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? The Logical Structure, Organization, ?
? and Management of Hard Disk Drives ?
? ?
? by ?
? Steve Gibson ?
? GIBSON RESEARCH CORPORATION ?
? ?
? Portions of this text originally appeared in Steve's ?
? InfoWorld Magazine TechTalk Column. ?
? ?
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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
head
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
regions.
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
controller.
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
controller.
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
"sectors"
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
disk.
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
chain.
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
belong.
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 **