During startup, the JT tries to clean up mapred.system.dir by recursively removing it and then recreating it. This requires that mapred.system.dir is inside a directory owned by the mapred user. For example, if set to /system/mapred then /system must be owned by the mapred account. This isn't documented properly and also seems unnecessary. Instead we can remove the contents of mapred.system.dir instead of the directory itself.