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The Logical Structure, Organization, and Management of Hard Disk Drives

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        К                                                              К
        К             The Logical Structure, Organization,             К
        К              and Management of Hard Disk Drives              К
        К                                                              К
        К                              by                              К
        К                         Steve Gibson                         К
        К                  GIBSON RESEARCH CORPORATION                 К
        К                                                              К
        К     Portions of this text originally appeared in Steve's     К
        К               InfoWorld Magazine TechTalk Column.            К
        К                                                              К

        As our operating systems and application software have continued
        to grow in size, their memory requirements have increased
        steadily. A vital memory in our system is hard disk storage.

        Bound within the hard disk's structure lie the answers to
        questions like: What is a low level format? What does FDISK do?
        What is a hard disk partition and why does DOS limit us to 32
        megabytes in a partition? What does it mean to have "lost
        cluster chains" or "cross-linked files?" What does it mean to
        have our disks "defragmented?" Let's explore MS-DOS and PC-DOS
        hard disk organization to answer these questions and others.

        The first stage in preparing any hard disk for operation is
        known as low level formatting.  Low level formatting takes any
        hard disk from its virgin "fresh from the factory" state and
        prepares it for operation with a particular hard disk
        controller and computer system.

        Low level formatting divides each circular track into equal size
        SECTORS by placing SECTOR ID HEADERS at uniform positions around
        each track. The start of a sector ID is marked with a special
        magnetic pattern which cannot be generated by normal recorded
        data. This ADDRESS MARK allows the beginning of each sector to
        be uniquely discriminated from all recorded data.

        The sector ID information, which immediately follows the address
        mark contains each sector's Cylinder, Head, and Sector number
        which is completely unique for each sector on the disk. When the
        hard disk controller is late reading or writing to these disk
        sectors, it compares the sector's pre-recorded cylinder number
        to make sure that the heads haven't "mis-stepped" and that
        they're flying over the proper cylinder.  It then compares the
        number to verify that unreliable cabling is not causing an
        improper head to be selected and waits for the proper sector to
        start by comparing the pre-recorded sector number as it passes
        by with the sector number for which it is searching.

        Since many hard disk surfaces are not flawless, low level
        formatting programs include a means for entering the hard disk
        drive's defect list. The defect list specifies tracks (by
        cylinder and head number) that the manufacturer's sensitive drive
        certification equipment found to stray from the normal which
        indicates some form of physical flaw that might prevent data from
        being reliably written and read. The list of such defects
        is typically printed and attached to the outside of the drive.

        When these tracks are entered into the low level formatter, the
        defective tracks receive a special code in their sector ID
        headers which indicates that the track has been flagged as bad
        and cannot be used for any data storage. Later, as we shall see,
        high level formatting moves this defective track information
        into the system's File Allocation Table (FAT) to prevent the
        operating system from allocating files within these defective

        When the low level format has been established, we have a
        completely empty drive, devoid of stored information, which can
        accept and retrieve data with the specification of any valid
        cylinder, head, and sector number.

        There's an important issue about the low level formatting of a
        hard disk which is frequently overlooked, but which can be quite
        important to appreciate. Since the hard disk controller works in
        intimate concert with its hard disk drive to transfer the data
        within its numbered sectors to and from the computer's memory,
        the exact details of the address mark, sector ID header, and
        rotational sector timing can be completely arbitrary for any
        controller and drive. Since these details are initially
        established when the drive receives its low level formatting,
        they are forever hence agreed upon by both the hard disk drive
        and the controller. But more importantly, there's absolutely no
        reason to assume that the relatively arbitrary low level
        formatting specifics used by any particular hard disk controller
        would be compatible with any other model of hard disk

        In practice this means that differing makes or models of hard
        disk controllers are completely unable to read, write, or
        interpret the formatted information created by any other make or
        model of controller. Consequently, whenever it is
        necessary or desirable to exchange hard disk controllers, a
        complete backup of the hard disk's data, while attached to the
        initial controller, MUST BE followed by creating a new low level
        format with the new controller on the drive before any of the
        backed-up information can be restored to the drive with the new

        So we've given our drives a low level format, since we see that
        it is this process which first establishes "communication"
        between a hard disk and its controller by creating 512-byte
        where none existed before. Now lets take up the next phase of
        hard disk structuring: The hard disk PARTITION.

