Hi Team,
Did you use hdfs dfsadmin -report command to check the dfs and non-dfs used, dfs is used by HDFS so i blieve 9TB is complete storage with dfs and nondfs. Now when you copying the file to hdfs have you enable the debug
HADOOP_ROOT_LOGGER=DEBUG,console
Also try to run the below command it will copy the file from local to hdfs
hdfs dfs -Ddfs.replication=#noofdatanodes -put /tmp/<3mbfile> /tmp