ubuntu upgrade makes my Dataverse down
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Zhang Yue
Jan 13, 2025, 3:21:42 PM1/13/25
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Dear all,
[2025-01-13T19:55:07.314+0000] [Payara 5.2022.5] [INFO] [] [org.jvnet.hk2.osgiadapter] [tid: _ThreadID=31 _ThreadName=FelixStartLevel] [timeMillis: 1736798107314] [levelValue: 800] [[
Skipping registration of inhabitant for service reference [org.osgi.service.metatype.MetaTypeProvider] as the service object could not be obtained.]]
[2025-01-13T19:55:07.444+0000] [Payara 5.2022.5] [INFO] [NCLS-JMX-00005] [javax.enterprise.system.jmx] [tid: _ThreadID=158 _ThreadName=Thread-12] [timeMillis: 1736798107444] [levelValue: 800] [[
JMXStartupService has started JMXConnector on JMXService URL service:jmx:rmi://0.0.0.0:8686/jndi/rmi://0.0.0.0:8686/jmxrmi]]
Currently my ubuntu has been upgraded from 04.22 to 04.24 and after this, my payara cannot deploy dataverse-5.14 after that and localhost just shows the default payara page. The service.log is shown below:
[2025-01-13T19:54:55.712+0000] [Payara 5.2022.5] [INFO] [AS-WEB-GLUE-00198] [javax.enterprise.web] [tid: _ThreadID=46 _ThreadName=RunLevelControllerThread-1736798092057] [timeMillis: 1736798095712] [levelValue: 800] [[
Created HTTP listener http-listener-1 on host/port 0.0.0.0:8080]]
[2025-01-13T19:54:55.717+0000] [Payara 5.2022.5] [INFO] [AS-WEB-GLUE-00198] [javax.enterprise.web] [tid: _ThreadID=46 _ThreadName=RunLevelControllerThread-1736798092057] [timeMillis: 1736798095717] [levelValue: 800] [[
Created HTTP listener http-listener-2 on host/port 0.0.0.0:8181]]
[2025-01-13T19:54:55.718+0000] [Payara 5.2022.5] [INFO] [AS-WEB-GLUE-00198] [javax.enterprise.web] [tid: _ThreadID=46 _ThreadName=RunLevelControllerThread-1736798092057] [timeMillis: 1736798095718] [levelValue: 800] [[
Created HTTP listener admin-listener on host/port 0.0.0.0:4848]]
[2025-01-13T19:54:55.721+0000] [Payara 5.2022.5] [INFO] [AS-WEB-GLUE-00198] [javax.enterprise.web] [tid: _ThreadID=46 _ThreadName=RunLevelControllerThread-1736798092057] [timeMillis: 1736798095721] [levelValue: 800] [[
Created HTTP listener jk-connector on host/port 0.0.0.0:8009]]
[2025-01-13T19:54:55.740+0000] [Payara 5.2022.5] [INFO] [AS-WEB-GLUE-00200] [javax.enterprise.web] [tid: _ThreadID=46 _ThreadName=RunLevelControllerThread-1736798092057] [timeMillis: 1736798095740] [levelValue: 800] [[
Created virtual server server]]
[2025-01-13T19:54:55.742+0000] [Payara 5.2022.5] [INFO] [AS-WEB-GLUE-00200] [javax.enterprise.web] [tid: _ThreadID=46 _ThreadName=RunLevelControllerThread-1736798092057] [timeMillis: 1736798095742] [levelValue: 800] [[
Created virtual server __asadmin]]
[2025-01-13T19:54:56.644+0000] [Payara 5.2022.5] [INFO] [AS-WEB-GLUE-00201] [javax.enterprise.web] [tid: _ThreadID=46 _ThreadName=RunLevelControllerThread-1736798092057] [timeMillis: 1736798096644] [levelValue: 800] [[
Virtual server server loaded default web module ]]
[2025-01-13T19:55:01.439+0000] [Payara 5.2022.5] [INFO] [AS-CORE-JAVAEE-0002] [javax.enterprise.system.core.ee] [tid: _ThreadID=46 _ThreadName=RunLevelControllerThread-1736798092057] [timeMillis: 1736798101439] [levelValue: 800] [[
Done with starting web container.]]
[2025-01-13T19:55:06.707+0000] [Payara 5.2022.5] [SEVERE] [] [javax.enterprise.system.core] [tid: _ThreadID=45 _ThreadName=RunLevelControllerThread-1736798092043] [timeMillis: 1736798106707] [levelValue: 1000] [[
Exception while deploying the app [dataverse-5.14]]]
[2025-01-13T19:55:06.708+0000] [Payara 5.2022.5] [SEVERE] [NCLS-CORE-00026] [javax.enterprise.system.core] [tid: _ThreadID=45 _ThreadName=RunLevelControllerThread-1736798092043] [timeMillis: 1736798106708] [levelValue: 1000] [[
Exception during lifecycle processing
java.lang.IllegalArgumentException: Unsupported class file major version 65
at org.objectweb.asm.ClassReader.<init>(ClassReader.java:199)
at org.objectweb.asm.ClassReader.<init>(ClassReader.java:180)
at org.objectweb.asm.ClassReader.<init>(ClassReader.java:166)
at org.objectweb.asm.ClassReader.<init>(ClassReader.java:287)
at org.glassfish.hk2.classmodel.reflect.Parser$1.on(Parser.java:133)
at org.glassfish.hk2.classmodel.reflect.impl.TypesCtr.onNotVisitedEntries(TypesCtr.java:134)
at org.glassfish.hk2.classmodel.reflect.Parser.awaitTermination(Parser.java:116)
at org.glassfish.hk2.classmodel.reflect.Parser.awaitTermination(Parser.java:68)
at com.sun.enterprise.v3.server.ApplicationLifecycle.getDeployableParser(ApplicationLifecycle.java:741)
at com.sun.enterprise.v3.server.ApplicationLifecycle.getDeployableTypes(ApplicationLifecycle.java:678)
Created HTTP listener http-listener-1 on host/port 0.0.0.0:8080]]
[2025-01-13T19:54:55.717+0000] [Payara 5.2022.5] [INFO] [AS-WEB-GLUE-00198] [javax.enterprise.web] [tid: _ThreadID=46 _ThreadName=RunLevelControllerThread-1736798092057] [timeMillis: 1736798095717] [levelValue: 800] [[
Created HTTP listener http-listener-2 on host/port 0.0.0.0:8181]]
[2025-01-13T19:54:55.718+0000] [Payara 5.2022.5] [INFO] [AS-WEB-GLUE-00198] [javax.enterprise.web] [tid: _ThreadID=46 _ThreadName=RunLevelControllerThread-1736798092057] [timeMillis: 1736798095718] [levelValue: 800] [[
Created HTTP listener admin-listener on host/port 0.0.0.0:4848]]
[2025-01-13T19:54:55.721+0000] [Payara 5.2022.5] [INFO] [AS-WEB-GLUE-00198] [javax.enterprise.web] [tid: _ThreadID=46 _ThreadName=RunLevelControllerThread-1736798092057] [timeMillis: 1736798095721] [levelValue: 800] [[
Created HTTP listener jk-connector on host/port 0.0.0.0:8009]]
[2025-01-13T19:54:55.740+0000] [Payara 5.2022.5] [INFO] [AS-WEB-GLUE-00200] [javax.enterprise.web] [tid: _ThreadID=46 _ThreadName=RunLevelControllerThread-1736798092057] [timeMillis: 1736798095740] [levelValue: 800] [[
Created virtual server server]]
[2025-01-13T19:54:55.742+0000] [Payara 5.2022.5] [INFO] [AS-WEB-GLUE-00200] [javax.enterprise.web] [tid: _ThreadID=46 _ThreadName=RunLevelControllerThread-1736798092057] [timeMillis: 1736798095742] [levelValue: 800] [[
Created virtual server __asadmin]]
[2025-01-13T19:54:56.644+0000] [Payara 5.2022.5] [INFO] [AS-WEB-GLUE-00201] [javax.enterprise.web] [tid: _ThreadID=46 _ThreadName=RunLevelControllerThread-1736798092057] [timeMillis: 1736798096644] [levelValue: 800] [[
Virtual server server loaded default web module ]]
[2025-01-13T19:55:01.439+0000] [Payara 5.2022.5] [INFO] [AS-CORE-JAVAEE-0002] [javax.enterprise.system.core.ee] [tid: _ThreadID=46 _ThreadName=RunLevelControllerThread-1736798092057] [timeMillis: 1736798101439] [levelValue: 800] [[
Done with starting web container.]]
