Steffen's answer is good and works. On the other hand if you just want something quick-and-dirty and just want to replace one or two variables, then you're probably looking to just change it via the command line like the following:
elastic-mapreduce --create \
--bootstrap-action s3://elasticmapreduce/bootstrap-actions/configure-hadoop \
--args "-m,mapred.child.java.opts=-Xmx999m"
I've seen another documentation, albeit an older one, that simply quotes the entire expression within one quote like the following:
--bootstrap-action "s3://elasticmapreduce/bootstrap-actions/configure-hadoop -m \
mapred.child.java.opts=-Xmx999m" ### I tried this style, it no longer works!
At any rate, this is not easily found in the AWS EMR documentation. I suspect that mapred.child.java.opts is one of the most overridden variables-- I was also looking for an answer when I got a GC error: "java.lang.OutOfMemoryError: GC overhead limit exceeded" and stumbled on this page. The default of 200m is just too small (documentation on defaults).
Good luck!