To collect a thread dump for a Controller App Server process, use the Glassfish "asadmin" tool.
<controller_home>/appserver/glassfish/bin/asadmin -u admin --passwordfile=<controller_home>/.passwordfile generate-jvm-report --type=thread > threaddump.txt
mkdir /tmp/threaddumps
cd /tmp/threaddumps
for i in {1..20}; do /opt/AppDynamics/Controller/appserver/glassfish/bin/asadmin -u admin --passwordfile=/opt/AppDynamics/Controller/.passwordfile generate-jvm-report --type=thread > threaddump$i.txt; sleep 60; done
generate-jvm-report
command can generate other types of reports including memory or summary. For more information, view Glassfish documentation.