You can run major compaction manually by running the following commands:
hbase shell major_compact 'TABLE_NAME'
You can also configure that compaction runs automatically by adding this properties in hbase-site.xml:
hbase.regionserver.compaction.enabled hbase.hregion.majorcompaction hbase.hregion.majorcompaction.jitter hbase.hstore.compactionThreshold
You can find more informations here:
But be careful, do only major compaction if all region are assigend. No Region should be in RIT (Region in Transition). Also major compaction is a heavyweight operation. So you should run it, when the cluster load is low.
You can monitor the compaction in the HBase Master UI.