Execution of Deletes constructed with thousands of calls to Delete.deleteColumn(family, qualifier) are very expensive and slow.
On our (quiet) cluster, a Delete w/ 20k qualifiers took about 13s to complete (as measured by client).
When 10 such Deletes were sent to the cluster via HTable.delete(List<Delete>), one of RegionServers ended up w/ 5 of the requests and became 100% CPU utilized for about 1 hour.
This lead to the client timing out after 20min (2min x 10 retries). In one case, the client was able to fill the RPC callqueue and received the following error:
Based on feedback (http://search-hadoop.com/m/yITsc1WcDWP), I switched to Delete.deleteColumn(family, qual, timestamp) where timestamp came from KeyValue retrieved from scan based on domain objects. This version of the delete ran in about 500ms.
User group thread titled "RS unresponsive after series of deletes" has related logs and stacktraces.
Link to thread: http://search-hadoop.com/m/RmIyr1WcDWP
Here is the stack dump of region server: http://pastebin.com/8y5x4xU7