        The notion of hard disk (or "fixed disk" as IBM calls them)
        partitions was created to allow a hard disk based computer
        system to contain and "boot up" several completely different
        operating systems. Partitioning divides a single physical hard
        disk into multiple LOGICAL partitions.

        A birthday cake is divided into multiple pieces by slicing it
        radially whereas a hard disk's divisions are circular. For
        example, a drive's first partition might extend from cylinder
        zero through 299 with the second partition beginning on cylinder
        300 and extending through 599. This circular partitioning is far
        more efficient since it minimizes the disk head travel when
        moving within a single partition.

        The partitions on a drive, even if there's only one, are managed
        by a special sector called the PARTITION TABLE which is located
        at the very beginning of every hard disk. It defines the
        starting and ending locations for each of the disk's partitions
        and specifies which of the partitions is to gain control of the
        system during system boot up. When the hard disk drive is booted
        a tiny program at the beginning of the partition table locates
        the partition which is flagged as being the "bootable partition"
        in the table and executes the program located in the first
        sector, the "boot sector," of that partition. This boot sector
        loads the balance of the partition's operating system then
        transfers control to it.

        Each partition on a hard disk is blind to the existence of any
        other.  By universal agreement, the operation of software inside
        a partition is completely contained within the bounds of the
        partition.  Adherence to this agreement prevents multiple
        operating systems from colliding and allows strange environments
        to cohabitate on a single hard disk.

        The sectors within a partition are numbered sequentially
        starting at zero and extending to the end of the partition. In
        kind with DOS's original belief that 640K of RAM would be more
        than we'd EVER need, there was a time in the not-so-distant past
        when a ten megabyte hard disk was an unheard of luxury and was
        considered huge. How could any single person ever fill up 10
        megabytes? No way.

        Consequently DOS was designed to access sectors within its hard
        disk partition with a single sixteen-bit quantity. One "word"
        was set aside for the specification of partition sectors. As
        many of you know, a single sixteen-bit binary word can represent
        values from 0 through 65,535. So this limited a partition's
        total sector count to 65,536. Since hard disk sectors are 512
        bytes long, a partition could contain 33,554,432 bytes. When you
        remember that binary megabytes are really 1,048,576 bytes each,
        that's exactly 32 megabytes.

        This is the origin of DOS's infamous 32 megabyte barrier. Today
        of course we have affordable drives with capacities well
        exceeding DOS's 32 megabyte limit. The industry has invented
        three solutions to this partition size dilemma.

        The first solution invented to the partition size problem
        utilizes DOS's inherent extendibility with external device
        drivers. Programs such as OnTrack's DISK MANAGER, Storage
        Dimensions' SPEEDSTOR, and Golden Bow's VFEATURE DELUXE utilize a
        clever trick to circumvent the 32 megabyte DOS limit: They trick
        DOS into believing that sectors are larger than 512 bytes! By
        interposing themselves between DOS and the hard disk, these
        partitioning device drivers lead DOS to believe that individual
        sectors are much larger than they really are. Then when DOS asks
        for one "logical" 4k-byte sector they hand DOS eight 512-byte
        physical sectors. This transforms the 65,536 sector count limit
        into a single partition containing more than 268 megabytes!

        The second solution was introduced by IBM's PC-DOS 3.3 operating
        system with its ability to allow DOS to have simultaneous access
        to multiple logical partitions on a single drive. With DOS 3.3,
        the standard FDISK command can establish any number of 32-
        megabyte or smaller partitions on a drive. While this doesn't
        create a single unified huge partition, it also doesn't require
        any external resident device drivers.

        The final solution has recently been introduced by Compaq
        Computer with their introduction of DOS 3.31. Being big enough
        to get away with sacrificing some software compatiblity, Compaq
        has redefined the way DOS numbers its partition sectors thereby
        removing the limitation at its source.