[2025-01-13T19:55:06.707+0000] [Payara 5.2022.5] [SEVERE] [] [javax.enterprise.system.core] [tid: _ThreadID=45 _ThreadName=RunLevelControllerThread-1736798092043] [timeMillis: 1736798106707] [levelValue: 1000] [[
Exception while deploying the app [dataverse-5.14]]]
[2025-01-13T19:55:06.708+0000] [Payara 5.2022.5] [SEVERE] [NCLS-CORE-00026] [javax.enterprise.system.core] [tid: _ThreadID=45 _ThreadName=RunLevelControllerThread-1736798092043] [timeMillis: 1736798106708] [levelValue: 1000] [[
Exception during lifecycle processing
java.lang.IllegalArgumentException: Unsupported class file major version 65
at org.objectweb.asm.ClassReader.<init>(ClassReader.java:199)
at org.objectweb.asm.ClassReader.<init>(ClassReader.java:180)
at org.objectweb.asm.ClassReader.<init>(ClassReader.java:166)
at org.objectweb.asm.ClassReader.<init>(ClassReader.java:287)
at org.glassfish.hk2.classmodel.reflect.Parser$1.on(Parser.java:133)
at org.glassfish.hk2.classmodel.reflect.impl.TypesCtr.onNotVisitedEntries(TypesCtr.java:134)
at org.glassfish.hk2.classmodel.reflect.Parser.awaitTermination(Parser.java:116)
at org.glassfish.hk2.classmodel.reflect.Parser.awaitTermination(Parser.java:68)
at com.sun.enterprise.v3.server.ApplicationLifecycle.getDeployableParser(ApplicationLifecycle.java:741)
at com.sun.enterprise.v3.server.ApplicationLifecycle.getDeployableTypes(ApplicationLifecycle.java:678)
at com.sun.enterprise.v3.server.ApplicationLifecycle.prepare(ApplicationLifecycle.java:409)
at com.sun.enterprise.v3.server.ApplicationLoaderService.processApplication(ApplicationLoaderService.java:427)
at com.sun.enterprise.v3.server.ApplicationLoaderService.postConstruct(ApplicationLoaderService.java:259)
at org.jvnet.hk2.internal.ClazzCreator.postConstructMe(ClazzCreator.java:303)
at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:351)
at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:463)
at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:281)
at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:65)
at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2102)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:93)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:67)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1213)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
]]
[2025-01-13T19:55:06.717+0000] [Payara 5.2022.5] [SEVERE] [NCLS-CORE-00041] [javax.enterprise.system.core] [tid: _ThreadID=45 _ThreadName=RunLevelControllerThread-1736798092043] [timeMillis: 1736798106717] [levelValue: 1000] [[
Application deployment failed: Exception while deploying the app [dataverse-5.14]]]
[2025-01-13T19:55:06.720+0000] [Payara 5.2022.5] [INFO] [NCLS-CORE-00017] [javax.enterprise.system.core] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1736798106720] [levelValue: 800] [[
Payara Server 5.2022.5 #badassfish (492) startup time : Felix (3308ms), startup services(14685ms), total(17993ms)]]
[2025-01-13T19:55:06.723+0000] [Payara 5.2022.5] [INFO] [] [fish.payara.nucleus.cluster.PayaraCluster] [tid: _ThreadID=142 _ThreadName=Executor-Service-1] [timeMillis: 1736798106723] [levelValue: 800] [[
Data Grid Status
Payara Data Grid State: DG Version: 4 DG Name: development DG Size: 1
Instances: {
DataGrid: development Name: server Lite: false This: true UUID: 0558ba99-70bf-4048-8744-380a44eb87c7 Address: /193.174.154.138:4900
}]]
[2025-01-13T19:55:06.724+0000] [Payara 5.2022.5] [INFO] [NCLS-CORE-00101] [javax.enterprise.system.core] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1736798106724] [levelValue: 800] [[
Network Listener jk-connector started in: 3ms - bound to [/0.0.0.0:8009]]]
[2025-01-13T19:55:06.746+0000] [Payara 5.2022.5] [INFO] [] [fish.payara.nucleus.notification.NotificationService] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1736798106746] [levelValue: 800] [[
Payara Notification Service bootstrapped.]]
[2025-01-13T19:55:06.746+0000] [Payara 5.2022.5] [INFO] [] [monitoring-console-core] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1736798106746] [levelValue: 800] [[
Bootstrapping Monitoring Console Runtime]]
[2025-01-13T19:55:06.771+0000] [Payara 5.2022.5] [INFO] [] [monitoring-console-core] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1736798106771] [levelValue: 800] [[
Starting monitoring data collection for server]]
[2025-01-13T19:55:06.772+0000] [Payara 5.2022.5] [INFO] [] [monitoring-console-core] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1736798106772] [levelValue: 800] [[
Starting monitoring watch collection for server]]
[2025-01-13T19:55:06.957+0000] [Payara 5.2022.5] [INFO] [NCLS-CORE-00101] [javax.enterprise.system.core] [tid: _ThreadID=46 _ThreadName=RunLevelControllerThread-1736798092057] [timeMillis: 1736798106957] [levelValue: 800] [[
Network Listener JMS_PROXY_default_JMS_host started in: 1ms - bound to [/0.0.0.0:7676]]]
[2025-01-13T19:55:06.977+0000] [Payara 5.2022.5] [INFO] [NCLS-JMX-00024] [javax.enterprise.system.jmx] [tid: _ThreadID=158 _ThreadName=Thread-12] [timeMillis: 1736798106977] [levelValue: 800] [[
Creating a SecureRMIServerSocketFactory @ 0.0.0.0 with ssl config = GlassFishConfigBean.org.glassfish.grizzly.config.dom.Ssl]]
[2025-01-13T19:55:06.980+0000] [Payara 5.2022.5] [WARNING] [NCLS-JMX-00020] [javax.enterprise.system.jmx] [tid: _ThreadID=158 _ThreadName=Thread-12] [timeMillis: 1736798106980] [levelValue: 900] [[
All SSL cipher suites disabled for network-listener(s). Using SSL implementation specific defaults]]
[2025-01-13T19:55:07.069+0000] [Payara 5.2022.5] [WARNING] [NCLS-JMX-00020] [javax.enterprise.system.jmx] [tid: _ThreadID=158 _ThreadName=Thread-12] [timeMillis: 1736798107069] [levelValue: 900] [[
All SSL cipher suites disabled for network-listener(s). Using SSL implementation specific defaults]]
[2025-01-13T19:55:07.100+0000] [Payara 5.2022.5] [INFO] [NCLS-JMX-00025] [javax.enterprise.system.jmx] [tid: _ThreadID=158 _ThreadName=Thread-12] [timeMillis: 1736798107100] [levelValue: 800] [[
SSLServerSocket /0.0.0.0:8686 and [SSL: ServerSocket[addr=/0.0.0.0,localport=8686]] created]]
at com.sun.enterprise.v3.server.ApplicationLoaderService.processApplication(ApplicationLoaderService.java:427)
at com.sun.enterprise.v3.server.ApplicationLoaderService.postConstruct(ApplicationLoaderService.java:259)
at org.jvnet.hk2.internal.ClazzCreator.postConstructMe(ClazzCreator.java:303)
at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:351)
at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:463)
at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:281)
at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:65)
at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2102)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:93)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:67)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1213)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
]]
[2025-01-13T19:55:06.717+0000] [Payara 5.2022.5] [SEVERE] [NCLS-CORE-00041] [javax.enterprise.system.core] [tid: _ThreadID=45 _ThreadName=RunLevelControllerThread-1736798092043] [timeMillis: 1736798106717] [levelValue: 1000] [[
Application deployment failed: Exception while deploying the app [dataverse-5.14]]]
[2025-01-13T19:55:06.720+0000] [Payara 5.2022.5] [INFO] [NCLS-CORE-00017] [javax.enterprise.system.core] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1736798106720] [levelValue: 800] [[
Payara Server 5.2022.5 #badassfish (492) startup time : Felix (3308ms), startup services(14685ms), total(17993ms)]]
[2025-01-13T19:55:06.723+0000] [Payara 5.2022.5] [INFO] [] [fish.payara.nucleus.cluster.PayaraCluster] [tid: _ThreadID=142 _ThreadName=Executor-Service-1] [timeMillis: 1736798106723] [levelValue: 800] [[
Data Grid Status
Payara Data Grid State: DG Version: 4 DG Name: development DG Size: 1
Instances: {
DataGrid: development Name: server Lite: false This: true UUID: 0558ba99-70bf-4048-8744-380a44eb87c7 Address: /193.174.154.138:4900
}]]
[2025-01-13T19:55:06.724+0000] [Payara 5.2022.5] [INFO] [NCLS-CORE-00101] [javax.enterprise.system.core] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1736798106724] [levelValue: 800] [[
Network Listener jk-connector started in: 3ms - bound to [/0.0.0.0:8009]]]
[2025-01-13T19:55:06.746+0000] [Payara 5.2022.5] [INFO] [] [fish.payara.nucleus.notification.NotificationService] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1736798106746] [levelValue: 800] [[
Payara Notification Service bootstrapped.]]
[2025-01-13T19:55:06.746+0000] [Payara 5.2022.5] [INFO] [] [monitoring-console-core] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1736798106746] [levelValue: 800] [[
Bootstrapping Monitoring Console Runtime]]
[2025-01-13T19:55:06.771+0000] [Payara 5.2022.5] [INFO] [] [monitoring-console-core] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1736798106771] [levelValue: 800] [[
Starting monitoring data collection for server]]
[2025-01-13T19:55:06.772+0000] [Payara 5.2022.5] [INFO] [] [monitoring-console-core] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1736798106772] [levelValue: 800] [[
Starting monitoring watch collection for server]]
[2025-01-13T19:55:06.957+0000] [Payara 5.2022.5] [INFO] [NCLS-CORE-00101] [javax.enterprise.system.core] [tid: _ThreadID=46 _ThreadName=RunLevelControllerThread-1736798092057] [timeMillis: 1736798106957] [levelValue: 800] [[
Network Listener JMS_PROXY_default_JMS_host started in: 1ms - bound to [/0.0.0.0:7676]]]
[2025-01-13T19:55:06.977+0000] [Payara 5.2022.5] [INFO] [NCLS-JMX-00024] [javax.enterprise.system.jmx] [tid: _ThreadID=158 _ThreadName=Thread-12] [timeMillis: 1736798106977] [levelValue: 800] [[
Creating a SecureRMIServerSocketFactory @ 0.0.0.0 with ssl config = GlassFishConfigBean.org.glassfish.grizzly.config.dom.Ssl]]
[2025-01-13T19:55:06.980+0000] [Payara 5.2022.5] [WARNING] [NCLS-JMX-00020] [javax.enterprise.system.jmx] [tid: _ThreadID=158 _ThreadName=Thread-12] [timeMillis: 1736798106980] [levelValue: 900] [[
All SSL cipher suites disabled for network-listener(s). Using SSL implementation specific defaults]]
[2025-01-13T19:55:07.069+0000] [Payara 5.2022.5] [WARNING] [NCLS-JMX-00020] [javax.enterprise.system.jmx] [tid: _ThreadID=158 _ThreadName=Thread-12] [timeMillis: 1736798107069] [levelValue: 900] [[
All SSL cipher suites disabled for network-listener(s). Using SSL implementation specific defaults]]
[2025-01-13T19:55:07.100+0000] [Payara 5.2022.5] [INFO] [NCLS-JMX-00025] [javax.enterprise.system.jmx] [tid: _ThreadID=158 _ThreadName=Thread-12] [timeMillis: 1736798107100] [levelValue: 800] [[
SSLServerSocket /0.0.0.0:8686 and [SSL: ServerSocket[addr=/0.0.0.0,localport=8686]] created]]
[2025-01-13T19:55:07.314+0000] [Payara 5.2022.5] [INFO] [] [org.jvnet.hk2.osgiadapter] [tid: _ThreadID=31 _ThreadName=FelixStartLevel] [timeMillis: 1736798107314] [levelValue: 800] [[
Skipping registration of inhabitant for service reference [org.osgi.service.metatype.MetaTypeProvider] as the service object could not be obtained.]]
