I'm rather inexperienced with databases and have just read about the "n+1 selects issue". My follow-up question: Assuming the database resides on the same machine as my program, is cached in RAM and properly indexed, why is the n+1 query pattern slow?
As an example let's take the code from the accepted answer:
SELECT * FROM Cars;
/* for each car */
SELECT * FROM Wheel WHERE CarId = ?
With my mental model of the database cache, each of the SELECT * FROM Wheel WHERE CarId = ? queries should need:
1 lookup to reach the "Wheel" table (one hashmap get())
1 lookup to reach the list of k wheels with the specified CarId (another hashmap get())
k lookups to get the wheel rows for each matching wheel (k pointer dereferenciations)
Even if we multiply that by a small constant factor for an additional overhead because of the internal memory structure, it still should be unnoticeably fast. Is the interprocess communication the bottleneck?
Edit: I just found this related article via Hacker News: Following a Select Statement Through Postgres Internals. - HN discussion thread.
Edit 2: To clarify, I do assume N to be large. A non-trivial overhead will add up to a noticeable delay then, yes. I am asking why the overhead is non-trivial in the first place, for the setting described above.
You are correct that avoiding n+1 selects is less important in the scenario you describe. If the database is on a remote machine, communication latencies of > 1ms are common, i.e. the cpu would spend millions of clock cycles waiting for the network.
If we are on the same machine, the communication delay is several orders of magnitude smaller, but synchronous communication with another process necessarily involves a context switch, which commonly costs > 0.01 ms (source), which is tens of thousands of clock cycles.
In addition, both the ORM tool and the database will have some overhead per query.
To conclude, avoiding n+1 selects is far less important if the database is local, but still matters if n is large.
Assuming the database resides on the same machine as my program
Never assume this. Thinking about special cases like this is never a good idea. It's quite likely that your data will grow, and you will need to put your database on another server. Or you will want redundancy, which involves (you guessed it) another server. Or for security, you might want not want your app server on the same box as the DB.
why is the n+1 query pattern slow?
You don't think it's slow because your mental model of performance is probably all wrong.
1) RAM is horribly slow. Your CPU is wasting around 200-400 CPU cycles each time it needs to read something something from RAM. CPUs have a lot of tricks to hide this (caches, pipelining, hyperthreading)
2) Reading from RAM is not "Random Access". It's like a hard drive: sequential reads are faster.
See this article about how accessing RAM in the right order is 76.6% faster http://lwn.net/Articles/255364/ (Read the whole article if you want to know how horrifyingly complex RAM actually is.)
CPU cache
In your "N+1 query" case, the "loop" for each N includes many megabytes of code (on client and server) swapping in and out of caches on each iteration, plus context switches (which usually dumps the caches anyway).
The "1 query" case probably involves a single tight loop on the server (finding and copying each row), then a single tight loop on the client (reading each row). If those loops are small enough, they can execute 10-100x faster running from cache.
RAM sequential access
The "1 query" case will read everything from the DB to one linear buffer, send it to the client who will read it linearly. No random accesses during data transfer.
The "N+1 query" case will be allocating and de-allocating RAM N times, which (for various reasons) may not be the same physical bit of RAM.
Various other reasons
The networking subsystem only needs to read one or two TCP headers, instead of N.
Your DB only needs to parse one query instead of N.
When you throw in multi-users, the "locality/sequential access" gets even more fragmented in the N+1 case, but stays pretty good in the 1-query case.
Lots of other tricks that the CPU uses (e.g. branch prediction) work better with tight loops.
See: http://blogs.msdn.com/b/oldnewthing/archive/2014/06/13/10533875.aspx
Having the database on a local machine reduces the problem; however, most applications and databases will be on different machines, where each round trip takes at least a couple of milliseconds.
A database will also need a lot of locking and latching checks for each individual query. Context switches have already been mentioned by meriton. If you don't use a surrounding transaction, it also has to build implicit transactions for each query. Some query parsing overhead is still there, even with a parameterized, prepared query or one remembered by string equality (with parameters).