        So now our hard disks have a low level format, with 
        "addressability" to the disk's individual physical sectors 
        established.  We have also defined and established partitions on 
        our drive, which gives DOS a sub-range of the hard disk within 
        which to build its filing system. Now let's examine the 
        structure of MS-/PC-DOS filing systems. The following discussion 
        also applies to DOS diskettes which aren't partitioned but 
        otherwise have an identical structure. 

        Let's begin by looking at the problem that DOS's filing system
        solves: Its task is to allow us, through the vehicle of DOS
        application programs, to create named collections of bytes of
        data, called files, and to help with their management by
        providing directories of these named files.

        The directory entry for any DOS file contains the file's name
        and extension, the date and time when the file was last written
        and closed, an assortment of Yes/No "attributes" which indicate
        whether the file has been modified since last backup, whether it
        can be written to, whether it's even visible in the directory,
        etc. The directory entry for the file also contains the address
        of the start of the file.

        We already know that hard disks are divided into numbered
        sectors 512 bytes in length. Since most of the files DOS manages
        are much larger than a single sector, disk space is allocated in
        "clumps" of sectors called clusters. Various versions of DOS
        utilize clusters of 4, 8 or 16 sectors each, or 2048, 4096, or
        8192 bytes in length.

        When a hard disk is completely empty, its clusters of sectors
        are all available for storing file data. As files are created
        and deleted on the hard disk, a bookkeeping system is needed
        which keeps track of which clusters are in use by which existing
        files, and which clusters are still available for allocation to
        new or growing files. This is the vital role played by the File
        Allocation Table. The "FAT," as it's frequently called, is the
        table DOS uses to manage the allocation of space on the hard

        As we know, the hard disk is arranged as a long stream of
        sectors.  After being clumped together into clusters, it can be
        viewed as a long stream of clusters. Now picture a table
        consisting of a
        long stream of entries, with one entry in the table for each
        cluster on the disk. The first FAT table entry corresponds to
        the first hard disk cluster, and the last FAT entry corresponds
        to the last hard disk cluster.

        Now imagine that DOS needs to create a new text or spreadsheet
        file for us. It must first find a free cluster on the hard disk,
        so it searches through the File Allocation Table looking for an
        empty FAT table entry, which corresponds to an empty hard disk
        cluster. When DOS finds the empty table entry it memorizes its
        number, then places a special "end of chain" marker in the FAT
        entry to show that this cluster has been allocated and is no
        longer free for use. DOS then goes out to the sectors which
        comprise this cluster and writes the file's new data there.

        This is all great until the file grows longer than a single
        cluster of sectors. DOS now needs to allocate a second cluster
        for this file. So it once again searches through the File
        Allocation Table for a free cluster. When found, it again places
        the special "end of chain" marker in this cluster and memorizes
        its number.

        Now things begin to get interesting... and just a little bit
        tricky. Since files might be really long, consisting of
        thousands of individually allocated clusters, there's no way for
        DOS to memorize all of the clusters used by each file. So DOS
        uses each File Allocation Table entry to store the number of the
        file's next cluster!

        Following along with our example, after finding and allocating
        the second cluster for the growing file, DOS goes back to the
        first cluster's FAT entry where it had placed that first "end of
        chain" marker and replaces it with the number of the file's
        second cluster. If a third cluster were then needed, its FAT
        entry would be marked "not available" by placing the special
        "end of chain" marker in it, then this third cluster number
        would be placed into the second cluster's FAT entry. Get it?

        This creates a "chain" of clusters with each cluster entry
        pointing to the next one, and the last one containing a special
        "end of chain" entry which signals that the end of the file's
        allocation chain has been reached.

        Finally, when the file is "closed," an entry is created in a DOS
        directory which names the file and contains the number of the
        file's first cluster. Then, using that first cluster's FAT
        entry, the entire allocation "chain" can  be "traversed" to find
        the clusters which contain the file's data.

        So now let's do a bit of review....

