Are you using X-Pack Monitoring to see what the cluster is doing, and if not, then you should :)

Basically, your cluster is overloaded and you need to find out why and where. And the stats it delivers will be useful.

NEW: Monitor These Apps!
elasticsearch, apache solr, apache hbase, hadoop, redis, casssandra, amazon cloudwatch, mysql, memcached, apache kafka, apache zookeeper, apache storm, ubuntu, centOS, red hat, debian, puppet labs, java, senseiDB