A high density storage enclosure houses first and second pluralities of hard disk drives (HDDs). The enclosure may be partitioned into a plurality of virtual enclosures, the first plurality of HDDs being associated with a first virtual enclosure and the second plurality of HDDs being associated with a second virtual enclosure. Configuration of the storage enclosure is performed by an SES processor in the storage enclosure accessing configuration parameters received from an external configuration unit coupled to the storage enclosure. The virtual enclosures may be configured as two (or more) independent virtual enclosures on two (or more) independent fabrics or may be configured in a trunked manner. Power supplies and cooling blowers in the storage enclosure may also be partitioned and assigned to be managed by SES processors in the virtual enclosures.