jira startup problem

[Kai Schaffors]

Hello experts, can you please help?
I have recently upgraded to 9.5.0 without issues.
I have experienced a disk failure and recovered from a backup.
Confluence is running without issues.
However JIRA has this startup error. I have searched the community and tried some fixes but none is working. The file jpm.xml is there and perfectly readable by the JIRA user.
I have added the JIRA_HOME to setenv.sh. Starting as jira user. Permissions are all o.k.

Thanks Rgds Kai

023-01-17 21:25:32,793+0100 JIRA-Bootstrap INFO [c.a.jira.startup.TemporaryDirectoryCleaner] The temporary directory cleaner is disabled. It can be
enabled by setting the system property 'tmpdir.clean.on.startup' to true
17-Jan-2023 21:25:32.805 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8089"]
17-Jan-2023 21:25:32.826 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8083"]
17-Jan-2023 21:25:32.831 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [2999] milliseconds
2023-01-17 21:25:32,991+0100 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /var/
atlassian/application-data/jira/dbconfig.xml
2023-01-17 21:25:33,075+0100 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /var/
atlassian/application-data/jira/dbconfig.xml
2023-01-17 21:25:33,076+0100 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /var/
atlassian/application-data/jira/dbconfig.xml
2023-01-17 21:25:33,162+0100 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /var/
atlassian/application-data/jira/dbconfig.xml
2023-01-17 21:25:33,308+0100 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger]

___ Starting the JIRA Plugin System _________________

2023-01-17 21:25:33,523+0100 JIRA-Bootstrap ERROR [c.a.jira.startup.BootstrapContainerLauncher] A fatal error occurred during bootstrapping. JIRA ha
s been locked.
io.atlassian.util.concurrent.LazyReference$InitializationException: io.atlassian.util.concurrent.LazyReference$InitializationException: com.atlassian.jira.exception.DataAccessException: Cannot load the application properties metadata file jpm.xml
at io.atlassian.util.concurrent.LazyReference.getInterruptibly(LazyReference.java:156)
at io.atlassian.util.concurrent.LazyReference.get(LazyReference.java:116)
at io.atlassian.util.concurrent.ResettableLazyReference.get(ResettableLazyReference.java:95)
at com.atlassian.jira.config.properties.ApplicationPropertiesStore.getOverlayedString(ApplicationPropertiesStore.java:307)

---- configcheck

jira1@globus:/opt/atlassian/jira$ bin/configtest.sh

`sMMMMMMMMMMMMMM+
MMMMMMMMMMMMMM
:sdMMMMMMMMMMM
MMMMMM
`sMMMMMMMMMMMMMM+ MMMMMM
MMMMMMMMMMMMMM +MMMMM
:sMMMMMMMMMMM MMMMM
MMMMMM `UOJ
`sMMMMMMMMMMMMM+ MMMMMM
MMMMMMMMMMMMMM +MMMMM
:sdMMMMMMMMMM MMMMM
MMMMMM `UOJ
MMMMMM
+MMMMM
MMMMM
`UOJ

Atlassian Jira
Version : 9.5.0

If you encounter issues starting or stopping Jira, please see the Troubleshooting guide at https://docs.atlassian.com/jira/jadm-docs-095/Troubleshooting+installation

Using JIRA_HOME: /var/atlassian/application-data/jira

Server startup logs are located in /opt/atlassian/jira/logs/catalina.out
Using CATALINA_BASE: /opt/atlassian/jira
Using CATALINA_HOME: /opt/atlassian/jira
Using CATALINA_TMPDIR: /opt/atlassian/jira/temp
Using JRE_HOME: /opt/atlassian/jira-9.5.0/jre/
Using CLASSPATH: /opt/atlassian/jira/bin/bootstrap.jar:/opt/atlassian/jira/bin/tomcat-juli.jar
Using CATALINA_OPTS:
Using CATALINA_PID: /opt/atlassian/jira/work/catalina.pidNOTE: 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
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version name: Apache Tomcat/9.0.68
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server built: Oct 3 2022 19:06:10 UTC
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version number: 9.0.68.0
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name: Linux
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version: 4.19.0-6-amd64
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture: amd64
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home: /opt/atlassian/jira-9.5.0/jre
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version: 11.0.13+8
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Vendor: Eclipse Adoptium
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE: /opt/atlassian/jira-9.5.0
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME: /opt/atlassian/jira-9.5.0
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: --add-opens=java.base/java.lang=ALL-UNNAMED
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: --add-opens=java.base/java.io=ALL-UNNAMED
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: --add-opens=java.base/java.util=ALL-UNNAMED
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: --add-opens=java.base/java.util.concurrent=ALL-UNNAMED
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: --add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xms384m
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Xmx2048m
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:InitialCodeCacheSize=32m
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:ReservedCodeCacheSize=512m
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dlog4j2.contextSelector=org.apache.logging.log4j.core.selector.BasicContextSelector
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log

INFO: Command line argument: -Dlog4j2.isWebapp=false
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.awt.headless=true
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Datlassian.standalone=JIRA
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dmail.mime.decodeparameters=true
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -XX:-OmitStackTraceInFastThrow
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.locale.providers=COMPAT
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djira.home=/var/atlassian/application-data/jira
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dignore.endorsed.dirs=
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.base=/opt/atlassian/jira
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.home=/opt/atlassian/jira
Jan 17, 2023 9:34:35 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.io.tmpdir=/opt/atlassian/jira/temp
Jan 17, 2023 9:34:35 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
INFO: The Apache Tomcat Native library which allows using OpenSSL was not found on the java.library.path: [/usr/java/packages/lib:/usr/lib64:/lib64:/lib:/usr/lib]
Jan 17, 2023 9:34:36 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-nio-8089"]
Jan 17, 2023 9:34:36 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-nio-8083"]
Jan 17, 2023 9:34:36 PM org.apache.catalina.startup.Catalina load
INFO: Server initialization in [934] milliseconds