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5 x decrease in performance with new Julia build #7000

Closed jfrolich closed 10 years ago

jfrolich commented 10 years ago

I am currently working on a high performance text analytics package for Julia.

When today I installed the new release I got a 5 times decrease in performance with the current Julia build (Version 0.3.0-prerelease+3225 (2014-05-27 03:45 UTC)) when compared to an older build (Version 0.3.0-prerelease+2727 (2014-04-23 18:25 UTC)). It is not clear why this is happening. When reinstalling the old version it works as expected. I used the windows x64 build.

The code is quite long but perhaps the bottleneck is clear. Otherwise I can try to make a more simple showcase of the performance problem. I am still learning Julia so perhaps it is an obvious mistake.

using DataFrames
using Base
using Datetime

import Base.length

PATH = "C:\\Users\\JFrolich\\Documents\\Data sets\\Reuters\\fetch\\full_dataset"
metadata = readtable(string(PATH, "/", "metadata.csv"))
y = array(metadata[:acq])

typealias Vocabulary Dict{UTF8String, Uint32}
typealias UnweightedDTM SparseMatrixCSC{Uint32}
typealias WeightedDTM SparseMatrixCSC{Float64}
typealias DTM Union(WeightedDTM, UnweightedDTM)
typealias Document UTF8String

function preprocess(d::Document)
    lowercase(d)
end

function tokenize(s::Document)
    [utf8(s) for s in matchall(r"\b\w\w+\b", preprocess(s))]
end

# A document collection is a collection of documents.
# The implementation needs the following interface:
#
# text: returns the plain text for the given document
# length: returns the length of the collection
#
abstract DocumentCollection

# Text files implementation
# This implementation of documentcollection iterate through
# text files to create the DTM
type TextFiles <: DocumentCollection
    filenames::Vector{String}
    buffer_ptr::Int
    buffer_size::Int
    buffer::Vector{Document}
end

TEXT_BUFFER_SIZE = 30000

function text_files(files)
    TextFiles(files, -1, TEXT_BUFFER_SIZE, [])
end

# returns the text for index 'i', it pre-filles a buffer of text
# for all the files in the collection when necesary, because
# loading it file by file is much slower (factor 3)
function text(dc::TextFiles, i::Int)
    if dc.buffer_ptr < 0 || i >= (dc.buffer_ptr + dc.buffer_size) || i < dc.buffer_ptr
        fill_buffer!(dc, i)
    end

    dc.buffer[i-dc.buffer_ptr+1]
end

function fill_buffer!(dc::TextFiles, i::Int)
    dc.buffer_ptr = i
    dc.buffer = Document[]
    for i in dc.buffer_ptr:(dc.buffer_ptr + dc.buffer_size)
        if i > length(dc)
            break
        end
        push!(dc.buffer, open(dc.filenames[i]) do f
            Document(readbytes(f))
        end)
    end
end

length(dc::TextFiles) = Base.length(dc.filenames)

# TextArray: This implementation of documentcollection is simply
# given as an array of strings
type TextArray <: DocumentCollection
    texts::Vector{Document}
end

function text(dc::TextArray, i::Int)
    dc.texts[i]
end

function text_array(texts)
    TextArray(texts)
end

length(dc::TextArray) = Base.length(dc.texts)

Base.start(dc::DocumentCollection) = 1
Base.next(dc::DocumentCollection, i) = (text(dc, i), i+1)
Base.done(dc::DocumentCollection, i) = i > length(dc)

# calculates Chi squared scores of a sparse matrix on a binary variable (y)
function chi2(X::DTM, y::Array{Int, 1})
    f_obs = y * X
    feature_count = ones(Float64, size(X)[1]) * X
    class_prob    = mean(y)
    f_exp = (class_prob * feature_count)'
    chisq = Float64[]
    for i in 1:length(f_obs)
        push!(chisq, (f_obs[i] - f_exp[i])^2/(f_exp[i]))
    end
    chisq
end

