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Now Make It Fast - Thoughts on physical table layout and performance for SQL Server

  2014-11-21


by Kerneels Roos

"He began to copy one of our tables, which contained partial user information, including email IDs, hashed passwords, and last tested URL. His copy operation
locked the database table, which raised alerts on our monitoring system. On receiving the alerts, we checked the logs, saw an unrecognized IP, and blocked
it right away. In that time, the hacker had been able to retrieve only a

portion of the data.” – From the postmortem of the Browser Stack hack of 9th November, 2014 at 23:30 GMT

Since relational database management systems (RDBMS) have been used in production environments since 1970 (Micro DBMS), and the theory on which they run was developed in the preceding decade,and perfected in the three remaining decades of the previous century (long ago), it was not surprising that, as a subject, it received very little attention in our curriculum - at least where I studied.

To further degrade the already apparently low relevance of the poor subject, we had to cope with a very thick and overly theoretical textbook we could not yet appreciate, and subscribe to, if you wanted to be cool and smart, to the snooty perception held by many peers that the lowly database was useful, but entirely boring.

A database was considered the type of thing you rigged up for a family member in Access in a few hours. Any larger system was the domain of ‘informatics’ - the less inspired, more practical brother field of study to the sexy ‘computer science’ with its focus on AI, advanced programming in C++, the new Java and the emerging world of Linux and Open Source.

Stepping outside into the real world, and the rest was history - databases everywhere, for everything! In my working career since 2001, every single business system I worked on had a RDBMS - primarily MS SQL Server, and sometimes MySQL or Oracle as the persistence store. Through the years I accumulated skill in modelling domains and manipulating the information through SQL, but optimisation of the storage structures for efficiency was a task I chose to ignore. I reasoned along the lines of it is the DBA’s / RDBMS’s work, or the mostly false assumption that computers are fast and how much data will the system realistically have anyways?

Really? Is that professional, to say this far will I go and no further, while you as the programmer is directly responsible for those horribly slow queries? Yes, the system works, some things are slow, but hey, they have a lot of data you say, it’s going to be slow at times! Now you are suppressing that little voice inside of you, quietly telling you it’s wrong aren’t you - it can be faster… Think of the waiting user, the wasted time, times hundreds for internal systems, times thousands for customers, times hundreds of thousands or even millions in the case of the web… All that wasted time, all that wasted energy, all the trees… Don’t think about it too much. You feel pretty bad by now don’t you…

Well, I have more bad news for you. At the end of this article you are going to feel even worse, because you are going to see how simple it is to start to turn things around.

Dramatics aside, we will have a quick look at the choices for table physical layout and ponder the implications on performance.

Be warned that we will of course only scratch the surface of SQL performance optimisation on SQL Server, and that this article is aimed at software developers with limited skill in this area, so I’m going to explain a bit - i.e. sit down, this might take a while.

Many folks have written many fine articles on this subject, and I’ll refer to some of those as we go along.

My primary justification for writing this article is that I’d like to cement this stuff in my mind, and the best way for me is to write it all out. I hope you can gain something from this also, and please comment if you disagree or whatever.

It’s out there… Somewhere… But has it order?

Contrary to popular current belief, the data isn’t somewhere in a [cloud] but it actually resides on one or more physical storage media (think disk drives), and importantly, it’s laid down either sorted or just as it was received - for all practical purposes, unsorted.

You probably knew this already, but I needed that sentence because it contained the word cloud so that I had an excuse to quote Stallman on cloud computing from 2008:

"It's stupidity. It's worse than stupidity: it's a marketing hype campaign,"

Back to tables… It is probably because SQL Server’s default is to choose the physically sorted way of laying down the data, when you define a primary key on a new table, that this table organisation prevails and is common in most systems. There is nothing like one size fits all and although the ordered layout of records is a great fit most of the time, it is not the best layout in all cases (more on that later). However, keep in mind there is wisdom in the choice of this default none the less.

Some terminology

For the purpose of the discussion we’ll stick to the most widely used terminology in the SQL Server world and call the ordered layout of records a clustered index, and the layout without any physical ordering a heap table, or simply a heap. The structure existing purely to speed up locating records we will refer to as a nonclustered index, and how the clustered index should be ordered we will call the clustering key.

Clustered index - the sorted one

The term clustered index is unfortunate, and probably the reason a lot of people develop a blurred notion of cluster vs. non clustered, and table vs. index. You could think of a clustered index as a database table for maintaining data in an ordered fashion (ordered by one or more columns) thereby giving efficient access to all the data for one record if the values of some of the sorting columns are known. Alternatively you could think of a clustered index as an database index to efficiently gain access to more data, organised by a subset of all the columns, yet it has all that added data in itself. Either way, Viewed as an ordered tabular representation of data, or an index existing for efficient access to itself - the important point is the physical sorted layout, and that the most efficient way to retrieve records from it is via the index that is itself given the primary key.