        The allocation of file space within a DOS partition is recorded
        and maintained within DOS's File Allocation Tables (FATs). The
        FATs make up a map of the utilization of space on any floppy or
        hard disk with one entry in the FAT for each allocatable cluster
        of sectors. Each entry in the FAT can indicate one of four
        possible conditions for the clusters of sectors it represents:
        It can be unused and available for allocation, unused and marked
        as bad to prevent its use, in use and pointing to the next
        cluster of the file, or in use as the last cluster of a file.

        If each entry in the FAT points to the next, who points to the
        first entry? This is the role of the file's directory entry. It
        contains the name of the file, the file's exact length, the time
        and date of the file's last modification, file attribute flags,
        and the identity of file's first cluster. In a sense, a file's
        directory entry forms the head of the file's allocation chain
        with each link thereafter pointing to the next link in the

        This system, while quite workable and efficient, does have its
        dangers. These dangers center around the fact that the FAT
        contains the ONLY record of disk space utilization and a
        stubborn failure to correctly read a single sector of the FAT
        could render hundreds of files unrecoverable. This danger
        explains the popularity of several utility programs which create
        a back-up copy of the File Allocation Table and Root Directory
        with each system boot-up. They provide some hope of recovery
        from the cataclysmic loss of the FAT's data.

        The original designers of DOS were aware of the importance of
        the FAT and do provide a duplicate copy immediately following
        the first, but its physical proximity to the original renders it
        little better than none, and DOS has long been notorious for
        failing to intelligently utilize this extra copy of FAT
        information even in the event of a primary FAT failure. (DOS 3.3
        seems to be much smarter in this regard.)

        Important as FAT reliability is, it's not generally the prime
        source of DOS file corruption, since even with perfect data
        retrieval, it's still possible to scramble DOS's files like
        crazy. The primary cause of DOS file system troubles are user
        error, program bugs, and "glitches." The advent of TSR "rule
        breaking" resident multitasking-style software has further
        complicated the scene.

        When a new file is created or "opened," information about it is
        maintained inside DOS. The file's name, status, and first
        cluster are all held in internal tables. Then, as the file
        grows, free clusters are "checked out" of the File Allocation
        Table and allocated to the file's chain of clusters.

        Now here's the crucial fact which causes so much trouble: No
        matter how big the newly created file becomes, a directory entry
        for the file is ONLY created when the file is finally and
        properly CLOSED. Until then the file exists only as a chain of
        allocated clusters filled with the file's data. If anything
        occurs to prevent the error-free closing of this file we have a
        real problem because the file's data is occupying a chain of
        "checked out" disk clusters, but there is no anchoring directory
        entry to point to the first cluster in the chain!

        A chain of clusters without an anchoring directory entry is
        called a "lost chain." It exists, it contains data, but there's
        no record of the file's name, exact size, or purpose.

        Lost cluster chains are frequently created when programs abort
        abnormally, when TSR's crash the system suddenly, when the
        computer user forgets to write a TSR's files out to disk before
        shutting the system down, or when a task in a multi-tasking
        system is not terminated. (It's easy to forget that a file was
        left open in a suspended background task.) Additionally, any
        damage to DOS's root directory or subdirectories can "liberate"
        chains of lost clusters.

        DOS provides the CHKDSK (pronounced Check Disk) command to help
        its users keep an eye on just these sorts of problems. CHKDSK
        provides a comprehensive verification of DOS's filing system
        integrity and provides a means for straightening things out.
        When the CHKDSK command is given, the parentage of all cluster
        chains is checked, allocation chains are "followed" to be sure
        they don't cross over other chains (creating cross-linked
        files), and several other system integrity checks are performed.

        In the case of lost chains, CHKDSK will offer to convert these
        into files by anchoring them to the root directory. Then any
        suitable text editor can be used to open these new files for the
        sake of identifying them and moving them back to where they

        Unfortunately the structure of DOS filing systems lacks the
        fundamental redundancy required to provide simple and error-free
        recovery from many forms of damage. Even the tools and
        techniques available from third party suppliers can't surmount
        these problems. The best bet is to understand DOS's weak spots,
        make certain that all opened files are closed successfully,
        perform a weekly CHKDSK command to collect accumulating file
        fragment "debris" and back up your hard disks regularly.