If the database gets filled up, query times may increase, compared to an almost empty database in the beginning.
If your database is to be used by other application, you will likely hammer it: even if your application works, others may slow down or even get an increasing number of failures, such as timeouts and deadlocks.
Also, consider having more than two levels of data. Imagine three levels: Blogs, Entries, Comments, with 100 blogs, each with 10 entries and 10 comments on each entry (for average). That's a SELECT 1+N+(NxM) situation. It will require 100 queries to retrieve the blog entries, and another 1000 to get all comments. Some more complex data, and you'll run into the 10000s or even 100000s.
Of course, bad programming may work in some cases and to some extent. If the database will always be on the same machine, nobody else uses it and the number of cars is never much more than 100, even a very sub-optimal program might be sufficient. But beware of the day any of these preconditions changes: refactoring the whole thing will take you much more time than doing it correctly in the beginning. And likely, you'll try some other workarounds first: a few more IF clauses, memory cache and the like, which help in the beginning, but mess up your code even more. In the end, you may be stuck in a "never touch a running system" position, where the system performance is becoming less and less acceptable, but refactoring is too risky and far more complex than changing correct code.
Also, a good ORM offers you ways around N+1: (N)Hibernate, for example, allows you to specify a batch-size (merging many SELECT * FROM Wheels WHERE CarId=? queries into one SELECT * FROM Wheels WHERE CarId IN (?, ?, ..., ?) ) or use a subselect (like: SELECT * FROM Wheels WHERE CarId IN (SELECT Id FROM Cars)).
The most simple option to avoid N+1 is a join, with the disadvantage that each car row is multiplied by the number of wheels, and multiple child/grandchild items likely ending up in a huge cartesian product of join results.
There is still overhead, even if the database is on the same machine, cached in RAM and properly indexed. The size of this overhead will depend on what DBMS you're using, the machine it's running on, the amount of users, the configuration of the DBMS (isolation level, ...) and so on.
When retrieving N rows, you can choose to pay this cost once or N times. Even a small cost can become noticeable if N is large enough.
One day someone might want to put the database on a separate machine or to use a different dbms. This happens frequently in the business world (to be compliant with some ISO standard, to reduce costs, to change vendors, ...)
So, sometimes it's good to plan for situations where the database isn't lightning fast.
All of this depends very much on what the software is for. Avoiding the "select n+1 problem" isn't always necessary, it's just a rule of thumb, to avoid a commonly encountered pitfall.
Related
We are in the case of using a SQL database for a single node storage of roughly 1 hour of high frequency metrics (several k inserts a second). We quickly ran into I/O issues which proper buffering would not simply handle, and we are willing to put time into solving the performance issue.
I suggested to switch to a specialised database for handling time series, but my colleague stayed pretty skeptical. His argument is that the gain "out of the box" is not guaranteed as he knows SQL well and already spent time optimizing the storage, and we in comparison do not have any kind of TSDB experience to properly optimize it.
My intuition is that using a TSDB would be much more efficient even with an out of box configuration but I don't have any data to measure this, and internet benchs such as InfluxDB's are nowhere near trustable. We should run our own, except we can't affoard to loose time in a dead end or a mediocre improvement.
What would be, in my use case but very roughly, the performance gap between relational storage and TSDB, when it comes to single node throughput ?
This question may be bordering on a software recommendation. I just want to point one important thing out: You have an existing code base so switching to another data store is expensive in terms of development costs and time. If you have someone experienced with the current technology, you are probably better off with a good-faith effort to make that technology work.
Whether you switch or not depends on the actual requirements of your application. For instance, if you don't need the data immediately, perhaps writing batches to a file is the most efficient mechanism.
Your infrastructure has ample opportunity for in-place growth -- more memory, more processors, solid-state disk (for example). These might meet your performance needs with a minimal amount of effort.
If you cannot make the solution work (and 10k inserts per second should be quite feasible), then there are numerous solutions. Some NOSQL databases relax some of the strict ACID requirements of traditional RDBMSs, providing faster throughout.
