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DistributedArrays

Distributed Arrays in Julia

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DistributedArrays.jl

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Distributed Arrays for Julia

NOTE Distributed Arrays will only work on Julia v0.4.0 or later.

DArrays have been removed from Julia Base library in v0.4 so it is now necessary to import the DistributedArrays package on all spawned processes.

@everywhere using DistributedArrays

Distributed Arrays

Large computations are often organized around large arrays of data. In these cases, a particularly natural way to obtain parallelism is to distribute arrays among several processes. This combines the memory resources of multiple machines, allowing use of arrays too large to fit on one machine. Each process operates on the part of the array it owns, providing a ready answer to the question of how a program should be divided among machines.

Julia distributed arrays are implemented by the DArray type. A DArray has an element type and dimensions just like an Array. A DArray can also use arbitrary array-like types to represent the local chunks that store actual data. The data in a DArray is distributed by dividing the index space into some number of blocks in each dimension.

Common kinds of arrays can be constructed with functions beginning with d:

    dzeros(100,100,10)
    dones(100,100,10)
    drand(100,100,10)
    drandn(100,100,10)
    dfill(x,100,100,10)

In the last case, each element will be initialized to the specified value x. These functions automatically pick a distribution for you. For more control, you can specify which processes to use, and how the data should be distributed:

    dzeros((100,100), workers()[1:4], [1,4])

The second argument specifies that the array should be created on the first four workers. When dividing data among a large number of processes, one often sees diminishing returns in performance. Placing DArray\ s on a subset of processes allows multiple DArray computations to happen at once, with a higher ratio of work to communication on each process.

The third argument specifies a distribution; the nth element of this array specifies how many pieces dimension n should be divided into. In this example the first dimension will not be divided, and the second dimension will be divided into 4 pieces. Therefore each local chunk will be of size (100,25). Note that the product of the distribution array must equal the number of processes.

  • distribute(a::Array) converts a local array to a distributed array.

  • localpart(d::DArray) obtains the locally-stored portion of a DArray.

  • Localparts can be retrived and set via the indexing syntax too. Indexing via symbols is used for this, specifically symbols :L,:LP,:l,:lp which are all equivalent. For example, d[:L] returns the localpart of d while d[:L]=v sets v as the localpart of d.

  • localindexes(a::DArray) gives a tuple of the index ranges owned by the local process.

  • convert(Array, a::DArray) brings all the data to the local process.

Indexing a DArray (square brackets) with ranges of indexes always creates a SubArray, not copying any data.

Constructing Distributed Arrays

The primitive DArray constructor has the following somewhat elaborate signature:

    DArray(init, dims[, procs, dist])

init is a function that accepts a tuple of index ranges. This function should allocate a local chunk of the distributed array and initialize it for the specified indices. dims is the overall size of the distributed array. procs optionally specifies a vector of process IDs to use. dist is an integer vector specifying how many chunks the distributed array should be divided into in each dimension.

The last two arguments are optional, and defaults will be used if they are omitted.

As an example, here is how to turn the local array constructor fill into a distributed array constructor:

    dfill(v, args...) = DArray(I->fill(v, map(length,I)), args...)

In this case the init function only needs to call fill with the dimensions of the local piece it is creating.

DArrays can also be constructed from multidimensional Array comprehensions with the @DArray macro syntax. This syntax is just sugar for the primitive DArray constructor:

julia> [i+j for i = 1:5, j = 1:5]
5x5 Array{Int64,2}:
 2  3  4  5   6
 3  4  5  6   7
 4  5  6  7   8
 5  6  7  8   9
 6  7  8  9  10

julia> @DArray [i+j for i = 1:5, j = 1:5]
5x5 DistributedArrays.DArray{Int64,2,Array{Int64,2}}:
 2  3  4  5   6
 3  4  5  6   7
 4  5  6  7   8
 5  6  7  8   9
 6  7  8  9  10

