Logstash output to Elasticsearch on AWS EC2
The problem is that the embedded elasticsearch instance of logstash was using its default discovery mode. Since the elasticsearch cluster is configured with cloud-aws the embedded elasticsearch of logstash needs to as well.
To do that you have to add an elasticsearch.yml configuration file to the working directory of logstash. You also need to supply the cloud-aws plugin by adding it to the class path.
java -cp logstash-1.1.7-monolithic.jar:cloud-aws/* logstash.runner agent -f shipper.confUsing this configuration I managed to get logstash to output to my elasticsearch cluster.