Revision 553c9205901310b994fddf16b99ec657ee817089 authored by kshyatt on 31 March 2017, 23:18:08 UTC, committed by kshyatt on 31 March 2017, 23:18:08 UTC
1 parent bd84fa1
sharedarray.jl
# This file is a part of Julia. License is MIT: http://julialang.org/license
import .Serializer: serialize_cycle_header, serialize_type, writetag, UNDEFREF_TAG
mutable struct SharedArray{T,N} <: DenseArray{T,N}
dims::NTuple{N,Int}
pids::Vector{Int}
refs::Vector
# The segname is currently used only in the test scripts to ensure that
# the shmem segment has been unlinked.
segname::String
# Fields below are not to be serialized
# Local shmem map.
s::Array{T,N}
# idx of current worker's pid in the pids vector, 0 if this shared array is not mapped locally.
pidx::Int
# the local partition into the array when viewed as a single dimensional array.
# this can be removed when @parallel or its equivalent supports looping on
# a subset of workers.
loc_subarr_1d::SubArray{T,1,Array{T,1},Tuple{UnitRange{Int}},true}
function SharedArray{T,N}(d,p,r,sn,s) where {T,N}
new(d,p,r,sn,s,0,view(Array{T}(ntuple(d->0,N)), 1:0))
end
end
"""
SharedArray{T}(dims::NTuple; init=false, pids=Int[])
SharedArray{T,N}(...)
Construct a `SharedArray` of a bits type `T` and size `dims` across the
processes specified by `pids` - all of which have to be on the same
host. If `N` is specified by calling `SharedArray{T,N}(dims)`, then
`N` must match the length of `dims`.
If `pids` is left unspecified, the shared array will be mapped across all processes on the
current host, including the master. But, `localindexes` and `indexpids` will only refer to
worker processes. This facilitates work distribution code to use workers for actual
computation with the master process acting as a driver.
If an `init` function of the type `initfn(S::SharedArray)` is specified, it is called on all
the participating workers.
SharedArray{T}(filename::AbstractString, dims::NTuple, [offset=0]; mode=nothing, init=false, pids=Int[])
SharedArray{T,N}(...)
Construct a `SharedArray` backed by the file `filename`, with element
type `T` (must be a bits type) and size `dims`, across the processes
specified by `pids` - all of which have to be on the same host. This
file is mmapped into the host memory, with the following consequences:
- The array data must be represented in binary format (e.g., an ASCII
format like CSV cannot be supported)
- Any changes you make to the array values (e.g., `A[3] = 0`) will
also change the values on disk
If `pids` is left unspecified, the shared array will be mapped across
all processes on the current host, including the master. But,
`localindexes` and `indexpids` will only refer to worker
processes. This facilitates work distribution code to use workers for
actual computation with the master process acting as a driver.
`mode` must be one of `"r"`, `"r+"`, `"w+"`, or `"a+"`, and defaults
to `"r+"` if the file specified by `filename` already exists, or
`"w+"` if not. If an `init` function of the type
`initfn(S::SharedArray)` is specified, it is called on all the
participating workers. You cannot specify an `init` function if the
file is not writable.
`offset` allows you to skip the specified number of bytes at the
beginning of the file.
"""
SharedArray
function (::Type{SharedArray{T,N}}){T,N}(dims::Dims{N}; init=false, pids=Int[])
isbits(T) || throw(ArgumentError("type of SharedArray elements must be bits types, got $(T)"))
pids, onlocalhost = shared_pids(pids)
local shm_seg_name = ""
local s = Array{T}(ntuple(d->0,N))
local S
local shmmem_create_pid
try
# On OSX, the shm_seg_name length must be <= 31 characters (including the terminating NULL character)
shm_seg_name = @sprintf("/jl%06u%s", getpid() % 10^6, randstring(20))
if onlocalhost
shmmem_create_pid = myid()
s = shm_mmap_array(T, dims, shm_seg_name, JL_O_CREAT | JL_O_RDWR)
else
# The shared array is created on a remote machine
shmmem_create_pid = pids[1]
remotecall_fetch(pids[1]) do
shm_mmap_array(T, dims, shm_seg_name, JL_O_CREAT | JL_O_RDWR)
nothing
end
end
func_mapshmem = () -> shm_mmap_array(T, dims, shm_seg_name, JL_O_RDWR)
refs = Array{Future}(length(pids))
for (i, p) in enumerate(pids)
refs[i] = remotecall(func_mapshmem, p)
end
# Wait till all the workers have mapped the segment
for ref in refs
wait(ref)