[2025-01-13T19:55:07.444+0000] [Payara 5.2022.5] [INFO] [NCLS-JMX-00005] [javax.enterprise.system.jmx] [tid: _ThreadID=158 _ThreadName=Thread-12] [timeMillis: 1736798107444] [levelValue: 800] [[
JMXStartupService has started JMXConnector on JMXService URL service:jmx:rmi://0.0.0.0:8686/jndi/rmi://0.0.0.0:8686/jmxrmi]]
If anyone has a suggestion to fix this, please let me know.
Philip Durbin
Jan 13, 2025, 3:35:53 PM1/13/25
to dataverse...@googlegroups.com
Hmm, I don't know if Google's AI overview for my search of 'ubuntu 22 vs 24 "java"' can be trusted but it says, "Ubuntu 22.04 might default to an older version of OpenJDK (e.g., OpenJDK 11), whereas Ubuntu 24.04 likely defaults to a newer version (e.g., OpenJDK 17)."
Since you're on Dataverse 5.14 you should ensure you're using Java 11, not Java 17. Perhaps that's why you're seeing that "Unsupported class file major version 65" error?
I hope this helps!
Phil
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Philip Durbin
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http://www.iq.harvard.edu/people/philip-durbin
Software Developer for http://dataverse.org
http://www.iq.harvard.edu/people/philip-durbin
Seeger, Bethany
Jan 13, 2025, 4:55:33 PM1/13/25
to Dataverse Users Community
Hi,
"java.lang.IllegalArgumentException: Unsupported class file major version 65"
Generally, this error means there is a problem with the version of Java you're trying to run on.
I believe version 5.14 relies on Java 11; can you check to see that the upgrade to ubuntu didn't also upgrade Java? (java -version) If so, then I think you'll need to install Java 11 again and make sure the server is using that one.
I believe version 5.14 relies on Java 11; can you check to see that the upgrade to ubuntu didn't also upgrade Java? (java -version) If so, then I think you'll need to install Java 11 again and make sure the server is using that one.
-Bethany
From: dataverse...@googlegroups.com <dataverse...@googlegroups.com> on behalf of Zhang Yue <yuezha...@gmail.com>
Sent: Monday, January 13, 2025 3:09 PM
To: Dataverse Users Community <dataverse...@googlegroups.com>
Subject: [Dataverse-Users] ubuntu upgrade makes my Dataverse down
Sent: Monday, January 13, 2025 3:09 PM
To: Dataverse Users Community <dataverse...@googlegroups.com>
Subject: [Dataverse-Users] ubuntu upgrade makes my Dataverse down
Zhang Yue
Jan 14, 2025, 6:45:38 AM1/14/25
to Dataverse Users Community
Dear all,
at org.jvnet.hk2.internal.ClazzCreator.postConstructMe(ClazzCreator.java:303)
at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:351)
at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:463)
at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:281)
at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:65)
at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2102)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:93)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:67)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1213)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1144)
at org.jvnet.hk2.internal.ClazzCreator.postConstructMe(ClazzCreator.java:303)
at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:351)
at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:463)
at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:281)
at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:65)
at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2102)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:93)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:67)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1213)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1144)
at org.jvnet.hk2.internal.ClazzCreator.postConstructMe(ClazzCreator.java:303)
at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:351)
at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:463)
at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:281)
at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:65)
at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2102)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:93)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:67)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1213)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1144)
at org.jvnet.hk2.internal.ClazzCreator.postConstructMe(ClazzCreator.java:303)
at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:351)
at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:463)
at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:281)
at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:65)
at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2102)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:93)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:67)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1213)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1144)
Sure I downgrade my java version till 11.0.25. But now more error raises:
[2025-01-14T10:47:46.476+0000] [Payara 5.2022.5] [WARNING] [] [javax.enterprise.resource.resourceadapter.com.sun.enterprise.resource.allocator] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666476] [levelValue: 900] [[
RAR5038:Unexpected exception while creating resource for pool __TimerPool. Exception : javax.resource.spi.ResourceAllocationException: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]]]
[2025-01-14T10:47:46.476+0000] [Payara 5.2022.5] [WARNING] [] [javax.enterprise.resource.resourceadapter.com.sun.enterprise.connectors] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666476] [levelValue: 900] [[
RAR5117 : Failed to obtain/create connection from connection pool [ __TimerPool ]. Reason : com.sun.appserv.connectors.internal.api.PoolingException: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]]]
[2025-01-14T10:47:46.478+0000] [Payara 5.2022.5] [WARNING] [] [javax.enterprise.resource.resourceadapter.com.sun.gjc.spi] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666478] [levelValue: 900] [[
RAR5114 : Error allocating connection : [Error in allocating a connection. Cause: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]]]]
[2025-01-14T10:47:46.479+0000] [Payara 5.2022.5] [SEVERE] [] [org.eclipse.persistence.session./file:/usr/local/payara5/glassfish/domains/domain1/applications/ejb-timer-service-app/WEB-INF/classes/___EJB__Timer__App.ejb] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666479] [levelValue: 1000] [[
Local Exception Stack:
Exception [EclipseLink-4002] (Eclipse Persistence Services - 2.7.11.payara-p1): org.eclipse.persistence.exceptions.DatabaseException
Internal Exception: java.sql.SQLException: Error in allocating a connection. Cause: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
Error Code: 0
at org.eclipse.persistence.exceptions.DatabaseException.sqlException(DatabaseException.java:318)
at org.eclipse.persistence.sessions.JNDIConnector.connect(JNDIConnector.java:150)
at org.eclipse.persistence.sessions.DatasourceLogin.connectToDatasource(DatasourceLogin.java:172)
at org.eclipse.persistence.internal.sessions.DatabaseSessionImpl.setOrDetectDatasource(DatabaseSessionImpl.java:226)
at org.eclipse.persistence.internal.sessions.DatabaseSessionImpl.loginAndDetectDatasource(DatabaseSessionImpl.java:810)
at org.eclipse.persistence.internal.jpa.EntityManagerFactoryProvider.login(EntityManagerFactoryProvider.java:261)
at org.eclipse.persistence.internal.jpa.EntityManagerSetupImpl.deploy(EntityManagerSetupImpl.java:771)
at org.eclipse.persistence.internal.jpa.EntityManagerFactoryDelegate.getAbstractSession(EntityManagerFactoryDelegate.java:222)
at org.eclipse.persistence.internal.jpa.EntityManagerFactoryDelegate.createEntityManagerImpl(EntityManagerFactoryDelegate.java:330)
at org.eclipse.persistence.internal.jpa.EntityManagerFactoryImpl.createEntityManagerImpl(EntityManagerFactoryImpl.java:350)
at org.eclipse.persistence.internal.jpa.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:313)
at org.glassfish.persistence.jpa.JPADeployer$2.visitPUD(JPADeployer.java:507)
at org.glassfish.persistence.jpa.JPADeployer$PersistenceUnitDescriptorIterator.iteratePUDs(JPADeployer.java:571)
at org.glassfish.persistence.jpa.JPADeployer.iterateInitializedPUsAtApplicationPrepare(JPADeployer.java:553)
at org.glassfish.persistence.jpa.JPADeployer.event(JPADeployer.java:454)
at org.glassfish.kernel.event.EventsImpl.send(EventsImpl.java:131)
at com.sun.enterprise.v3.server.ApplicationLifecycle.prepare(ApplicationLifecycle.java:570)
at com.sun.enterprise.v3.server.ApplicationLifecycle.deploy(ApplicationLifecycle.java:657)
at com.sun.enterprise.v3.server.ApplicationLifecycle.deploy(ApplicationLifecycle.java:651)
at org.glassfish.ejb.persistent.timer.PersistentEJBTimerService.deployEJBTimerService(PersistentEJBTimerService.java:1463)
at org.glassfish.ejb.persistent.timer.PersistentEJBTimerService.initEJBTimerService(PersistentEJBTimerService.java:1369)
at org.glassfish.ejb.persistent.timer.DatabaseEJBTimerService.initPersistentTimerService(DatabaseEJBTimerService.java:98)
at com.sun.ejb.containers.EJBTimerService.initPersistentTimerService(EJBTimerService.java:423)
at com.sun.ejb.containers.EJBTimerService.getEJBTimerService(EJBTimerService.java:257)
at com.sun.ejb.containers.BaseContainer.initialize(BaseContainer.java:871)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1541)
at org.glassfish.ejb.startup.EjbApplication.initialize(EjbApplication.java:250)
at org.glassfish.internal.data.EngineRef.initialize(EngineRef.java:203)
