Confluence 7.4.10 to 7.13.0 failed to upgrade, please support.
Asked by ZhaoChunsheng:

Confluence 7.4.10 to 7.13.0 failed to upgrade, please support.  
After the upgrade, the message was successful, but the page could not be accessed. I re-executed the installation file and re-upgraded, but I still cannot use Confluence.

All the working documents are here, please tell me how to resume use. Thank you.

NOTE: Picked up JDK_JAVA_OPTIONS: --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.util.concurrent=ALL-UNNAMED --add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED  
\[0.001s\]\[warning\]\[gc\] -Xloggc is deprecated. Will use -Xlog:gc:/opt/atlassian/confluence/logs/gc-2021-08-20_15-17-15.log instead.  
20-Aug-2021 15:17:15.522 WARNING \[main\] org.apache.tomcat.util.digester.SetPropertiesRule.begin Match \[Server\] failed to set property \[debug\] to \[0\]  
20-Aug-2021 15:17:15.555 WARNING \[main\] org.apache.tomcat.util.digester.SetPropertiesRule.begin Match \[Server/Service/Connector\] failed to set property \[debug\] to \[0\]  
20-Aug-2021 15:17:15.563 WARNING \[main\] org.apache.tomcat.util.digester.SetPropertiesRule.begin Match \[Server/Service/Engine\] failed to set property \[debug\] to \[0\]  
20-Aug-2021 15:17:15.566 WARNING \[main\] org.apache.tomcat.util.digester.SetPropertiesRule.begin Match \[Server/Service/Engine/Host\] failed to set property \[debug\] to \[0\]  
20-Aug-2021 15:17:15.587 WARNING \[main\] org.apache.tomcat.util.digester.SetPropertiesRule.begin Match \[Server/Service/Engine/Host/Context\] failed to set property \[debug\] to \[0\]  
20-Aug-2021 15:17:15.602 WARNING \[main\] org.apache.tomcat.util.digester.SetPropertiesRule.begin Match \[Server/Service/Engine/Host/Context\] failed to set property \[debug\] to \[0\]  
20-Aug-2021 15:17:15.758 INFO \[main\] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler \["http-nio-8090"\]  
20-Aug-2021 15:17:15.767 SEVERE \[main\] org.apache.catalina.util.LifecycleBase.handleSubClassException Failed to initialize component \[Connector\[HTTP/1.1-8090\]\]  
org.apache.catalina.LifecycleException: Protocol handler initialization failed  
at org.apache.catalina.connector.Connector.initInternal(Connector.java:1048)  
at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:136)  
at org.apache.catalina.core.StandardService.initInternal(StandardService.java:556)  
at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:136)  
at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:1045)  
at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:136)  
at org.apache.catalina.startup.Catalina.load(Catalina.java:724)  
at org.apache.catalina.startup.Catalina.load(Catalina.java:746)  
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)  
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)  
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)  
at java.base/java.lang.reflect.Method.invoke(Unknown Source)  
at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:302)  
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:472)  
Caused by: java.net.BindException: Address already in use  
at java.base/sun.nio.ch.Net.bind0(Native Method)  
at java.base/sun.nio.ch.Net.bind(Unknown Source)  
at java.base/sun.nio.ch.Net.bind(Unknown Source)  
at java.base/sun.nio.ch.ServerSocketChannelImpl.bind(Unknown Source)  
at org.apache.tomcat.util.net.NioEndpoint.initServerSocket(NioEndpoint.java:300)  
at org.apache.tomcat.util.net.NioEndpoint.bind(NioEndpoint.java:253)  
at org.apache.tomcat.util.net.AbstractEndpoint.bindWithCleanup(AbstractEndpoint.java:1204)  
at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:1217)  
at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:603)  