Distributed Array Operations

At this time, distributed arrays do not have much functionality. Their major utility is allowing communication to be done via array indexing, which is convenient for many problems. As an example, consider implementing the "life" cellular automaton, where each cell in a grid is updated according to its neighboring cells. To compute a chunk of the result of one iteration, each process needs the immediate neighbor cells of its local chunk. The following code accomplishes this::

    function life_step(d::DArray)
        DArray(size(d),procs(d)) do I
            top   = mod(first(I[1])-2,size(d,1))+1
            bot   = mod( last(I[1])  ,size(d,1))+1
            left  = mod(first(I[2])-2,size(d,2))+1
            right = mod( last(I[2])  ,size(d,2))+1

            old = Array(Bool, length(I[1])+2, length(I[2])+2)
            old[1      , 1      ] = d[top , left]   # left side
            old[2:end-1, 1      ] = d[I[1], left]
            old[end    , 1      ] = d[bot , left]
            old[1      , 2:end-1] = d[top , I[2]]
            old[2:end-1, 2:end-1] = d[I[1], I[2]]   # middle
            old[end    , 2:end-1] = d[bot , I[2]]
            old[1      , end    ] = d[top , right]  # right side
            old[2:end-1, end    ] = d[I[1], right]
            old[end    , end    ] = d[bot , right]

            life_rule(old)
        end
    end

As you can see, we use a series of indexing expressions to fetch data into a local array old. Note that the do block syntax is convenient for passing init functions to the DArray constructor. Next, the serial function life_rule is called to apply the update rules to the data, yielding the needed DArray chunk. Nothing about life_rule is DArray\ -specific, but we list it here for completeness::

    function life_rule(old)
        m, n = size(old)
        new = similar(old, m-2, n-2)
        for j = 2:n-1
            for i = 2:m-1
                nc = +(old[i-1,j-1], old[i-1,j], old[i-1,j+1],
                       old[i  ,j-1],             old[i  ,j+1],
                       old[i+1,j-1], old[i+1,j], old[i+1,j+1])
                new[i-1,j-1] = (nc == 3 || nc == 2 && old[i,j])
            end
        end
        new
    end

Numerical Results of Distributed Computations

Floating point arithmetic is not associative and this comes up when performing distributed computations over DArrays. All DArray operations are performed over the localpart chunks and then aggregated. The change in ordering of the operations will change the numeric result as seen in this simple example:

julia> addprocs(8);

julia> @everywhere using DistributedArrays

julia> A = fill(1.1, (100,100));

julia> sum(A)
11000.000000000013

julia> DA = distribute(A);

julia> sum(DA)
11000.000000000127

julia> sum(A) == sum(DA)
false

The ultimate ordering of operations will be dependent on how the Array is distributed.

Garbage Collection and DArrays

When a DArray is constructed (typically on the master process), the returned DArray objects stores information on how the array is distributed, which procesor holds which indexes and so on. When the DArray object on the master process is garbage collected, all particpating workers are notified and localparts of the DArray freed on each worker.

Since the size of the DArray object itself is small, a problem arises as gc on the master faces no memory pressure to collect the DArray immediately. This results in a delay of the memory being released on the participating workers.

Therefore it is highly recommended to explcitly call close(d::DArray) as soon as user code has finished working with the distributed array.

It is also important to note that the localparts of the DArray is collected from all particpating workers when the DArray object on the process creating the DArray is collected. It is therefore important to maintain a reference to a DArray object on the creating process for as long as it is being computed upon.

d_closeall() is another useful function to manage distributed memory. It releases all darrays created from the calling process, including any temporaries created during computation.

Working with distributed non-array data (requires Julia 0.6)

The function ddata(;T::Type=Any, init::Function=I->nothing, pids=workers(), data::Vector=[]) can be used to created a distributed vector whose localparts need not be Arrays.

It returns a DArray{T,1,T}, i.e., the element type and localtype of the array are the same.

ddata() constructs a distributed vector of length nworkers() where each localpart can hold any value, initially initialized to nothing.

Argument data if supplied is distributed over the pids. length(data) must be a multiple of length(pids). If the multiple is 1, returns a DArray{T,1,T} where T is eltype(data). If the multiple is greater than 1, returns a DArray{T,1,Array{T,1}}, i.e., it is equivalent to calling distribute(data).

gather{T}(d::DArray{T,1,T}) returns an Array{T,1} consisting of all distributed elements of d

Given a DArray{T,1,T} object d, d[:L] returns the localpart on a worker. d[i] returns the localpart on the ith worker that d is distributed over.

SPMD Mode (An MPI Style SPMD mode with MPI like primitives, requires Julia 0.6)

SPMD, i.e., a Single Program Multiple Data mode is implemented by submodule DistributedArrays.SPMD. In this mode the same function is executed in parallel on all participating nodes. This is a typical style of MPI programs where the same program is executed on all processors. A basic subset of MPI-like primitives are currently supported. As a programming model it should be familiar to folks with an MPI background.

The same block of code is executed concurrently on all workers using the spmd function.

