SQLite insert speed slows as number of records increases due to an index

Question

Original question

Background

It is well-known that SQLite needs to be fine tuned to achieve insert speeds on the order of 50k inserts/s. There are many questions here regarding slow insert speeds and a wealth of advice and benchmarks.

There are also claims that SQLite can handle large amounts of data, with reports of 50+ GB not causing any problems with the right settings.

I have followed the advice here and elsewhere to achieve these speeds and I'm happy with 35k-45k inserts/s. The problem I have is that all of the benchmarks only demonstrate fast insert speeds with < 1m records. What I am seeing is that insert speed seems to be inversely proportional to table size.

Issue

My use case requires storing 500m to 1b tuples ([x_id, y_id, z_id]) over a few years (1m rows / day) in a link table. The values are all integer IDs between 1 and 2,000,000. There is a single index on z_id.

Performance is great for the first 10m rows, ~35k inserts/s, but by the time the table has ~20m rows, performance starts to suffer. I'm now seeing about 100 inserts/s.

The size of the table is not particularly large. With 20m rows, the size on disk is around 500MB.

The project is written in Perl.

Question

Is this the reality of large tables in SQLite or are there any secrets to maintaining high insert rates for tables with > 10m rows?

Known workarounds which I'd like to avoid if possible

Drop the index, add the records, and re-index: This is fine as a workaround, but doesn't work when the DB still needs to be usable during updates. It won't work to make the database completely inaccessible for x minutes / day
Break the table into smaller subtables / files: This will work in the short term and I have already experimented with it. The problem is that I need to be able to retrieve data from the entire history when querying which means that eventually I'll hit the 62 table attachment limit. Attaching, collecting results in a temp table, and detaching hundreds of times per request seems to be a lot of work and overhead, but I'll try it if there are no other alternatives.
Set SQLITE_FCNTL_CHUNK_SIZE: I don't know C (?!), so I'd prefer to not learn it just to get this done. I can't see any way to set this parameter using Perl though.

UPDATE

Following Tim's suggestion that an index was causing increasingly slow insert times despite SQLite's claims that it is capable of handling large data sets, I performed a benchmark comparison with the following settings:

inserted rows: 14 million
commit batch size: 50,000 records
cache_size pragma: 10,000
page_size pragma: 4,096
temp_store pragma: memory
journal_mode pragma: delete
synchronous pragma: off

In my project, as in the benchmark results below, a file-based temporary table is created and SQLite's built-in support for importing CSV data is used. The temporary table is then attached to the receiving database and sets of 50,000 rows are inserted with an insert-select statement. Therefore, the insert times do not reflect file to database insert times, but rather table to table insert speed. Taking the CSV import time into account would reduce the speeds by 25-50% (a very rough estimate, it doesn't take long to import the CSV data).

Clearly having an index causes the slowdown in insert speed as table size increases.

Plot of SQLite insert speed and table size

It's quite clear from the data above that the correct answer can be assigned to Tim's answer rather than the assertions that SQLite just can't handle it. Clearly it can handle large datasets if indexing that dataset is not part of your use case. I have been using SQLite for just that, as a backend for a logging system, for a while now which does not need to be indexed, so I was quite surprised at the slowdown I experienced.

Conclusion

If anyone finds themselves wanting to store a large amount of data using SQLite and have it indexed, using shards may be the answer. I eventually settled on using the first three characters of an MD5 hash a unique column in z to determine assignment to one of 4,096 databases. Since my use case is primarily archival in nature, the schema will not change and queries will never require shard walking. There is a limit to database size since extremely old data will be reduced and eventually discarded, so this combination of sharding, pragma settings, and even some denormalisation gives me a nice balance that will, based on the benchmarking above, maintain an insert speed of at least 10k inserts / second.

How are you using transactions? How large have you configured the page cache? — CL.
@CL. cache_size is set to 10000. All inserts are in one transaction with commits every 50k inserts. These values were chosen after extensive testing to find the fastest insert speed (35k-45k inserts/s), but that speed drops as the number of records increases past about 10m. — user918938
Going beyond your specific question here: may I ask, are you using the index on z_id to find individual records or to select ranges? — Tim
@Tim it's a link table, so items get selected from table_z then linked to table_y and table_x via z_id through this table. So, to answer your question, it helps find individual records. — user918938
@veryhungrymike: In that case, you could look into a non-indexed hash-table nested-relational db that would allow you to instantly find your way to z_id rows and the y_ids and x_ids linked to a particular z_id without the indexing overhead and the concomitant degraded performance during inserts as the index grows. One that puts greater weight on the digits of z_id with greatest variation (right-weighted) would give you good distribution. — Tim

Tim Tim · Accepted Answer · 2013-04-04T11:25:50

If your requirement is to find a particular z_id and the x_ids and y_ids linked to it (as distinct from quickly selecting a range of z_ids) you could look into a non-indexed hash-table nested-relational db that would allow you to instantly find your way to a particular z_id in order to get its y_ids and x_ids -- without the indexing overhead and the concomitant degraded performance during inserts as the index grows. In order to avoid clumping (aka bucket collisions), choose a key hashing algorithm that puts greatest weight on the digits of z_id with greatest variation (right-weighted).

P.S. A database that uses a b-tree may at first appear faster than a db that uses linear hashing, say, but the insert performance will remain level with the linear hash as performance on the b-tree begins to degrade.

P.P.S. To answer @kawing-chiu's question: the core feature relevant here is that such a database relies on so-called "sparse" tables in which the physical location of a record is determined by a hashing algorithm which takes the record key as input. This approach permits a seek directly to the record's location in the table without the intermediary of an index. As there is no need to traverse indexes or to re-balance indexes, insert-times remain constant as the table becomes more densely populated. With a b-tree, by contrast, insert times degrade as the index tree grows. OLTP applications with large numbers of concurrent inserts can benefit from such a sparse-table approach. The records are scattered throughout the table. The downside of records being scattered across the "tundra" of the sparse table is that gathering large sets of records which have a value in common, such as a postal code, can be slower. The hashed sparse-table approach is optimized to insert and retrieve individual records, and to retrieve networks of related records, not large sets of records that have some field value in common.

A nested relational database is one that permits tuples within a column of a row.

SQLite insert speed slows as number of records increases due to an index

Original question

Background

Issue

Question

Known workarounds which I'd like to avoid if possible

UPDATE

Conclusion

5 Answers

Schema:

Data - 2 Million Rows:

Databases: 1; Tables: 1; Indexes: 0

Databases: 1; Tables: 1; Indexes: 1 (`md5`)

Databases: 1; Tables: 20 (one per 100,000 records); Indexes: 1 (`md5`)

SQLite insert speed slows as number of records increases due to an index

Original question

Background

Issue

Question

Known workarounds which I'd like to avoid if possible

UPDATE

Conclusion

5 Answers

Schema:

Data - 2 Million Rows:

Databases: 1; Tables: 1; Indexes: 0

Databases: 1; Tables: 1; Indexes: 1 (md5)

Databases: 1; Tables: 20 (one per 100,000 records); Indexes: 1 (md5)

Databases: 1; Tables: 1; Indexes: 1 (`md5`)

Databases: 1; Tables: 20 (one per 100,000 records); Indexes: 1 (`md5`)