end
# All good, immediately unlink the segment.
if (prod(dims) > 0) && (sizeof(T) > 0)
if onlocalhost
rc = shm_unlink(shm_seg_name)
else
rc = remotecall_fetch(shm_unlink, shmmem_create_pid, shm_seg_name)
end
systemerror("Error unlinking shmem segment " * shm_seg_name, rc != 0)
end
S = SharedArray{T,N}(dims, pids, refs, shm_seg_name, s)
initialize_shared_array(S, onlocalhost, init, pids)
shm_seg_name = ""
finally
if shm_seg_name != ""
remotecall_fetch(shm_unlink, shmmem_create_pid, shm_seg_name)
end
end
S
end
(::Type{SharedArray{T,N}}){T,N}(I::Integer...; kwargs...) =
SharedArray{T,N}(I; kwargs...)
(::Type{SharedArray{T}}){T}(d::NTuple; kwargs...) =
SharedArray{T,length(d)}(d; kwargs...)
(::Type{SharedArray{T}}){T}(I::Integer...; kwargs...) =
SharedArray{T,length(I)}(I; kwargs...)
(::Type{SharedArray{T}}){T}(m::Integer; kwargs...) =
SharedArray{T,1}(m; kwargs...)
(::Type{SharedArray{T}}){T}(m::Integer, n::Integer; kwargs...) =
SharedArray{T,2}(m, n; kwargs...)
(::Type{SharedArray{T}}){T}(m::Integer, n::Integer, o::Integer; kwargs...) =
SharedArray{T,3}(m, n, o; kwargs...)
function (::Type{SharedArray{T,N}}){T,N}(filename::AbstractString, dims::NTuple{N,Int},
offset::Integer=0; mode=nothing, init=false, pids::Vector{Int}=Int[])
if !isabspath(filename)
throw(ArgumentError("$filename is not an absolute path; try abspath(filename)?"))
end
if !isbits(T)
throw(ArgumentError("type of SharedArray elements must be bits types, got $(T)"))
end
pids, onlocalhost = shared_pids(pids)
# If not supplied, determine the appropriate mode
have_file = onlocalhost ? isfile(filename) : remotecall_fetch(isfile, pids[1], filename)
if mode === nothing
mode = have_file ? "r+" : "w+"
end
workermode = mode == "w+" ? "r+" : mode # workers don't truncate!
# Ensure the file will be readable
if !(mode in ("r", "r+", "w+", "a+"))
throw(ArgumentError("mode must be readable, but $mode is not"))
end
if init !== false
typeassert(init, Function)
if !(mode in ("r+", "w+", "a+"))
throw(ArgumentError("cannot initialize unwritable array (mode = $mode)"))
end
end
if mode == "r" && !isfile(filename)
throw(ArgumentError("file $filename does not exist, but mode $mode cannot create it"))
end
# Create the file if it doesn't exist, map it if it does
refs = Array{Future}(length(pids))
func_mmap = mode -> open(filename, mode) do io
Mmap.mmap(io, Array{T,N}, dims, offset; shared=true)
end
s = Array{T}(ntuple(d->0,N))
if onlocalhost
s = func_mmap(mode)
refs[1] = remotecall(pids[1]) do
func_mmap(workermode)
end
else
refs[1] = remotecall_wait(pids[1]) do
func_mmap(mode)
end
end
# Populate the rest of the workers
for i = 2:length(pids)
refs[i] = remotecall(pids[i]) do
func_mmap(workermode)
end
end
# Wait till all the workers have mapped the segment
for ref in refs
wait(ref)
end
S = SharedArray{T,N}(dims, pids, refs, filename, s)
initialize_shared_array(S, onlocalhost, init, pids)
S
end
(::Type{SharedArray{T}}){T,N}(filename::AbstractString, dims::NTuple{N,Int}, offset::Integer=0;
mode=nothing, init=false, pids::Vector{Int}=Int[]) =
SharedArray{T,N}(filename, dims, offset; mode=mode, init=init, pids=pids)
function initialize_shared_array(S, onlocalhost, init, pids)
if onlocalhost
init_loc_flds(S)
else
S.pidx = 0
end
# if present, init function is called on each of the parts
if isa(init, Function)
@sync begin
for p in pids
@async remotecall_wait(init, p, S)
end
end
end
finalizer(S, finalize_refs)
S
end
function finalize_refs{T,N}(S::SharedArray{T,N})
if length(S.pids) > 0
for r in S.refs
finalize(r)
end
empty!(S.pids)
empty!(S.refs)
init_loc_flds(S)
S.s = Array{T}(ntuple(d->0,N))
end
S
end
SharedVector{T} = SharedArray{T,1}
SharedMatrix{T} = SharedArray{T,2}
length(S::SharedArray) = prod(S.dims)
size(S::SharedArray) = S.dims
ndims(S::SharedArray) = length(S.dims)
IndexStyle(::Type{<:SharedArray}) = IndexLinear()
function reshape{T,N}(a::SharedArray{T}, dims::NTuple{N,Int})
if length(a) != prod(dims)
throw(DimensionMismatch("dimensions must be consistent with array size"))
end
refs = Array{Future}(length(a.pids))
for (i, p) in enumerate(a.pids)
refs[i] = remotecall(p, a.refs[i], dims) do r,d
reshape(fetch(r),d)
end
end
A = SharedArray{T,N}(dims, a.pids, refs, a.segname, reshape(a.s, dims))
init_loc_flds(A)
A
end
"""
procs(S::SharedArray)
Get the vector of processes mapping the shared array.