Heap - the unsorted one

A heap is simpler to understand. Think of a file that grows by repeatedly appending new lines to it without trying to maintain any kind of order. Obviously, for efficient access to the data in a heap we need one or more nonclustered indexes targeting the heap’s data, and built up from one or more components of that data.

When comparing clustered indexes with heaps we will assume that at least for the primary key, a nonclustered index is defined on the heap that would make the clustered index and heap nearly equally efficient when retrieving a record, given a single primary key value.

Nonclustered index - the real index

The term nonclustered index we will use to refer to the structure that exists primarily to provide indexed lookup to clustered indexes and heaps alike. In SQL Server a heap or clustered index can have many nonclustered indexes targeting it.

Clustering key - how the clustered index is clustered, or sorted

Apart from the notion of a primary key, for a clustered index, the clustering key defines the subset of columns that instruct the system on how to cluster or sort the records. A clustering key should be chosen to be as unique as possible, but uniqueness is not required (unlike for the primary key),since the system will add four bytes called the uniquifier to the clustering key if it is not indicated as being unique already.

Implications of heap vs. clustered index for DML

To compare the efficiency implications of DML statements on these two broad ways of physical data layout we have to look closer at the nature of the operations we would like to perform.

It is fairly intuitive to reason about this if we keep in mind:

  • The physical layout of a heap vs. a clustered index.
  • Indexes should stay up to date after the operation completes.
  • Is the operation on one or on multiple records.
  • What piece of data is required for the fastest retrieval of records.

The single index, primary key as clustering key scenario.

It turns out that it is generally the best choice to use a clustered index instead of a heap, for the scenario where you need only one index on one or more indexing columns. For this scenario, a clustered index takes up less space, performs better overall, and releases space better when records get deleted.

The short answer to why this is the case is that for a clustered index, the data is the index, so lookups on the clustering key finds the relevant records directly (after climbing the index B-tree), and alterations affecting the clustering key requires alterations to one structure - the clustered index. For a heap plus one nonclustered index however, lookups given the index key is a two-step process. First the nonclustered index is queried to find the RID, the uniquely identifying key for each heap row corresponding to the clustering key, and then the RID is used to fetch the record from the heap. In addition to this, although alterations involving the index key might not require much work on the heap, the nonclustered index needs to be updated - again a two-step process.

Nevertheless, there is a great case to be made for choosing a heap over a clustered index, which we’ll get to shortly, but for the scenario as explained above (one index on the clustering key), a clustered index is the better choice.

See this Microsoft best practices white paper, but be warned that it is proving the superiority of choosing a clustered index in favor of a heap in a scenario where a clustered index is the best choice. Do not be fooled by this article into thinking heaps are overall inferior to clustered indexes, as a casual reading might lead you into believing.

Let’s look at the various DML operations quickly on clusterd index and heap…

INSERT

INSERT into a heap is simply a case of appending where there is space available in a data page (or creating a new page at the end). After this, a second write operation is required - insertion of the index key into the B-tree of the nonclustered index.

Now for a clustered index, the new record must be inserted in the correct location. If this correct location is on a data page that is full, that page needs to be split in two . This might be more time-consuming than the simple insert on the heap, but for a clustered index there is no second write operation to maintain the index - the data and index are one. Note that this might even turn out to make a clustered index perform better overall since it only requires one write operation.

Any additional nonclustered indexes on a clustered index or heap would take roughly the same time to update or keep in sync with the actual data, so we can ignore their maintenance penalty when comparing.

But surely we should be able to gain performance with inserts by choosing either of the two table layouts, given that heaps and clustered indexes differ so fundamentally? In this particular scenario they are equally good because both options still require that indexes be kept up to date. If we were to choose a heap and define absolutely no nonclustered index on it we will gain the fastest insert performance since inserting would simply be adding data on anywhere where there is space.

There is actually a great use case for this: logs and other archival type of storage that do not require immediate querying.

But optimisation is a tricky problem, since even for this use case, if many concurrent inserts are expected, it might very well be better to choose a clustered index instead, on some non unique but range-like clustering key that will jump around a bit, to achieve an effect of inserting in different locations to prevent everything from trying to insert in the same data page all the time (as would be the case for a heap).

SELECT, UPDATE and DELETE

SELECT, UPDATE and DELETE first requires locating where the records to operate on need to be physically found, followed by the actual action on the data.

Assuming that the operation simply applies to data given a single primary key value that is the clustering key, the finding or first part of this operation is slightly less efficient for a heap compared to a clustered index. For a clustered index, after the tree is climbed the information is there and ready to be retrieved, while for a heap, after climbing the tree of the nonclustered index, you only get the RID, and then require a second operation to (all be it directly) get at the data in the heap - one additional level of indirection.

