A method and system are provided for partitioning a file system. The system may include one or more server computer systems and a plurality of physical file systems. The physical file systems may be hosted by the one or more server computer systems. The physical file systems may be accessible to clients through a virtual file system having a single namespace. The virtual file system may include metadata which are partitioned across the plurality of physical file systems. The server computer systems may be configured to independently perform file system consistency checks on each of the physical file systems, in order to independently validate each partition of the metadata.