Disk Storage, Basic File Structures, and Hashing

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Disk Storage, Basic File Structures, and Hashing
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Introduction

• In a computerized database, the data is stored on
  computer storage medium, which includes
• Primary Storage
• can be processed directly by the CPU
• e.g., the main memory, cache
• fast, expensive, but of limited capacity
• Secondary Storage
• cannot be processed directly by the CPU
• magnetic disks, optical disks, tapes
• slow, cost less, but have a large capacity.

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Storage Hierarchy

Volatile
Cache
Primary storage
unit price
Memory
Flash Memory
Secondary storage
Magnetic Disk
speed
Non-volatile
Optical Disk
Tertiary storage
Magnetic Tape
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Storage of Databases

• For the following reasons, most databases are
  stored permanently on secondary storage
• They are too large to fit entirely in main memory
• They must persist over long period of times, but
  the main memory is a volatile storage
• Secondary storage costs less

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Secondary Storage

• Magnetic-disk cannot be directly processed by
  the CPU it must be brought to the main memory
  first.
• Data is stored on spinning disk, and read/written
  magnetically
• Primary medium for the long-term storage of data
  typically stores entire database.
• Non-volatile
• slow access to data
• large storage capacity (on the order of gigabytes)

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Disk Storage Devices

• Preferred secondary storage device for high
  storage capacity and low cost.
• Data stored as magnetized areas on magnetic disk
  surfaces.
• A disk pack contains several magnetic disks
  connected to a rotating spindle.
• Disks are divided into concentric circular tracks
  on each disk surface.
• Track capacities vary typically from 4 to 50
  Kbytes or more

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Disk Storage Devices (contd.)

• A track is divided into smaller blocks or sectors
• because it usually contains a large amount of
  information
• The division of a track into sectors is
  hard-coded on the disk surface and cannot be
  changed.
• One type of sector organization calls a portion
  of a track that subtends (faces) a fixed angle at
  the center as a sector.
• A track is divided into blocks.
• The block size B is fixed for each system.
• Typical block sizes range from B512 bytes to
  B4096 bytes.
• Whole blocks are transferred between disk and
  main memory for processing.

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Disk Storage Devices (contd.)

• A read-write head moves to the track that
  contains the block to be transferred.
• Disk rotation moves the block under the
  read-write head for reading or writing.
• A physical disk block (hardware) address consists
  of
• a cylinder number (imaginary collection of tracks
  of same radius from all recorded surfaces)
• the track number or surface number (within the
  cylinder)
• and block number (within track).
• Reading or writing a disk block is time consuming
  because of the seek time s and rotational delay
  (latency) rd.
• Double buffering can be used to speed up the
  transfer of contiguous disk blocks.

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Physical Characteristics of Disks
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Components of a Disk

• The platters spin (say, 90rps).
• The arm assembly is moved in or out to position a
  head on a desired track.
• Read-write head
• Positioned very close to the platter surface
  (almost touching it)
• Reads or writes magnetically encoded information.
• Only one head reads/writes at any one time.
• Surface of platter divided into circular tracks

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Physical Characteristics of Disks

• Track
• an information storage circle on the surface of a
  disk.
• Over 16,000 tracks per platter
• each track can store between 4KB and 50KB of
  data.
• Each track is divided into sectors.
• Tracks under heads make a cylinder (imaginary!)
• Cylinder
• the tracks with the same diameter on all surfaces
  of a disk pack.
• Cylinder i consists of i-th track of all the
  platters

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Physical Characteristics of Disks

• Sector
• a part of a track with fixed size
• separated by fixed-size interblock gaps
• Typical sectors per track
• 200 (on inner tracks) to 400 (on outer tracks)

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Sectors
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Disk I/O Model of Computation

• Disk I/O is equivalent to one read or write
  operation of a single block
• It is very expensive compared with what is likely
  to be done once the block gets in main memory
• one random disk I/O about 1,000,000 machine
  instructions in terms of time
• Cost for computation that requires secondary
  storage is computed only by disk I/Os.

