Under the Covers: Tuning and Physical Storage

# Under the Covers: Tuning and Physical Storage

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## Under the Covers: Tuning and Physical Storage

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1. Under the Covers:Tuning and Physical Storage Zachary G. Ives University of Pennsylvania CIS 550 – Database & Information Systems November 3, 2003 Some slide content may be courtesy of Susan Davidson, Dan Suciu, & Raghu Ramakrishnan

2. Resuming Last Week’s Discussionof Data Integration… • Query: q(a,t) :- author(a, i, _), book(i, t, p) • Mapping rule: s1(a,t)  author(a, i, _), book(i, t, p), t = “123” • Inverse rules: author(a, f(a,t), NULL)  s1(a,t) book(f(a,t), t, p)  s1(a,t), t = “123” • We can now expand the query: • q(a,t) :- author(a, i, NULL), book(i, t, p), i = f(a,t) • q(a,t) :- s1(a,t), s1(a,t), t = “123”, i = f(a,t)

3. Query Answering Using Inverse Rules • Invert all rules • Take the query and the possible rule expansions and execute them in a Datalog interpreter: • This creates a union of all possible “view unfoldings”: every possible way of combining and cross-correlating info from different sources • all combinations of expansions of book and of author in our example • Then it throws away all unsatisfiable rewritings (some expansions will be logically inconsistent) • The answer is the result of executing the query

4. Faster Algorithms • “Bucket algorithm” from Levy et al.: • Given a query Q with relations and predicates • Create a bucket for each subgoal in Q • Iterate over each view (source mapping) • If source includes bucket’s subgoal: • Create mapping between Q’s vars and the view’s var at the same position • If satisfiable with substitutions, add to bucket • Do cross-product of buckets, see if result is contained in the query (recall we saw an algorithm to do that) • “MiniCon algorithm” (Pottinger & Levy)

5. Source Capabilities • The simplest form is to annotate the attributes of a relation: • Bookbff(auth,title,pub) • But many data integration efforts had more sophisticated models • Can a data source support joins between its relations? • Can a data source be sent a relation that it should join with? • In the end, we need to perform parts of the query in the mediator, and other parts at the sources

6. Local-as-View and the Info Manifold • More robust way of defining mediated schemas and sources • Mediated schema is clearly defined, less likely to change • Sources can be more accurately described • Relatively efficient algorithms for query reformulation, creating executable plans • Still requires standardization on a single schema • Can be hard to get consensus • Some other data integration aspects were captured in related papers • Overlap between sources; coverage of data at sources • Semi-automated creation of mappings • Semi-automated construction of wrappers

7. Data Integration, Concluded • A very important problem today – perhaps the central problem faced by most IT departments, scientific collaborations • A basic set of techniques cover many kinds of mappings • Concordance tables • View-based mappings: local- and global-as-view • Still a field with much ongoing research • Especially at Penn, U. Washington, U. Illinois, UC San Diego

8. Under the Covers:Tuning and Physical Storage Zachary G. Ives University of Pennsylvania CIS 550 – Database & Information Systems November 3, 2003 Some slide content may be courtesy of Susan Davidson, Dan Suciu, & Raghu Ramakrishnan

9. Performance: What Governs It? • Speed of the machine – of course! • But also many software-controlled factors that we must understand: • Caching and buffer management • How the data is stored – physical layout, partitioning • Auxiliary structures – indices • Locking and concurrency control (we’ll talk about this later) • Different algorithms for operations – query execution • Different orderings for execution – query optimization • Reuse of materialized views, merging of query subexpressions – answering queries using views; multi-query optimization

10. General Emphasis of Today’s Lecture • Goal: cover basic principles that are applied throughout database system design • Use the appropriate strategy in the appropriate place Every (reasonable) algorithm is good somewhere • … And a corollary: database people reinvent a lot of things and add minor tweaks…

