[WIP] add source of fastest c++ benches

c_vs_julia.jl

@@ -0,0 +1,39 @@
+cd(@__DIR__)
+fasta_input = "fasta.txt"
+fasta_gen = joinpath("fasta", "fasta.jl")
+run(pipeline(`$(Base.julia_cmd()) $fasta_gen 25000000` ;stdout = fasta_input))
+
+benchmarks = [
+    ("binarytrees", 21),
+    ("fannkuchredux", 12),
+    ("fasta", 25000000),
+    ("knucleotide", fasta_input),
+    ("mandelbrot", 16000),
+    ("nbody", 50000000),
+    ("pidigits", 10000),
+    ("regexredux", fasta_input),
+    ("revcomp", fasta_input),
+    ("spectralnorm", 5500),
+]
+
+timings = map(benchmarks) do (bench, arg)
+  println(bench)
+  isfile("result.bin") && rm("result.bin")
+  args = [:stdout => "result.bin"]
+  argcmd = ``
+  cmd = if arg isa String
+    @assert isfile(arg)
+    push!(args, :stdin => arg)
+  else
+    argcmd = `$arg`
+  end
+  jltime = withenv("JULIA_NUM_THREADS" => 16) do
+    exe = joinpath("jl_build", bench, "cmain")
+     @elapsed run(pipeline(`$() $argcmd`; args...))
+  end
+  ctime = @elapsed run(pipeline(`./$bench $argcmd`; args...))
+  (jltime, ctime)
+end
+
+
+run(pipeline(`./revcomp $argcmd`, stdin = fasta_gen))

cpp_src/.gitignore

@@ -0,0 +1,11 @@
+binarytrees
+fannkuchredux
+fasta
+knucleotide
+mandelbrot
+nbody
+pidigits
+regexredux
+revcomp
+spectralnorm
+*.o

cpp_src/make.jl

@@ -9,17 +9,21 @@ for cmd in make_cmds
   end
 end
 
+fasta_input = "fasta.txt"
+fasta_gen = joinpath(@__DIR__, "..", "fasta", "fasta.jl")
+run(pipeline(`$(Base.julia_cmd()) $fasta_gen 25000000` ;stdout = fasta_input))
+
 
 benchmarks = [
     ("binarytrees", 21),
     ("fannkuchredux", 12),
     ("fasta", 25000000),
-    ("knucleotide", "knucleotide-input.txt"),
+    ("knucleotide", fasta_input),
     ("mandelbrot", 16000),
     ("nbody", 50000000),
     ("pidigits", 10000),
-    ("regexredux", "regexredux-input.txt"),
-    ("revcomp", "revcomp-input.txt"),
+    ("regexredux", fasta_input),
+    ("revcomp", fasta_input),
     ("spectralnorm", 5500),
 ]
 
@@ -31,60 +35,32 @@ map(benchmarks) do (bench, arg)
   else
     `./$bench $arg`
   end
-  @elapsed read(cmd, String)
 end
-
-map(benchmarks) do (bench, arg)
+cd(@__DIR__)
+timings = map(benchmarks) do (bench, arg)
   println(bench)
   root = joinpath(dir, bench)
   jl = joinpath(root, string(bench, "-fast.jl"))
   if !isfile(jl)
     jl = replace(jl, "-fast" => "")
   end
   @assert isfile(jl)
+  isfile("result.bin") && rm("result.bin")
   args = [:stdout => "result.bin"]
   argcmd = ``
   cmd = if arg isa String
-    push!(args, :stdin => joinpath(dir, bench, arg))
+    @assert isfile(arg)
+    push!(args, :stdin => arg)
   else
     argcmd = `$arg`
   end
-  jltime = withenv("JULIA_NUM_THREADS" => 16) do
-     @elapsed run(pipeline(`julia -O3 $jl $argcmd`; args...))
-  end
+  # jltime = withenv("JULIA_NUM_THREADS" => 16) do
+  #    @elapsed run(pipeline(`julia -O3 $jl $argcmd`; args...))
+  # end
+  jltime = 0.0
   ctime = @elapsed run(pipeline(`./$bench $argcmd`; args...))
   (jltime, ctime)
 end
 