at java.base/java.lang.Iterable.forEach(Iterable.java:75)
at org.glassfish.internal.data.ApplicationInfo.lambda$initialize$0(ApplicationInfo.java:393)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1541)
at org.glassfish.internal.data.ApplicationInfo.initialize(ApplicationInfo.java:393)
at com.sun.enterprise.v3.server.ApplicationLifecycle.initialize(ApplicationLifecycle.java:625)
at com.sun.enterprise.v3.server.ApplicationLoaderService.postConstruct(ApplicationLoaderService.java:346)
RAR5038:Unexpected exception while creating resource for pool __TimerPool. Exception : javax.resource.spi.ResourceAllocationException: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]]]
[2025-01-14T10:47:46.476+0000] [Payara 5.2022.5] [WARNING] [] [javax.enterprise.resource.resourceadapter.com.sun.enterprise.connectors] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666476] [levelValue: 900] [[
RAR5117 : Failed to obtain/create connection from connection pool [ __TimerPool ]. Reason : com.sun.appserv.connectors.internal.api.PoolingException: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]]]
[2025-01-14T10:47:46.478+0000] [Payara 5.2022.5] [WARNING] [] [javax.enterprise.resource.resourceadapter.com.sun.gjc.spi] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666478] [levelValue: 900] [[
RAR5114 : Error allocating connection : [Error in allocating a connection. Cause: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]]]]
[2025-01-14T10:47:46.479+0000] [Payara 5.2022.5] [SEVERE] [] [org.eclipse.persistence.session./file:/usr/local/payara5/glassfish/domains/domain1/applications/ejb-timer-service-app/WEB-INF/classes/___EJB__Timer__App.ejb] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666479] [levelValue: 1000] [[
Local Exception Stack:
Exception [EclipseLink-4002] (Eclipse Persistence Services - 2.7.11.payara-p1): org.eclipse.persistence.exceptions.DatabaseException
Internal Exception: java.sql.SQLException: Error in allocating a connection. Cause: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
Error Code: 0
at org.eclipse.persistence.exceptions.DatabaseException.sqlException(DatabaseException.java:318)
at org.eclipse.persistence.sessions.JNDIConnector.connect(JNDIConnector.java:150)
at org.eclipse.persistence.sessions.DatasourceLogin.connectToDatasource(DatasourceLogin.java:172)
at org.eclipse.persistence.internal.sessions.DatabaseSessionImpl.setOrDetectDatasource(DatabaseSessionImpl.java:226)
at org.eclipse.persistence.internal.sessions.DatabaseSessionImpl.loginAndDetectDatasource(DatabaseSessionImpl.java:810)
at org.eclipse.persistence.internal.jpa.EntityManagerFactoryProvider.login(EntityManagerFactoryProvider.java:261)
at org.eclipse.persistence.internal.jpa.EntityManagerSetupImpl.deploy(EntityManagerSetupImpl.java:771)
at org.eclipse.persistence.internal.jpa.EntityManagerFactoryDelegate.getAbstractSession(EntityManagerFactoryDelegate.java:222)
at org.eclipse.persistence.internal.jpa.EntityManagerFactoryDelegate.createEntityManagerImpl(EntityManagerFactoryDelegate.java:330)
at org.eclipse.persistence.internal.jpa.EntityManagerFactoryImpl.createEntityManagerImpl(EntityManagerFactoryImpl.java:350)
at org.eclipse.persistence.internal.jpa.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:313)
at org.glassfish.persistence.jpa.JPADeployer$2.visitPUD(JPADeployer.java:507)
at org.glassfish.persistence.jpa.JPADeployer$PersistenceUnitDescriptorIterator.iteratePUDs(JPADeployer.java:571)
at org.glassfish.persistence.jpa.JPADeployer.iterateInitializedPUsAtApplicationPrepare(JPADeployer.java:553)
at org.glassfish.persistence.jpa.JPADeployer.event(JPADeployer.java:454)
at org.glassfish.kernel.event.EventsImpl.send(EventsImpl.java:131)
at com.sun.enterprise.v3.server.ApplicationLifecycle.prepare(ApplicationLifecycle.java:570)
at com.sun.enterprise.v3.server.ApplicationLifecycle.deploy(ApplicationLifecycle.java:657)
at com.sun.enterprise.v3.server.ApplicationLifecycle.deploy(ApplicationLifecycle.java:651)
at org.glassfish.ejb.persistent.timer.PersistentEJBTimerService.deployEJBTimerService(PersistentEJBTimerService.java:1463)
at org.glassfish.ejb.persistent.timer.PersistentEJBTimerService.initEJBTimerService(PersistentEJBTimerService.java:1369)
at org.glassfish.ejb.persistent.timer.DatabaseEJBTimerService.initPersistentTimerService(DatabaseEJBTimerService.java:98)
at com.sun.ejb.containers.EJBTimerService.initPersistentTimerService(EJBTimerService.java:423)
at com.sun.ejb.containers.EJBTimerService.getEJBTimerService(EJBTimerService.java:257)
at com.sun.ejb.containers.BaseContainer.initialize(BaseContainer.java:871)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1541)
at org.glassfish.ejb.startup.EjbApplication.initialize(EjbApplication.java:250)
at org.glassfish.internal.data.EngineRef.initialize(EngineRef.java:203)
at java.base/java.lang.Iterable.forEach(Iterable.java:75)
at org.glassfish.internal.data.ApplicationInfo.lambda$initialize$0(ApplicationInfo.java:393)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1541)
at org.glassfish.internal.data.ApplicationInfo.initialize(ApplicationInfo.java:393)
at com.sun.enterprise.v3.server.ApplicationLifecycle.initialize(ApplicationLifecycle.java:625)
at com.sun.enterprise.v3.server.ApplicationLoaderService.postConstruct(ApplicationLoaderService.java:346)
at org.jvnet.hk2.internal.ClazzCreator.postConstructMe(ClazzCreator.java:303)
at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:351)
at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:463)
at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:281)
at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:65)
at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2102)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:93)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:67)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1213)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: java.sql.SQLException: Error in allocating a connection. Cause: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
at com.sun.gjc.spi.base.AbstractDataSource.getConnection(AbstractDataSource.java:119)
at org.eclipse.persistence.sessions.JNDIConnector.connect(JNDIConnector.java:138)
... 45 more
Caused by: javax.resource.spi.ResourceAllocationException: Error in allocating a connection. Cause: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
at com.sun.enterprise.connectors.ConnectionManagerImpl.internalGetConnection(ConnectionManagerImpl.java:319)
at com.sun.enterprise.connectors.ConnectionManagerImpl.allocateConnection(ConnectionManagerImpl.java:196)
at com.sun.enterprise.connectors.ConnectionManagerImpl.allocateConnection(ConnectionManagerImpl.java:171)
at com.sun.enterprise.connectors.ConnectionManagerImpl.allocateConnection(ConnectionManagerImpl.java:166)
at com.sun.gjc.spi.base.AbstractDataSource.getConnection(AbstractDataSource.java:113)
... 46 more
Caused by: com.sun.appserv.connectors.internal.api.PoolingException: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
at com.sun.enterprise.resource.pool.datastructure.RWLockDataStructure.addResource(RWLockDataStructure.java:108)
at com.sun.enterprise.resource.pool.ConnectionPool.addResource(ConnectionPool.java:288)
at com.sun.enterprise.resource.pool.ConnectionPool.createResourceAndAddToPool(ConnectionPool.java:1532)
at com.sun.enterprise.resource.pool.ConnectionPool.createResources(ConnectionPool.java:957)
at com.sun.enterprise.resource.pool.ConnectionPool.initPool(ConnectionPool.java:236)
at com.sun.enterprise.resource.pool.ConnectionPool.internalGetResource(ConnectionPool.java:527)
at com.sun.enterprise.resource.pool.ConnectionPool.getResource(ConnectionPool.java:388)
at com.sun.enterprise.resource.pool.PoolManagerImpl.getResourceFromPool(PoolManagerImpl.java:244)
at com.sun.enterprise.resource.pool.PoolManagerImpl.getResource(PoolManagerImpl.java:171)
at com.sun.enterprise.connectors.ConnectionManagerImpl.getResource(ConnectionManagerImpl.java:354)
at com.sun.enterprise.connectors.ConnectionManagerImpl.internalGetConnection(ConnectionManagerImpl.java:307)
... 50 more
Caused by: com.sun.appserv.connectors.internal.api.PoolingException: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
at com.sun.enterprise.resource.pool.ConnectionPool.createSingleResource(ConnectionPool.java:932)
at com.sun.enterprise.resource.pool.ConnectionPool.createResource(ConnectionPool.java:1209)
at com.sun.enterprise.resource.pool.datastructure.RWLockDataStructure.addResource(RWLockDataStructure.java:100)
... 60 more
Caused by: com.sun.appserv.connectors.internal.api.PoolingException: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
at com.sun.enterprise.resource.allocator.ConnectorAllocator.createResource(ConnectorAllocator.java:184)
at com.sun.enterprise.resource.pool.ConnectionPool.createSingleResource(ConnectionPool.java:919)
... 62 more
Caused by: javax.resource.spi.ResourceAllocationException: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
at com.sun.gjc.spi.XAManagedConnectionFactory.createManagedConnection(XAManagedConnectionFactory.java:132)
at com.sun.enterprise.resource.allocator.ConnectorAllocator.createResource(ConnectorAllocator.java:164)
... 63 more
Caused by: org.h2.jdbc.JdbcSQLFeatureNotSupportedException: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:507)
at org.h2.message.DbException.getJdbcSQLException(DbException.java:429)
at org.h2.message.DbException.get(DbException.java:205)
at org.h2.message.DbException.get(DbException.java:181)
at org.h2.message.DbException.getUnsupportedException(DbException.java:269)
