Merge pull request #15 from JuliaGraphs/sbromberger/julia1.0

julia 1.0 compat

Author: sbromberger

.travis.yml

@@ -5,8 +5,8 @@ os:
   - linux
 
 julia:
-  - 0.6
-
+  - 1.0
+  - nightly
 notifications:
   email: false
 
@@ -27,10 +27,10 @@ matrix:
 
 # uncomment the following lines to override the default test script
 script:
- - julia -e 'Pkg.clone(pwd()); Pkg.build("Graph500"); Pkg.test("Graph500"; coverage=true)'
+ - julia -e 'using Pkg; Pkg.clone(pwd()); Pkg.build("Graph500"); Pkg.test("Graph500"; coverage=true)'
 
 after_success:
   # push coverage results to Coveralls
   # - julia -e 'cd(Pkg.dir("Graph500")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
   # push coverage results to Codecov
-  - julia -e 'cd(Pkg.dir("Graph500")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
+  - julia -e 'using Pkg; cd(Pkg.dir("Graph500")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'

REQUIRE

@@ -1,4 +1,4 @@
-julia 0.6
-LightGraphs 0.10.0
-StatsBase 0.8.2
+julia 0.7
+LightGraphs 1.0
+StatsBase
 ProgressMeter

src/Graph500.jl

@@ -1,11 +1,15 @@
-__precompile__(true)
 module Graph500
 
   # Dependencies
   using LightGraphs
   using StatsBase
   using ProgressMeter
   import LightGraphs.sample
+  using Distributed: @everywhere, @spawnat, @distributed, nprocs, myid
+  using Markdown: @doc_str
+  using Random
+  using Statistics: std
+
 
   export
   # kronecker_generator

src/driver.jl

@@ -10,7 +10,7 @@ end
 ### required for initialising Dict{Graph{T},Graph500Results}() constructor
 Graph500Results() = Graph500Results(0, 0, 0.0, zeros(0), zeros(0))
 
-@doc_str """
+doc"""
     driver(scale, edgefactor; replicate, seed)
 
 Run Graph500 benchmark(http://graph500.org/?page_id=12) on a graph with `2^scale` vertices and
@@ -29,9 +29,8 @@ function driver(
     ij = kronecker_generator(scale, edgefactor; replicate=replicate, seed=seed)   # generate edge list
 
     println("Starting Kernel 1.")
-    tic()
-    g = kernel_1(ij)    # kernel1
-    kernel_1_time = toq()
+    
+    g, kernel_1_time = @timed kernel_1(ij)    # kernel1
 
     T = eltype(g)
     search_key = key_sampling(g)    # sample min(nv(g),64) vertices for dfs
@@ -41,9 +40,7 @@ function driver(
 
     ### kernel_2
     @showprogress 1 "Kernel 2: " for (k, key) in enumerate(search_key)
-        tic()
-        parent_ = kernel_2(g, key)
-        kernel_2_time[k] = toq()
+        parent_, kernel_2_time[k] = @timed kernel_2(g, key)
         err = validate(g, parent_, ij, key)
         err <= 0 && error("BFS ", k, " from search key ", key, " failed to validate: ", err)
 

src/kernel_1.jl

@@ -1,4 +1,4 @@
-@doc_str """
+"""
     get_next_type(T)
 Return a data with a Integer Datatype twice the size of `T`
 """
@@ -9,7 +9,7 @@ function get_next_type(T::DataType)
     (T== UInt64) && return (UInt128,64)
 end
 
-@doc_str """
+"""
     kernel_1(ij)
 Create Graph from edge list `ij` based on kernel_1 benchmark(http://graph500.org/?page_id=12#sec-4)
 Return `LightGraphs.SimpleGraph` structure

src/kernel_2.jl

@@ -1,4 +1,4 @@
-@doc_str """
+doc"""
     key_sampling(g)
 Sample `min(nv(g), 64)` keys in `[1,nv(g)]`
 Returns a vector of randomly sampled keys
@@ -25,7 +25,7 @@ function key_sampling(
   return keys
 end
 
-@doc_str """
+doc"""
     kernel_2(g, s)
 Perform bfs on graph `g` starting at vertex `s`
 Returns vector containing parent info for each vertex

src/kronecker_generator.jl

@@ -50,17 +50,26 @@ function kronecker_generator(
     T_two = T(2)
 