11. What’s the “Base” in “Database”? • Could just be a file with random access • What are the advantages and disadvantages? • DBs generally require “raw” disk access • Need to know when a page is actually written to disk, vs. queued by the OS • Predictable performance, less fragmentation • May want to exploit striping or contiguous regions • Typically divided into “extents” and pages

12. Buffer Management • Could keep DB in RAM • “Main-memory DBs” like TimesTen • But many DBs are still too big; we read & replace pages • May need to force to disk or pin in buffer • Policies for page replacement, prefetching • LRU, as in Operating Systems (not as good as you might think – why not?) • MRU (one-time sequential scans) • Clock, etc. • DBMIN (min # pages, local policy) Tuple Reads/Writes Buffer Mgr

13. Storing Tuples in Pages Tuples • Many possible layouts • Dynamic vs. fixed lengths • Ptrs, lengths vs. slots • Tuples grow down, directories grow up • Identity and relocation Objects and XML are harder • Horizontal, path, vertical partitioning • Generally no algorithmic way of deciding Generally want to leave some space for insertions t1 t2 t3

14. Alternatives for Organizing Files Many alternatives, each ideal for some situation, and poor for others: • Heap files:for full file scans or frequent updates • Data unordered • Write new data at end • Sorted Files: if retrieved in sort order or want range • Need external sort or an index to keep sorted • Hashed Files: if selection on equality • Collection of buckets with primary & overflow pages • Hashing functionover search key attributes

15. Model for Analyzing Access Costs We ignore CPU costs, for simplicity: • p(T):The number of data pages in table T • r(T):Number of records in table T • D:(Average) time to read or write disk page • Measuring number of page I/O’s ignores gains of pre-fetching blocks of pages; thus, I/O cost is only approximated. • Average-case analysis; based on several simplistic assumptions. • Good enough to show the overall trends!

16. Assumptions in Our Analysis • Single record insert and delete • Heap files: • Equality selection on key; exactly one match • Insert always at end of file • Sorted files: • Files compacted after deletions • Selections on sort field(s) • Hashed files: • No overflow buckets, 80% page occupancy

17. Cost of Operations

18. Cost of Operations • Several assumptions underlie these (rough) estimates!

19. Speeding Operations over Data • Three general data organization techniques: • Indexing • Sorting • Hashing

20. Technique I: Indexing • An index on a file speeds up selections on the searchkeyattributesfor the index (trade space for speed). • Any subset of the fields of a relation can be the search key for an index on the relation. • Searchkeyis not the same as key(minimal set of fields that uniquely identify a record in a relation). • An index contains a collection of data entries, and supports efficient retrieval of all data entries k* with a given key value k.

21. Alternatives for Data Entry k* in Index • Three alternatives: • Data record with key value k • Clustered  fast lookup • Index is large; only 1 can exist • <k, rid of data record with search key value k>, OR • <k, list of rids of data records with search key k> • Can have secondary indices • Smaller index may mean faster lookup • Often not clustered  more expensive to use • Choice of alternative for data entries is orthogonal to the indexing technique used to locate data entries with a given key value k.

22. Classes of Indices • Primaryvs.secondary: primary has primary key • Clusteredvs.unclustered: order of records and index approximately same • Alternative 1 implies clustered, but not vice-versa • A file can be clustered on at most one search key • Densevs.Sparse: dense has index entry per data value; sparse may “skip” some • Alternative 1 always leads to dense index • Every sparse index is clustered! • Sparse indexes are smaller; however, some useful optimizations are based on dense indexes

23. Clustered vs. Unclustered Index Suppose Index Alternative (2) used, records are stored in Heap file • Perhaps initially sort data file, leave some gaps • Inserts may require overflow pages Index entries UNCLUSTERED CLUSTERED direct search for dataentries Data entries Data entries (Index File) (Data file) Data Records Data Records

24. B+ Tree: The DB World’s Favorite Index • Insert/delete at log F N cost • (F = fanout, N = # leaf pages) • Keep tree height-balanced • Minimum 50% occupancy (except for root). • Each node contains d <= m <= 2d entries. d is called the order of the tree. • Supports equality and range searches efficiently. Index Entries (Direct search) Data Entries ("Sequence set")

25. Example B+ Tree • Search begins at root, and key comparisons direct it to a leaf. • Search for 5*, 15*, all data entries >= 24* ... Root 30 24 13 17 39* 22* 24* 27* 38* 3* 5* 19* 20* 29* 33* 34* 2* 7* 14* 16* • Based on the search for 15*, we know it is not in the tree!

