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Hi,
Please make sure the user you are using to run glassfish also owns all the directories including /glassfish4 and below. Also, be aware that running glassfish at anytime as another user, such as root, may create temporary files that may block starting the application as your usual user. Last, try undeploying the application, removing the /usr/local/glassfish4/glassfish/domains/domain1/generated directory, restart glassfish and redeploy the application.
We've received your RT ticket and will continue communicating with you there but since there have been several similar installation issues recently, I thought it would help to post some general tips here.
Regards,
Kevin