# Feature selection
function select_k_best(X::DTM, y::Vector{Int}, score_fnc, k::Int)
    scores = score_fnc(X,y)
    sortperm(scores::Array{Float64,1}, rev=true, alg=MergeSort)[1:k]
end

function ngramize(tokens::Array{UTF8String,1}, n_grams::Int64=2)
    n_tokens::Int64 = length(tokens)
    for i in 1:n_tokens
        gram = ""
        for j in 1:n_grams
            token = tokens[i+j-1]
            if j == 1
                gram = token
            elseif j > 1 && i+j-1 <= n_tokens
                gram = string(gram, " ", token)
                push!(tokens, gram)
            end
        end
    end
    tokens
end

function text_from_files(files)
    texts = UTF8String[]
    for file in files
        push!(texts, open(file) do f
            UTF8String(readbytes(f))
        end)
    end
    texts
end

# TODO: Add ngram range feature
function dtm(dc::DocumentCollection, n_grams::Int)
    vocabulary = Vocabulary()
    is = Uint32[]
    js = Uint32[]
    vs = Uint32[]
    for (i, text) in enumerate(dc)
        tokens::Array{UTF8String,1} = ngramize(tokenize(text), n_grams)
        for token in tokens
            push!(is, i)
            push!(js, get!(vocabulary, token, length(vocabulary)+1))
            push!(vs, 1)
        end
    end
    (sparse(is, js, vs, length(dc), maximum(js)),
     vocabulary_to_feature_names(vocabulary))
end

function vocabulary_to_feature_names(vocabulary::Vocabulary)
    inv_voc = Dict{Uint32, UTF8String}()
    for (k,v) in vocabulary
        inv_voc[v] = k
    end
    [inv_voc[convert(Uint32, i)] for i in 1:length(inv_voc)]
end

files = [string(PATH, "/text/", id) for id in (metadata[:id])]

dc = text_array(text_from_files(files))

@time X, feature_names = dtm(dc,3)
lindahua commented 10 years ago

Can you do git bisect to pin down the culprit?

jfrolich commented 10 years ago

I use the binary builds, so I guess I cannot do that?

JeffBezanson commented 10 years ago

You could try running the fast and slow versions each with @profile followed by Profile.print(). That might help identify the bottleneck.

jfrolich commented 10 years ago

I can tell the slowdown is in this part:

for (i, text) in enumerate(dc)
  tokens::Array{UTF8String,1} = ngramize(tokenize(text), n_grams)
  for token in tokens
    push!(is, i)
    push!(js, get!(vocabulary, token, length(vocabulary)+1))
    push!(vs, 1)
  end
end

Will do a profile now..

jfrolich commented 10 years ago

Good:

5    ...lia RF\text_proc_2.jl; tokenize; line: 22
  1 string.jl; bytestring; line: 653
    1 ...lia RF\text_proc_2.jl; ngramize; line: 123
7    array.jl; lexcmp; line: 817
14   array.jl; push!; line: 445
2    array.jl; push!; line: 446
1    inference.jl; builtin_tfunction; line: 511
2    inference.jl; typeinf; line: 1212
1    iobuffer.jl; ensureroom; line: 147
68   profile.jl; anonymous; line: 9
    68 profile.jl; anonymous; line: 14
                   2  ...\text_proc_2.jl; dtm; line: 145
1    reflection.jl; _methods; line: 80
1    regex.jl; matchall; line: 131
1    regex.jl; matchall; line: 133
1    regex.jl; matchall; line: 134
1    regex.jl; matchall; line: 136
7    regex.jl; matchall; line: 138
1    regex.jl; matchall; line: 146
1    regex.jl; matchall; line: 154
 1 array.jl; push!; line: 447
28   regex.jl; matchall; line: 167
        1  regex.jl; matchall; line: 164
                              21 regex.jl; matchall; line: 138
                              1  regex.jl; matchall; line: 146
                              4  regex.jl; matchall; line: 154
                                 1 array.jl; push!; line: 440
                                     1 string.jl; SubString; line: 601
                                     +2 1 array.jl; push!; line: 445
                                     +4 1 string.jl; SubString; line: 600
                              1  regex.jl; matchall; line: 155
2    string.jl; isequal; line: 521
4    string.jl; map; line: 804
        1 utf8.jl; getindex; line: 56
        1 utf8.jl; getindex; line: 72
10   string.jl; map; line: 805
        1 string.jl; lowercase; line: 787
             1 string.jl; lowercase; line: 787
10   string.jl; map; line: 809
     1 iobuffer.jl; write; line: 220
     2 iobuffer.jl; write; line: 221
             1 string.jl; lowercase; line: 787
               1 array.jl; append!; line: 462
                 1 iobuffer.jl; ensureroom; line: 131
     2 iobuffer.jl; write; line: 226
     1 iobuffer.jl; write; line: 228
      1 utf8.jl; endof; line: 33
      1 utf8.jl; endof; line: 35
          1 io.jl; write; line: 68
           1 iobuffer.jl; write; line: 220
          1 io.jl; write; line: 70
1    utf8.jl; endof; line: 32
1    utf8.jl; endof; line: 35
4    utf8.jl; isvalid; line: 95
 2    ...lia RF\text_proc_2.jl; tokenize; line: 22
                     1 string.jl; map; line: 805
                     1 string.jl; map; line: 809
 1    array.jl; getindex; line: 111
 2    array.jl; push!; line: 445
     2 array.jl; push!; line: 440
 1    inference.jl; without_linenums; line: 1819
 1    iobuffer.jl; ensureroom; line: 131
 3    iobuffer.jl; ensureroom; line: 145
 1    iobuffer.jl; ensureroom; line: 146
 2    iobuffer.jl; ensureroom; line: 149
 2    reflection.jl; _methods; line: 80
 1    reflection.jl; _methods; line: 97
                 1 reflection.jl; _methods; line: 80
 1    string.jl; isequal; line: 521
 1    utf8.jl; string; line: 135
 61   utf8.jl; string; line: 138
 4    utf8.jl; string; line: 139
 77   utf8.jl; string; line: 140
    2  array.jl; append!; line: 457
     1 array.jl; append!; line: 457
     8 array.jl; append!; line: 462
       1 array.jl; copy!; line: 55
             2 array.jl; copy!; line: 52
             5 array.jl; copy!; line: 55
              2 array.jl; unsafe_copy!; line: 42
      1 array.jl; append!; line: 463
 11   utf8.jl; string; line: 142
  6    array.jl; append!; line: 457
  1    array.jl; append!; line: 460
  120  array.jl; append!; line: 461
  12   array.jl; append!; line: 462
   1 array.jl; copy!; line: 52
   2 array.jl; copy!; line: 55
    2 array.jl; copy!; line: 52
  2    array.jl; lexcmp; line: 817
      2 dict.jl; hashindex; line: 360
  39   array.jl; push!; line: 445
      39 array.jl; push!; line: 440
  1    dict.jl; _setindex!; line: 503
  4    dict.jl; _setindex!; line: 505
  1    inference.jl; typeinf; line: 1465
                               1 inference.jl; stupdate; line: 1146
  9    string.jl; bytestring; line: 34
  1    string.jl; isequal; line: 521
  1    string.jl; lowercase; line: 787
      1 iobuffer.jl; ensureroom; line: 145
   15   ...ia RF\text_proc_2.jl; tokenize; line: 22