There is an option to include columns of the heap or clustered index in the nonclustered indexes. The effect of this is that, after climbing the tree of the nonclustered index, those included column’s data is immediately available - a mini clustered index in the form of a nonclustered index with included columns. All very straight forward and unambiguous wouldn’t you say?

Except for SELECT, the efficiency of the second part, the action part of the operation can vary much more between heap and clustered index. For UPDATE, if the column being updated happens to be one or more of the columns comprising the clustering key, and the table is a clustered index, then in order to keep the data sorted, the system might have to do page splits. This in turn mean that potentially, large amounts of data need to be copied around. For a heap this is never the case, and the columns can simply be updated in place - order is of no importance.

For both heap and clustered index, if any of the columns are part of any defined nonclustered indexes then altering them might have nonclustered index maintenance time as a further performance penalty.

Fortunately, for both heap and clustered index, if the columns being updated are not part of the clustering key the efficiency of the action part of the operation is nearly similar.

Performing a DELETE on a heap or clustered index should be simply a case of marking that record as deleted and making the space available for potential future inserts. For a clustered index, no index maintenance is yet again needed while for the heap, the nonclustered index needs updating.

Welcome to the real world, where tree climbing is to be avoided - the multiple indexes scenario

The single index, primary key as clustering key and lookup scenario described earlier might appear early on, and a lot in most models, but very soon you will also want to efficiently query on other columns on wider (more columns) and deeper (more rows) tables.

To prevent full table scans, you start adding nonclustered indexes, and this is where heaps start to become the more attractive alternative.

Suppose for a moment that your table (let’s call it table T) that became wide and deep overnight is a clustered index, and the primary key (K) is also the clustering key.

Each additional nonclustered index (N1, N2, …) on T will store in its leaf nodes the values of K. This means that a query on T utilising some nonclustered index N results in a tree climb of N that yields some value of K. Following this we require another tree climb of the clustered index that is T, given a value for K, and only then is the actual data reached.

On the other hand, suppose now that your wide and deep table H is a heap instead, with one or more nonclustered indexes N1, N2, … and so on. This time, each nonclustered index N will store at the leaf node the RID of the relevant row, and not simply yet another key into a further index. This means that if some query on H utilise one of the nonclustered indexes, only one tree climb of that nonclustered index is required, after which the RID is obtained, and unlike a clustering key, a RID represents the physical position of the record in the heap, and thus can be directly accessed - no further tree climbing required.

For a more in-depth look at this, and some hard numbers comprising a compelling case, do yourself a favor and read Markus Wienand’s fine article, Unreasonable Defaults: Primary Key as Clustering Key.

Summary and closing thoughts - Optimising performance is an interesting and very relevant problem

"Premature optimisation is the root of all evil"
 -- Donald E. Knuth

As much as I concur with that statement, especially how it applies to code, I do think that a good understanding of the options available to you when turning a data model into an actual database schema can proactively prevent vicious cycles of poor performing monster database servers. Yes, there is a lot of things one can do, and the precise case where one technique or option would be the better option is hard to identify, but the better your understanding of the internals, the more likely you are to get it right first time, and the more it will start to happen that you are writing a query and you suddenly realise that a specific index would benefit that query tremendously.

I’ve rambled a bit, but to summarise:

  • There are two main choices for the physical layout of data for tables.
  • If only one index on the primary key is required it’s probably the best to choose a clustered index.
  • For a many index scenario choose a heap.
  • For best insert performance on high loads choose a heap with no nonclustered indexes.
  • Use the include columns feature of nonclustered indexes.

Today there are exciting new alternative data storage technologies like fully in memory databases, distributed systems such as Hadoop, Google’s BigTable approach, and document oriented noSQL options such as ElasticSearch to name only a very few. These alternative solutions to the problem of working with large data sets have and will continue to be applied more and more, but if the last decade is anything to go by, the relational database is going to stick around for quite some time still, so investing time into learning how to optimise it is time well spent.

The reason for SQL systems remaining central to all serious data storage applications is not by accident. There is a theoretical reason, routed in the so-called CAP theorem. For an overview of how the CAP theorem restricted the growth and adoption of noSQL systems, have a look at Whats left of NoSQL?.

An interesting response to this is FoundationDB (see NoSQL’s CAP theorem busters: We don’t drop ACID).

An exciting emerging trend is to harness the strengths of both the traditional RDBMS and the more recent big data distributed, more normalised data storage technologies. For an interesting application of this, see Use Updatable Tables for Responsive Real-Time Reporting.

I hope this short info burst tickled your interest enough that you will go ahead and look into all of it a bit more. Personally I have been pleasantly surprised by the depth of this subject area.

I can highly recommend the book SQL Performance Optimisation for an in-depth look at this subject, and the Use The Index Luke site.

This article also appears on my goodfast.info site - a work in progress.

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