https://github.com/JuliaLang/julia
Tip revision: 637cc5fe3f20355615b952742f669892269e468c authored by Andy Ferris on 29 August 2017, 12:20:55 UTC
Added a MappedArray wrapper
Added a MappedArray wrapper
Tip revision: 637cc5f
mmap.jl
# This file is a part of Julia. License is MIT: https://julialang.org/license
module Mmap
const PAGESIZE = Int(Sys.isunix() ? ccall(:jl_getpagesize, Clong, ()) : ccall(:jl_getallocationgranularity, Clong, ()))
# for mmaps not backed by files
mutable struct Anonymous <: IO
name::AbstractString
readonly::Bool
create::Bool
end
"""
Mmap.Anonymous(name, readonly, create)
Create an `IO`-like object for creating zeroed-out mmapped-memory that is not tied to a file
for use in `Mmap.mmap`. Used by `SharedArray` for creating shared memory arrays.
"""
Anonymous() = Anonymous("",false,true)
Base.isopen(::Anonymous) = true
Base.isreadable(::Anonymous) = true
Base.iswritable(a::Anonymous) = !a.readonly
const INVALID_HANDLE_VALUE = -1
# const used for zeroed, anonymous memory; same value on Windows & Unix; say what?!
gethandle(io::Anonymous) = INVALID_HANDLE_VALUE
# platform-specific mmap utilities
if Sys.isunix()
const PROT_READ = Cint(1)
const PROT_WRITE = Cint(2)
const MAP_SHARED = Cint(1)
const MAP_PRIVATE = Cint(2)
const MAP_ANONYMOUS = Cint(Sys.isbsd() ? 0x1000 : 0x20)
const F_GETFL = Cint(3)
gethandle(io::IO) = fd(io)
# Determine a stream's read/write mode, and return prot & flags appropriate for mmap
function settings(s::Int, shared::Bool)
flags = shared ? MAP_SHARED : MAP_PRIVATE
if s == INVALID_HANDLE_VALUE
flags |= MAP_ANONYMOUS
prot = PROT_READ | PROT_WRITE
else
mode = ccall(:fcntl,Cint,(Cint,Cint),s,F_GETFL)
systemerror("fcntl F_GETFL", mode == -1)
mode = mode & 3
prot = mode == 0 ? PROT_READ : mode == 1 ? PROT_WRITE : PROT_READ | PROT_WRITE
if prot & PROT_READ == 0
throw(ArgumentError("mmap requires read permissions on the file (choose r+)"))
end
end
return prot, flags, (prot & PROT_WRITE) > 0
end
# Before mapping, grow the file to sufficient size
# Note: a few mappable streams do not support lseek. When Julia
# supports structures in ccall, switch to fstat.
grow!(::Anonymous,o::Integer,l::Integer) = return
function grow!(io::IO, offset::Integer, len::Integer)
pos = position(io)
filelen = filesize(io)
if filelen < offset + len
failure = ccall(:jl_ftruncate, Cint, (Cint, Int64), fd(io), offset+len)
Base.systemerror(:ftruncate, failure != 0)
end
seek(io, pos)
return
end
elseif Sys.iswindows()
const DWORD = Culong
const PAGE_READONLY = DWORD(0x02)
const PAGE_READWRITE = DWORD(0x04)
const PAGE_WRITECOPY = DWORD(0x08)
const PAGE_EXECUTE_READ = DWORD(0x20)
const PAGE_EXECUTE_READWRITE = DWORD(0x40)
const PAGE_EXECUTE_WRITECOPY = DWORD(0x80)
const FILE_MAP_COPY = DWORD(0x01)
const FILE_MAP_WRITE = DWORD(0x02)
const FILE_MAP_READ = DWORD(0x04)
const FILE_MAP_EXECUTE = DWORD(0x20)
function gethandle(io::IO)
handle = Libc._get_osfhandle(RawFD(fd(io))).handle
systemerror("could not get handle for file to map: $(Libc.FormatMessage())", handle == -1)
return Int(handle)
end
settings(sh::Anonymous) = sh.name, sh.readonly, sh.create
settings(io::IO) = Ptr{Cwchar_t}(0), isreadonly(io), true
else
error("mmap not defined for this OS")
end # os-test
# core implementation of mmap
"""
Mmap.mmap(io::Union{IOStream,AbstractString,Mmap.AnonymousMmap}[, type::Type{Array{T,N}}, dims, offset]; grow::Bool=true, shared::Bool=true)
Mmap.mmap(type::Type{Array{T,N}}, dims)
Create an `Array` whose values are linked to a file, using memory-mapping. This provides a
convenient way of working with data too large to fit in the computer's memory.
The type is an `Array{T,N}` with a bits-type element of `T` and dimension `N` that
determines how the bytes of the array are interpreted. Note that the file must be stored in
binary format, and no format conversions are possible (this is a limitation of operating
systems, not Julia).
`dims` is a tuple or single [`Integer`](@ref) specifying the size or length of the array.
The file is passed via the stream argument, either as an open `IOStream` or filename string.
