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Glassfish setup issues

 
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Apologies if this should be in the beginners section - I wasn't entirely sure.

I am trying to learn my way around EE/Glassfish for the purposes of GUI development. I started with the my first cup because the trail has always seen me right in SE.

Unfortunately, I have come to the part where it asks me to Right-click the GlassFish Server instance and select View Update Center to display the Update Tool. and when I go to do this I seen an option View Domain Update Centre. When I first ran this it made a big fuss and installed a lot of stuff which sounded a lot like it was going rather well. However, when I come to rerun it I am finding that it, apparently, does nothing. I see nothing pop up anywhere to indicate any activity.

I have googled this a bit but I am so new to this I am not really sure what I am looking for. I tried running the server and accessing via 4848 and I got a few error messages (or what I assume to be error messages). The problem is that these appear in the netbeans window and I was in the browser so I am not entirely sure which actions triggered which messages. I also get a popup telling me that a long running process has been identified but this just seems to hang and another to tell me that Java DB is not set up correctly. I have posted the stack underneath in case it makes more sense to someone here than it does to me (it can't make less!)

Sorry if this is vague - I'm having difficultly disentangling all of these issues If you let me know what might be pertinent information or how better to structure my question I will endeavour to provide/do so.

Thanks,

Phil

Edit: Fixed the JavaDB issue using this. One less popup, same issue though.

Glassfish messages:

INFO: Running GlassFish Version: GlassFish Server Open Source Edition 3.1.2.2 (build 5)
INFO: Registered org.glassfish.ha.store.adapter.cache.ShoalBackingStoreProxy for persistence-type = replicated in BackingStoreFactoryRegistry
INFO: Grizzly Framework 1.9.50 started in: 47ms - bound to [0.0.0.0:7676]
INFO: Grizzly Framework 1.9.50 started in: 107ms - bound to [0.0.0.0:8181]
INFO: Grizzly Framework 1.9.50 started in: 50ms - bound to [0.0.0.0:3700]
INFO: Grizzly Framework 1.9.50 started in: 98ms - bound to [0.0.0.0:4848]
INFO: Grizzly Framework 1.9.50 started in: 142ms - bound to [0.0.0.0:8080]
INFO: GlassFish Server Open Source Edition 3.1.2.2 (5) startup time : Felix (6,556ms), startup services(868ms), total(7,424ms)
INFO: HV000001: Hibernate Validator 4.3.0.Final
INFO: JMX005: JMXStartupService had Started JMXConnector on JMXService URL service:jmx:rmi://Linux1:8686/jndi/rmi://Linux1:8686/jmxrmi
INFO: Grizzly Framework 1.9.50 started in: 20ms - bound to [0.0.0.0:8080]
INFO: unable to read instance state file /home/phil/GlassFish_Server/glassfish/domains/domain1/config/.instancestate, recreating
INFO: Grizzly Framework 1.9.50 started in: 1ms - bound to [0.0.0.0:8181]
INFO: Domain Pinged: stable.glassfish.org
INFO: Grizzly Framework 1.9.50 started in: 1ms - bound to [0.0.0.0:8080]
INFO: Grizzly Framework 1.9.50 started in: 1ms - bound to [0.0.0.0:8181]
INFO: The Admin Console is installing...
INFO: The Admin Console is already installed, but not yet loaded.
INFO: The Admin Console is starting. Please wait.
INFO: Created EjbThreadPoolExecutor with thread-core-pool-size 16 thread-max-pool-size 32 thread-keep-alive-seconds 60 thread-queue-capacity 2147483647 allow-core-thread-timeout false
INFO: WEB0169: Created HTTP listener [http-listener-1] on host/port [0.0.0.0:8080]
INFO: WEB0169: Created HTTP listener [http-listener-2] on host/port [0.0.0.0:8181]
INFO: WEB0169: Created HTTP listener [admin-listener] on host/port [0.0.0.0:4848]
INFO: WEB0171: Created virtual server [server]
INFO: WEB0171: Created virtual server [__asadmin]
INFO: WEB0172: Virtual server [server] loaded default web module []
INFO: Initiating Jersey application, version 'Jersey: 1.11.1 03/31/2012 06:49 PM'
INFO: SEC1002: Security Manager is OFF.
INFO: SEC1010: Entering Security Startup Service
INFO: SEC1143: Loading policy provider com.sun.enterprise.security.provider.PolicyWrapper.
INFO: SEC1115: Realm [admin-realm] of classtype [com.sun.enterprise.security.auth.realm.file.FileRealm] successfully created.
INFO: SEC1115: Realm [file] of classtype [com.sun.enterprise.security.auth.realm.file.FileRealm] successfully created.
INFO: SEC1115: Realm [certificate] of classtype [com.sun.enterprise.security.auth.realm.certificate.CertificateRealm] successfully created.
INFO: SEC1011: Security Service(s) Started Successfully
INFO: REST00001: Listening to REST requests at context: /management/domain
INFO: Initializing Mojarra 2.1.6 (SNAPSHOT 20111206) for context ''
INFO: WEB0671: Loading application [__admingui] at [/]
INFO: CORE10010: Loading application __admingui done in 4,534 ms
INFO: The Admin Console application is loaded.
WARNING: PWC4011: Unable to set request character encoding to UTF-8 from context , because request parameters have already been read, or ServletRequest.getReader() has already been called
INFO: Redirecting to /
INFO: Admin Console: Initializing Session Attributes...
WARNING: Prefs file removed in background /home/phil/.java/.userPrefs/glassfish/layout/prefs.xml
process 16136: Array or variant type requires that type struct be written, but object_path was written.
The overall signature expected here was 'l' and we are on byte 26 of that signature.
type unknown not a basic type
type unknown not a basic type
type unknown not a basic type
type unknown not a basic type
type unknown not a basic type
type unknown not a basic type
*** glibc detected *** /home/phil/Java/jdk1.7.0_07/bin/java: invalid fastbin entry (free): 0x843445f0 ***
*** glibc detected *** /home/phil/Java/jdk1.7.0_07/bin/java: malloc(): memory corruption (fast): 0x84301287 ***
 
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