Multithreaded custom grouped operations with single-row result

docs/src/man/split_apply_combine.md

@@ -122,11 +122,13 @@ It is allowed to mix single values and vectors if multiple transformations
 are requested. In this case single value will be repeated to match the length
 of columns specified by returned vectors.
 
-A separate task is spawned for each specified transformation, allowing for
-parallel operation when several transformations are requested and Julia was
-started with more than one thread. Passed transformation functions should
-therefore not modify global variables (i.e. they should be pure), or use
-locks to control parallel accesses.
+A separate task is spawned for each specified transformation; each transformation
+then spawns as many tasks as Julia threads, and splits processing of groups across
+them (however, currently transformations with optimized implementations like `sum`
+and transformations that return multiple rows use a single task for all groups).
+This allows for parallel operation when Julia was started with more than one
+thread. Passed transformation functions should therefore not modify global variables
+(i.e. they should be pure), or use locks to control parallel accesses.
 
 To apply `function` to each row instead of whole columns, it can be wrapped in a
 `ByRow` struct. `cols` can be any column indexing syntax, in which case

src/abstractdataframe/selection.jl

@@ -145,10 +145,13 @@ const TRANSFORMATION_COMMON_RULES =
     `copycols=false`, a `SubDataFrame` is returned without copying columns.
 
     If a `GroupedDataFrame` is passed, a separate task is spawned for each
-    specified transformation, allowing for parallel operation when several
-    transformations are requested and Julia was started with more than one thread.
-    Passed transformation functions should therefore not modify global variables
-    (i.e. they should be pure), or use locks to control parallel accesses.
+    specified transformation; each transformation then spawns as many tasks
+    as Julia threads, and splits processing of groups across them
+    (however, currently transformations with optimized implementations like `sum`
+    and transformations that return multiple rows use a single task for all groups).
+    This allows for parallel operation when Julia was started with more than one
+    thread. Passed transformation functions should therefore not modify global
+    variables (i.e. they should be pure), or use locks to control parallel accesses.
     In the future, parallelism may be extended to other cases, so this requirement
     also holds for `DataFrame` inputs.
     """

src/groupeddataframe/complextransforms.jl

@@ -57,7 +57,7 @@ function _combine_with_first(first::Union{NamedTuple, DataFrameRow, AbstractData
                                                              f, gd, incols, targetcolnames,
                                                              firstmulticol)
     else
-        outcols, finalcolnames = _combine_rows_with_first!(first, initialcols, 1, 1,
+        outcols, finalcolnames = _combine_rows_with_first!(first, initialcols,
                                                            f, gd, incols, targetcolnames,
                                                            firstmulticol)
     end
@@ -92,9 +92,92 @@ function fill_row!(row, outcols::NTuple{N, AbstractVector},
     return nothing
 end
 