     15 string.jl; bytestring; line: 653
       3  ...a RF\text_proc_2.jl; ngramize; line: 123
       12 ...a RF\text_proc_2.jl; ngramize; line: 124
               11 string.jl; bytestring; line: 653
                   10 array.jl; push!; line: 445
                   1  array.jl; push!; line: 446
   47   array.jl; append!; line: 462
           47 array.jl; copy!; line: 55
              1  array.jl; unsafe_copy!; line: 42
               2  array.jl; unsafe_copy!; line: 42
                3  array.jl; unsafe_copy!; line: 48
                 1  array.jl; unsafe_copy!; line: 48
                  37 array.jl; unsafe_copy!; line: 42
                  3  array.jl; unsafe_copy!; line: 48
   25   array.jl; lexcmp; line: 817
       2 dict.jl; hashindex; line: 360
           2 string.jl; isequal; line: 521
   6    array.jl; lexcmp; line: 819
   530  dict.jl; hashindex; line: 360
      137 utf8.jl; endof; line: 32
      165 utf8.jl; endof; line: 33
      173 utf8.jl; endof; line: 35
      1   utf8.jl; endof; line: 36
       54 string.jl; isequal; line: 521
         1  utf8.jl; endof; line: 32
             17 utf8.jl; endof; line: 32
             15 utf8.jl; endof; line: 33
             16 utf8.jl; endof; line: 35
   2    dict.jl; ht_keyindex2; line: 467
   6    dict.jl; ht_keyindex2; line: 470
     1 dict.jl; int64hash; line: 219
     1 dict.jl; int64hash; line: 220
     2 dict.jl; int64hash; line: 224
   29   dict.jl; ht_keyindex2; line: 475
   9    dict.jl; ht_keyindex2; line: 486
   1    dict.jl; skip_deleted; line: 639
   3    dict.jl; skip_deleted; line: 640
   1    dict.jl; skip_deleted; line: 641
   2    dict.jl; skip_deleted; line: 643
   1    string.jl; bytestring; line: 653
       1 array.jl; push!; line: 440
   1    string.jl; lowercase; line: 787
     1 array.jl; append!; line: 462
       1 iobuffer.jl; ensureroom; line: 146
   2    string.jl; map; line: 802
       1 dict.jl; hashindex; line: 360
         1 utf8.jl; endof; line: 35
   24   string.jl; map; line: 804
    1  utf8.jl; getindex; line: 54
     1  utf8.jl; getindex; line: 65
      3  utf8.jl; getindex; line: 54
           1 utf8.jl; getindex; line: 54
           1 utf8.jl; getindex; line: 56
           1 utf8.jl; getindex; line: 67
           2 utf8.jl; getindex; line: 68
           3 utf8.jl; getindex; line: 72
           3 utf8.jl; getindex; line: 74
           3 utf8.jl; getindex; line: 77
   77   string.jl; map; line: 805
           4  string.jl; lowercase; line: 787
                8 string.jl; lowercase; line: 787
   51   string.jl; map; line: 809
    1  utf8.jl; endof; line: 32
     3  io.jl; write; line: 70
      1  io.jl; write; line: 70
        2  iobuffer.jl; write; line: 220
        9  iobuffer.jl; write; line: 221
         1 iobuffer.jl; ensureroom; line: 149
          2 iobuffer.jl; ensureroom; line: 131
           1 iobuffer.jl; ensureroom; line: 131
            3 iobuffer.jl; ensureroom; line: 131
            1 iobuffer.jl; ensureroom; line: 149
        1  iobuffer.jl; write; line: 222
        3  iobuffer.jl; write; line: 224
        2  iobuffer.jl; write; line: 226
        1  iobuffer.jl; write; line: 229
        3  iobuffer.jl; write; line: 230
         2 utf8.jl; endof; line: 32
         6 utf8.jl; endof; line: 35
             6 io.jl; write; line: 68
              1 iobuffer.jl; write; line: 220
               1 iobuffer.jl; write; line: 220
               1 iobuffer.jl; write; line: 224
                1 iobuffer.jl; write; line: 220
             1 io.jl; write; line: 70
             1 io.jl; write; line: 77
             1 io.jl; write; line: 86
    131  array.jl; push!; line: 445
      2  dict.jl; get!; line: 535
      42 dict.jl; get!; line: 536
       2  string.jl; isequal; line: 521
        5  string.jl; isequal; line: 521
         5  string.jl; isequal; line: 521
            4  string.jl; isequal; line: 521
             2  string.jl; isequal; line: 521
                      22 string.jl; isequal; line: 521
                       1  array.jl; lexcmp; line: 817
                        1 array.jl; lexcmp; line: 817
                           1 array.jl; lexcmp; line: 817
