Trying to install dataverse 5.6 - can not start domain

Adilia Alves

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Sep 16, 2021, 7:49:29 PM9/16/21

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I want to install dataverse v 5.6 .

I upgrated java 8 to java 11 version and installed Payara 5.2021.5 (https://guides.dataverse.org/en/latest/installation/prerequisites.html).

when I tried to start domain (payara/bin> ./asadmin start-domain domain1) i got the following log and this task does not finish (time out). Can someone tell me, what is going on?

Thanks in advance.

Adília Alves

"Launching Payara Server on Felix platform
Sep 17, 2021 12:07:26 AM com.sun.enterprise.glassfish.bootstrap.osgi.BundleProvisioner createBundleProvisioner
INFO: Create bundle provisioner class = class com.sun.enterprise.glassfish.bootstrap.osgi.BundleProvisioner.
Registered com.sun.enterprise.glassfish.bootstrap.osgi.EmbeddedOSGiGlassFishRuntime@6effed4 in service registry.

#!## LogManagerService.postConstruct : rootFolder=/usr/local/payara5/glassfish
#!## LogManagerService.postConstruct : templateDir=/usr/local/payara5/glassfish/lib/templates
#!## LogManagerService.postConstruct : src=/usr/local/payara5/glassfish/lib/templates/logging.properties
#!## LogManagerService.postConstruct : dest=/usr/local/payara5/glassfish/domains/domain1/config/logging.properties
[#|2021-09-17T00:07:27.990+0100|INFO|Payara 5.2020|javax.enterprise.logging|_ThreadID=23;_ThreadName=RunLevelControllerThread-1631833647825;_TimeMillis=1631833647990;_LevelValue=800;_MessageID=NCLS-LOGGING-00009;|
Running Payara Version: Payara Server 5.2020.2 #badassfish (build 547)|#]

[#|2021-09-17T00:07:28.003+0100|INFO|Payara 5.2020|javax.enterprise.logging|_ThreadID=23;_ThreadName=RunLevelControllerThread-1631833647825;_TimeMillis=1631833648003;_LevelValue=800;_MessageID=NCLS-LOGGING-00010;|
Server log file is using Formatter class: com.sun.enterprise.server.logging.ODLLogFormatter|#]

[#|2021-09-17T00:07:28.667+0100|INFO|Payara 5.2020|org.glassfish.ha.store.spi.BackingStoreFactoryRegistry|_ThreadID=23;_ThreadName=RunLevelControllerThread-1631833647825;_TimeMillis=1631833648667;_LevelValue=800;|
Registered fish.payara.ha.hazelcast.store.HazelcastBackingStoreFactoryProxy for persistence-type = hazelcast in BackingStoreFactoryRegistry|#]

[#|2021-09-17T00:07:30.967+0100|INFO|Payara 5.2020|fish.payara.nucleus.hazelcast.HazelcastCore|_ThreadID=22;_ThreadName=RunLevelControllerThread-1631833647821;_TimeMillis=1631833650967;_LevelValue=800;|
Hazelcast Instance Bound to JNDI at payara/Hazelcast|#]

[#|2021-09-17T00:07:30.969+0100|INFO|Payara 5.2020|fish.payara.nucleus.hazelcast.HazelcastCore|_ThreadID=22;_ThreadName=RunLevelControllerThread-1631833647821;_TimeMillis=1631833650969;_LevelValue=800;|
JSR107 Caching Provider Bound to JNDI at payara/CachingProvider|#]

[#|2021-09-17T00:07:30.969+0100|INFO|Payara 5.2020|fish.payara.nucleus.hazelcast.HazelcastCore|_ThreadID=22;_ThreadName=RunLevelControllerThread-1631833647821;_TimeMillis=1631833650969;_LevelValue=800;|
JSR107 Default Cache Manager Bound to JNDI at payara/CacheManager|#]

[#|2021-09-17T00:07:31.214+0100|INFO|Payara 5.2020|javax.enterprise.system.core|_ThreadID=22;_ThreadName=RunLevelControllerThread-1631833647821;_TimeMillis=1631833651214;_LevelValue=800;_MessageID=NCLS-CORE-00101;|
Network Listener http-listener-1 started in: 5ms - bound to [/0.0.0.0:8080]|#]

[#|2021-09-17T00:07:31.229+0100|WARNING|Payara 5.2020|org.glassfish.grizzly.http2.Http2AddOn|_ThreadID=22;_ThreadName=RunLevelControllerThread-1631833647821;_TimeMillis=1631833651229;_LevelValue=900;|
TLS ALPN (Application-Layer Protocol Negotiation) support is not available. HTTP/2 support will not be enabled.|#]