"""
procs(S::SharedArray) = S.pids
"""
indexpids(S::SharedArray)
Returns the current worker's index in the list of workers
mapping the `SharedArray` (i.e. in the same list returned by `procs(S)`), or
0 if the `SharedArray` is not mapped locally.
"""
indexpids(S::SharedArray) = S.pidx
"""
sdata(S::SharedArray)
Returns the actual `Array` object backing `S`.
"""
sdata(S::SharedArray) = S.s
sdata(A::AbstractArray) = A
"""
localindexes(S::SharedArray)
Returns a range describing the "default" indexes to be handled by the
current process. This range should be interpreted in the sense of
linear indexing, i.e., as a sub-range of `1:length(S)`. In
multi-process contexts, returns an empty range in the parent process
(or any process for which [`indexpids`](@ref) returns 0).
It's worth emphasizing that `localindexes` exists purely as a
convenience, and you can partition work on the array among workers any
way you wish. For a `SharedArray`, all indexes should be equally fast
for each worker process.
"""
localindexes(S::SharedArray) = S.pidx > 0 ? range_1dim(S, S.pidx) : 1:0
unsafe_convert{T}(::Type{Ptr{T}}, S::SharedArray{T}) = unsafe_convert(Ptr{T}, sdata(S))
unsafe_convert{T}(::Type{Ptr{T}}, S::SharedArray ) = unsafe_convert(Ptr{T}, sdata(S))
function convert(::Type{SharedArray}, A::Array)
S = SharedArray{eltype(A),ndims(A)}(size(A))
copy!(S, A)
end
function convert{T}(::Type{SharedArray{T}}, A::Array)
S = SharedArray{T,ndims(A)}(size(A))
copy!(S, A)
end
function convert{TS,TA,N}(::Type{SharedArray{TS,N}}, A::Array{TA,N})
S = SharedArray{TS,ndims(A)}(size(A))
copy!(S, A)
end
function deepcopy_internal(S::SharedArray, stackdict::ObjectIdDict)
haskey(stackdict, S) && return stackdict[S]
R = SharedArray{eltype(S),ndims(S)}(size(S); pids = S.pids)
copy!(sdata(R), sdata(S))
stackdict[S] = R
return R
end
function shared_pids(pids)
if isempty(pids)
# only use workers on the current host
pids = procs(myid())
if length(pids) > 1
pids = filter(x -> x != 1, pids)
end
onlocalhost = true
else
if !check_same_host(pids)
throw(ArgumentError("SharedArray requires all requested processes to be on the same machine."))