When you initialize the stream, use `"r"` for a "read-only" array, and `"w+"` to create a
new array used to write values to disk.
If no `type` argument is specified, the default is `Vector{UInt8}`.
Optionally, you can specify an offset (in bytes) if, for example, you want to skip over a
header in the file. The default value for the offset is the current stream position for an
`IOStream`.
The `grow` keyword argument specifies whether the disk file should be grown to accommodate
the requested size of array (if the total file size is < requested array size). Write
privileges are required to grow the file.
The `shared` keyword argument specifies whether the resulting `Array` and changes made to it
will be visible to other processes mapping the same file.
For example, the following code
```julia
# Create a file for mmapping
# (you could alternatively use mmap to do this step, too)
A = rand(1:20, 5, 30)
s = open("/tmp/mmap.bin", "w+")
# We'll write the dimensions of the array as the first two Ints in the file
write(s, size(A,1))
write(s, size(A,2))
# Now write the data
write(s, A)
close(s)
# Test by reading it back in
s = open("/tmp/mmap.bin") # default is read-only
m = read(s, Int)
n = read(s, Int)
A2 = Mmap.mmap(s, Matrix{Int}, (m,n))
```
creates a `m`-by-`n` `Matrix{Int}`, linked to the file associated with stream `s`.
A more portable file would need to encode the word size -- 32 bit or 64 bit -- and endianness
information in the header. In practice, consider encoding binary data using standard formats
like HDF5 (which can be used with memory-mapping).
"""
function mmap(io::IO,
::Type{Array{T,N}}=Vector{UInt8},
dims::NTuple{N,Integer}=(div(filesize(io)-position(io),sizeof(T)),),
offset::Integer=position(io); grow::Bool=true, shared::Bool=true) where {T,N}
# check inputs
isopen(io) || throw(ArgumentError("$io must be open to mmap"))
isbits(T) || throw(ArgumentError("unable to mmap $T; must satisfy isbits(T) == true"))
len = prod(dims) * sizeof(T)
len >= 0 || throw(ArgumentError("requested size must be ≥ 0, got $len"))
len == 0 && return Array{T}(ntuple(x->0,Val(N)))
len < typemax(Int) - PAGESIZE || throw(ArgumentError("requested size must be < $(typemax(Int)-PAGESIZE), got $len"))
offset >= 0 || throw(ArgumentError("requested offset must be ≥ 0, got $offset"))
# shift `offset` to start of page boundary
offset_page::Int64 = div(offset, PAGESIZE) * PAGESIZE
# add (offset - offset_page) to `len` to get total length of memory-mapped region
mmaplen = (offset - offset_page) + len
file_desc = gethandle(io)
# platform-specific mmapping
@static if Sys.isunix()
prot, flags, iswrite = settings(file_desc, shared)
iswrite && grow && grow!(io, offset, len)
# mmap the file
ptr = ccall(:jl_mmap, Ptr{Void}, (Ptr{Void}, Csize_t, Cint, Cint, Cint, Int64), C_NULL, mmaplen, prot, flags, file_desc, offset_page)
systemerror("memory mapping failed", reinterpret(Int,ptr) == -1)
else
name, readonly, create = settings(io)
szfile = convert(Csize_t, len + offset)
readonly && szfile > filesize(io) && throw(ArgumentError("unable to increase file size to $szfile due to read-only permissions"))
handle = create ? ccall(:CreateFileMappingW, stdcall, Ptr{Void}, (Cptrdiff_t, Ptr{Void}, DWORD, DWORD, DWORD, Cwstring),
file_desc, C_NULL, readonly ? PAGE_READONLY : PAGE_READWRITE, szfile >> 32, szfile & typemax(UInt32), name) :
ccall(:OpenFileMappingW, stdcall, Ptr{Void}, (DWORD, Cint, Cwstring),
readonly ? FILE_MAP_READ : FILE_MAP_WRITE, true, name)
handle == C_NULL && error("could not create file mapping: $(Libc.FormatMessage())")
ptr = ccall(:MapViewOfFile, stdcall, Ptr{Void}, (Ptr{Void}, DWORD, DWORD, DWORD, Csize_t),
handle, readonly ? FILE_MAP_READ : FILE_MAP_WRITE, offset_page >> 32, offset_page & typemax(UInt32), (offset - offset_page) + len)
ptr == C_NULL && error("could not create mapping view: $(Libc.FormatMessage())")
end # os-test
# convert mmapped region to Julia Array at `ptr + (offset - offset_page)` since file was mapped at offset_page
A = unsafe_wrap(Array, convert(Ptr{T}, UInt(ptr) + UInt(offset - offset_page)), dims)
finalizer(A, function(x)
@static if Sys.isunix()
systemerror("munmap", ccall(:munmap, Cint, (Ptr{Void}, Int), ptr, mmaplen) != 0)