[#|2021-09-17T00:07:31.235+0100|INFO|Payara 5.2020|javax.enterprise.system.core|_ThreadID=22;_ThreadName=RunLevelControllerThread-1631833647821;_TimeMillis=1631833651235;_LevelValue=800;_MessageID=NCLS-CORE-00101;|
Network Listener http-listener-2 started in: 1ms - bound to [/0.0.0.0:8181]|#]

[#|2021-09-17T00:07:31.245+0100|INFO|Payara 5.2020|javax.enterprise.system.core|_ThreadID=22;_ThreadName=RunLevelControllerThread-1631833647821;_TimeMillis=1631833651245;_LevelValue=800;_MessageID=NCLS-CORE-00101;|
Network Listener admin-listener started in: 4ms - bound to [/0.0.0.0:4848]|#]

[#|2021-09-17T00:07:31.247+0100|INFO|Payara 5.2020|javax.enterprise.system.core|_ThreadID=22;_ThreadName=RunLevelControllerThread-1631833647821;_TimeMillis=1631833651247;_LevelValue=800;_MessageID=NCLS-CORE-00087;|
Grizzly 2.4.4 started in: 3,052ms - bound to [http-listener-1:8080, http-listener-2:8181, admin-listener:4848]|#]

[#|2021-09-17T00:07:31.284+0100|INFO|Payara 5.2020|javax.enterprise.system.core|_ThreadID=23;_ThreadName=RunLevelControllerThread-1631833647825;_TimeMillis=1631833651284;_LevelValue=800;_MessageID=NCLS-CORE-00101;|
Network Listener iiop-service started in: 1ms - bound to [/0.0.0.0:3700]|#]

[#|2021-09-17T00:07:31.292+0100|INFO|Payara 5.2020|javax.enterprise.system.core|_ThreadID=1;_ThreadName=main;_TimeMillis=1631833651292;_LevelValue=800;_MessageID=NCLS-CORE-00017;|
Payara Server 5.2020.2 #badassfish (547) startup time : Felix (2,376ms), startup services(3,477ms), total(5,853ms)|#]

[#|2021-09-17T00:07:31.292+0100|INFO|Payara 5.2020|fish.payara.nucleus.cluster.PayaraCluster|_ThreadID=76;_ThreadName=Executor-Service-7;_TimeMillis=1631833651292;_LevelValue=800;|
Data Grid Status
Payara Data Grid State: DG Version: 35 DG Name: development DG Size: 1
Instances: {
DataGrid: development Instance Group: MicroShoal Name: server Lite: false This: true UUID: 043ded67-2803-4933-8066-6b14cdfbb927 Address: /193.136.195.131:4900
}|#]

[#|2021-09-17T00:07:31.319+0100|INFO|Payara 5.2020|fish.payara.nucleus.notification.NotificationService|_ThreadID=1;_ThreadName=main;_TimeMillis=1631833651319;_LevelValue=800;|
Payara Notification Service bootstrapped with configuration: NotificationExecutionOptions{enabled=true, notifierConfigurationExecutionOptionsList={LOG=LogNotifierConfigurationExecutionOptions{useSeparateLogFile=false} NotifierConfigurationExecutionOptions{notifierType=LOG, enabled=true, noisy=true}}}|#]

[#|2021-09-17T00:07:31.341+0100|INFO|Payara 5.2020|monitoring-console-core|_ThreadID=1;_ThreadName=main;_TimeMillis=1631833651341;_LevelValue=800;|
Bootstrapping Monitoring Console Runtime|#]

[#|2021-09-17T00:07:31.376+0100|INFO|Payara 5.2020|monitoring-console-core|_ThreadID=1;_ThreadName=main;_TimeMillis=1631833651376;_LevelValue=800;|
Starting monitoring data collection for server|#]

[#|2021-09-17T00:07:31.735+0100|INFO|Payara 5.2020|org.hibernate.validator.internal.util.Version|_ThreadID=24;_ThreadName=RunLevelControllerThread-1631833647834;_TimeMillis=1631833651735;_LevelValue=800;|
HV000001: Hibernate Validator 6.1.2.Final|#]

[#|2021-09-17T00:07:31.843+0100|INFO|Payara 5.2020|javax.enterprise.system.jmx|_ThreadID=115;_ThreadName=Thread-11;_TimeMillis=1631833651843;_LevelValue=800;_MessageID=NCLS-JMX-00005;|
JMXStartupService has started JMXConnector on JMXService URL service:jmx:rmi://0.0.0.0:8686/jndi/rmi://0.0.0.0:8686/jmxrmi|#]

