1) Start Atlas in debug mode
first you want to add extra JVM options in the startup script , so in atlas_start.py replace this line
DEFAULT_JVM_OPTS="-Dlog4j.configuration=atlas-log4j.xml -Djava.net.preferIPv4Stack=true -server"
with this
DEFAULT_JVM_OPTS="-Dlog4j.configuration=atlas-log4j.xml -Djava.net.preferIPv4Stack=true -server -Xdebug -Xnoagent -Xrunjdwp:transport=dt_socket,address=54371,server=y,suspend=y "
Now, when you start Atlas, it will hang until you connect with the debugger (because of the suspend=y).
2) connect from Eclipse remote debugger
Make sure you have imported the Atlas project into Eclipse based on this document: http://atlas.apache.org/EclipseSetup.html
Then create a new debug configurations under the following menu: /Run/Debug Configurations...
Make sure the port is set to the same above (54371) and connection type is Standard (socket attach)
Use Eclipse JDT launcher.