I'm working with MS-SQL Server, and we have several views that have the potential to return enormous amounts of processed data, enough to spike our servers to 100% resource usage for 30 minutes straight with a single query (if queried irresponsibly).
There is absolutely no business case in which such huge amounts of data would need to be returned from these views, so we'd like to lock it down to make sure nobody can DoS our SQL servers (intentionally or otherwise) by simply querying these particular views without proper where clauses etc.
Is it possible, via triggers or another method, to check the where clause etc. and confirm whether a given query is "safe" to execute (based on thresholds we determine), and reject the query if it doesn't meet our guidelines?
Or can we configure the server to reject given execution plans based on estimated time-to-completion etc.?
One potential way to reduce the overall cost of certain queries coming from a certain group of people is to use the resource governor. You can throttle how much CPU and/or memory is used up be a particular user/group. This is effective if you have a "wild west" kind of environment where some users submit bad queries that eat your resources alive. See here.
Another thing to consider is to set your MAXDOP (max degree of parallelism) to prevent any single query from taking all of the available CPU threads. That is, if MAXDOP is 1, then any query can only take 2 CPU threads to process. This is useful to prevent a large query from letting smaller quick ones processing. See here.
Kind of hacky but put a top x in every view
You cannot enforce it at the SQL side but on the app size they could use a TimeOut. But if they lack QC they probably lack the discipline for TimeOut. If you have some queries going 30 minutes they are probably setting a value longer than the default.
I'm not convinced about Blam's top X in each view. Without a corresponding ORDER BY clause the data will be returned in an indeterminate order. There may benefits to CDC's MAXDOP suggestion. Not so much for itself, but for the other queries that want to run at the same time.
I'd be inclined to look at moving to stored procedures. Then you can require input parameters and evaluate them before the query gets run in earnest. If, for example, a date range is too big, you can restrict it. You should also find out who is running the expensive query and what they really need. Seems like they might benefit from some ETL. Just some ideas.
Me got 15 x 100 million 32-byte records. Only sequential access and appends needed. The key is a Long. The value is a tuple - (Date, Double, Double). Is there something in this universe which can do this? I am willing to have 15 seperate databases (sql/nosql) or files for each of those 100 million records. I only have a i7 core and 8 GB RAM and 2 TB hard disk.
I have tried PostgreSQL, MySQL, Kyoto Cabinet (with fine tuning) with Protostuff encoding.
SQL DBs (with indices) take forever to do the silliest query.
Kyoto Cabinet's B-Tree can handle upto 15-18 million records beyond which appends take forever.
I am fed up so much that I am thinking of falling back on awk + CSV which I remember used to work for this type of data.
If you scenario means always going through all records in sequence then it may be an overkill to use a database. If you start to need random lookups, replacing/deleting records or checking if a new record is not a duplicate of an older one, a database engine would make more sense.
For the sequential access, a couple of text files or hand-crafted binary files will be easier to handle. You sound like a developer - I would probably go for an own binary format and access it with help of memory-mapped files to improve the sequential read/append speed. No caching, just a sliding window to read the data. I think that it would perform better and even on usual hardware than any DB would; I did such data analysis once. It would also be faster than awking CSV files; however, I am not sure how much and if it satisfied the effort to develop the binary storage, first of all.
As soon as the database becomes interesting, you can have a look at MongoDB and CouchDB. They are used for storing and serving very large amounts of data. (There is a flattering evaluation that compares one of them to traditional DBs.). Databases usually need a reasonable hardware power to perform better; maybe you could check out how those two would do with your data.
--- Ferda
Ferdinand Prantl's answer is very good. Two points:
By your requirements I recommend that you create a very tight binary format. This will be easy to do because your records are fixed size.
If you understand your data well you might be able to compress it. For example, if your key is an increasing log value you don't need to store it entirely. Instead, store the difference to the previous value (which is almost always going to be one). Then, use a standard compression algorithm/library to save on data size big time.