[#|2021-09-17T00:07:32.161+0100|INFO|Payara 5.2020|javax.enterprise.system.core|_ThreadID=24;_ThreadName=RunLevelControllerThread-1631833647834;_TimeMillis=1631833652161;_LevelValue=800;_MessageID=NCLS-CORE-00101;|
Network Listener JMS_PROXY_default_JMS_host started in: 1ms - bound to [/0.0.0.0:7676]|#]

[#|2021-09-17T00:07:32.200+0100|INFO|Payara 5.2020|org.jvnet.hk2.osgiadapter|_ThreadID=20;_ThreadName=FelixStartLevel;_TimeMillis=1631833652200;_LevelValue=800;|
Skipping registration of inhabitant for service reference [org.osgi.service.metatype.MetaTypeProvider] as the service object could not be obtained.|#]"

James Myers

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Sep 16, 2021, 10:21:31 PM9/16/21

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One thing I see is that the log shows payara 5.2020.2 running, not 5.2021.5. I'm not sure if that's the only issue - the log is hard to read on a phone.

-- Jim

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Adilia Alves

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Sep 17, 2021, 5:47:24 PM9/17/21

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Thank you Jim Myers.You are correct. Unfortunately, the problem persists with payara 5.2021.5.

Here is the log when I start the domain.

/usr/lib/jvm/java-11-openjdk-11.0.12.0.7-0.el7_9.x86_64/bin/java
-cp
/usr/local/payara5/glassfish/modules/glassfish.jar
-XX:+UnlockDiagnosticVMOptions
--add-opens=java.base/java.net=ALL-UNNAMED
--add-opens=java.base/sun.net.www.protocol.jrt=ALL-UNNAMED
--add-opens=java.management/sun.management=ALL-UNNAMED
--add-exports=java.base/jdk.internal.ref=ALL-UNNAMED
--add-opens=java.naming/javax.naming.spi=ALL-UNNAMED
--add-opens=jdk.management/com.sun.management.internal=ALL-UNNAMED
--add-opens=java.base/java.nio=ALL-UNNAMED
--add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED
--add-opens=java.base/java.lang=ALL-UNNAMED
--add-opens=java.logging/java.util.logging=ALL-UNNAMED
--add-opens=java.base/sun.net.www.protocol.jar=ALL-UNNAMED
--add-opens=java.base/jdk.internal.loader=ALL-UNNAMED
--add-opens=java.base/java.util=ALL-UNNAMED
--add-opens=java.base/sun.nio.ch=ALL-UNNAMED
-XX:NewRatio=2
-Xbootclasspath/a:/usr/local/payara5/glassfish/lib/grizzly-npn-api.jar
-Xmx512m
-server
-javaagent:/usr/local/payara5/glassfish/lib/monitor/flashlight-agent.jar
-Djavax.xml.accessExternalSchema=all
-Djavax.net.ssl.trustStore=/usr/local/payara5/glassfish/domains/domain1/config/cacerts.jks
-Djdk.tls.rejectClientInitiatedRenegotiation=true
-Djdk.corba.allowOutputStreamSubclass=true
-Dfelix.fileinstall.dir=/usr/local/payara5/glassfish/modules/autostart/
-Dorg.glassfish.additionalOSGiBundlesToStart=org.apache.felix.shell,org.apache.f elix.gogo.runtime,org.apache.felix.gogo.shell,org.apache.felix.gogo.command,org.

apache.felix.shell.remote,org.apache.felix.fileinstall
-Dcom.sun.aas.installRoot=/usr/local/payara5/glassfish
-Dfelix.fileinstall.poll=5000
-Djava.security.policy=/usr/local/payara5/glassfish/domains/domain1/config/server.policy
-Dosgi.shell.telnet.maxconn=1
-Dfelix.fileinstall.bundles.startTransient=true
-Dcom.sun.enterprise.config.config_environment_factory_class=com.sun.enterprise.