     # seeding the processors if replicate is true
-    if replicate
-      for i in 1:nprocs()
-         @spawnat i srand(seed[i])
-      end
-    end
+    # if replicate
+    #     for i in 1:nprocs()
+    #         if replicate
+    #             @spawnat i rng =  MersenneTwister(seed[i])
+    #         else
+    #             @spawnat i rng = MersenneTwister()
+    #         end
+    #     end
+    # end
 
-    temp =  @parallel (+) for ib in 1:T(scale)
+    temp =  @distributed (+) for ib in 1:T(scale)
         # Compare with probabilities and set bits of indices.
+        if replicate
+            rng = Random.seed!(seed[myid()])
+        else
+            rng = Random.seed!()
+        end
         random_bits = falses(2, M)
-        random_bits[1, :] = rand(M) .> (ab)
-        random_bits[2, :] = rand(M) .> ( c_norm.*(random_bits[1, :]) + a_norm.*.!(random_bits[1, :]) )
+        random_bits[1, :] = rand(rng, M) .> (ab)
+        random_bits[2, :] = rand(rng, M) .> ( c_norm.*(random_bits[1, :]) + a_norm.*.!(random_bits[1, :]) )
         T_two^(ib-T_one).*random_bits
     end
 

src/output.jl

@@ -1,56 +1,57 @@
-@doc_str """
+doc"""
     output(result, nv, ne)
 