For sequential reads and writes, leveldb will handle your dataset pretty well.
I think that's about 48 gigs of data in one table.
When you get into large databases, you have to look at things a little differently. With an ordinary database (say, tables less than a couple million rows), you can do just about anything as a proof of concept. Even if you're stone ignorant about SQL databases, server tuning, and hardware tuning, the answer you come up with will probably be right. (Although sometimes you might be right for the wrong reason.)
That's not usually the case for large databases.
Unfortunately, you can't just throw 1.5 billion rows straight at an untuned PostgreSQL server, run a couple of queries, and say, "PostgreSQL can't handle this." Most SQL dbms have ways of dealing with lots of data, and most people don't know that much about them.
Here are some of the things that I have to think about when I have to process a lot of data over the long term. (Short-term or one-off processing, it's usually not worth caring a lot about speed. A lot of companies won't invest in more RAM or a dozen high-speed disks--or even a couple of SSDs--for even a long-term solution, let alone a one-time job.)
Server CPU.
Server RAM.
Server disks.
RAID configuration. (RAID 3 might be worth looking at for you.)
Choice of operating system. (64-bit vs 32-bit, BSD v. AT&T derivatives)
Choice of DBMS. (Oracle will usually outperform PostgreSQL, but it costs.)
DBMS tuning. (Shared buffers, sort memory, cache size, etc.)
Choice of index and clustering. (Lots of different kinds nowadays.)
Normalization. (You'd be surprised how often 5NF outperforms lower NFs. Ditto for natural keys.)
Tablespaces. (Maybe putting an index on its own SSD.)
Partitioning.
I'm sure there are others, but I haven't had coffee yet.
But the point is that you can't determine whether, say, PostgreSQL can handle a 48 gig table unless you've accounted for the effect of all those optimizations. With large databases, you come to rely on the cumulative effect of small improvements. You have to do a lot of testing before you can defensibly conclude that a given dbms can't handle a 48 gig table.
Now, whether you can implement those optimizations is a different question--most companies won't invest in a new 64-bit server running Oracle and a dozen of the newest "I'm the fastest hard disk" hard drives to solve your problem.
But someone is going to pay either for optimal hardware and software, for dba tuning expertise, or for programmer time and waiting on suboptimal hardware. I've seen problems like this take months to solve. If it's going to take months, money on hardware is probably a wise investment.
I have a database containing a single huge table. At the moment a query can take anything from 10 to 20 minutes and I need that to go down to 10 seconds. I have spent months trying different products like GridSQL. GridSQL works fine, but is using its own parser which does not have all the needed features. I have also optimized my database in various ways without getting the speedup I need.
I have a theory on how one could scale out queries, meaning that I utilize several nodes to run a single query in parallel. A precondition is that the data is partitioned (vertically), one partition placed on each node. The idea is to take an incoming SQL query and simply run it exactly like it is on all the nodes. When the results are returned to a coordinator node, the same query is run on the union of the resultsets. I realize that an aggregate function like average need to be rewritten into a count and sum to the nodes and that the coordinator divides the sum of the sums with the sum of the counts to get the average.
What kinds of problems could not easily be solved using this model. I believe one issue would be the count distinct function.
Edit: I am getting so many nice suggestions, but none have addressed the method.
It's a data volume problem, not necessarily an architecture problem.
Whether on 1 machine or 1000 machines, if you end up summarizing 1,000,000 rows, you're going to have problems.
Rather than normalizing you data, you need to de-normalize it.
You mention in a comment that your data base is "perfect for your purpose", when, obviously, it's not. It's too slow.
So, something has to give. Your perfect model isn't working, as you need to process too much data in too short of a time. Sounds like you need some higher level data sets than your raw data. Perhaps a data warehousing solution. Who knows, not enough information to really say.
But there are a lot of things you can do to satisfy a specific subset of queries with a good response time, while still allowing ad hoc queries that respond in "10-20 minutes".
Edit regarding comment:
I am not familiar with "GridSQL", or what it does.