at org.apache.coyote.http11.AbstractHttp11Protocol.init(AbstractHttp11Protocol.java:80)  
at org.apache.catalina.connector.Connector.initInternal(Connector.java:1045)  
... 13 more  
20-Aug-2021 15:17:15.768 INFO \[main\] org.apache.catalina.startup.Catalina.load Server initialization in \[302\] milliseconds  
20-Aug-2021 15:17:15.771 INFO \[main\] org.apache.catalina.core.StandardService.startInternal Starting service \[Tomcat-Standalone\]  
20-Aug-2021 15:17:15.771 INFO \[main\] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: \[Apache Tomcat/9.0.45\]  
20-Aug-2021 15:17:16.466 INFO \[Catalina-utility-2\] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.  
20-Aug-2021 15:17:16.581 INFO \[Catalina-utility-2\] org.apache.catalina.core.ApplicationContext.log 1 Spring WebApplicationInitializers detected on classpath  
log4j:ERROR Could not find value for key log4j.appender.luceneQuery  
log4j:ERROR Could not instantiate appender named "luceneQuery".  
20-Aug-2021 15:17:16.682 INFO \[Catalina-utility-2\] org.apache.catalina.core.ApplicationContext.log Initializing Spring DispatcherServlet 'dispatcher'  
15:17:16 \[Catalina-utility-2\] o.a.c.c.C.\[.\[.\[/synchrony-proxy\]\[INFO\] log - Initializing Spring DispatcherServlet 'dispatcher'  
2021-08-20 15:17:16,804 INFO \[Catalina-utility-1\] \[com.atlassian.confluence.lifecycle\] contextInitialized Starting Confluence 7.13.0 \[build 8703 based on commit hash 791df1c41ad1e432a490f9fc6f60e3ea49358bee\] - synchrony version 4.0.0-master-f680ea21  
Loading class \`com.mysql.jdbc.Driver'. This is deprecated. The new driver class is \`com.mysql.cj.jdbc.Driver'. The driver is automatically registered via the SPI and manual loading of the driver class is generally unnecessary.  
WARNING: An illegal reflective access operation has occurred  
WARNING: Illegal reflective access by com.atlassian.hibernate.adapter.proxy.BytecodeProviderImpl_ImplementV2Proxy (file:/opt/atlassian/confluence/confluence/WEB-INF/lib/hibernate.adapter-1.0.3.jar) to field java.lang.reflect.Field.modifiers  
WARNING: Please consider reporting this to the maintainers of com.atlassian.hibernate.adapter.proxy.BytecodeProviderImpl_ImplementV2Proxy  
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations  
WARNING: All illegal access operations will be denied in a future release  
20-Aug-2021 15:17:26.309 SEVERE \[Catalina-utility-1\] org.apache.catalina.core.StandardContext.startInternal One or more Filters failed to start. Full details will be found in the appropriate container log file  
20-Aug-2021 15:17:26.310 SEVERE \[Catalina-utility-1\] org.apache.catalina.core.StandardContext.startInternal Context \[\] startup failed due to previous errors  
20-Aug-2021 15:17:26.354 WARNING \[Catalina-utility-1\] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application \[ROOT\] registered the JDBC driver \[com.mysql.cj.jdbc.Driver\] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.  
20-Aug-2021 15:17:26.354 WARNING \[Catalina-utility-1\] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application \[ROOT\] registered the JDBC driver \[com.github.gquintana.metrics.sql.Driver\] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.  
20-Aug-2021 15:17:26.354 WARNING \[Catalina-utility-1\] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application \[ROOT\] registered the JDBC driver \[org.hsqldb.jdbc.JDBCDriver\] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.  
20-Aug-2021 15:17:26.354 WARNING \[Catalina-utility-1\] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application \[ROOT\] registered the JDBC driver \[com.microsoft.sqlserver.jdbc.SQLServerDriver\] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.  