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Pages and Blocks

• Data files decomposed into pages (blocks)
• fixed size piece of contiguous information in the
  file
• sizes range from 512 bytes to several kilobytes
• block is the smallest unit for transferring data
  between the main memory and the disk.
• Address of a page (block)
• (cylinder, track (within cylinder), sector
  (within track)

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Pages and Blocks
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Page I/O

• Page I/O --- one page I/O is the cost (or time
  needed) to transfer one page of data between the
  memory and the disk.
• The cost of a (random) page I/O
• seek time rotational delay block transfer
  time
• Seek time
• time needed to position read/write head on
  correct track.
• Rotational delay (latency)
• time needed to rotate the beginning of page under
  read/write head.
• Block transfer time
• time needed to transfer data in the page/block.

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Page I/O

• Average rotational delay (rd)
• rd ½ (1/p) min (601000)/(2p) msec
• OR
• rd ½ cost of 1 revolution
• ½ (601000/p) msec
• where
• p is speed of disk rotation (how many revolutions
  per minute - rpm)
• Example
• Speed of disk rotatioon is p 3600 rpm
• 60 revolutions/sec
• 1 rev. 16.66 msec. (1 second 1000 msec)
• rd 8.33 ms

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Page I/O

• Transfer rate (tr)
• tr track size / cost of one revolution
• track size / (601000/p) in msec
• Bulk transfer rate (btr)
• btr (B/(BG)) tr bytes/msec
• Where B is the block size in bytes
• G is interblock gap size in bytes
• Block transfer time (btt)
• btt B / tr not taking into acount G
• btt B / btr taking into acount G

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Page I/O

• Example
• Track size 50 KB and p 3600 rpm
• Block size B 3KB 3000 bytes
• tr (501000)/(601000/3600) 3000 bytes/msec
• btt B / tr 3000/3000 1 msec

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Page I/O

• Average time for reading/writing n consecutive
  pages that are in the same track or cylinder s
  rd n btt
• Average time for reading/writing consecutively n
  noncontigues pages/blocks that are in the same
  cylinder s n (rd btt)

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An Example

• A hard disk specifications
• 4 platters, 8 Surfaces, 3.5 Inch diameter
• 213 8192 tracks/surface
• 28 256 sectors/track
• 29 512 bytes/sector
• Average seek time s 25 ms
• Rotation rate rd 3600 rpm 60 rps
• 1 rev. 16.66 msec
• Transfer rate
• tr 1 KB in 0.117 ms
• tr 1 KB in 0.130 ms with gap

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An Example

• What is the total capacity of this disk
• 8 GB (82132829233)
• How many bytes does one track hold?
• 256 sectors/track512 bytes/sector 128KB
• How many blocks per track?
• one block 4096 bytes 8 sectors (4096/512)
• 256/8 32 blocks/track

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An Example

• How long does it take to access one block?
• One block 4096 bytes
• 8 sectors 4096/512
• Rotation rate r
• 1 rev. 16.66 msec.
• Time to access 1 sector (s r/2
  tr/(secters/KB)
• 25 (16.66/2) .117/2 33.3885 ms.
• time to access 1 block
• time to access the first sector of the block
  time to access the subsequent 7 sectors.

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An Example

• T 25 (16.66/2) (0.117/2) 1 (0.13/2) 7
  
• 33.3885 0.455 ms 33.8435ms
• Compare to one sector access time 33.3885 ms

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Buffering

• A buffer
• is a contiguous reserved area in main memory
  available for storage of copies of disk blocks.
• to speed up the processes.
• For a read command
• the block from disk is copied into the buffer.
• For a write command
• the contents of the buffer are copied into the
  disk.

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Accessing Data Through RAM Buffer
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Buffer Manager

• Programs call on the buffer manager when they
  need a block from disk.
• If the block is already in the buffer,
• the requesting program is given the address of
  the block in main memory
• If the block is not in the buffer,
• the buffer manager allocates space in the buffer
  for the block, replacing (throwing out) some
  other block, if required, to make space for the
  new block.
• The block that is thrown out is written back to
  disk only if it was modified since the most
  recent time that it was written to/fetched from
  the disk.

