Data Structures that Power up your Database

Sanket Patil
9 min readSep 18, 2022

Many databases use a log, which is append-only data file. Real databases have more issues to deal with (concurrency control, reclaiming disk space so the log doesn’t grow forever and handling errors and partially written records).

A log is an append-only sequence of records

In order to efficiently find the value for a particular key, we need a different data structure: an index. An index is an additional structure that is derived from the primary data. Well-chosen indexes speed up read queries but every index slows down writes. That’s why databases don’t index everything by default, but require you to choose indexes manually using your knowledge on typical query patterns.

Hash indexes

Key-value stores are quite similar to the dictionary type (hash map or hash table). Let’s say our storage consists only of appending to a file. The simplest indexing strategy is to keep an in-memory hash map where every key is mapped to a byte offset in the data file. Whenever you append a new key-value pair to the file, you also update the hash map to reflect the offset of the data you just wrote. Bitcask (the default storage engine in Riak) does it like that. The only requirement it has is that all the keys fit in the available RAM. Values can use more space than there is available in memory, since they can be loaded from disk.

A storage engine like Bitcask is well suited to situations where the value for each key is updated frequently. There are a lot of writes, but there are too many distinct keys, you have a large number of writes per key, but it’s feasible to keep all keys in memory.

As we only ever append to a file, so how do we avoid eventually running out of disk space? A good solution is to break the log into segments of certain size by closing the segment file when it reaches a certain size, and making subsequent writes to a new segment file. We can then perform compaction on these segments. Compaction means throwing away duplicate keys in the log, and keeping only the most recent update for each key.

We can also merge several segments together at the save time as performing the compaction. Segments are never modified after they have been written, so the merged segment is written to a new file. Merging and compaction of frozen segments can be done in a background thread. After the merging process is complete, we switch read requests to use the new merged segment instead of the old segments, and the old segment files can simply be deleted.

Each segment now has its own in-memory hash table, mapping keys to file offsets. In order to find a value for a key, we first check the most recent segment hash map; if the key is not present we check the second-most recent segment and so on. The merging process keeps the number of segments small, so lookups don’t need to check many hash maps.

Some issues that are important in a real implementation:

  • File format. It is simpler to use binary format.
  • Deleting records. Append special deletion record to the data file (tombstone) that tells the merging process to discard previous values.
  • Crash recovery. If restarted, the in-memory hash maps are lost. You can recover from reading each segment but that would take long time. Bitcask speeds up recovery by storing a snapshot of each segment hash map on disk.
  • Partially written records. The database may crash at any time. Bitcask includes checksums allowing corrupted parts of the log to be detected and ignored.
  • Concurrency control. As writes are appended to the log in a strictly sequential order, a common implementation is to have a single writer thread. Segments are immutable, so they can be read concurrently by multiple threads.

Append-only design turns out to be good for several reasons:

  • Appending and segment merging are sequential write operations, much faster than random writes, especially on magnetic spinning-disks.
  • Concurrency and crash recovery are much simpler.
  • Merging old segments avoids files getting fragmented over time.

Hash table has its limitations too:

  • The hash table must fit in memory. It is difficult to make an on-disk hash map perform well.
  • Range queries are not efficient.

SSTables and LSM-Trees

We introduce a new requirement to segment files: we require that the sequence of key-value pairs is sorted by key. We call this Sorted String Table, or SSTable. We require that each key only appears once within each merged segment file (compaction already ensures that). SSTables have few big advantages over log segments with hash indexes

  1. Merging segments is simple and efficient (we can use algorithms like mergesort). When multiple segments contain the same key, we can keep the value from the most recent segment and discard the values in older segments.
  2. You no longer need to keep an index of all the keys in memory. For a key like handiwork, when you know the offsets for the keys handback and handsome, you know handiwork must appear between those two. You can jump to the offset for handback and scan from there until you find handiwork, if not, the key is not present. You still need an in-memory index to tell you the offsets for some of the keys. One key for every few kilobytes of segment file is sufficient.
  3. Since read requests need to scan over several key-value pairs in the requested range anyway, it is possible to group those records into a block and compress it before writing it to disk.

How do we get the data sorted in the first place? With red-black trees or AVL trees, you can insert keys in any order and read them back in sorted order.

  • When a write comes in, add it to an in-memory balanced tree structure (memtable).
  • When the memtable gets bigger than some threshold (megabytes), write it out to disk as an SSTable file. Writes can continue to a new memtable instance.
  • On a read request, try to find the key in the memtable, then in the most recent on-disk segment, then in the next-older segment, etc.
  • From time to time, run merging and compaction in the background to discard overwritten and deleted values.

If the database crashes, the most recent writes are lost. We can keep a separate log on disk to which every write is immediately appended. That log is not in sorted order, but that doesn’t matter, because its only purpose is to restore the memtable after crash. Every time the memtable is written out to an SSTable, the log can be discarded. Storage engines that are based on this principle of merging and compacting sorted files are often called LSM structure engines (Log Structure Merge-Tree).