else
status = ccall(:UnmapViewOfFile, stdcall, Cint, (Ptr{Void},), ptr)!=0
status |= ccall(:CloseHandle, stdcall, Cint, (Ptr{Void},), handle)!=0
status || error("could not unmap view: $(Libc.FormatMessage())")
end
end)
return A
end
mmap(file::AbstractString,
::Type{T}=Vector{UInt8},
dims::NTuple{N,Integer}=(div(filesize(file),sizeof(eltype(T))),),
offset::Integer=Int64(0); grow::Bool=true, shared::Bool=true) where {T<:Array,N} =
open(io->mmap(io, T, dims, offset; grow=grow, shared=shared), file, isfile(file) ? "r+" : "w+")::Array{eltype(T),N}
# using a length argument instead of dims
mmap(io::IO, ::Type{T}, len::Integer, offset::Integer=position(io); grow::Bool=true, shared::Bool=true) where {T<:Array} =
mmap(io, T, (len,), offset; grow=grow, shared=shared)
mmap(file::AbstractString, ::Type{T}, len::Integer, offset::Integer=Int64(0); grow::Bool=true, shared::Bool=true) where {T<:Array} =
open(io->mmap(io, T, (len,), offset; grow=grow, shared=shared), file, isfile(file) ? "r+" : "w+")::Vector{eltype(T)}
# constructors for non-file-backed (anonymous) mmaps
mmap(::Type{T}, dims::NTuple{N,Integer}; shared::Bool=true) where {T<:Array,N} = mmap(Anonymous(), T, dims, Int64(0); shared=shared)
mmap(::Type{T}, i::Integer...; shared::Bool=true) where {T<:Array} = mmap(Anonymous(), T, convert(Tuple{Vararg{Int}},i), Int64(0); shared=shared)
"""
Mmap.mmap(io, BitArray, [dims, offset])
Create a `BitArray` whose values are linked to a file, using memory-mapping; it has the same
purpose, works in the same way, and has the same arguments, as [`mmap`](@ref Mmap.mmap), but
the byte representation is different.
**Example**: `B = Mmap.mmap(s, BitArray, (25,30000))`
This would create a 25-by-30000 `BitArray`, linked to the file associated with stream `s`.
"""
function mmap(io::IOStream, ::Type{<:BitArray}, dims::NTuple{N,Integer},
offset::Int64=position(io); grow::Bool=true, shared::Bool=true) where N
n = prod(dims)
nc = Base.num_bit_chunks(n)
chunks = mmap(io, Vector{UInt64}, (nc,), offset; grow=grow, shared=shared)
if !isreadonly(io)
chunks[end] &= Base._msk_end(n)
else
if chunks[end] != chunks[end] & Base._msk_end(n)
throw(ArgumentError("the given file does not contain a valid BitArray of size $(join(dims, 'x')) (open with \"r+\" mode to override)"))
end
end
B = BitArray{N}(ntuple(i->0,Val(N))...)
B.chunks = chunks
B.len = n
if N != 1
B.dims = dims
end
return B
end
mmap(file::AbstractString, ::Type{T}, dims::NTuple{N,Integer}, offset::Integer=Int64(0);grow::Bool=true, shared::Bool=true) where {T<:BitArray,N} =
open(io->mmap(io, T, dims, offset; grow=grow, shared=shared), file, isfile(file) ? "r+" : "w+")::BitArray{N}
# using a length argument instead of dims
mmap(io::IO, ::Type{T}, len::Integer, offset::Integer=position(io); grow::Bool=true, shared::Bool=true) where {T<:BitArray} =
mmap(io, T, (len,), offset; grow=grow, shared=shared)
mmap(file::AbstractString, ::Type{T}, len::Integer, offset::Integer=Int64(0); grow::Bool=true, shared::Bool=true) where {T<:BitArray} =
open(io->mmap(io, T, (len,), offset; grow=grow, shared=shared), file, isfile(file) ? "r+" : "w+")::BitVector
# constructors for non-file-backed (anonymous) mmaps
mmap(::Type{T}, dims::NTuple{N,Integer}; shared::Bool=true) where {T<:BitArray,N} = mmap(Anonymous(), T, dims, Int64(0); shared=shared)
mmap(::Type{T}, i::Integer...; shared::Bool=true) where {T<:BitArray} = mmap(Anonymous(), T, convert(Tuple{Vararg{Int}},i), Int64(0); shared=shared)
# msync flags for unix
const MS_ASYNC = 1
const MS_INVALIDATE = 2
const MS_SYNC = 4
"""
Mmap.sync!(array)
Forces synchronization between the in-memory version of a memory-mapped `Array` or
`BitArray` and the on-disk version.
"""
function sync!(m::Array{T}, flags::Integer=MS_SYNC) where T
offset = rem(UInt(pointer(m)), PAGESIZE)
ptr = pointer(m) - offset
@static if Sys.isunix()
systemerror("msync",
ccall(:msync, Cint, (Ptr{Void}, Csize_t, Cint), ptr, length(m) * sizeof(T), flags) != 0)
else
systemerror("could not FlushViewOfFile: $(Libc.FormatMessage())",
ccall(:FlushViewOfFile, stdcall, Cint, (Ptr{Void}, Csize_t), ptr, length(m)) == 0)
end
end
sync!(B::BitArray, flags::Integer=MS_SYNC) = sync!(B.chunks, flags)
end # module