UnalignedVectors.jl

Create arrays from memory buffers that lack appropriate alignment
Author JuliaArrays
Popularity
4 Stars
Updated Last
2 Years Ago
Started In
May 2017

UnalignedVectors

NOTE: This package is deprecated. On Julia 0.7 or higher, use reinterpret directly.

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Julia allows you to create arrays from a pointer to a memory buffer, but an Array{T} requires a pointer that is a multiple of sizeof(T). This package allows you to create an AbstractArray with element type T even when the pointer lacks proper alignment.

Usage example: memory mapping

A common usage might be memory mapping, using Julia's Mmap.mmap functionality. Let's create a fake file format with the following structure:

  • magic bytes "BIGARRAY" followed a newline
  • the number of dimensions in the array
  • the size of the array
  • the data of the array (always Float64)

The rub is that the data will always start with an odd offset, because the magic bytes (plus the newline) total 9 bytes, and the dimension information always adds an even number of types. As a consequence, the memory buffer is not properly aligned for Float64 (which requires the pointer address to be a multiple of 8) and consequently ordinary mmap operations will fail.

To try this out, first let's write such a file:

open("/tmp/testfile.bga", "w") do io
    write(io, "BIGARRAY\n")
    A = [1.0 2.0;
         3.0 4.0]
    write(io, ndims(A))
    for s in size(A)
        write(io, s)
    end
    write(io, A)
end

Now let's create a format reader (note that the best way to define a new format is using FileIO, but for simplicity we'll keep things very low level):

function reader(io)
    String(read(io, 9)) == "BIGARRAY\n" || error("file is not a BIGARRAY file")
    n = read(io, Int)             # read the number of dimensions
    sz = (read(io, Int, n)...)    # read the size
    # Mmap the buffer:
    a = Mmap.mmap(io, Vector{UInt8}, sizeof(Float64)*prod(sz), position(io))
    # Create an array of the desired eltype and size:
    v = UnalignedVector{Float64}(a)
    reshape(v, sz)
end

The key thing to note about this implementation is that we mmaped the buffer as a Vector{UInt8}; had we tried a Vector{Float64}, more recent versions of Julia would have given us an error that would look something like this:

ERROR: ArgumentError: unsafe_wrap: pointer 0x7f89817ae021 is not properly aligned to 8 bytes
Stacktrace:
 [1] #mmap#1(::Bool, ::Bool, ::Function, ::IOStream, ::Type{Array{Float64,2}}, ::Tuple{Int64,Int64}, ::Int64) at ./mmap.jl:139
 [2] mmap(::IOStream, ::Type{Array{Float64,2}}, ::Tuple{Int64,Int64}, ::Int64) at ./mmap.jl:102
 [3] reader(::IOStream) at ./REPL[4]:5
 [4] open(::##5#6, ::String) at ./iostream.jl:152

In contrast, since UInt8 has an alignment of 1, it's always safe for mmapping.

To create the array with desired element type, the UnalignedVector{Float64}(a) call creates an AbstractVector{Float64} out of the memory buffer, which we then reshape to the desired size. If you want to try this, just read the file with

B = open("/tmp/testfile.bga") do io
    reader(io)
end

and you should see that B == A.