If you send several, identical SQL queries to individual "shard" databases, each containing a subset, then the simple selection query will scale to the network (i.e. you will eventually become network bound to the controller), as this is a truly, parallel, stateless process.
The problem becomes, as you mentioned, the secondary processing, notably sorting and aggregates, as this can only be done on the final, "raw" result set.
That means that your controller ends up, inevitably, becoming your bottleneck and, in the end, regardless of how "scaled out" you are, you still have to contend with a data volume issue. If you send your query out to 1000 node and inevitably have to summarize or sort the 1000 row result set from each node, resulting in 1M rows, you still have a long result time and large data processing demand on a single machine.
I don't know what database you are using, and I don't know the specifics about individual databases, but you can see how if you actually partition your data across several disk spindles, and have a decent, modern, multi-core processor, the database implementation itself can handle much of this scaling in terms of parallel disk spindle requests for you. Which implementations actually DO do this, I can't say. I'm just suggesting that it's possible for them to (and some may well do this).
But, my general point, is if you are running, specifically, aggregates, then you are likely processing too much data if you're hitting the raw sources each time. If you analyze your queries, you may well be able to "pre-summarize" your data at various levels of granularity to help avoid the data saturation problem.
For example, if you are storing individual web hits, but are more interested in activity based on each hour of the day (rather than the subsecond data you may be logging), summarizing to the hour of the day alone can reduce your data demand dramatically.
So, scaling out can certainly help, but it may well not be the only solution to the problem, rather it would be a component. Data warehousing is designed to address these kinds of problems, but does not work well with "ad hoc" queries. Rather you need to have a reasonable idea of what kinds of queries you want to support and design it accordingly.
One huge table - can this be normalised at all?
If you are doing mostly select queries, have you considered either normalising to a data warehouse that you then query, or running analysis services and a cube to do your pre-processing for you?
From your question, what you are doing sounds like the sort of thing a cube is optimised for, and could be done without you having to write all the plumbing.
By trying custom solution (grid) you introduce a lot of complexity. Maybe, it's your only solution, but first did you try partitioning the table (native solution)?
I'd seriously be looking into an OLAP solution. The trick with the Cube is once built it can be queried in lots of ways that you may not have considered. And as #HLGEM mentioned, have you addressed indexing?
Even at in millions of rows, a good search should be logarithmic not linear. If you have even one query which results in a scan then your performance will be destroyed. We might need an example of your structure to see if we can help more?
I also agree fully with #Mason, have you profiled your query and investigated the query plan to see where your bottlenecks are. Adding nodes improving speed makes me think that your query might be CPU bound.
David,
Are you using all of the features of GridSQL? You can also use constraint exclusion partitioning, effectively breaking out your big table into several smaller tables. Depending on your WHERE clause, when the query is processed it may look at a lot less data and return results much faster.
Also, are you using multiple logical nodes per physical server? Configuring it that way can take advantage of otherwise idle cores.
If you monitor the servers during execution, is the bottleneck IO or CPU?
Also alluded to here is that you may want to roll up rows in your fact table into summary tables/cubes. I do not know enough about Tableau, will it automatically use the appropriate cube and drill down only when necessary? If so, it seems like you would get big gains doing something like this.
My guess (based on nothing but my gut) is that any gains you might see from parallelization will be eaten up by reaggregation and subsequent queries of the results. Further, I would think that writing might get more complicated with pk/fk/constraints. If this were my world, I would probably create many indexed views on top of my table (and other views) that optimized for the particular queries I need to execute (which I have worked with successfully on 10million+ row tables.)
If you run the incoming query, unpartitioned, on each node, why will any node finish before a single node running the same query would finish? Am I misunderstanding your execution plan?
I think this is, in part, going to depend on the nature of the queries you're executing and, in particular, how many rows contribute to the final result set. But surely you'll need to partition the query somehow among the nodes.
Your method to scale out queries works fine.
In fact, I've implemented such a method in:
http://code.google.com/p/shard-query
It uses a parser, but it supports most SQL constructs.