config.serverbeans.AppserverConfigEnvironmentFactory
-Dfelix.fileinstall.log.level=2
-Djavax.net.ssl.keyStore=/usr/local/payara5/glassfish/domains/domain1/config/keystore.jks
-Djava.security.auth.login.config=/usr/local/payara5/glassfish/domains/domain1/config/login.conf
-Dfelix.fileinstall.disableConfigSave=false
-Dorg.glassfish.grizzly.DEFAULT_MEMORY_MANAGER=org.glassfish.grizzly.memory.HeapMemoryManager
-Dfelix.fileinstall.bundles.new.start=true
-Dcom.sun.aas.instanceRoot=/usr/local/payara5/glassfish/domains/domain1
-Dosgi.shell.telnet.port=6666
-Dgosh.args=--nointeractive
-Dcom.sun.enterprise.security.httpsOutboundKeyAlias=s1as
-Dorg.jboss.weld.serialization.beanIdentifierIndexOptimization=false
-Dosgi.shell.telnet.ip=127.0.0.1
-Djdk.attach.allowAttachSelf=true
-DANTLR_USE_DIRECT_CLASS_LOADING=true
-Djava.awt.headless=true
-Dcom.ctc.wstx.returnNullForDefaultNamespace=true
-Djdbc.drivers=org.h2.Driver
-Dorg.glassfish.grizzly.nio.DefaultSelectorHandler.force-selector-spin-detection=true
-Djava.library.path=/usr/local/payara5/glassfish/lib:/usr/java/packages/lib:/usr/lib64:/lib64:/lib:/usr/lib
com.sun.enterprise.glassfish.bootstrap.ASMain
-upgrade
false
-domaindir
/usr/local/payara5/glassfish/domains/domain1
-read-stdin
true
-asadmin-args
--host,,,localhost,,,--port,,,4848,,,--secure=false,,,--terse=false,,,--extraterse=false,,,--echo=false,,,--interactive=true,,,--autoname=false,,,start-domain,,

,--verbose=true,,,--watchdog=false,,,--debug=false,,,--domaindir,,,/usr/local/payara5/glassfish/domains,,,domain1
-domainname
domain1
-instancename
server
-type
DAS
-verbose
true
-asadmin-classpath
/usr/local/payara5/glassfish/lib/client/appserver-cli.jar
-debug
false
-asadmin-classname
com.sun.enterprise.admin.cli.AdminMain
-watchdog
false

Launching Payara Server on Felix platform

Sep 17, 2021 10:27:54 PM com.sun.enterprise.glassfish.bootstrap.osgi.BundleProvisioner createBundleProvisioner

INFO: Create bundle provisioner class = class com.sun.enterprise.glassfish.bootstrap.osgi.BundleProvisioner.

Registered com.sun.enterprise.glassfish.bootstrap.osgi.EmbeddedOSGiGlassFishRuntime@15a7cc in service registry.

#!## LogManagerService.postConstruct : rootFolder=/usr/local/payara5/glassfish
#!## LogManagerService.postConstruct : templateDir=/usr/local/payara5/glassfish/lib/templates
#!## LogManagerService.postConstruct : src=/usr/local/payara5/glassfish/lib/templates/logging.properties
#!## LogManagerService.postConstruct : dest=/usr/local/payara5/glassfish/domains/domain1/config/logging.properties

Server log file is using Formatter class: com.sun.enterprise.server.logging.ODLLogFormatter|#]

Registered fish.payara.ha.hazelcast.store.HazelcastBackingStoreFactoryProxy for persistence-type = hazelcast in BackingStoreFactoryRegistry|#]

Hazelcast Instance Bound to JNDI at payara/Hazelcast|#]

JSR107 Caching Provider Bound to JNDI at payara/CachingProvider|#]

JSR107 Default Cache Manager Bound to JNDI at payara/CacheManager|#]

Network Listener admin-listener started in: 4ms - bound to [/0.0.0.0:4848]|#]

[#|2021-09-17T22:28:00.508+0100|INFO|Payara 5.2021.5|javax.enterprise.system.core|_ThreadID=25;_ThreadName=RunLevelControllerThread-1631914076588;_TimeMillis=16               31914080508;_LevelValue=800;_MessageID=NCLS-CORE-00087;|
Grizzly 2.4.4 started in: 3,185ms - bound to [http-listener-1:8080, http-listener-2:8181, admin-listener:4848]|#]

[#|2021-09-17T22:28:00.620+0100|INFO|Payara 5.2021.5|javax.enterprise.system.core|_ThreadID=22;_ThreadName=RunLevelControllerThread-1631914076574;_TimeMillis=16              31914080620;_LevelValue=800;_MessageID=NCLS-CORE-00101;|
Network Listener iiop-service started in: 2ms - bound to [/0.0.0.0:3700]|#]

[#|2021-09-17T22:28:00.899+0100|INFO|Payara 5.2021.5|javax.enterprise.system.core|_ThreadID=1;_ThreadName=main;_TimeMillis=1631914080899;_LevelValue=800;_Messag               eID=NCLS-CORE-00017;|
Payara Server 5.2021.5 #badassfish (770) startup time : Felix (4,696ms), startup services(4,331ms), total(9,027ms)|#]