-function create_cmain(dir, bench, arg)
-  root = joinpath(dir, bench)
-  jl = joinpath(root, string(bench, "-fast.jl"))
-  if !isfile(jl)
-    jl = replace(jl, "-fast" => "")
-  end
-  src = read(jl, String)
-  str = split(read(jl, String), "\n", keepempty = false)
-  lastend = str[findlast(x-> occursin(x, "end"), str)]
-  start = lastend.offset + lastend.ncodeunits
-  main = src[(start + 1):end]
-  rest = src[1:start]
-  open(joinpath(root, "cmain.jl"), "w") do io
-    println(io, rest)
-    println(io, """
-    Base.@ccallable function julia_main(ARGS::Vector{String})::Cint
-    """)
-    for line in split(main, "\n", keepempty = false)
-      println(io, "    ", line)
-    end
-    println(io, """
-        return 0
-    end
-    """)
-    if arg isa Integer
-      println(io, "julia_main([\"$arg\"])")
-    end
-  end
-end
-for (bench, arg) in benchmarks
-  create_cmain(dir, bench, arg)
-end
+
+run(pipeline(`./revcomp $argcmd`, stdin = fasta_gen))

fasta/fasta-fast.jl

@@ -3,14 +3,7 @@
 
 const line_width = 60
 
-const alu = string(
-   "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG",
-   "GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA",
-   "CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT",
-   "ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA",
-   "GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG",
-   "AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC",
-   "AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA")
+const alu = b"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA"
 
 const iub1 = b"acgtBDHKMNRSVWY"
 const iub2 = [0.27, 0.12, 0.12, 0.27, 0.02,0.02, 0.02, 0.02, 0.02, 0.02,0.02, 0.02, 0.02, 0.02, 0.02]
@@ -31,18 +24,18 @@ function repeat_fasta(io, src, n)
     col = 1
     count = 1
     c, state = iterate(I)
-    write(io, c % UInt8)
+    write(io, c)
     while count < n
         col += 1
         c, state = iterate(I, state)
-        write(io, c % UInt8)
+        write(io, c)
         if col == line_width
-            write(io, '\n')
+            write(io, '\n' % UInt8)
             col = 0
         end
         count += 1
     end
-    write(io, '\n')
+    write(io, '\n' % UInt8)
     return
 end
 
@@ -77,7 +70,7 @@ function random_fasta(io, symb, pr, n)
     return
 end
 
-function perf_fasta(_n=25000000, io = stdout)
+function perf_fasta(n=25000000, io = stdout)
   write(io, ">ONE Homo sapiens alu\n")
   repeat_fasta(io, alu, 2n)
 
@@ -87,5 +80,5 @@ function perf_fasta(_n=25000000, io = stdout)
   random_fasta(io, homosapiens1, homosapiens2, 5n)
 end
 
-n = parse(Int,ARGS[1])
-perf_fasta(n)
+# n = parse(Int,ARGS[1])
+@time perf_fasta(25000000, IOBuffer())

jl_build/.gitignore

@@ -0,0 +1,10 @@
+binarytrees
+fannkuchredux
+fasta
+knucleotide
+mandelbrot
+nbody
+pidigits
+regexredux
+revcomp
+spectralnorm

knucleotide/cmain.jl

@@ -1,4 +1,4 @@
-# The Computer Language Benchmarks Game
+# Th# The Computer Language Benchmarks Game
 # https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
 #
 # contributed by David Campbell
@@ -7,12 +7,8 @@
 #
 # Bit-twiddle optimizations added by Kristoffer Carlsson
 
-using Distributed
 using Printf
 
-addprocs(4)
-
-@everywhere begin
 const NucleotideLUT = zeros(UInt8, 256)
 NucleotideLUT['A'%UInt8] = 0
 NucleotideLUT['C'%UInt8] = 1
@@ -114,57 +110,52 @@ function sorted_array(m)
     sort!(kn)
 end
 
-do_work(str::String, i::Int) = sorted_array(count_data(str, KNucleotides{i,determine_inttype(i)}))
+do_work(str::String, i::Int) = sorted_array(count_data(str, KNucleotides{i, determine_inttype(i)}))
 do_work(str::String, i::String) = count_one(str, i)
 
-end # @everywhere
-
-function print_knucs(a::Array{KNuc, 1})
+function print_knucs(io, a::Array{KNuc, 1})
     sum = 0
     for kn in a
         sum += kn.count
     end
     for kn in a
-        @printf("%s %.3f\n", kn.name, 100.0kn.count/sum)
+        @printf(io, "%s %.3f\n", kn.name, 100.0kn.count/sum)
     end
-    println()
+    println(io)
 end
 