20-Aug-2021 15:17:26.354 WARNING \[Catalina-utility-1\] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application \[ROOT\] registered the JDBC driver \[net.sourceforge.jtds.jdbc.Driver\] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.  
20-Aug-2021 15:17:26.354 WARNING \[Catalina-utility-1\] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application \[ROOT\] registered the JDBC driver \[org.h2.Driver\] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.  
20-Aug-2021 15:17:26.354 WARNING \[Catalina-utility-1\] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application \[ROOT\] registered the JDBC driver \[org.postgresql.Driver\] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.  
20-Aug-2021 15:17:26.355 WARNING \[Catalina-utility-1\] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application \[ROOT\] appears to have started a thread named \[mysql-cj-abandoned-connection-cleanup\] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:  
java.base@11.0.8/java.lang.Object.wait(Native Method)  
java.base@11.0.8/java.lang.ref.ReferenceQueue.remove(Unknown Source)  
com.mysql.cj.jdbc.AbandonedConnectionCleanupThread.run(AbandonedConnectionCleanupThread.java:85)  
java.base@11.0.8/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)  
java.base@11.0.8/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)  
java.base@11.0.8/java.lang.Thread.run(Unknown Source)  
20-Aug-2021 15:17:26.382 INFO \[main\] org.apache.catalina.startup.Catalina.start Server startup in \[10614\] milliseconds  
20-Aug-2021 15:17:29.065 INFO \[mysql-cj-abandoned-connection-cleanup\] org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading Illegal access: this web application instance has been stopped already. Could not load \[\]. The following stack trace is thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access.  
java.lang.IllegalStateException: Illegal access: this web application instance has been stopped already. Could not load \[\]. The following stack trace is thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access.  
at org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading(WebappClassLoaderBase.java:1384)  
at org.apache.catalina.loader.WebappClassLoaderBase.getResource(WebappClassLoaderBase.java:1037)  
at com.mysql.cj.jdbc.AbandonedConnectionCleanupThread.checkThreadContextClassLoader(AbandonedConnectionCleanupThread.java:117)  
at com.mysql.cj.jdbc.AbandonedConnectionCleanupThread.run(AbandonedConnectionCleanupThread.java:84)  
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)  
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)  
at java.base/java.lang.Thread.run(Unknown Source)  
20-Aug-2021 15:17:30.351 WARNING \[main\] org.apache.catalina.core.StandardServer.await Invalid shutdown command \[\] received  
20-Aug-2021 15:21:34.609 INFO \[Thread-4\] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler \["http-nio-8090"\]  
20-Aug-2021 15:21:34.610 INFO \[Thread-4\] org.apache.catalina.core.StandardService.stopInternal Stopping service \[Tomcat-Standalone\]  
20-Aug-2021 15:21:34.615 INFO \[Catalina-utility-2\] org.apache.catalina.core.ApplicationContext.log Destroying Spring FrameworkServlet 'dispatcher'  
15:21:34 \[Catalina-utility-2\] o.a.c.c.C.\[.\[.\[/synchrony-proxy\]\[INFO\] log - Destroying Spring FrameworkServlet 'dispatcher'  
20-Aug-2021 15:21:34.632 INFO \[Thread-4\] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler \["http-nio-8090"\]  
20-Aug-2021 15:21:34.633 INFO \[Thread-4\] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler \["http-nio-8090"\]  