-function _combine_rows_with_first!(first::Union{NamedTuple, DataFrameRow},
+function _combine_rows_with_first_task!(tid::Integer,
+                                        rowstart::Integer,
+                                        rowend::Integer,
+                                        rownext::Integer,
+                                        outcols::NTuple{<:Any, AbstractVector},
+                                        outcolsref::Ref{NTuple{<:Any, AbstractVector}},
+                                        type_widened::AbstractVector{Bool},
+                                        widen_type_lock::ReentrantLock,
+                                        f::Base.Callable,
+                                        gd::GroupedDataFrame,
+                                        starts::AbstractVector{<:Integer},
+                                        ends::AbstractVector{<:Integer},
+                                        incols::Union{Nothing, AbstractVector,
+                                                      Tuple, NamedTuple},
+                                        colnames::NTuple{<:Any, Symbol},
+                                        firstmulticol::Val)
+    j = nothing
+    gdidx = gd.idx
+    local newoutcols
+    for i in rownext:rowend
+        row = wrap_row(do_call(f, gdidx, starts, ends, gd, incols, i), firstmulticol)
+        j = fill_row!(row, outcols, i, 1, colnames)
+        if j !== nothing # Need to widen column
+            # If another thread is already widening outcols, wait until it's done
+            lock(widen_type_lock)
+            try
+                newoutcols = outcolsref[]
+                # Workaround for julia#15276
+                newoutcols = let i=i, j=j, newoutcols=newoutcols, row=row
+                    ntuple(length(newoutcols)) do k
+                        S = typeof(row[k])
+                        T = eltype(newoutcols[k])
+                        U = promote_type(S, T)
+                        if S <: T || U <: T
+                            newoutcols[k]
+                        else
+                            type_widened .= true
+                            Tables.allocatecolumn(U, length(newoutcols[k]))
+                        end
+                    end
+                end
+                for k in 1:length(outcols)
+                    if outcols[k] !== newoutcols[k]
+                        copyto!(newoutcols[k], rowstart,
+                                outcols[k], rowstart, i - rowstart + (k < j))
+                    end
+                end
+                j = fill_row!(row, newoutcols, i, j, colnames)
+                @assert j === nothing # eltype is guaranteed to match
+
+                outcolsref[] = newoutcols
+                type_widened[tid] = false
+            finally
+                unlock(widen_type_lock)
+            end
+            return _combine_rows_with_first_task!(tid, rowstart, rowend, i+1, newoutcols, outcolsref,
+                                                  type_widened, widen_type_lock,
+                                                  f, gd, starts, ends,
+                                                  incols, colnames, firstmulticol)
+        end
+        # If other thread widened columns, copy already processed data to new vectors
+        # This doesn't have to happen immediately (hence type_widened isn't atomic),
+        # but the more we wait the more data will have to be copied
+        if type_widened[tid]
+            lock(widen_type_lock) do
+                type_widened[tid] = false
+                newoutcols = outcolsref[]
+                for k in 1:length(outcols)
+                    # Check whether this particular column has been widened
+                    if outcols[k] !== newoutcols[k]
+                        copyto!(newoutcols[k], rowstart,
+                                outcols[k], rowstart, i - rowstart + 1)
+                    end
+                end
+            end
+            return _combine_rows_with_first_task!(tid, rowstart, rowend, i+1, newoutcols, outcolsref,
+                                                  type_widened, widen_type_lock,
+                                                  f, gd, starts, ends,
+                                                  incols, colnames, firstmulticol)
+        end
+    end
+    return outcols
+end
+
+function _combine_rows_with_first!(firstrow::Union{NamedTuple, DataFrameRow},
                                    outcols::NTuple{N, AbstractVector},
-                                   rowstart::Integer, colstart::Integer,
                                    f::Base.Callable, gd::GroupedDataFrame,
                                    incols::Union{Nothing, AbstractVector, Tuple, NamedTuple},
                                    colnames::NTuple{N, Symbol},
@@ -107,32 +190,60 @@ function _combine_rows_with_first!(first::Union{NamedTuple, DataFrameRow},
     # handle empty GroupedDataFrame
     len == 0 && return outcols, colnames
 
-    # Handle first group
-    j = fill_row!(first, outcols, rowstart, colstart, colnames)
-    @assert j === nothing # eltype is guaranteed to match
-    # Handle remaining groups
-    @inbounds for i in rowstart+1:len
-        row = wrap_row(do_call(f, gdidx, starts, ends, gd, incols, i), firstmulticol)
-        j = fill_row!(row, outcols, i, 1, colnames)
-        if j !== nothing # Need to widen column type
-            local newcols
-            let i = i, j = j, outcols=outcols, row=row # Workaround for julia#15276
-                newcols = ntuple(length(outcols)) do k
-                    S = typeof(row[k])
-                    T = eltype(outcols[k])
-                    U = promote_type(S, T)
-                    if S <: T || U <: T
-                        outcols[k]
-                    else
-                        copyto!(Tables.allocatecolumn(U, length(outcols[k])),
-                                1, outcols[k], 1, k >= j ? i-1 : i)
-                    end
+    # Handle groups other than the first one (which is handled below)
+    # Create up to one task per thread
+    # This has lower overhead than creating one task per group,
+    # but is optimal only if operations take roughly the same time for all groups
+    @static if VERSION >= v"1.4"
+        basesize = max(1, cld(len - 1, Threads.nthreads()))
+        partitions = Iterators.partition(2:len, basesize)
+    else
+        partitions = (2:len,)
+    end
+    widen_type_lock = ReentrantLock()
+    outcolsref = Ref{NTuple{<:Any, AbstractVector}}(outcols)
+    type_widened = fill(false, length(partitions))
+    tasks = Vector{Task}(undef, length(partitions))
+    for (tid, idx) in enumerate(partitions)
+        tasks[tid] =
+            @spawn _combine_rows_with_first_task!(tid, first(idx), last(idx), first(idx),
+                                                  outcols, outcolsref,
+                                                  type_widened, widen_type_lock,
+                                                  f, gd, starts, ends, incols, colnames,
+                                                  firstmulticol)
+    end
+
+    # Workaround JuliaLang/julia#38931:
+    # we want to preserve the exception type thrown in user code,
+    # and print the backtrace corresponding to it
+    for t in tasks
+        try
+            wait(t)
+        catch e
+            throw(t.exception)
+        end
+    end
+
+    # Copy data for any tasks that finished before others widened columns
+    outcols = outcolsref[]
+    for (tid, idx) in enumerate(partitions)
+        if type_widened[tid]
+            oldoutcols = fetch(tasks[tid])
+            for k in 1:length(outcols)
+                # Check whether this particular column has been widened
+                if oldoutcols[k] !== outcols[k]
+                    copyto!(outcols[k], first(idx), oldoutcols[k], first(idx),
+                            last(idx) - first(idx) + 1)
                 end
             end
-            return _combine_rows_with_first!(row, newcols, i, j,
-                                             f, gd, incols, colnames, firstmulticol)
         end
     end
+
+    # Handle first group
+    # This is done at the end to write directly to the final outcols
+    j1 = fill_row!(firstrow, outcols, 1, 1, colnames)
+    @assert j1 === nothing # eltype is guaranteed to match
+
     return outcols, colnames
 end
 