[#|2021-09-17T22:28:00.914+0100|INFO|Payara 5.2021.5|fish.payara.nucleus.cluster.PayaraCluster|_ThreadID=79;_ThreadName=Executor-Service-8;_TimeMillis=163191408                  0914;_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: f1de5161-d517-483b-a6e6-aefa780dc139 Address: /193.136.195.131:4900
}|#]

[#|2021-09-17T22:28:00.920+0100|INFO|Payara 5.2021.5|fish.payara.nucleus.notification.NotificationService|_ThreadID=1;_ThreadName=main;_TimeMillis=1631914080920             ;_LevelValue=800;|
Payara Notification Service bootstrapped.|#]

[#|2021-09-17T22:28:00.950+0100|INFO|Payara 5.2021.5|monitoring-console-core|_ThreadID=1;_ThreadName=main;_TimeMillis=1631914080950;_LevelValue=800;|

Bootstrapping Monitoring Console Runtime|#]

Starting monitoring data collection for server|#]

JMXStartupService has started JMXConnector on JMXService URL service:jmx:rmi://0.0.0.0:8686/jndi/rmi://0.0.0.0:8686/jmxrmi|#]

Skipping registration of inhabitant for service reference [org.osgi.service.metatype.MetaTypeProvider] as the service object could not be obtained.|#]

James Myers

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Sep 17, 2021, 5:58:22 PM9/17/21

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Hmm – now that I’m at a computer - in your log, I don’t see any jvm options related to Dataverse which would suggest you aren’t running the domain you’ve configured for Dataverse. I’m not sure why that is, but the release notes and guides describe what you need to do for a fresh install or when updating from a prior Dataverse version. (If you’re updating from an earlier Dataverse version, you need to run all the steps for all intermediate versions.).

Hope that helps,

-- Jim

To view this discussion on the web visit https://groups.google.com/d/msgid/dataverse-community/32522f00-2220-4ccc-9c0f-56904c33ec42n%40googlegroups.com.

Adilia Alves

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Sep 23, 2021, 5:05:30 AM9/23/21

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Thank you Jim for your precious help.

I completely removed pgsql and installed postgresql 13 version. Dataverse 5.3 is working.

Acharya Srinivas

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Dec 26, 2021, 1:52:43 PM12/26/21

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Hi I am getting same kind of issue here . while install dvinstall

Remote server does not listen for requests on [localhost:4848]. Is the server up?
Unable to get remote commands.
Closest matching local command(s):
help

Failed to deploy the application! WAR file: dataverse.war.
(exit code: 256)
Aborting.

=================================================================== LOG

Skipping registration of inhabitant for service reference [org.osgi.service.metatype.MetaTypeProvider] as the service object could not be obtained.|#]

when I am trying to start domain , getting below , please help

./asadmin start-domain

===============

openjdk version "11.0.13" 2021-10-19 LTS
OpenJDK Runtime Environment 18.9 (build 11.0.13+8-LTS)
OpenJDK 64-Bit Server VM 18.9 (build 11.0.13+8-LTS, mixed mode, sharing)
dException in thread "main" com.sun.jna.LastErrorException: [5] Input/output error
at com.sun.jna.Native.invokeVoid(Native Method)
at com.sun.jna.Function.invoke(Function.java:414)
at com.sun.jna.Function.invoke(Function.java:360)
at com.sun.jna.Library$Handler.invoke(Library.java:244)
at com.sun.proxy.$Proxy12.tcgetattr(Unknown Source)
at org.jline.terminal.impl.jna.linux.LinuxNativePty.doSetAttr(LinuxNativePty.java:84)
at org.jline.terminal.impl.AbstractPty.setAttr(AbstractPty.java:29)
at org.jline.terminal.impl.AbstractPosixTerminal.close(AbstractPosixTerminal.java:76)
at org.jline.terminal.impl.PosixSysTerminal.close(PosixSysTerminal.java:95)
at com.sun.enterprise.admin.cli.CLICommand.closeTerminal(CLICommand.java:1466)
at com.sun.enterprise.admin.cli.LoginCommand.getAdminUser(LoginCommand.java:143)
at com.sun.enterprise.admin.cli.LoginCommand.executeCommand(LoginCommand.java:79)
at com.sun.enterprise.admin.cli.CLICommand.execute(CLICommand.java:340)
at com.sun.enterprise.admin.cli.AdminMain.executeCommand(AdminMain.java:360)
at com.sun.enterprise.admin.cli.AdminMain.doMain(AdminMain.java:294)
at org.glassfish.admin.cli.AsadminMain.main(AsadminMain.java:56)
ption -Ddataverse.files.file.type=file already exists in the configuration.

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