NOTE: Picked up JDK_JAVA_OPTIONS: --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.util.concurrent=ALL-UNNAMED --add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED  
\[0.001s\]\[warning\]\[gc\] -Xloggc is deprecated. Will use -Xlog:gc:/opt/atlassian/confluence/logs/gc-2021-08-20_15-21-53.log instead.  
20-Aug-2021 15:21:53.414 WARNING \[main\] org.apache.tomcat.util.digester.SetPropertiesRule.begin Match \[Server\] failed to set property \[debug\] to \[0\]  
20-Aug-2021 15:21:53.449 WARNING \[main\] org.apache.tomcat.util.digester.SetPropertiesRule.begin Match \[Server/Service/Connector\] failed to set property \[debug\] to \[0\]  
20-Aug-2021 15:21:53.459 WARNING \[main\] org.apache.tomcat.util.digester.SetPropertiesRule.begin Match \[Server/Service/Engine\] failed to set property \[debug\] to \[0\]  
20-Aug-2021 15:21:53.461 WARNING \[main\] org.apache.tomcat.util.digester.SetPropertiesRule.begin Match \[Server/Service/Engine/Host\] failed to set property \[debug\] to \[0\]  
20-Aug-2021 15:21:53.487 WARNING \[main\] org.apache.tomcat.util.digester.SetPropertiesRule.begin Match \[Server/Service/Engine/Host/Context\] failed to set property \[debug\] to \[0\]  
20-Aug-2021 15:21:53.503 WARNING \[main\] org.apache.tomcat.util.digester.SetPropertiesRule.begin Match \[Server/Service/Engine/Host/Context\] failed to set property \[debug\] to \[0\]  
20-Aug-2021 15:21:53.689 INFO \[main\] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler \["http-nio-8090"\]  
20-Aug-2021 15:21:53.706 INFO \[main\] org.apache.catalina.startup.Catalina.load Server initialization in \[402\] milliseconds  
20-Aug-2021 15:21:53.710 INFO \[main\] org.apache.catalina.core.StandardService.startInternal Starting service \[Tomcat-Standalone\]  
20-Aug-2021 15:21:53.710 INFO \[main\] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: \[Apache Tomcat/9.0.45\]  
20-Aug-2021 15:21:54.510 INFO \[Catalina-utility-1\] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.  
20-Aug-2021 15:21:54.693 INFO \[Catalina-utility-1\] org.apache.catalina.core.ApplicationContext.log 1 Spring WebApplicationInitializers detected on classpath  
20-Aug-2021 15:21:54.867 INFO \[Catalina-utility-1\] org.apache.catalina.core.ApplicationContext.log Initializing Spring DispatcherServlet 'dispatcher'  
15:21:54 \[Catalina-utility-1\] o.a.c.c.C.\[.\[.\[/synchrony-proxy\]\[INFO\] log - Initializing Spring DispatcherServlet 'dispatcher'  
log4j:ERROR Could not find value for key log4j.appender.luceneQuery  
log4j:ERROR Could not instantiate appender named "luceneQuery".  
2021-08-20 15:21:55,436 INFO \[Catalina-utility-2\] \[com.atlassian.confluence.lifecycle\] contextInitialized Starting Confluence 7.13.0 \[build 8703 based on commit hash 791df1c41ad1e432a490f9fc6f60e3ea49358bee\] - synchrony version 4.0.0-master-f680ea21  
Loading class \`com.mysql.jdbc.Driver'. This is deprecated. The new driver class is \`com.mysql.cj.jdbc.Driver'. The driver is automatically registered via the SPI and manual loading of the driver class is generally unnecessary.  
WARNING: An illegal reflective access operation has occurred  
WARNING: Illegal reflective access by com.atlassian.hibernate.adapter.proxy.BytecodeProviderImpl_ImplementV2Proxy (file:/opt/atlassian/confluence/confluence/WEB-INF/lib/hibernate.adapter-1.0.3.jar) to field java.lang.reflect.Field.modifiers  
WARNING: Please consider reporting this to the maintainers of com.atlassian.hibernate.adapter.proxy.BytecodeProviderImpl_ImplementV2Proxy  
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations  
WARNING: All illegal access operations will be denied in a future release  
Security framework of XStream not explicitly initialized, using predefined black list on your own risk.