        "Disk Optimizers" which promise to increase the throughput and
        performance of old and well used hard disk drives number among
        the most popular of the general use hard disk utilities.

        We've seen how DOS's file allocation system operates. Files are
        composed of clusters which in turn are composed of sectors. And
        while the group of sectors which comprise a cluster are by
        definition contiguous, the cluster linking scheme which DOS
        employs allows a file's clusters to be scattered across the
        disk's surface. Since the file's directory entry specifies the
        file's first cluster, and each succeeding cluster entry in the
        file allocation table specifies the next one, the file's
        contents could be literally anywhere on the disk. The term "file
        fragmentation" refers to the condition where a file's clusters
        are not consecutively numbered. Let's first examine how a disk's
        files might become fragmented.

        When a file is deleted from a disk, its directory entry is
        flagged as unused and each cluster which the file occupied is
        flagged in the system's FAT as being free for use. If the
        surrounding clusters are still in use by other files, this
        creates a "hole" of free space in the disk.

        Now suppose that a new file is copied from a floppy disk onto
        the hard disk. As DOS reads the new file's data from the floppy,
        it must allocate space for this file on the hard disk. So each
        time another cluster of sectors is needed, DOS searches through
        the file allocation table to find the next available cluster. In
        our example, DOS would discover the clusters which had been
        freed by the first file we deleted and allocate them for use by
        the new file. Then, when all of the clusters in the free space
        hole had been used, DOS would be forced to continue its search
        deeper into the drive. When space was found further in, the
        file's contents would be partially stored near the beginning of
        the disk and partially nearer to the end. The file would then
        consist of at least two fragments.

        During the normal course of daily computer usage, many files are
        being constantly created, copied, extended, deleted, and
        replaced. When a wordprocessor creates an automatic backup file,
        the original file is typically renamed to identify it as a
        backup file and a new file is created. Every new file creation
        is an opportunity for fragmentation. The files which are being
        modified most often are most subject to extensive fragmentation
        since any search by DOS for a free file cluster is almost
        guaranteed to produce a new discontinuity. With continued use,
        it's typical for much of the disk's file data to become
        haphazardly scattered across the surface of the disk drive.

        But since DOS's cluster allocation scheme was specifically
        designed to manage such scattering, what's the problem? Any time
        the drive's head moves, two things occur: Time is consumed, and
        the drive experiences some mechanical wear and tear. If a file's
        data is scattered across the surface of the disk, the drive's
        head is forced to move a large distance many times to read a
        single file. If the file is a database whose records are being
        accessed at random, this excessive head motion can degrade the
        overall system performance tremendously and induce many other
        wear-related disk drive problems.

        The extra time wasted in cluster fragment chasing is directly
        proportional to the drive's average head access time. The prior
        generation of 65 to 80 millisecond stepping motor drives lose
        far more performance to fragmentation than the latest sub-28
        millisecond drives.

        Disk optimizers like SoftLogic Solutions' DISK OPTIMIZER,
        Norton's SPEEDDISK, Central Point's COMPRESS, and Golden Bow's
        VOPT operate by physically rearranging the allocation of files
        on the disk. They relocate file cluster fragments while
        simultaneously updating the system's File Allocation Tables to
        reflect the new cluster locations. When finished, every file on
        the disk consists of a single contiguous run of consecutively
        numbered clusters. Once the disk drive's head has been
        positioned to the beginning of the file, the entire file can be
        read or randomly accessed with an absolute minimum of head
        motion. Besides improving the system's overall performance, file
        defragmentation minimizes the mechanical wear and tear placed
        upon the drive's hardware. If some disaster should befall your
        system's Root Directory or File Allocation Table, contiguous
        files are also much easier to find and recover than files with
        severe fragmentation.

        Since file fragmentation is a continually occurring fact of
        living with DOS, periodic defragmentation, like hard disk
        backup, should become part of every serious DOS user's regimen.

                                   - The End -

                     Copyright (c) 1989 by Steven M. Gibson
                             Laguna Hills, CA 92653
                            **ALL RIGHTS RESERVED **