end
onlocalhost = myid() in procs(pids[1])
end
pids, onlocalhost
end
function range_1dim(S::SharedArray, pidx)
l = length(S)
nw = length(S.pids)
partlen = div(l, nw)
if l < nw
if pidx <= l
return pidx:pidx
else
return 1:0
end
elseif pidx == nw
return (((pidx-1) * partlen) + 1):l
else
return (((pidx-1) * partlen) + 1):(pidx*partlen)
end
end
sub_1dim(S::SharedArray, pidx) = view(S.s, range_1dim(S, pidx))
function init_loc_flds{T,N}(S::SharedArray{T,N}, empty_local=false)
if myid() in S.pids
S.pidx = findfirst(S.pids, myid())
if isa(S.refs[1], Future)
refid = remoteref_id(S.refs[S.pidx])
else
refid = S.refs[S.pidx]
end
c = channel_from_id(refid)
S.s = fetch(c)
S.loc_subarr_1d = sub_1dim(S, S.pidx)
else
S.pidx = 0
if empty_local
S.s = Array{T}(ntuple(d->0,N))
end
S.loc_subarr_1d = view(Array{T}(ntuple(d->0,N)), 1:0)
end
end
# Don't serialize s (it is the complete array) and
# pidx, which is relevant to the current process only
function serialize(s::AbstractSerializer, S::SharedArray)
serialize_cycle_header(s, S) && return
for n in fieldnames(SharedArray)
if n in [:s, :pidx, :loc_subarr_1d]
writetag(s.io, UNDEFREF_TAG)
elseif n == :refs
v = getfield(S, n)
if isa(v[1], Future)
# convert to ids to avoid distributed GC overhead
ids = [remoteref_id(x) for x in v]
serialize(s, ids)
else
serialize(s, v)
end
else
serialize(s, getfield(S, n))
end
end
end
function deserialize(s::AbstractSerializer, t::Type{<:SharedArray})
S = invoke(deserialize, Tuple{AbstractSerializer,DataType}, s, t)
init_loc_flds(S, true)
S
end
function show(io::IO, S::SharedArray)
if length(S.s) > 0
invoke(show, Tuple{IO,DenseArray}, io, S)
else
show(io, remotecall_fetch(sharr->sharr.s, S.pids[1], S))
end
end
function show(io::IO, mime::MIME"text/plain", S::SharedArray)
if length(S.s) > 0
invoke(show, Tuple{IO,MIME"text/plain",DenseArray}, io, MIME"text/plain"(), S)
else
# retrieve from the first worker mapping the array.
println(io, summary(S), ":")
showarray(io, remotecall_fetch(sharr->sharr.s, S.pids[1], S), false; header=false)
end
end
convert(::Type{Array}, S::SharedArray) = S.s
# pass through getindex and setindex! - unlike DArrays, these always work on the complete array
getindex(S::SharedArray, i::Real) = getindex(S.s, i)
setindex!(S::SharedArray, x, i::Real) = setindex!(S.s, x, i)
function fill!(S::SharedArray, v)
vT = convert(eltype(S), v)
f = S->fill!(S.loc_subarr_1d, vT)
@sync for p in procs(S)
@async remotecall_wait(f, p, S)
end
return S
end
function rand!{T}(S::SharedArray{T})
f = S->map!(x -> rand(T), S.loc_subarr_1d, S.loc_subarr_1d)
@sync for p in procs(S)
@async remotecall_wait(f, p, S)
end
return S
end
function randn!(S::SharedArray)
f = S->map!(x -> randn(), S.loc_subarr_1d, S.loc_subarr_1d)
@sync for p in procs(S)
@async remotecall_wait(f, p, S)
end
return S
end
# convenience constructors
function shmem_fill(v, dims; kwargs...)
SharedArray{typeof(v),length(dims)}(dims; init = S->fill!(S.loc_subarr_1d, v), kwargs...)
end
shmem_fill(v, I::Int...; kwargs...) = shmem_fill(v, I; kwargs...)
# rand variant with range
function shmem_rand(TR::Union{DataType, UnitRange}, dims; kwargs...)
if isa(TR, UnitRange)
SharedArray{Int,length(dims)}(dims; init = S -> map!(x -> rand(TR), S.loc_subarr_1d, S.loc_subarr_1d), kwargs...)
else
SharedArray{TR,length(dims)}(dims; init = S -> map!(x -> rand(TR), S.loc_subarr_1d, S.loc_subarr_1d), kwargs...)
end
end
shmem_rand(TR::Union{DataType, UnitRange}, i::Int; kwargs...) = shmem_rand(TR, (i,); kwargs...)
shmem_rand(TR::Union{DataType, UnitRange}, I::Int...; kwargs...) = shmem_rand(TR, I; kwargs...)
shmem_rand(dims; kwargs...) = shmem_rand(Float64, dims; kwargs...)
shmem_rand(I::Int...; kwargs...) = shmem_rand(I; kwargs...)
function shmem_randn(dims; kwargs...)