# define foo() on all workers
@everywhere function foo(arg1, arg2)
    ....
end

# call foo() everywhere using the `spmd` function
d_in=DArray(.....)
d_out=ddata()
spmd(foo,d_in,d_out; pids=workers()) # executes on all workers

spmd is defined as spmd(f, args...; pids=procs(), context=nothing)

args is one or more arguments to be passed to f. pids identifies the workers that f needs to be run on. context identifies a run context, which is explained later.

The following primitives can be used in SPMD mode.

  • sendto(pid, data; tag=nothing) - sends data to pid

  • recvfrom(pid; tag=nothing) - receives data from pid

  • recvfrom_any(; tag=nothing) - receives data from any pid

  • barrier(;pids=procs(), tag=nothing) - all tasks wait and then proceeed

  • bcast(data, pid; tag=nothing, pids=procs()) - broadcasts the same data over pids from pid

  • scatter(x, pid; tag=nothing, pids=procs()) - distributes x over pids from pid

  • gather(x, pid; tag=nothing, pids=procs()) - collects data from pids onto worker pid

Tag tag should be used to differentiate between consecutive calls of the same type, for example, consecutive bcast calls.

spmd and spmd related functions are defined in submodule DistributedArrays.SPMD. You will need to import it explcitly, or prefix functions that can can only be used in spmd mode with SPMD., for example, SPMD.sendto.

Example

This toy example exchanges data with each of its neighbors n times.

using DistributedArrays
addprocs(8)
@everywhere importall DistributedArrays
@everywhere importall DistributedArrays.SPMD

d_in=d=DArray(I->fill(myid(), (map(length,I)...)), (nworkers(), 2), workers(), [nworkers(),1])
d_out=ddata()

# define the function everywhere
@everywhere function foo_spmd(d_in, d_out, n)
    pids = sort(vec(procs(d_in)))
    pididx = findfirst(pids, myid())
    mylp = d_in[:L]
    localsum = 0

    # Have each worker exchange data with its neighbors
    n_pididx = pididx+1 > length(pids) ? 1 : pididx+1
    p_pididx = pididx-1 < 1 ? length(pids) : pididx-1

    for i in 1:n
        sendto(pids[n_pididx], mylp[2])
        sendto(pids[p_pididx], mylp[1])

        mylp[2] = recvfrom(pids[p_pididx])
        mylp[1] = recvfrom(pids[n_pididx])

        barrier(;pids=pids)
        localsum = localsum + mylp[1] + mylp[2]
    end

    # finally store the sum in d_out
    d_out[:L] = localsum
end

# run foo_spmd on all workers
spmd(foo_spmd, d_in, d_out, 10)

# print values of d_in and d_out after the run
println(d_in)
println(d_out)

SPMD Context

Each SPMD run is implictly executed in a different context. This allows for multiple spmd calls to be active at the same time. A SPMD context can be explicitly specified via keyword arg context to spmd.

context(pids=procs()) returns a new SPMD context.

A SPMD context also provides a context local storage, a dict, which can be used to store key-value pairs between spmd runs under the same context.

context_local_storage() returns the dictionary associated with the context.

NOTE: Implicitly defined contexts, i.e., spmd calls without specifying a context create a context which live only for the duration of the call. Explictly created context objects can be released early by calling close(ctxt::SPMDContext). This will release the local storage dictionaries on all participating pids. Else they will be released when the context object is gc'ed on the node that created it.

Nested spmd calls

As spmd executes the the specified function on all participating nodes, we need to be careful with nesting spmd calls.

An example of an unsafe(wrong) way:

function foo(.....)
    ......
    spmd(bar, ......)
    ......
end

function bar(....)
    ......
    spmd(baz, ......)
    ......
end

spmd(foo,....)

In the above example, foo, bar and baz are all functions wishing to leverage distributed computation. However, they themselves may be currenty part of a spmd call. A safe way to handle such a scenario is to only drive parallel computation from the master process.

The correct way (only have the driver process initiate spmd calls):

function foo()
    ......
    myid()==1 && spmd(bar, ......)
    ......
end

function bar()
    ......
    myid()==1 && spmd(baz, ......)
    ......
end

spmd(foo,....)

This is also true of functions which automatically distribute computation on DArrays.

function foo(d::DArray)
    ......
    myid()==1 && map!(bar, d)
    ......
end
spmd(foo,....)

Without the myid() check, the spmd call to foo would execute map! from all nodes, which is not what we probably want.

Similarly @everywhere from within a SPMD run should also be driven from the master node only.

First Commit

02/26/2015

Last Touched

8 days ago

Commits

275 commits

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