test/grouping.jl

@@ -3577,4 +3577,46 @@ end
     end
 end
 
+@testset "result eltype widening from different tasks" begin
+    if VERSION < v"1.5"
+        Base.convert(::Type{Union{Missing, Nothing, Float64}}, x::Int) = float(x)
+    end
+    Random.seed!(1)
+    for y in (Any[1, missing, missing, 2, 4],
+              Any[1, missing, nothing, 2.1, 'a'],
+              Any[1, 1, missing, 1, nothing, 1, 2.1, 1, 'a'],
+              Any[1, 2, 3, 4, 5, 6, 2.1, missing, 'a'],
+              Any[1, 2, 3.1, 4, 5, 6, 2.1, missing, 'a']),
+        x in (1:length(y), rand(1:2, length(y)), rand(1:3, length(y)))
+        df = DataFrame(x=x, y1=y, y2=reverse(y))
+        gd = groupby(df, :x)
+        res = combine(gd, :y1 => (y -> y[1]) => :y1, :y2 => (y -> y[end]) => :y2)
+        # sleep ensures one task will widen the result after the other is done,
+        # so that data has to be copied at the end
+        @test res ≅
+              combine(gd, [:x, :y1] => ((x, y) -> (sleep((x == [5])/10); y[1])) => :y1,
+                          [:x, :y2] => ((x, y) -> (sleep((x == [5])/10); y[end])) => :y2) ≅
+              combine(gd, [:x, :y1] => ((x, y) -> (sleep(x[1]/100); y[1])) => :y1,
+                          [:x, :y2] => ((x, y) -> (sleep(x[1]/100); y[end])) => :y2) ≅
+              combine(gd, [:x, :y1] => ((x, y) -> (sleep(rand()/10); y[1])) => :y1,
+                          [:x, :y2] => ((x, y) -> (sleep(rand()/10); y[end])) => :y2)
+
+        if df.x == 1:nrow(df)
+            @test res ≅ df
+        end
+
+        res = combine(gd, :y1 => (y -> (y1=y[1], y2=y[end])) => AsTable,
+                          :y2 => (y -> (y3=y[1], y4=y[end])) => AsTable)
+        # sleep ensures one task will widen the result after the other is done,
+        # so that data has to be copied at the end
+        @test res ≅
+              combine(gd, [:x, :y1] => ((x, y) -> (sleep((x == [5])/10); (y1=y[1], y2=y[end]))) => AsTable,
+                          [:x, :y2] => ((x, y) -> (sleep((x == [5])/10); (y3=y[1], y4=y[end]))) => AsTable) ≅
+              combine(gd, [:x, :y1] => ((x, y) -> (sleep(x[1]/100); (y1=y[1], y2=y[end]))) => AsTable,
+                          [:x, :y2] => ((x, y) -> (sleep(x[1]/100); (y3=y[1], y4=y[end]))) => AsTable) ≅
+              combine(gd, [:x, :y1] => ((x, y) -> (sleep(rand()/10); (y1=y[1], y2=y[end]))) => AsTable,
+                          [:x, :y2] => ((x, y) -> (sleep(rand()/10); (y3=y[1], y4=y[end]))) => AsTable)
+    end
+end
+
 end # module