I've used the directions here to successfully install Glassfish 3.0.1 on an virtualized (VirtualBox and VMWare) Ubuntu 10.10 Server instance without any real difficulty not resolved by more closely following the directions. However when I try applying them to Glassfish 3.1, I seem to keep getting stuck at section 6. "Security configuration before first startup". In particular, there are some differences I noted:

1) There are two keys in the default keystore. The 's1as' key is still there, but another named 'glassfish-instance' is also there. When I saw this, I deleted and recreated them both along with a 'myAlias' key which I was going to use where needed.

2) When turning the security on it seems like part of the server thinks it's on, but others don't. For instances:

$ /home/glassfish/bin/asadmin set server-config.network-config.protocols.protocol.admin-listener.security-enabled=true
server-config.network-config.protocols.protocol.admin-listener.security-enabled=true
Command set executed successfully.

$ /home/glassfish/bin/asadmin get server-config.network-config.protocols.protocol.admin-listener.security-enabled
server-config.network-config.protocols.protocol.admin-listener.security-enabled=true
Command get executed successfully.

$ /home/glassfish/bin/asadmin --secure list-jvm-options
It appears that server [localhost:4848] does not accept secure connections. Retry with --secure=false.
javax.net.ssl.SSLHandshakeException: Remote host closed connection during handshake
Command list-jvm-options failed.

$ /home/glassfish/bin/asadmin --secure=false list-jvm-options
-XX:MaxPermSize=192m
-client
-Djavax.management.builder.initial=com.sun.enterprise.v3.admin.AppServerMBeanServerBuilder
-XX: UnlockDiagnosticVMOptions
-Djava.endorsed.dirs=${com.sun.aas.installRoot}/modules/endorsed${path.separator}${com.sun.aas.installRoot}/lib/endorsed
-Djava.security.policy=${com.sun.aas.instanceRoot}/config/server.policy
-Djava.security.auth.login.config=${com.sun.aas.instanceRoot}/config/login.conf
-Dcom.sun.enterprise.security.httpsOutboundKeyAlias=s1as
-Xmx512m
-Djavax.net.ssl.keyStore=${com.sun.aas.instanceRoot}/config/keystore.jks
-Djavax.net.ssl.trustStore=${com.sun.aas.instanceRoot}/config/cacerts.jks
-Djava.ext.dirs=${com.sun.aas.javaRoot}/lib/ext${path.separator}${com.sun.aas.javaRoot}/jre/lib/ext${path.separator}${com.sun.aas.in
stanceRoot}/lib/ext
-Djdbc.drivers=org.apache.derby.jdbc.ClientDriver
-DANTLR_USE_DIRECT_CLASS_LOADING=true
-Dcom.sun.enterprise.config.config_environment_factory_class=com.sun.enterprise.config.serverbeans.AppserverConfigEnvironmentFactory
-Dorg.glassfish.additionalOSGiBundlesToStart=org.apache.felix.shell,org.apache.felix.gogo.runtime,org.apache.felix.gogo.shell,org.apache.felix.gogo.command
-Dosgi.shell.telnet.port=6666
-Dosgi.shell.telnet.maxconn=1
-Dosgi.shell.telnet.ip=127.0.0.1
-Dgosh.args=--nointeractive
-Dfelix.fileinstall.dir=${com.sun.aas.installRoot}/modules/autostart/
-Dfelix.fileinstall.poll=5000
-Dfelix.fileinstall.log.level=2
-Dfelix.fileinstall.bundles.new.start=true
-Dfelix.fileinstall.bundles.startTransient=true
-Dfelix.fileinstall.disableConfigSave=false
-XX:NewRatio=2
Command list-jvm-options executed successfully.

Also the admin console responds only to http (not https) requests. Thoughts?