-function perf_k_nucleotide(io = stdin)
+function perf_k_nucleotide(io = stdin, output = stdout)
     three = ">THREE "
     while true
         line = readline(io)
         if startswith(line, three)
             break
         end
     end
-    data = read(io, String)
-    str = filter(!isequal('\n'), data)
-
-    vs = [1, 2, "GGT", "GGTA", "GGTATT", "GGTATTTTAATT", "GGTATTTTAATTTATAGT"]
+    str = sprint() do sio
+        foreach(line-> write(sio, line), eachline(io))
+    end
+    vs = (1, 2, "GGT", "GGTA", "GGTATT", "GGTATTTTAATT", "GGTATTTTAATTTATAGT")
     results = Vector{Any}(undef, length(vs))
-    order = collect(enumerate(vs))
-
-    @sync for w in workers()
-        @async while !isempty(order)
-            v = pop!(order)
-            r = remotecall_fetch(do_work, w, str, v[2])
-            results[v[1]] = r
-        end
+    Threads.@threads for i in length(vs):-1:1
+        results[i] = do_work(str, vs[i])
     end
 
     for (v, result) in zip(vs, results)
         if result isa Array
-            print_knucs(result)
+            print_knucs(output, result)
         end
         if result isa Int
-            @printf("%d\t%s\n", result, v)
+            @printf(output, "%d\t%s\n", result, v)
         end
     end
 end
-Base.@ccallable function julia_main(ARGS::Vector{String})::Cint
 
+Base.@ccallable function julia_main(ARGS::Vector{String})::Cint
     perf_k_nucleotide()
     return 0
 end
 
+open(joinpath(@__DIR__, "knucleotide-input.txt")) do io
+    perf_k_nucleotide(io, IOBuffer())
+end

knucleotide/knucleotide-fast.jl

@@ -10,9 +10,6 @@
 using Distributed
 using Printf
 
-addprocs(4)
-
-@everywhere begin
 const NucleotideLUT = zeros(UInt8, 256)
 NucleotideLUT['A'%UInt8] = 0
 NucleotideLUT['C'%UInt8] = 1
@@ -117,8 +114,6 @@ end
 do_work(str::String, i::Int) = sorted_array(count_data(str, KNucleotides{i,determine_inttype(i)}))
 do_work(str::String, i::String) = count_one(str, i)
 
-end # @everywhere
-
 function print_knucs(a::Array{KNuc, 1})
     sum = 0
     for kn in a
@@ -141,16 +136,10 @@ function perf_k_nucleotide(io = stdin)
     data = read(io, String)
     str = filter(!isequal('\n'), data)
 
-    vs = [1, 2, "GGT", "GGTA", "GGTATT", "GGTATTTTAATT", "GGTATTTTAATTTATAGT"]
+    vs = (1, 2, "GGT", "GGTA", "GGTATT", "GGTATTTTAATT", "GGTATTTTAATTTATAGT")
     results = Vector{Any}(undef, length(vs))
-    order = collect(enumerate(vs))
-
-    @sync for w in workers()
-        @async while !isempty(order)
-            v = pop!(order)
-            r = remotecall_fetch(do_work, w, str, v[2])
-            results[v[1]] = r
-        end
+    for (i, v) in enumerate(vs)
+        results[i] = do_work(w, str, v[2])
     end
 
     for (v, result) in zip(vs, results)

mandelbrot/cmain.jl

@@ -70,10 +70,11 @@ function mandelbrot(n = 200, io = stdout)
     write(io, "P4\n$n $n\n")
     write(io, rows)
 end
-Base.@ccallable function julia_main(ARGS::Vector{String})::Cint
 
-    mandelbrot(parse(Int, ARGS[1]), stdout)
+Base.@ccallable function julia_main(ARGS::Vector{String})::Cint
+    n = parse(Int, ARGS[1])
+    mandelbrot(n, stdout)
     return 0
 end
 
-mandelbrot(160, IOBuffer())
+julia_main(["8"])

nbody/cmain.jl

@@ -125,12 +125,13 @@ function perf_nbody(N::Int=1000)
     end
     @printf("%.9f\n", energy(bodies))
 end
-Base.@ccallable function julia_main(ARGS::Vector{String})::Cint
 
-    end # module
+end
+
+Base.@ccallable function julia_main(ARGS::Vector{String})::Cint
     n = parse(Int,ARGS[1])
     NBody.perf_nbody(n)
     return 0
 end
 
-julia_main(["50000000"])
+julia_main(["50000"])