 Print Graph500 Benchmark statistics(http://graph500.org/?page_id=12#sec-9_3)
 """
 function output(result::Graph500Results,nv::Integer,ne::Integer)
-      print_with_color(:green, "\n", "Benchmark Info", "\n")
-      println("Scale : ", result.scale)
-      println("Number of vertices : ", nv)
-      println("Number of Edges : ", ne)
-      println("Number of Bfs : ", result.nbfs, "\n")
-
-      # kernel 1 Construction time
-      print_with_color(:green, "\n", "Graph construction time", "\n")
-      println("Graph Construction Time : ", result.kernel_1_time, "\n")
-
-      # bfs time statistics
-      bfs_time_stats = summarystats(result.kernel_2_time)
-      print_with_color(:green, "\n", "BFS time statistics", "\n")
-      println("BFS min time : ", bfs_time_stats.min)
-      println("BFS first quartile time : ", bfs_time_stats.q25)
-      println("BFS median time : ", bfs_time_stats.median)
-      println("BFS third quartile time : ", bfs_time_stats.q75)
-      println("BFS max time : ", bfs_time_stats.max)
-      println("BFS mean time : ", bfs_time_stats.mean)
-      println("BFS standard deviation time : ", std(result.kernel_2_time), "\n")
-
-      # bfs statistics based on number of edges
-      bfs_edgetraversed_stats = summarystats(result.kernel_2_nedge)
-      print_with_color(:green, "\n", "Edges traversed per BFS statistics", "\n")
-      println("BFS min nedge : ", bfs_edgetraversed_stats.min)
-      println("BFS first quartile nedge : ", bfs_edgetraversed_stats.q25)
-      println("BFS median nedge : ", bfs_edgetraversed_stats.median)
-      println("BFS third quartile nedge : ", bfs_edgetraversed_stats.q75)
-      println("BFS max nedge : ", bfs_edgetraversed_stats.max)
-      println("BFS mean nedge : ", bfs_edgetraversed_stats.mean)
-      println("BFS standard deviation nedge : ", std(result.kernel_2_nedge), "\n")
-
-      # statistics on traversed edges per second(teps)
-      bfs_teps = result.kernel_2_nedge ./ result.kernel_2_time
-      bfs_n = length(bfs_teps)
-      teps_stats = summarystats(bfs_teps)
-      print_with_color(:green, "\n", "Edges traversed per second statistics", "\n")
-      println("BFS min TEPS : ", teps_stats.min)
-      println("BFS first quartile TEPS : ", teps_stats.q25)
-      println("BFS median TEPS : ", teps_stats.median)
-      println("BFS third quartile TEPS : ", teps_stats.q75)
-      println("BFS max TEPS : ", teps_stats.max)
-
-      # harmomnic mean of teps
-      k2tmp = 1.0 ./ bfs_teps
-      k2tmp = k2tmp - (1/harmmean(bfs_teps))
-      harmonic_std = (sqrt(sum(k2tmp.^2)) / (bfs_n-1)) * harmmean(bfs_teps)^2
-      println("BFS harmonic mean TEPS : ", harmmean(bfs_teps))
-      println("BFS harmonic standard deviation TEPS : ", harmonic_std, "\n")
-  end
+    io = IOContext(stdout, :color=>true)
+    printstyled(io, "\n", "Benchmark Info", "\n", color=:green)
+    println("Scale : ", result.scale)
+    println("Number of vertices : ", nv)
+    println("Number of Edges : ", ne)
+    println("Number of Bfs : ", result.nbfs, "\n")
+    
+    # kernel 1 Construction time
+    printstyled(io, "\n", "Graph construction time", "\n", color=:green)
+    println("Graph Construction Time : ", result.kernel_1_time, "\n")
+    
+    # bfs time statistics
+    bfs_time_stats = summarystats(result.kernel_2_time)
+    printstyled(io, "\n", "BFS time statistics", "\n", color=:green)
+    println("BFS min time : ", bfs_time_stats.min)
+    println("BFS first quartile time : ", bfs_time_stats.q25)
+    println("BFS median time : ", bfs_time_stats.median)
+    println("BFS third quartile time : ", bfs_time_stats.q75)
+    println("BFS max time : ", bfs_time_stats.max)
+    println("BFS mean time : ", bfs_time_stats.mean)
+    println("BFS standard deviation time : ", std(result.kernel_2_time), "\n")
+    
+    # bfs statistics based on number of edges
+    bfs_edgetraversed_stats = summarystats(result.kernel_2_nedge)
+    printstyled(io, "\n", "Edges traversed per BFS statistics", "\n", color=:green)
+    println("BFS min nedge : ", bfs_edgetraversed_stats.min)
+    println("BFS first quartile nedge : ", bfs_edgetraversed_stats.q25)
+    println("BFS median nedge : ", bfs_edgetraversed_stats.median)
+    println("BFS third quartile nedge : ", bfs_edgetraversed_stats.q75)
+    println("BFS max nedge : ", bfs_edgetraversed_stats.max)
+    println("BFS mean nedge : ", bfs_edgetraversed_stats.mean)
+    println("BFS standard deviation nedge : ", std(result.kernel_2_nedge), "\n")
+    
+    # statistics on traversed edges per second(teps)
+    bfs_teps = result.kernel_2_nedge ./ result.kernel_2_time
+    bfs_n = length(bfs_teps)
+    teps_stats = summarystats(bfs_teps)
+    printstyled(io, "\n", "Edges traversed per second statistics", "\n", color=:green)
+    println("BFS min TEPS : ", teps_stats.min)
+    println("BFS first quartile TEPS : ", teps_stats.q25)
+    println("BFS median TEPS : ", teps_stats.median)
+    println("BFS third quartile TEPS : ", teps_stats.q75)
+    println("BFS max TEPS : ", teps_stats.max)
+    
+    # harmomnic mean of teps
+    k2tmp = 1.0 ./ bfs_teps
+    k2tmp = k2tmp .- (1/harmmean(bfs_teps))
+    harmonic_std = (sqrt(sum(k2tmp.^2)) / (bfs_n-1)) * harmmean(bfs_teps)^2
+    println("BFS harmonic mean TEPS : ", harmmean(bfs_teps))
+    println("BFS harmonic standard deviation TEPS : ", harmonic_std, "\n")
+end

src/validation.jl

@@ -1,4 +1,4 @@
-@doc_str """
+doc"""
     validate(g, parent_, ij, search_key)
 validate `parent_` info for bfs on graph `g` with key `search_key` based on Graph500 result
 validation(http://graph500.org/?page_id=12#sec-8)
@@ -20,16 +20,16 @@ function validate(
     end
 
     N = nv(g)
-    slice = find(x->(x > zero(T)), parent_)
+    slice = findall(x->(x > zero(T)), parent_)
 
     #Compute levels and check for cycles.
     level_ = zeros(T, length(parent_))
-    level_[slice] = 1
+    level_[slice] .= 1
     P = parent_[slice]
     mask = (P .!= search_key)
     k = 0
     while any(mask)
-      level_[slice[mask]] = level_[slice[mask]] + 1
+      level_[slice[mask]] .+= 1
       P = parent_[P]
       mask = (P .!= search_key)
       k = k + 1

test/runtests.jl

@@ -1,5 +1,5 @@
 using Graph500
-using Base.Test
+using Test
 
 @testset begin
   include("kronecker_generator.jl")