at org.h2.engine.Database.open(Database.java:639)
at org.h2.engine.Database.openDatabase(Database.java:307)
at org.h2.engine.Database.<init>(Database.java:301)
at org.h2.engine.Engine.openSession(Engine.java:74)
at org.h2.engine.Engine.openSession(Engine.java:192)
at org.h2.engine.Engine.createSessionAndValidate(Engine.java:171)
at org.h2.engine.Engine.createSession(Engine.java:166)
at org.h2.engine.Engine.createSession(Engine.java:29)
at org.h2.engine.SessionRemote.connectEmbeddedOrServer(SessionRemote.java:340)
at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:173)
at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:152)
at org.h2.Driver.connect(Driver.java:69)
at org.h2.jdbcx.JdbcDataSource.getJdbcConnection(JdbcDataSource.java:189)
at org.h2.jdbcx.JdbcDataSource.getXAConnection(JdbcDataSource.java:352)
at com.sun.gjc.spi.XAManagedConnectionFactory.createManagedConnection(XAManagedConnectionFactory.java:118)
... 64 more
]]
[2025-01-14T10:47:46.486+0000] [Payara 5.2022.5] [SEVERE] [] [javax.enterprise.system.core] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666486] [levelValue: 1000] [[
Exception [EclipseLink-4002] (Eclipse Persistence Services - 2.7.11.payara-p1): org.eclipse.persistence.exceptions.DatabaseException
Internal Exception: java.sql.SQLException: Error in allocating a connection. Cause: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
Error Code: 0]]
[2025-01-14T10:47:46.502+0000] [Payara 5.2022.5] [WARNING] [] [javax.enterprise.system.container.ejb.com.sun.ejb.containers] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666502] [levelValue: 900] [[
Cannot deploy or load EJBTimerService: ]]
[2025-01-14T10:47:46.647+0000] [Payara 5.2022.5] [SEVERE] [] [javax.enterprise.system.tools.deployment.common] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666647] [levelValue: 1000] [[
Exception while invoking class org.glassfish.ejb.startup.EjbApplication start method
java.lang.RuntimeException: EJB Timer Service is not available
at com.sun.ejb.containers.BaseContainer.startApplication(BaseContainer.java:3946)
at org.glassfish.ejb.startup.EjbApplication.start(EjbApplication.java:168)
at org.glassfish.internal.data.EngineRef.start(EngineRef.java:123)
at org.glassfish.internal.data.ModuleInfo.start(ModuleInfo.java:292)
at org.glassfish.internal.data.ApplicationInfo.start(ApplicationInfo.java:361)
at com.sun.enterprise.v3.server.ApplicationLifecycle.initialize(ApplicationLifecycle.java:629)
at com.sun.enterprise.v3.server.ApplicationLoaderService.postConstruct(ApplicationLoaderService.java:346)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: java.sql.SQLException: Error in allocating a connection. Cause: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
at com.sun.gjc.spi.base.AbstractDataSource.getConnection(AbstractDataSource.java:119)
at org.eclipse.persistence.sessions.JNDIConnector.connect(JNDIConnector.java:138)
... 45 more
Caused by: javax.resource.spi.ResourceAllocationException: Error in allocating a connection. Cause: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
at com.sun.enterprise.connectors.ConnectionManagerImpl.internalGetConnection(ConnectionManagerImpl.java:319)
at com.sun.enterprise.connectors.ConnectionManagerImpl.allocateConnection(ConnectionManagerImpl.java:196)
at com.sun.enterprise.connectors.ConnectionManagerImpl.allocateConnection(ConnectionManagerImpl.java:171)
at com.sun.enterprise.connectors.ConnectionManagerImpl.allocateConnection(ConnectionManagerImpl.java:166)
at com.sun.gjc.spi.base.AbstractDataSource.getConnection(AbstractDataSource.java:113)
... 46 more
Caused by: com.sun.appserv.connectors.internal.api.PoolingException: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
at com.sun.enterprise.resource.pool.datastructure.RWLockDataStructure.addResource(RWLockDataStructure.java:108)
at com.sun.enterprise.resource.pool.ConnectionPool.addResource(ConnectionPool.java:288)
at com.sun.enterprise.resource.pool.ConnectionPool.createResourceAndAddToPool(ConnectionPool.java:1532)
at com.sun.enterprise.resource.pool.ConnectionPool.createResources(ConnectionPool.java:957)
at com.sun.enterprise.resource.pool.ConnectionPool.initPool(ConnectionPool.java:236)
at com.sun.enterprise.resource.pool.ConnectionPool.internalGetResource(ConnectionPool.java:527)
at com.sun.enterprise.resource.pool.ConnectionPool.getResource(ConnectionPool.java:388)
at com.sun.enterprise.resource.pool.PoolManagerImpl.getResourceFromPool(PoolManagerImpl.java:244)
at com.sun.enterprise.resource.pool.PoolManagerImpl.getResource(PoolManagerImpl.java:171)
at com.sun.enterprise.connectors.ConnectionManagerImpl.getResource(ConnectionManagerImpl.java:354)
at com.sun.enterprise.connectors.ConnectionManagerImpl.internalGetConnection(ConnectionManagerImpl.java:307)
... 50 more
Caused by: com.sun.appserv.connectors.internal.api.PoolingException: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
at com.sun.enterprise.resource.pool.ConnectionPool.createSingleResource(ConnectionPool.java:932)
at com.sun.enterprise.resource.pool.ConnectionPool.createResource(ConnectionPool.java:1209)
at com.sun.enterprise.resource.pool.datastructure.RWLockDataStructure.addResource(RWLockDataStructure.java:100)
... 60 more
Caused by: com.sun.appserv.connectors.internal.api.PoolingException: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
at com.sun.enterprise.resource.allocator.ConnectorAllocator.createResource(ConnectorAllocator.java:184)
at com.sun.enterprise.resource.pool.ConnectionPool.createSingleResource(ConnectionPool.java:919)
... 62 more
Caused by: javax.resource.spi.ResourceAllocationException: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
at com.sun.gjc.spi.XAManagedConnectionFactory.createManagedConnection(XAManagedConnectionFactory.java:132)
at com.sun.enterprise.resource.allocator.ConnectorAllocator.createResource(ConnectorAllocator.java:164)
... 63 more
Caused by: org.h2.jdbc.JdbcSQLFeatureNotSupportedException: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:507)
at org.h2.message.DbException.getJdbcSQLException(DbException.java:429)
at org.h2.message.DbException.get(DbException.java:205)
at org.h2.message.DbException.get(DbException.java:181)
at org.h2.message.DbException.getUnsupportedException(DbException.java:269)
at org.h2.engine.Database.open(Database.java:639)
at org.h2.engine.Database.openDatabase(Database.java:307)
at org.h2.engine.Database.<init>(Database.java:301)
at org.h2.engine.Engine.openSession(Engine.java:74)
at org.h2.engine.Engine.openSession(Engine.java:192)
at org.h2.engine.Engine.createSessionAndValidate(Engine.java:171)
at org.h2.engine.Engine.createSession(Engine.java:166)
at org.h2.engine.Engine.createSession(Engine.java:29)
at org.h2.engine.SessionRemote.connectEmbeddedOrServer(SessionRemote.java:340)
at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:173)
at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:152)
at org.h2.Driver.connect(Driver.java:69)
at org.h2.jdbcx.JdbcDataSource.getJdbcConnection(JdbcDataSource.java:189)
at org.h2.jdbcx.JdbcDataSource.getXAConnection(JdbcDataSource.java:352)
at com.sun.gjc.spi.XAManagedConnectionFactory.createManagedConnection(XAManagedConnectionFactory.java:118)
... 64 more
]]
[2025-01-14T10:47:46.486+0000] [Payara 5.2022.5] [SEVERE] [] [javax.enterprise.system.core] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666486] [levelValue: 1000] [[
Exception [EclipseLink-4002] (Eclipse Persistence Services - 2.7.11.payara-p1): org.eclipse.persistence.exceptions.DatabaseException
Internal Exception: java.sql.SQLException: Error in allocating a connection. Cause: Connection could not be allocated because: Feature not supported: "autoServerMode && (readOnly || fileLockMethod == NO || fileLockMethod == FS || inMemory)" [50100-200]
Error Code: 0]]
[2025-01-14T10:47:46.502+0000] [Payara 5.2022.5] [WARNING] [] [javax.enterprise.system.container.ejb.com.sun.ejb.containers] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666502] [levelValue: 900] [[
Cannot deploy or load EJBTimerService: ]]
[2025-01-14T10:47:46.647+0000] [Payara 5.2022.5] [SEVERE] [] [javax.enterprise.system.tools.deployment.common] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666647] [levelValue: 1000] [[
Exception while invoking class org.glassfish.ejb.startup.EjbApplication start method
java.lang.RuntimeException: EJB Timer Service is not available
at com.sun.ejb.containers.BaseContainer.startApplication(BaseContainer.java:3946)
at org.glassfish.ejb.startup.EjbApplication.start(EjbApplication.java:168)
at org.glassfish.internal.data.EngineRef.start(EngineRef.java:123)
at org.glassfish.internal.data.ModuleInfo.start(ModuleInfo.java:292)
at org.glassfish.internal.data.ApplicationInfo.start(ApplicationInfo.java:361)
at com.sun.enterprise.v3.server.ApplicationLifecycle.initialize(ApplicationLifecycle.java:629)
at com.sun.enterprise.v3.server.ApplicationLoaderService.postConstruct(ApplicationLoaderService.java:346)
at org.jvnet.hk2.internal.ClazzCreator.postConstructMe(ClazzCreator.java:303)
at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:351)
at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:463)
at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:281)
at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:65)
at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2102)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:93)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:67)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1213)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