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Buffer Manager

• Once space is allocated in the buffer, the buffer
  manager reads the block from the disk to the
  buffer, and passes the address of the block in
  main memory to requester.
• Buffer Replacement Policy
• Frame is chosen for replacement by a replacement
  policy
• Least-recently-used (LRU), MRU, FIFO, etc.
• Policy can have big impact on of I/Os depends
  on the access pattern.

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File Organization

• The database is stored as a collection of files.
• Each file is a sequence of records.
• A record is a sequence of fields.
• Records are stored on disk blocks.
• A file can have fixed-length records or
  variable-length records.

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File Organization

• Fixed length records
• Each record is of fixed length. Pad with spaces.
• Variable length records
• different records in the file have different
  sizes.
• Arise in database systems in several ways
• different record types in a file.
• same record type with (variable-length fields,
  repeating field, or optional fields)

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File Organization
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Fixed-Length Records

• Insertion
• Store record i starting from byte n ? (i 1),
  where n is the size of each record.
• Deletion of record i
• Packed format
• move records i 1, . . ., n to i, . . . , n 1
• OR
• move record n to i
• Unpacked format (do not move records, but)
• link all free records on a free list
• OR
• Use bitmap vector

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Free Lists

• Store the address of the first deleted record in
  the file header.
• Use this first record to store the address of the
  second deleted record, and so on.

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Page Formats Fixed Length Records

• Record id ltpage id, slot gt.

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Variable-Length Records Representation

• Byte-String representation
• Attach an end-of-record (?) control character to
  the end of each record
• Difficulty with deletion and growth
• Slotted-page header contains
• number of record entries
• location and size of each record
• end of free space in the block

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Slotted Page Structure

• Records can be moved around within a page to keep
  them contiguous with no empty space between them
• entry in the header must be updated.
• Pointers should not point directly to record -
  instead they should point to the entry for the
  record in header.

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Fixed-Length Representation

• Reserved Space
• can use fixed-length records of a known maximum
  length
• unused space in shorter records filled with a
  null or end-of-record symbol.

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Fixed-Length Representation

• List Representation by Pointers
• A variable-length record is represented by a list
  of fixed-length records, chained together via
  pointers.
• Can be used even if the maximum record length is
  not known

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Fixed-Length Representation

• Disadvantage space is wasted in all records
  except the first in a a chain.
• Solution is to allow two kinds of block in file
• Anchor block contains the first records of chain
• Overflow block contains records other than those
  that are the first records of chairs.

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Blocking Factor

• Blocking Factor (bfr) - the number of records
  that can fit into a single block.
• bfr ?B/R?
• B Block size in bytes
• R Record size in bytes
• Example
• Record size R 100 bytes
• Block Size B 2,000 bytes
• Thus the blocking factor bfr 2000/100 20
• The number of blocks b needed to store a file of
  r records
• b ?r/bfr? blocks

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Spanned Unspanned Records

• A block is the unit of data transfer between disk
  and memory.
• Unspanned records
• A record is found in one and only one block.
• records do not span across block boundaries.
• Used with fixed-length records having B ? R
• Spanned records
• Records are allowed to span across block
  boundaries.
• Used with variable-length records having R ? B
• In variable-length records, either organization
  can be used.

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Placing File Records on Disk

• A file header or file descriptor contains
  information about a file (e.g., the disk address,
  record format descriptions, etc.)

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Allocating File Blocks on Disk

• The physical disk blocks that are allocated to
  hold the records of a file can be contiguous,
  linked, or indexed.
• In contiguous allocation, the file blocks are
  allocated to consecutive disk blocks.
• In linked allocation, each file block contains a
  pointer to the next file block.
• In indexed allocation, one or more index blocks
  contain pointers to the actual file blocks.

