For some data point. In our cluster, we do not automatically split regions and keep our region count low. Therefore, we have StoreFiles that reach in the 10GB range. Obviously, if all the compaction threads were processing a 10GB compaction, the queue would get stopped up. We put the throttle point at 500MB. Since compactions are network-bound. We have 1Gbps network links & are seeing roughly 40MBps speed (3x == 1Gbps), so about 12 sec per compaction max on the small threadpool. Therefore, our use case doesn't directly correspond to the common auto-split use case.
My original thought is to default the throttle to:
min("hbase.hregion.memstore.flush.size" * 2, "hbase.hregion.max.filesize" / 2)
Note that the default split/flush ratio is 4, so this number should be in the middle. Since most users do compression, the actual flush size should be ~20% of the MemStore size (so flushSize*2 is really more like flushSize*10). I will submit a patch with this default. Please feel free to chime in with your experience using it and we'll see if we can improve this default.