.com/jirakb/mysql-communication-link-failure-214338032.html however it does not help.

I have following MySQL server installed on my server is  5.7.21-0ubuntu0.16.04.1 and already tried following drivers:
5.1.35, 5.1.36 and 5.1.45

[Michael Wolfe]

If you haven't already, check out this article on setting up the mysql database for Atlassian products.  This article details setting up the individual database, and modifying the settings within mysql's my.cnf file.

https://confluence.atlassian.com/adminjiraserver073/connecting-jira-applications-to-mysql-861253043.html

I have found that the mysql driver version 5.1.44 has worked the best for me.  These are the settings I have in my 'my.cnf' file.

[mysqld]
character-set-server=utf8
collation-server=utf8_bin
default-storage-engine=INNODB
max_allowed_packet=256M
innodb_log_file_size=2GB
transaction-isolation=READ-COMMITTED

I just setup a development jira server and attempted to use the .45 driver and the installation seemed to have trouble finding it, but found it immediately when I used the .44 driver.