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Organization of Records in Files

• Heap File Organization
• a record can be placed anywhere in the file where
  there is space, or at the end
• for full file scans or frequent updates
• Data unordered (unsorted)
• Sorted/Ordered File Organization
• store records sorted in order, based on the value
  of the search key of each record
• Need external sort or an index to keep sorted
• Hashing File Organization
• a hash function computed on some attribute of
  each record
• the result specifies in which block of the file
  the record should be placed

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Heap File Organization

• Records are placed in the file in the order in
  which they are inserted. Such an organization is
  called a heap file.
• Insertion is at the end
• takes constant time O(1) (very efficient)
• Searching
• requires a linear search (expensive)
• Deleting
• requires a search, then delete
• Select, Update and Delete
• take b/2 time (linear time) in average
• b is the number of blocks

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Heap File Organization

• For a file of unordered fixed-length records
  using unspanned blocks and contiguous allocation,
  it is straightforward to access any record by its
  position in the file.
• If the records are numbered 0,1,2, , r-1 and
• The records in each block are numbered 0,1,2, ,
  f-1, where f is the blocking factor
• The the i-th record of the file is located in
• Block ?i/f? and in the
• (i mod f)-th record in that block

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Heap File Organization

• A Heap file allows us to retrieve records
• by specifying the rid, or
• by scanning all records sequentially
• Accessing a record by its position does not help
  locate a record based on a search condition.

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File Stored as a Heap File
666666 MGT123 F1994 4.0 123456
CS305 S1996 4.0 page 0 987654
CS305 F1995 2.0 717171 CS315
S1997 4.0 666666 EE101 S1998
3.0 page 1 765432 MAT123 S1996
2.0 515151 EE101 F1995
3.0 234567 CS305 S1999 4.0

page 2 878787 MGT123 S1996
3.0
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Sequential File Organization

• Suitable for applications that require sequential
  processing of the entire file
• The records in the file are ordered by a
  search-key

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Files of Ordered Records

• Some blocks of an ordered (sequential) file of
  EMPLOYEE records with NAME as the ordering key
  field.

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File Stored as a Sorted File
111111 MGT123 F1994 4.0 111111
CS305 S1996 4.0 page 0 123456
CS305 F1995 2.0 123456 CS315
S1997 4.0 123456 EE101 S1998
3.0 page 1 232323 MAT123 S1996
2.0 234567 EE101 F1995
3.0 234567 CS305 S1999 4.0

page 2 313131 MGT123 S1996
3.0
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Sequential File Organization

• Insertion is expensive
• records must be inserted in the correct order
• locate the position where the record is to be
  inserted
• if there is free space insert there
• if no free space insert the record in an overflow
  block
• In either case, pointer chain must be updated
• Insert takes lg(b) plus the time to re-organize
  records.
• b is the number of blocks
• Deletion
• use pointer chains
• Searching
• very efficient (Binary search)
• This requires lg(b) on the average

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Sequential File Organization
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Hashing Techniques

• A hash function maps the hash field of a record
  into the address of the storage media in which
  the record is stored.
• Hashing provides very fast access to records,
  where the search condition is an equality
  condition on the hash field.
• For internal files, hashing is implemented as a
  hash table. The mapping that assigns each element
  of the data a cell of the hash table is called a
  hash function.

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Hashing Techniques

• Two records that yield the same hash value are
  said to collide.
• A good hash function must be easy to compute and
  generate a low number of collisions.
• The process of finding another position (for
  colliding data) is called collision resolution.
• There are several methods for collision
  resolution, including open addressing, chaining,
  and multiple hashing.

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Hashing Techniques

• Open addressing
• Proceeding from the occupied position specified
  by the hash function, check the subsequent
  positions in order until an unused position is
  found.
• Chaining
• Associate an overflow area (or a linked list) to
  any cell (hashing address) and then simply store
  the data in this medium.
• Multiple hashing
• Apply a second hash function if the first results
  in a collision.
• If another collision results, use open
  addressing, or apply a third hash function, and
  then use open addressing.