]]
[2025-01-14T10:47:46.648+0000] [Payara 5.2022.5] [SEVERE] [NCLS-CORE-00026] [javax.enterprise.system.core] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666648] [levelValue: 1000] [[
Exception during lifecycle processing
java.lang.RuntimeException: EJB Timer Service is not available
at com.sun.ejb.containers.BaseContainer.startApplication(BaseContainer.java:3946)
at org.glassfish.ejb.startup.EjbApplication.start(EjbApplication.java:168)
at org.glassfish.internal.data.EngineRef.start(EngineRef.java:123)
at org.glassfish.internal.data.ModuleInfo.start(ModuleInfo.java:292)
at org.glassfish.internal.data.ApplicationInfo.start(ApplicationInfo.java:361)
at com.sun.enterprise.v3.server.ApplicationLifecycle.initialize(ApplicationLifecycle.java:629)
at com.sun.enterprise.v3.server.ApplicationLoaderService.postConstruct(ApplicationLoaderService.java:346)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
]]
[2025-01-14T10:47:46.648+0000] [Payara 5.2022.5] [SEVERE] [NCLS-CORE-00026] [javax.enterprise.system.core] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666648] [levelValue: 1000] [[
Exception during lifecycle processing
java.lang.RuntimeException: EJB Timer Service is not available
at com.sun.ejb.containers.BaseContainer.startApplication(BaseContainer.java:3946)
at org.glassfish.ejb.startup.EjbApplication.start(EjbApplication.java:168)
at org.glassfish.internal.data.EngineRef.start(EngineRef.java:123)
at org.glassfish.internal.data.ModuleInfo.start(ModuleInfo.java:292)
at org.glassfish.internal.data.ApplicationInfo.start(ApplicationInfo.java:361)
at com.sun.enterprise.v3.server.ApplicationLifecycle.initialize(ApplicationLifecycle.java:629)
at com.sun.enterprise.v3.server.ApplicationLoaderService.postConstruct(ApplicationLoaderService.java:346)
at org.jvnet.hk2.internal.ClazzCreator.postConstructMe(ClazzCreator.java:303)
at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:351)
at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:463)
at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:281)
at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:65)
at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2102)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:93)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:67)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1213)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
]]
[2025-01-14T10:47:46.649+0000] [Payara 5.2022.5] [SEVERE] [] [javax.enterprise.system.core] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666649] [levelValue: 1000] [[
Exception while loading the app]]
[2025-01-14T10:47:46.650+0000] [Payara 5.2022.5] [WARNING] [NCLS-MON-00506] [javax.enterprise.system.tools.monitor] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666650] [levelValue: 900] [[
Error unregistering ProbeProvider
java.lang.NullPointerException
at org.glassfish.flashlight.impl.provider.FlashlightProbeProviderFactory.unregisterProbeProvider(FlashlightProbeProviderFactory.java:377)
at com.sun.ejb.containers.util.pool.AbstractPool.unregisterProbeProvider(AbstractPool.java:268)
at com.sun.ejb.containers.util.pool.NonBlockingPool.close(NonBlockingPool.java:405)
at com.sun.ejb.containers.StatelessSessionContainer.doConcreteContainerShutdown(StatelessSessionContainer.java:633)
at com.sun.ejb.containers.BaseContainer.onShutdown(BaseContainer.java:4329)
at org.glassfish.ejb.startup.EjbApplication.stop(EjbApplication.java:313)
at org.glassfish.internal.data.EngineRef.stop(EngineRef.java:176)
at com.sun.enterprise.v3.server.ApplicationLifecycle$3.actOn(ApplicationLifecycle.java:310)
at com.sun.enterprise.v3.server.ApplicationLifecycle.initialize(ApplicationLifecycle.java:635)
at com.sun.enterprise.v3.server.ApplicationLoaderService.postConstruct(ApplicationLoaderService.java:346)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
]]
[2025-01-14T10:47:46.649+0000] [Payara 5.2022.5] [SEVERE] [] [javax.enterprise.system.core] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666649] [levelValue: 1000] [[
Exception while loading the app]]
[2025-01-14T10:47:46.650+0000] [Payara 5.2022.5] [WARNING] [NCLS-MON-00506] [javax.enterprise.system.tools.monitor] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851666650] [levelValue: 900] [[
Error unregistering ProbeProvider
java.lang.NullPointerException
at org.glassfish.flashlight.impl.provider.FlashlightProbeProviderFactory.unregisterProbeProvider(FlashlightProbeProviderFactory.java:377)
at com.sun.ejb.containers.util.pool.AbstractPool.unregisterProbeProvider(AbstractPool.java:268)
at com.sun.ejb.containers.util.pool.NonBlockingPool.close(NonBlockingPool.java:405)
at com.sun.ejb.containers.StatelessSessionContainer.doConcreteContainerShutdown(StatelessSessionContainer.java:633)
at com.sun.ejb.containers.BaseContainer.onShutdown(BaseContainer.java:4329)
at org.glassfish.ejb.startup.EjbApplication.stop(EjbApplication.java:313)
at org.glassfish.internal.data.EngineRef.stop(EngineRef.java:176)
at com.sun.enterprise.v3.server.ApplicationLifecycle$3.actOn(ApplicationLifecycle.java:310)
at com.sun.enterprise.v3.server.ApplicationLifecycle.initialize(ApplicationLifecycle.java:635)
at com.sun.enterprise.v3.server.ApplicationLoaderService.postConstruct(ApplicationLoaderService.java:346)
at org.jvnet.hk2.internal.ClazzCreator.postConstructMe(ClazzCreator.java:303)
at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:351)
at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:463)
at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:281)
at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:65)
at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2102)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:93)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:67)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1213)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
]]
(This WARNING raises many times)
[2025-01-14T10:47:47.014+0000] [Payara 5.2022.5] [SEVERE] [AS-WEB-GLUE-00192] [javax.enterprise.web] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851667014] [levelValue: 1000] [[
Undeployment failed for context ]]
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
]]
(This WARNING raises many times)
[2025-01-14T10:47:47.014+0000] [Payara 5.2022.5] [SEVERE] [AS-WEB-GLUE-00192] [javax.enterprise.web] [tid: _ThreadID=29 _ThreadName=RunLevelControllerThread-1736851599173] [timeMillis: 1736851667014] [levelValue: 1000] [[
Undeployment failed for context ]]
qqm...@hotmail.com
Jan 14, 2025, 5:23:10 PM1/14/25
to Dataverse Users Community
I'm not sure what is causing that but we often suggest the following as part of deployment:
- service payara stop
- rm -rf <payara install path>/glassfish/domains/domain1/generated
- rm -rf <payara install path>/glassfish/domains/domain1/lib/databases/ejbtimer
- service payara start
That may help get rid of errors with the ELBtimers.
-- Jim
Zhang Yue
Jan 15, 2025, 6:43:12 AM1/15/25
to Dataverse Users Community
Dear Jim,
I found 2 files: ejbtimer.mv.db ejbtimer.trace.db in the database dir. Shall I delete all of them?
Best,
Yue
Zhang Yue
Jan 15, 2025, 7:02:28 AM1/15/25
to Dataverse Users Community
I finally fixed this my using asadmin start-domain because ejbtimer need root permission to create and change. Simply delete everything about ejb and restart payara service cannot work.
Thanks for all your help!
Yue
James Myers
Jan 15, 2025, 8:37:01 AM1/15/25
to dataverse...@googlegroups.com
Yue,
Glad you got it working. The account running Payara definitely needs to be able to write to the domain1 dir and its children. (If anyone’s interested, I bet we could add some permissions tests to the ConfigCheckService to make sure Dataverse can write where it needs to and provide a clearer error message at startup. Feel free to add an issue or PR.)
As for deleting – in general you can delete everything in either of those two directories without an issue. Dataverse will recreate their contents at startup. I don’t think we know exactly why this is ever needed. I think we’ve seen problems when upgrading (so perhaps differences in what Payara wrote in them in different versions) and it may be that temporary permission problems (e.g. starting Payara with the wrong user) could affect them as well. In any case, if things are working, there’s no need to clear them.
Cheers,
-- Jim
To view this discussion visit https://groups.google.com/d/msgid/dataverse-community/64c132fc-2cb3-4a6f-981f-8681406abdf2n%40googlegroups.com.
Don Sizemore
Jan 15, 2025, 8:45:28 AM1/15/25
to dataverse...@googlegroups.com
Hello,
Did you downgrade to openjdk-11-jdk-headless, or the full JRE?
I ask because the corresponding headless package in Red Hat land is
enough to launch Payara but not deploy Dataverse.
Thank you,
Don
> To view this discussion visit https://groups.google.com/d/msgid/dataverse-community/ba2c8bd7-627e-43f6-bd73-9ec2990d6235n%40googlegroups.com.
Did you downgrade to openjdk-11-jdk-headless, or the full JRE?
I ask because the corresponding headless package in Red Hat land is
enough to launch Payara but not deploy Dataverse.
Thank you,
Don
Zhang Yue
Jan 20, 2025, 6:43:36 AM1/20/25
to Dataverse Users Community
Hi all,
Sorry to bother you all again.
I have problem asadmin-deploying the same dataverse-5.14.war. Ejb error with many SQL Exception occurs:
remote failure: Error occurred during deployment: Exception while loading the app : EJB Timer Service is not available. Please see server.log for more details.