Lucene, an indexing engine for full-text search used by Elasticsearch and Solr, uses a similar method for storing its term dictionary. LSM-tree algorithm can be slow when looking up keys that don’t exist in the database. To optimise this, storage engines often use additional Bloom filters (a memory-efficient data structure for approximating the contents of a set).

There are also different strategies to determine the order and timing of how SSTables are compacted and merged. Mainly two size-tiered and leveled compaction. LevelDB and RocksDB use leveled compaction, HBase use size-tiered, and Cassandra supports both. In size-tiered compaction, newer and smaller SSTables are successively merged into older and larger SSTables. In leveled compaction, the key range is split up into smaller SSTables and older data is moved into separate “levels”, which allows the compaction to use less disk space.

B-trees

This is the most widely used indexing structure. B-tress keep key-value pairs sorted by key, which allows efficient key-value lookups and range queries. The log-structured indexes break the database down into variable-size segments typically several megabytes or more. B-trees break the database down into fixed-size blocks or pages, traditionally 4KB.

One page is designated as the root and you start from there. The page contains several keys and references to child pages. If you want to update the value for an existing key in a B-tree, you search for the leaf page containing that key, change the value in that page, and write the page back to disk. If you want to add new key, find the page and add it to the page. If there isn’t enough free space in the page to accommodate the new key, it is split in two half-full pages, and the parent page is updated to account for the new subdivision of key ranges.

Trees remain balanced. A B-tree with n keys always has a depth of O(log n). The basic underlying write operation of a B-tree is to overwrite a page on disk with new data. It is assumed that the overwrite does not change the location of the page, all references to that page remain intact. This is a big contrast to log-structured indexes such as LSM-trees, which only append to files.

Some operations require several different pages to be overwritten. When you split a page, you need to write the two pages that were split, and also overwrite their parent. If the database crashes after only some of the pages have been written, you end up with a corrupted index. It is common to include an additional data structure on disk: a write-ahead log (WAL, also know as the redo log). Careful concurrency control is required if multiple threads are going to access, typically done protecting the tree internal data structures with latches (lightweight locks).

B-trees and LSM-trees

LSM-trees are typically faster for writes, whereas B-trees are thought to be faster for reads. Reads are typically slower on LSM-tress as they have to check several different data structures and SSTables at different stages of compaction.

Advantages of LSM-trees:

  • LSM-trees are typically able to sustain higher write throughput than B-trees, party because they sometimes have lower write amplification: a write to the database results in multiple writes to disk. The more a storage engine writes to disk, the fewer writes per second it can handle.
  • LSM-trees can be compressed better, and thus often produce smaller files on disk than B-trees. B-trees tend to leave disk space unused due to fragmentation.

Downsides of LSM-trees:

  • Compaction process can sometimes interfere with the performance of ongoing reads and writes. B-trees can be more predictable. The bigger the database, the the more disk bandwidth is required for compaction. Compaction cannot keep up with the rate of incoming writes, if not configured properly you can run out of disk space.
  • On B-trees, each key exists in exactly one place in the index. This offers strong transactional semantics. Transaction isolation is implemented using locks on ranges of keys, and in a B-tree index, those locks can be directly attached to the tree.

Other indexing structures

We’ve only discussed key-value indexes, which are like primary key index. There are also secondary indexes. A secondary index can be easily constructed from a key-value index. The main difference is that in a secondary index, the indexed values are not necessarily unique. There are two ways of doing this: making each value in the index a list of matching row identifiers or by making a each entry unique by appending a row identifier to it.

Full-text search and fuzzy indexes

Indexes don’t allow you to search for similar keys, such as misspelled words. Such fuzzy querying requires different techniques. Full-text search engines allow synonyms, grammatical variations, occurrences of words near each other.

Keeping everything in memory

Disks have two significant advantages: they are durable, and they have lower cost per gigabyte than RAM. It’s quite feasible to keep them entirely in memory, this has lead to in-memory databases. Key-value stores, such as Memcached are intended for cache only, it’s acceptable for data to be lost if the machine is restarted. Other in-memory databases aim for durability, with special hardware, writing a log of changes to disk, writing periodic snapshots to disk or by replicating in-memory sate to other machines.

When an in-memory database is restarted, it needs to reload its state, either from disk or over the network from a replica. The disk is merely used as an append-only log for durability, and reads are served entirely from memory. Products such as VoltDB, MemSQL, and Oracle TimesTime are in-memory databases. Redis and Couchbase provide weak durability.

In-memory databases can be faster because they can avoid the overheads of encoding in-memory data structures in a form that can be written to disk. Another interesting area is that in-memory databases may provide data models that are difficult to implement with disk-based indexes.

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