It doesn't yet support count(distinct expr) but this is doable and I plan to add support in the future.
I also have a tool called Flexviews (google for flexviews materialized views)
This tool lets you create materialized views (summary tables) which include various aggregate functions and joins.
Those tools combined together can yield massive scalability improvements for OLAP type queries.
I'm sure it repeats everywhere. You can 'feel' network is slow, or machine or slow or something. But the server/chassis logs are not showing anything, so IT doesn't believe you. What do you do?
Your regressions are taking twice the time ... but that's not enough
Okay you transfer 100 GB using dd etc, but ... that's not enough.
Okay you get server placed in different chassis for 2 week, it works fine ... but .. that's not enough...
so HOW do you get IT to replace the chassis ?
More specifically:
Is there any suite which I can run on two setups ( supposed to be identical ), which can show up difference in network/cpu/disk access .. which IT will believe ?
Computers don't age and slow down the same way we do. If your server is getting slower -- actually slower, not just feels slower because every other computer you use is getting faster -- then there is a reason and it is possible that you may be able to fix it. I'd try cleaning up some disk space, de-fragmenting the disk, and checking what other processes are running (perhaps someone's added more apps to the system and you're just not getting as many cycles).
If your app uses a database, you may want to analyze your query performance and see if some indices are in order. Queries that perform well when you have little data can start taking a long time as the amount of data grows if they have to use table scans. As a former "IT" guy, I'd also be reluctant to throw hardware at a problem because someone tells me the system is slowing down. I'd want to know what has changed and see if I could get the system running the way it should be. If the app has simply out grown the hardware -- after you've made suitable optimizations -- then upgrading is a reasonable choice.
Run a standard benchmark suite. See if it pinpoints memory, cpu, bus or disk, when compared to a "working" similar computer.
See http://en.wikipedia.org/wiki/Benchmark_(computing)#Common_benchmarks for some tips.
The only way to prove something is to do a stringent audit.
Now traditionally, we should keep the system constant between two different sets while altering the variable we are interested. In this case the variable is the hardware that your code is running on. So in simple terms, you should audit the running of your software on two different sets of hardware, one being the hardware you are unhappy about. And see the difference.
Now if you are to do this properly, which I am sure you are, you will first need to come up with a null hypothesis, something like:
"The slowness of the application is
unrelated to the specific hardware we
are using"
And now you set about disproving that hypothesis in favour of an alternative hypothesis. Once you have collected enough results, you can apply statistical analyses on them, to decide whether any differences are statistically significant. There are analyses to find out how much data you need, and then compare the two sets to decide if the differences are random, or not random (which would disprove your null hypothesis). The type of tests you do will mostly depend on your data, but clever people have made checklists to help us decide.
It sounds like your main problem is being listened to by IT, but raw technical data may not be persuasive to the right people. Getting backup from the business may help you and that means talking about money.
Luckily, both platforms already contain a common piece of software - the application itself - designed to make or save money for someone. Why not measure how quickly it can do that e.g. how long does it take to process an order?
By measuring how long your application spends dealing with each sub task or data source you can get a rough idea of the underlying hardware which is under performing. Writing to a local database, or handling a data structure larger than RAM will impact the disk, making network calls will impact the network hardware, CPU bound calculations will impact there.
This data will never be as precise as a benchmark, and it may require expensive coding, but its easier to translate what it finds into money terms. Log4j's NDC and MDC features, and Springs AOP might be good enabling tools for you.
Run perfmon.msc from Start / Run in Windows 2000 through to Vista. Then just add counters for CPU, disk etc..
For SQL queries you should capture the actual queries then run them manually to see if they are slow.
For instance if using SQL Server, run the profiler from Tools, SQL Server Profiler. Then perform some operations in your program and look at the capture for any suspicous database calls. Copy and paste one of the queries into a new query window in management studio and run it.
For networking you should try artificially limiting your network speed to see how it affects your code (e.g. Traffic Shaper XP is a simple freeware limiter).