PER01003: Deployment encountered SQL Exceptions:
PER01000: Got SQLException executing statement "CREATE TABLE EXTERNALTOOLTYPE (ID SERIAL NOT NULL, TYPE VARCHAR(255) NOT NULL, EXTERNALTOOL_ID BIGINT NOT NULL, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "externaltooltype" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_EXTERNALTOOLTYPE_externaltool_id ON EXTERNALTOOLTYPE (externaltool_id)": org.postgresql.util.PSQLException: ERROR: relation "index_externaltooltype_externaltool_id" already exists
PER01000: Got SQLException executing statement "CREATE TABLE DATAVERSETHEME (ID SERIAL NOT NULL, BACKGROUNDCOLOR VARCHAR(255), LINKCOLOR VARCHAR(255), LINKURL VARCHAR(255), LOGO VARCHAR(255), LOGOALIGNMENT VARCHAR(255), LOGOBACKGROUNDCOLOR VARCHAR(255), LOGOFOOTER VARCHAR(255), LOGOFOOTERALIGNMENT INTEGER, LOGOFOOTERBACKGROUNDCOLOR VARCHAR(255), LOGOFORMAT VARCHAR(255), TAGLINE VARCHAR(255), TEXTCOLOR VARCHAR(255), dataverse_id BIGINT, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "dataversetheme" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_DATAVERSETHEME_dataverse_id ON DATAVERSETHEME (dataverse_id)": org.postgresql.util.PSQLException: ERROR: relation "index_dataversetheme_dataverse_id" already exists
PER01000: Got SQLException executing statement "CREATE TABLE DATAFILECATEGORY (ID SERIAL NOT NULL, NAME VARCHAR(255) NOT NULL, DATASET_ID BIGINT NOT NULL, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "datafilecategory" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_DATAFILECATEGORY_dataset_id ON DATAFILECATEGORY (dataset_id)": org.postgresql.util.PSQLException: ERROR: relation "index_datafilecategory_dataset_id" already exists
PER01000: Got SQLException executing statement "CREATE TABLE ROLEASSIGNMENT (ID SERIAL NOT NULL, ASSIGNEEIDENTIFIER VARCHAR(255) NOT NULL, PRIVATEURLANONYMIZEDACCESS BOOLEAN, PRIVATEURLTOKEN VARCHAR(255), DEFINITIONPOINT_ID BIGINT NOT NULL, ROLE_ID BIGINT NOT NULL, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "roleassignment" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_ROLEASSIGNMENT_assigneeidentifier ON ROLEASSIGNMENT (assigneeidentifier)": org.postgresql.util.PSQLException: ERROR: relation "index_roleassignment_assigneeidentifier" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_ROLEASSIGNMENT_definitionpoint_id ON ROLEASSIGNMENT (definitionpoint_id)": org.postgresql.util.PSQLException: ERROR: relation "index_roleassignment_definitionpoint_id" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_ROLEASSIGNMENT_role_id ON ROLEASSIGNMENT (role_id)": org.postgresql.util.PSQLException: ERROR: relation "index_roleassignment_role_id" already exists
PER01000: Got SQLException executing statement "CREATE TABLE DATASETEXTERNALCITATIONS (ID BIGINT NOT NULL, CITEDBYURL VARCHAR(255) NOT NULL, DATASET_ID BIGINT NOT NULL, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "datasetexternalcitations" already exists
PER01000: Got SQLException executing statement "CREATE TABLE WORKFLOW (ID SERIAL NOT NULL, NAME VARCHAR(255), PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "workflow" already exists
PER01000: Got SQLException executing statement "CREATE TABLE OAISET (ID SERIAL NOT NULL, DEFINITION TEXT, DELETED BOOLEAN, DESCRIPTION TEXT, NAME TEXT, SPEC TEXT, UPDATEINPROGRESS BOOLEAN, VERSION BIGINT, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "oaiset" already exists
PER01000: Got SQLException executing statement "CREATE TABLE BANNERMESSAGE (ID SERIAL NOT NULL, ACTIVE BOOLEAN, DISMISSIBLEBYUSER BOOLEAN, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "bannermessage" already exists
PER01000: Got SQLException executing statement "CREATE TABLE DATAVERSELINKINGDATAVERSE (ID SERIAL NOT NULL, LINKCREATETIME TIMESTAMP, DATAVERSE_ID BIGINT NOT NULL, LINKINGDATAVERSE_ID BIGINT NOT NULL, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "dataverselinkingdataverse" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_DATAVERSELINKINGDATAVERSE_dataverse_id ON DATAVERSELINKINGDATAVERSE (dataverse_id)": org.postgresql.util.PSQLException: ERROR: relation "index_dataverselinkingdataverse_dataverse_id" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_DATAVERSELINKINGDATAVERSE_linkingDataverse_id ON DATAVERSELINKINGDATAVERSE (linkingDataverse_id)": org.postgresql.util.PSQLException: ERROR: relation "index_dataverselinkingdataverse_linkingdataverse_id" already exists
PER01000: Got SQLException executing statement "CREATE TABLE METADATABLOCK (ID SERIAL NOT NULL, DISPLAYNAME VARCHAR(255) NOT NULL, NAME VARCHAR(255) NOT NULL, namespaceuri TEXT, owner_id BIGINT, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "metadatablock" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_METADATABLOCK_name ON METADATABLOCK (name)": org.postgresql.util.PSQLException: ERROR: relation "index_metadatablock_name" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_METADATABLOCK_owner_id ON METADATABLOCK (owner_id)": org.postgresql.util.PSQLException: ERROR: relation "index_metadatablock_owner_id" already exists
PER01000: Got SQLException executing statement "CREATE TABLE CONFIRMEMAILDATA (ID SERIAL NOT NULL, CREATED TIMESTAMP NOT NULL, EXPIRES TIMESTAMP NOT NULL, TOKEN VARCHAR(255), AUTHENTICATEDUSER_ID BIGINT NOT NULL UNIQUE, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "confirmemaildata" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_CONFIRMEMAILDATA_token ON CONFIRMEMAILDATA (token)": org.postgresql.util.PSQLException: ERROR: relation "index_confirmemaildata_token" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_CONFIRMEMAILDATA_authenticateduser_id ON CONFIRMEMAILDATA (authenticateduser_id)": org.postgresql.util.PSQLException: ERROR: relation "index_confirmemaildata_authenticateduser_id" already exists
PER01000: Got SQLException executing statement "CREATE TABLE OAUTH2TOKENDATA (ID SERIAL NOT NULL, ACCESSTOKEN TEXT, EXPIRYDATE TIMESTAMP, OAUTHPROVIDERID VARCHAR(255), RAWRESPONSE TEXT, REFRESHTOKEN VARCHAR(64), TOKENTYPE VARCHAR(32), USER_ID BIGINT, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "oauth2tokendata" already exists
PER01000: Got SQLException executing statement "CREATE TABLE DVOBJECT (ID SERIAL NOT NULL, DTYPE VARCHAR(31), AUTHORITY VARCHAR(255), CREATEDATE TIMESTAMP NOT NULL, GLOBALIDCREATETIME TIMESTAMP, IDENTIFIER VARCHAR(255), IDENTIFIERREGISTERED BOOLEAN, INDEXTIME TIMESTAMP, MODIFICATIONTIME TIMESTAMP NOT NULL, PERMISSIONINDEXTIME TIMESTAMP, PERMISSIONMODIFICATIONTIME TIMESTAMP, PREVIEWIMAGEAVAILABLE BOOLEAN, PROTOCOL VARCHAR(255), PUBLICATIONDATE TIMESTAMP, STORAGEIDENTIFIER VARCHAR(255), CREATOR_ID BIGINT, OWNER_ID BIGINT, RELEASEUSER_ID BIGINT, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "dvobject" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_DVOBJECT_dtype ON DVOBJECT (dtype)": org.postgresql.util.PSQLException: ERROR: relation "index_dvobject_dtype" already exists
PER01003: Deployment encountered SQL Exceptions:
PER01000: Got SQLException executing statement "CREATE TABLE EXTERNALTOOLTYPE (ID SERIAL NOT NULL, TYPE VARCHAR(255) NOT NULL, EXTERNALTOOL_ID BIGINT NOT NULL, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "externaltooltype" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_EXTERNALTOOLTYPE_externaltool_id ON EXTERNALTOOLTYPE (externaltool_id)": org.postgresql.util.PSQLException: ERROR: relation "index_externaltooltype_externaltool_id" already exists
PER01000: Got SQLException executing statement "CREATE TABLE DATAVERSETHEME (ID SERIAL NOT NULL, BACKGROUNDCOLOR VARCHAR(255), LINKCOLOR VARCHAR(255), LINKURL VARCHAR(255), LOGO VARCHAR(255), LOGOALIGNMENT VARCHAR(255), LOGOBACKGROUNDCOLOR VARCHAR(255), LOGOFOOTER VARCHAR(255), LOGOFOOTERALIGNMENT INTEGER, LOGOFOOTERBACKGROUNDCOLOR VARCHAR(255), LOGOFORMAT VARCHAR(255), TAGLINE VARCHAR(255), TEXTCOLOR VARCHAR(255), dataverse_id BIGINT, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "dataversetheme" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_DATAVERSETHEME_dataverse_id ON DATAVERSETHEME (dataverse_id)": org.postgresql.util.PSQLException: ERROR: relation "index_dataversetheme_dataverse_id" already exists
PER01000: Got SQLException executing statement "CREATE TABLE DATAFILECATEGORY (ID SERIAL NOT NULL, NAME VARCHAR(255) NOT NULL, DATASET_ID BIGINT NOT NULL, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "datafilecategory" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_DATAFILECATEGORY_dataset_id ON DATAFILECATEGORY (dataset_id)": org.postgresql.util.PSQLException: ERROR: relation "index_datafilecategory_dataset_id" already exists
