How do you know how much memory your java application is taking on Linux?

pmap or top is probably the simplest. Just be sure not to confuse virtual memory with physical.

jps |awk "{print $1}" | xargs -L 1 ps -ef -o %mem

ps aux | grep -i

Just search for the pid created by that java process. And then you get to know the memory usage by top or ps -ef/ps -auxx commands.

jvmtop is a command-line tool which provides a live-view at several metrics, including heap.