BSONqs.jl

Mostly compatible Fork of BSON package with focus on composite type performance
Author richiejp
Popularity
1 Star
Updated Last
9 Months Ago
Started In
January 2019

BSONqs

This is a fork of BSON.jl, with much better performance for loading composite data types in particular. The 'qs' stands for "quick structs".

BSONqs appears to be between 2-4x faster than BSON in read benchmarks. See the performance section below for more info.

Usage

Usage is mostly the same as the original package. You should be able to use this as a drop in replacement, except that you may need to alias the package name.

using BSONqs

const BSON = BSONqs

Currently the load function does not support some of the more exotic data types, however you may use load_compat instead. There are also now two forms of the parse function.

parse(x::Union{IO, String})
parse(x::Union{IO, String}, ctx::ParseCtx; mmap=false)

The later provides the best performance in most circumstances and is the least compatible. It should be noted that load(x; args...) = parse(x, ParseCtx(); args...), but that parse(x) is not the same as load_compat(x).

On Linux atleast you can set mmap=true for better perfomance when loading from a file.

Partial loading

Finally there is an experimental interface for lazily loading a BSON document one member at a time. This also allows you to specify the type of each document member.

import Mmap

open("a_file.bson") do fio
  io = IOBuffer(Mmap.mmap(fio))
  doc = Document(io, DefaultMemberType)

  # Get a doc member, parsing it as the DefaultMemberType
  val = doc[:a_member_key]
  # Get a doc member, parsing it as T
  val = doc[T, :a_member_key]

  # iterate over all the members, parsing them as DefaultMemberType
  for (k, v) in doc
    ...
  end

# Load the entire document into a Dict, again using DefaultMemberType
  Dict(doc)
end

Lazy or partial loading could be useful if you have a large document with many large members. I have used the word 'partial', because calling Document will scan the input stream and build an index which may not be considered lazy enough. Note that there is no automatic caching of parsed results.

Specifying a concrete type allows some parsing to be skipped.

Performance hints

This library works best with large, repetitive datasets with concrete types. You should always try to use concrete types in structs in Julia (see the official docs).

This library makes heavy use of @generated and type specific functions, so the compilation time is longer than the original. This means that (in theory) for smaller or highly irregular datasets, the original library may be faster for the first call to load where the dataset is small and contains one or more uncached data types.

Also for generic BSON documents, without any Julia type data, this library may or may not be faster.

If your platform supports it, use mmap. It is generally faster anyway, but in this case it also allows us to avoid unecessary copies and allocations. Below is a comparison of the original library and BSONqs with and without mmap on a common dataset (on the second pass).

julia> @time BSON.load("vgg19.bson");
  0.626661 seconds (1.97 k allocations: 1.071 GiB, 33.95% gc time)

julia> @time BSONqs.load("vgg19.bson");
  0.482821 seconds (1.82 k allocations: 1.071 GiB, 42.69% gc time)

julia> @time BSONqs.load("vgg19.bson"; mmap=true);
  0.237986 seconds (1.82 k allocations: 548.121 MiB, 26.12% gc time)

In any case, if performance is important to you, you should create a benchmark with your data. Finally note that this library mainly uses the same serialization code as the original, so write performance should be the same (although at the time of writing the original has a bug which makes it much worse). If you are interested in write performance then please let me know.