PER01000: Got SQLException executing statement "CREATE TABLE ROLEASSIGNMENT (ID SERIAL NOT NULL, ASSIGNEEIDENTIFIER VARCHAR(255) NOT NULL, PRIVATEURLANONYMIZEDACCESS BOOLEAN, PRIVATEURLTOKEN VARCHAR(255), DEFINITIONPOINT_ID BIGINT NOT NULL, ROLE_ID BIGINT NOT NULL, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "roleassignment" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_ROLEASSIGNMENT_assigneeidentifier ON ROLEASSIGNMENT (assigneeidentifier)": org.postgresql.util.PSQLException: ERROR: relation "index_roleassignment_assigneeidentifier" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_ROLEASSIGNMENT_definitionpoint_id ON ROLEASSIGNMENT (definitionpoint_id)": org.postgresql.util.PSQLException: ERROR: relation "index_roleassignment_definitionpoint_id" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_ROLEASSIGNMENT_role_id ON ROLEASSIGNMENT (role_id)": org.postgresql.util.PSQLException: ERROR: relation "index_roleassignment_role_id" already exists
PER01000: Got SQLException executing statement "CREATE TABLE DATASETEXTERNALCITATIONS (ID BIGINT NOT NULL, CITEDBYURL VARCHAR(255) NOT NULL, DATASET_ID BIGINT NOT NULL, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "datasetexternalcitations" already exists
PER01000: Got SQLException executing statement "CREATE TABLE WORKFLOW (ID SERIAL NOT NULL, NAME VARCHAR(255), PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "workflow" already exists
PER01000: Got SQLException executing statement "CREATE TABLE OAISET (ID SERIAL NOT NULL, DEFINITION TEXT, DELETED BOOLEAN, DESCRIPTION TEXT, NAME TEXT, SPEC TEXT, UPDATEINPROGRESS BOOLEAN, VERSION BIGINT, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "oaiset" already exists
PER01000: Got SQLException executing statement "CREATE TABLE BANNERMESSAGE (ID SERIAL NOT NULL, ACTIVE BOOLEAN, DISMISSIBLEBYUSER BOOLEAN, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "bannermessage" already exists
PER01000: Got SQLException executing statement "CREATE TABLE DATAVERSELINKINGDATAVERSE (ID SERIAL NOT NULL, LINKCREATETIME TIMESTAMP, DATAVERSE_ID BIGINT NOT NULL, LINKINGDATAVERSE_ID BIGINT NOT NULL, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "dataverselinkingdataverse" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_DATAVERSELINKINGDATAVERSE_dataverse_id ON DATAVERSELINKINGDATAVERSE (dataverse_id)": org.postgresql.util.PSQLException: ERROR: relation "index_dataverselinkingdataverse_dataverse_id" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_DATAVERSELINKINGDATAVERSE_linkingDataverse_id ON DATAVERSELINKINGDATAVERSE (linkingDataverse_id)": org.postgresql.util.PSQLException: ERROR: relation "index_dataverselinkingdataverse_linkingdataverse_id" already exists
PER01000: Got SQLException executing statement "CREATE TABLE METADATABLOCK (ID SERIAL NOT NULL, DISPLAYNAME VARCHAR(255) NOT NULL, NAME VARCHAR(255) NOT NULL, namespaceuri TEXT, owner_id BIGINT, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "metadatablock" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_METADATABLOCK_name ON METADATABLOCK (name)": org.postgresql.util.PSQLException: ERROR: relation "index_metadatablock_name" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_METADATABLOCK_owner_id ON METADATABLOCK (owner_id)": org.postgresql.util.PSQLException: ERROR: relation "index_metadatablock_owner_id" already exists
PER01000: Got SQLException executing statement "CREATE TABLE CONFIRMEMAILDATA (ID SERIAL NOT NULL, CREATED TIMESTAMP NOT NULL, EXPIRES TIMESTAMP NOT NULL, TOKEN VARCHAR(255), AUTHENTICATEDUSER_ID BIGINT NOT NULL UNIQUE, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "confirmemaildata" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_CONFIRMEMAILDATA_token ON CONFIRMEMAILDATA (token)": org.postgresql.util.PSQLException: ERROR: relation "index_confirmemaildata_token" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_CONFIRMEMAILDATA_authenticateduser_id ON CONFIRMEMAILDATA (authenticateduser_id)": org.postgresql.util.PSQLException: ERROR: relation "index_confirmemaildata_authenticateduser_id" already exists
PER01000: Got SQLException executing statement "CREATE TABLE OAUTH2TOKENDATA (ID SERIAL NOT NULL, ACCESSTOKEN TEXT, EXPIRYDATE TIMESTAMP, OAUTHPROVIDERID VARCHAR(255), RAWRESPONSE TEXT, REFRESHTOKEN VARCHAR(64), TOKENTYPE VARCHAR(32), USER_ID BIGINT, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "oauth2tokendata" already exists
PER01000: Got SQLException executing statement "CREATE TABLE DVOBJECT (ID SERIAL NOT NULL, DTYPE VARCHAR(31), AUTHORITY VARCHAR(255), CREATEDATE TIMESTAMP NOT NULL, GLOBALIDCREATETIME TIMESTAMP, IDENTIFIER VARCHAR(255), IDENTIFIERREGISTERED BOOLEAN, INDEXTIME TIMESTAMP, MODIFICATIONTIME TIMESTAMP NOT NULL, PERMISSIONINDEXTIME TIMESTAMP, PERMISSIONMODIFICATIONTIME TIMESTAMP, PREVIEWIMAGEAVAILABLE BOOLEAN, PROTOCOL VARCHAR(255), PUBLICATIONDATE TIMESTAMP, STORAGEIDENTIFIER VARCHAR(255), CREATOR_ID BIGINT, OWNER_ID BIGINT, RELEASEUSER_ID BIGINT, PRIMARY KEY (ID))": org.postgresql.util.PSQLException: ERROR: relation "dvobject" already exists
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_DVOBJECT_dtype ON DVOBJECT (dtype)": org.postgresql.util.PSQLException: ERROR: relation "index_dvobject_dtype" already exists
(and many "already exist" problem occurs)
Zhang Yue
Jan 20, 2025, 6:43:46 AM1/20/25
to Dataverse Users Community
James Myers
Jan 20, 2025, 11:37:52 AM1/20/25
to dataverse...@googlegroups.com
This could be a case where deleting the contents of the directories I mentioned before and restarting Payara may help. (The contents of the osgi-cache directory can also be deleted, but I don’t think that affects the timers.)
The SQL exceptions are not related and are not a real problem – Dataverse is trying to create all the tables it needs, but if you have an existing database, those tables are already there and the CREATE calls fail. Other than confusing log messages, there’s no effect. (I think there is an issue about fixing this, but no PR yet.)
-- Jim
To view this discussion visit https://groups.google.com/d/msgid/dataverse-community/dbbec52d-0976-46e5-a3f4-6b2e9980558cn%40googlegroups.com.
Zhang Yue
Jan 20, 2025, 2:03:56 PM1/20/25
to Dataverse Users Community
Dear Jim,
Thanks for your answer. Yeap I tried your method which is also mentioned in other posts. But the same EJB bug happens again. Maybe I should re-install payara5? Shall I backup datafiles, solr and sql database before re-install?
Good to know that these SQL message doesn't matter much.
Best,
Yue
Zhang Yue
Jan 20, 2025, 5:08:09 PM1/20/25
to Dataverse Users Community
Dear all,
Now I have reinstalled the payara5 and re-deployed dataverse-5.14.war without any datafile, sql dataset and solr loss, with the same domain.xml file before only setting password-alias in addition. But as my dataverse instance is started by "sudo -u dataverse ./asadmin start-domain", my "systemctl start payara" part is broken and I would like to know how to make "sudo systemctl restart payara" work again.
Best,
Yue
James Myers
Jan 21, 2025, 10:25:51 AM1/21/25
to dataverse...@googlegroups.com
Yue,
One thing I’ve seen that can cause this is when you’ve changed the Payara admin password and your startup script uses it. With a new Payara with the default password, the script fails because it uses the ‘wrong’ password. If it isn’t that, hopefully you can find some information about where the problem is following internet guidance on debugging startup script failures.
To view this discussion visit https://groups.google.com/d/msgid/dataverse-community/43809d9a-d769-4405-9202-a16722bfaea8n%40googlegroups.com.
Zhang Yue
Jan 24, 2025, 9:50:28 AM1/24/25
to Dataverse Users Community
Dear Jim,
Thank you for your advice. After I correct the payara admin password systemctl service passed successfully.
However the next day, the service start again with EJB error... Now I stopped and disable the service and then simply start domain under root, which works good but not as recommended as guide says.
Maybe I will just let it be this, after a while I will consider to update payara5 to payara6.
Best,
Yue
James Myers
Jan 24, 2025, 10:11:50 AM1/24/25
to dataverse...@googlegroups.com
Glad you’re making progress. My guess is that if you have to run as root, there’s a permission/ownership problem somewhere. You might want to try the commands in the install guide (or the payara5 equivalents):
chown -R root:root /usr/local/payara6
chown dataverse /usr/local/payara6/glassfish/lib
chown -R dataverse:dataverse /usr/local/payara6/glassfish/domains/domain1
To view this discussion visit https://groups.google.com/d/msgid/dataverse-community/6221bb97-285c-4839-807c-02fec6753921n%40googlegroups.com.
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