SharedArray{Float64,length(dims)}(dims; init = S-> map!(x -> randn(), S.loc_subarr_1d, S.loc_subarr_1d), kwargs...)
end
shmem_randn(I::Int...; kwargs...) = shmem_randn(I; kwargs...)
similar(S::SharedArray, T::Type, dims::Dims) = similar(S.s, T, dims)
similar(S::SharedArray, T::Type) = similar(S.s, T, size(S))
similar(S::SharedArray, dims::Dims) = similar(S.s, eltype(S), dims)
similar(S::SharedArray) = similar(S.s, eltype(S), size(S))
reduce(f, S::SharedArray) =
mapreduce(fetch, f,
Any[ @spawnat p reduce(f, S.loc_subarr_1d) for p in procs(S) ])
function map!(f, S::SharedArray, Q::SharedArray)
if !(S === Q) && (procs(S) != procs(Q) || localindexes(S) != localindexes(Q))
throw(ArgumentError("incompatible source and destination arguments"))
end
@sync for p in procs(S)
@spawnat p begin
for idx in localindexes(S)
S.s[idx] = f(Q.s[idx])
end
end
end
return S
end
copy!(S::SharedArray, A::Array) = (copy!(S.s, A); S)
function copy!(S::SharedArray, R::SharedArray)
length(S) == length(R) || throw(BoundsError())
ps = intersect(procs(S), procs(R))
isempty(ps) && throw(ArgumentError("source and destination arrays don't share any process"))
l = length(S)
length(ps) > l && (ps = ps[1:l])
nw = length(ps)
partlen = div(l, nw)
@sync for i = 1:nw
p = ps[i]
idx = i < nw ? ((i-1)*partlen+1:i*partlen) : ((i-1)*partlen+1:l)
@spawnat p begin
S.s[idx] = R.s[idx]
end
end
return S
end
function print_shmem_limits(slen)
try
if is_linux()
pfx = "kernel"
elseif is_apple()
pfx = "kern.sysv"
elseif Sys.KERNEL == :FreeBSD || Sys.KERNEL == :DragonFly
pfx = "kern.ipc"
elseif Sys.KERNEL == :OpenBSD
pfx = "kern.shminfo"
else
# seems NetBSD does not have *.shmall
return
end
shmmax_MB = div(parse(Int, split(readstring(`sysctl $(pfx).shmmax`))[end]), 1024*1024)
page_size = parse(Int, split(readstring(`getconf PAGE_SIZE`))[end])
shmall_MB = div(parse(Int, split(readstring(`sysctl $(pfx).shmall`))[end]) * page_size, 1024*1024)
println("System max size of single shmem segment(MB) : ", shmmax_MB,
"\nSystem max size of all shmem segments(MB) : ", shmall_MB,
"\nRequested size(MB) : ", div(slen, 1024*1024),
"\nPlease ensure requested size is within system limits.",
"\nIf not, increase system limits and try again."
)
catch e
nothing # Ignore any errors in this
end
end
# utilities
function shm_mmap_array(T, dims, shm_seg_name, mode)
local s = nothing
local A = nothing
if (prod(dims) == 0) || (sizeof(T) == 0)
return Array{T}(dims)
end
try
A = _shm_mmap_array(T, dims, shm_seg_name, mode)
catch e
print_shmem_limits(prod(dims)*sizeof(T))
rethrow(e)
finally
if s !== nothing
close(s)
end
end
A
end
# platform-specific code
if is_windows()
function _shm_mmap_array(T, dims, shm_seg_name, mode)
readonly = !((mode & JL_O_RDWR) == JL_O_RDWR)
create = (mode & JL_O_CREAT) == JL_O_CREAT
s = Mmap.Anonymous(shm_seg_name, readonly, create)
Mmap.mmap(s, Array{T,length(dims)}, dims, zero(Int64))
end
# no-op in windows
shm_unlink(shm_seg_name) = 0
else # !windows
function _shm_mmap_array(T, dims, shm_seg_name, mode)
fd_mem = shm_open(shm_seg_name, mode, S_IRUSR | S_IWUSR)
systemerror("shm_open() failed for " * shm_seg_name, fd_mem < 0)
s = fdio(fd_mem, true)
# On OSX, ftruncate must to used to set size of segment, just lseek does not work.
# and only at creation time
if (mode & JL_O_CREAT) == JL_O_CREAT
rc = ccall(:jl_ftruncate, Cint, (Cint, Int64), fd_mem, prod(dims)*sizeof(T))
systemerror("ftruncate() failed for shm segment " * shm_seg_name, rc != 0)
end
Mmap.mmap(s, Array{T,length(dims)}, dims, zero(Int64); grow=false)
end
shm_unlink(shm_seg_name) = ccall(:shm_unlink, Cint, (Cstring,), shm_seg_name)
shm_open(shm_seg_name, oflags, permissions) = ccall(:shm_open, Cint,
(Cstring, Cint, Cmode_t), shm_seg_name, oflags, permissions)
end # os-test
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