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Why did you created IBM server instance since your application is Remote Application (remote to eclipse), the following step is not needed:
Now in debug perspective, I created a new server with selection/values such as -
IBM--->IBM Websphere v6---->
port - 9081
server profile directory - C:/DEV/WebSphere/AppServer/profiles/default
cell - GCWSNTRANode01Cell
node - GCWSNTRANode01
server - server1
Next---->Added the project to configured project ----->FINISH
after creating remote application, just go and start server1 from web sphere console which will start your application deployed in server1, and in eclipse just debug your application like Run -> Debug ->Remote Java Application -><your application name> -> Debug or else you can just select application from Debug Dropdownlist from debug perspective, this will start in debug mode.
If still face any problems let me know I ll add screen shots.
I did all things as your comment, but my portlet project still not debug.
The remote application is running but when I try set break point and click some button on portlet the application still not go to debug mode.
Can you add screen shot please? Thanks for you advance.