26. B+ Trees in Practice • Typical order: 100. Typical fill-factor: 67%. • average fanout = 133 • Typical capacities: • Height 4: 1334 = 312,900,700 records • Height 3: 1333 = 2,352,637 records • Can often hold top levels in buffer pool: • Level 1 = 1 page = 8 Kbytes • Level 2 = 133 pages = 1 Mbyte • Level 3 = 17,689 pages = 133 MBytes

27. Inserting Data into a B+ Tree • Find correct leaf L. • Put data entry onto L. • If L has enough space, done! • Else, must split L (into L and a new node L2) • Redistribute entries evenly, copy up middle key. • Insert index entry pointing to L2 into parent of L. • This can happen recursively • To split index node, redistribute entries evenly, but push up middle key. (Contrast with leaf splits.) • Splits “grow” tree; root split increases height. • Tree growth: gets wider or one level taller at top.

28. Inserting 8* into Example B+ Tree • Observe how minimum occupancy is guaranteed in both leaf and index pg splits. • Recall that all data items are in leaves, and partition values for keys are in intermediate nodes Note difference between copy-upand push-up.

29. Inserting 8* Example: Copy up Root 30 24 13 17 39* 22* 24* 27* 38* 3* 5* 19* 20* 29* 33* 34* 2* 7* 14* 16* Want to insert here; no room, so split & copy up: 8* Entry to be inserted in parent node. (Note that 5 is copied up and 5 continues to appear in the leaf.) 5* 3* 7* 2* 8*

30. Inserting 8* Example: Push up Need to split node & push up Root 30 24 13 17 5 39* 3* 22* 24* 27* 38* 19* 20* 2* 29* 33* 34* 14* 16* 5* 7* 8* Entry to be inserted in parent node. (Note that 17 is pushed up and only appears once in the index. Contrast this with a leaf split.) 17 24 30 5 13

31. Deleting Data from a B+ Tree • Start at root, find leaf L where entry belongs. • Remove the entry. • If L is at least half-full, done! • If L has only d-1 entries, • Try to re-distribute, borrowing from sibling (adjacent node with same parent as L). • If re-distribution fails, merge L and sibling. • If merge occurred, must delete entry (pointing to L or sibling) from parent of L. • Merge could propagate to root, decreasing height.

32. B+ Tree Summary B+ tree and other indices ideal for range searches, good for equality searches. • Inserts/deletes leave tree height-balanced; logF N cost. • High fanout (F) means depth rarely more than 3 or 4. • Almost always better than maintaining a sorted file. • Typically, 67% occupancy on average. • Note: Order (d) concept replaced by physical space criterion in practice (“at least half-full”). • Records may be variable sized • Index pages typically hold more entries than leaves

33. Other Kinds of Indices • Multidimensional indices • R-trees, kD-trees, … • Text indices • Inverted indices • Structural indices • Object indices: access support relations, path indices • XML and graph indices: dataguides, 1-indices, d(k) indices

34. DataGuides (McHugh, Goldman, Widom) • Idea: create a summary graph structure representing all possible paths through the XML tree or graph • A deterministic finite state machine representing all paths • Vaguely like the DTD graph from the Shanmugasundaram et al. paper • At each node in the DataGuide, include an extent structure that points to all nodes in the original tree • These are the nodes that match the path

35. Example DataGuide db <db> <book> <auth>1</auth> <auth>2</auth> <title>DBs</title> </book> <book> <auth>2</auth> <title>AI</title> </book> <author> <id>1</id> <name>Smith</name></author> <author> <id>2</id> <name>Lee</name> </author> </db> author book name id auth title