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It is because when we turn on Phoenix in HBase, HBase will add some additional properties (e.g. org.apache.hadoop.hbase.ipc.controller.ServerRpcControllerFactory) related to Phoenix in the hbase-site.xml. Users suppose to add these new dependencies in their pom.xml file, otherwise the hbase connection will fail, even if user does not use Phoenix at all.
In order to avoid this "class not found error", the easiest way is to make sure you turn Phoenix off when connecting HBase from Storm. This solution is still valid in HDP 2.5.