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "I/O dispatcher 4"

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "I/O dispatcher 5"  
Exception in thread "I/O dispatcher 10" java.lang.OutOfMemoryError: Java heap space  
Exception in thread "I/O dispatcher 19" java.lang.OutOfMemoryError: Java heap space  
Exception in thread "I/O dispatcher 16" java.lang.OutOfMemoryError: Java heap space  
Exception in thread "C3P0PooledConnectionPoolManager\[identityToken-\>z8kfsxajrb9vy31xmokz0\|75d725f0\]-HelperThread-#2" java.lang.OutOfMemoryError: Java heap space  
Exception in thread "httpclient-io:thread-1" java.lang.OutOfMemoryError: Java heap space

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "AsyncFileHandlerWriter-234698513"


Answers:
author: Nic Brough -Adaptavist-
body: -Xmx1024m is 1Gb - try increasing it to 2Gb.

comments: author: ZhaoChunsheng
body: Oh my god, it started successfully! Thank you! ! !


author: cruise
body: How to set up, where is the configuration file


author: ZhaoChunsheng
body: /opt/atlassian/confluence/bin/setenv.sh


author: ZhaoChunsheng
body: setenv.sh

# Set the Java heap size  
CATALINA_OPTS="-Xms1024m -Xmx1024m ${CATALINA_OPTS}"

# Default values for small to medium size instances  
CATALINA_OPTS="-XX:ReservedCodeCacheSize=256m ${CATALINA_OPTS}"

mysqld.cnf

\[mysqld\]  
pid-file = /var/run/mysqld/mysqld.pid  
socket = /var/run/mysqld/mysqld.sock  
datadir = /var/lib/mysql  
log-error = /var/log/mysql/error.log

collation-server=utf8mb4_bin  
max_allowed_packet=256M  
transaction-isolation=READ-COMMITTED  
innodb_log_file_size=2GB


author: Nic Brough -Adaptavist-
body: So, you've got two massive problems here.

java.lang.OutOfMemoryError: Java heap space - this means what it says. You have not allocated enough memory for your Jira to run in. Take a look at the setenv.sh, changing the maximum memory (Xmx in most systems) to a higher value. Your log doesn't say what memory was allocated when it started, so I can't suggest a new value directly, but I would try adding 512Mb or 1Gb to it to start with. Don't increase it by more than 1Gb on any step, giving it too much memory can also cause problems. Also remember to allow the OS some working space (on a Linux machine with 4Gb memory for example, I would not take the Java heap above 3Gb. On Windows, I'd be looking to add more memory because the OS is really bad at this sort of thing and struggles with less than 2.5Gb for itself)

SQL state \[HY000\]; error code \[1419\]; You do not have the SUPER privilege and binary logging is enabled - this means your database is misconfigured, although it **might** also happen if you run out of memory. Fix the memory first, and if this one still happens, re-read the docs on how to configure your database for Confluence.


author: ZhaoChunsheng
body: Upgrade failed. Please consult the system logs for details. You will need to fix these problems, restore your database and confluence home directory to the pre upgrade state. Then retry the upgrade. Upgrade error message: Upgrade task com.atlassian.confluence.upgrade.upgradetask.DenormalisedSpacePermissionsUpgradeTask@606c2c79 failed during the SCHEMA_UPGRADE phase due to: StatementCallback; uncategorized SQLException for SQL \[CREATE TRIGGER denormalised_space_trigger_on_update AFTER UPDATE ON SPACES FOR EACH ROW sp: BEGIN DECLARE isServiceDisabled BOOL DEFAULT TRUE; CALL space_procedure_for_denormalised_permissions(isServiceDisabled); IF (isServiceDisabled) THEN LEAVE sp; END IF; IF (NEW.LOWERSPACEKEY = OLD.LOWERSPACEKEY) THEN LEAVE sp; END IF; INSERT INTO DENORMALISED_SPACE_CHANGE_LOG(SPACE_ID) VALUES (NEW.SPACEID); END;\]; SQL state \[HY000\]; error code \[1419\]; You do not have the SUPER privilege and binary logging is enabled (you \*might\* want to use the less safe log_bin_trust_function_creators variable); nested exception is java.sql.SQLException: You do not have the SUPER privilege and binary logging is enabled (you \*might\* want to use the less safe log_bin_trust_function_creators variable)