                           2 array.jl; lexcmp; line: 819
                            1 array.jl; lexcmp; line: 817
                             1 array.jl; lexcmp; line: 817
                                  2 array.jl; lexcmp; line: 817
                                  2 array.jl; lexcmp; line: 819
      16 dict.jl; get!; line: 540
       1  dict.jl; ht_keyindex2; line: 467
        1  dict.jl; ht_keyindex2; line: 467
         1  dict.jl; ht_keyindex2; line: 467
          1 dict.jl; ht_keyindex2; line: 467
            1 dict.jl; ht_keyindex2; line: 487
              1 dict.jl; ht_keyindex2; line: 467
              1 dict.jl; ht_keyindex2; line: 487
                      6 string.jl; isequal; line: 521
                          1 dict.jl; ht_keyindex2; line: 467
                          2 dict.jl; ht_keyindex2; line: 486
                              1 string.jl; isequal; line: 521
                          3 dict.jl; ht_keyindex2; line: 487
      59 dict.jl; get!; line: 542
      1  dict.jl; get!; line: 545
      1  string.jl; SubString; line: 600
       1 utf8.jl; endof; line: 34
      1  string.jl; SubString; line: 607
       1 utf8.jl; isvalid; line: 95
      1  string.jl; SubString; line: 608
      8  string.jl; SubString; line: 612
    1    dict.jl; hashindex; line: 360
        1 string.jl; isequal; line: 521
    1    inference.jl; typeinf; line: 1212
    1    regex.jl; matchall; line: 138
    1    regex.jl; matchall; line: 154
      1 array.jl; push!; line: 440
    57   string.jl; isequal; line: 521
        2  dict.jl; ht_keyindex2; line: 469
        55 dict.jl; ht_keyindex2; line: 470
         1  dict.jl; hashindex; line: 360
          1  dict.jl; hashindex; line: 360
             1  dict.jl; hashindex; line: 360
                50 array.jl; lexcmp; line: 817
                    50 dict.jl; hashindex; line: 360
                     1  array.jl; sizeof; line: 23
                      6  array.jl; sizeof; line: 23
      28   ...a RF\text_proc_2.jl; tokenize; line: 22
                          1  regex.jl; matchall; line: 133
                          4  string.jl; map; line: 804
                                  2 utf8.jl; getindex; line: 56
                                  1 utf8.jl; getindex; line: 67
                                  1 utf8.jl; getindex; line: 77
                          9  string.jl; map; line: 805
                                       2 string.jl; lowercase; line: 787
                          14 string.jl; map; line: 809
                           1  utf8.jl; endof; line: 34
                              1  io.jl; write; line: 86
                               1 iobuffer.jl; write; line: 220
                               2 iobuffer.jl; write; line: 221
                                  1 iobuffer.jl; ensureroom; line: 131
                               2 iobuffer.jl; write; line: 226
                               1 iobuffer.jl; write; line: 229
                                2 utf8.jl; endof; line: 35
                                    2 io.jl; write; line: 68
                                       1 ...ffer.jl; write; line: 220
                                        1 ...ffer.jl; write; line: 224
                                    1 io.jl; write; line: 70
      1    array.jl; cumsum_pairwise; line: 1354
          1 array.jl; cumsum_pairwise; line: 1350
      1    dict.jl; _setindex!; line: 503
      156  string.jl; isequal; line: 521
          2   dict.jl; ht_keyindex2; line: 469
          3   dict.jl; ht_keyindex2; line: 472
          114 dict.jl; ht_keyindex2; line: 475
          1   dict.jl; ht_keyindex2; line: 476
          34  dict.jl; ht_keyindex2; line: 486
          1   dict.jl; ht_keyindex2; line: 490
          1   dict.jl; ht_keyindex2; line: 492
       1    ...a RF\text_proc_2.jl; tokenize; line: 22
       1    array.jl; push!; line: 445
       21   dict.jl; hashindex; line: 360
           21 string.jl; isequal; line: 521
            1  array.jl; lexcmp; line: 819
               1  array.jl; lexcmp; line: 819
                  3  array.jl; lexcmp; line: 817
                       15 array.jl; lexcmp; line: 817
                       1  array.jl; lexcmp; line: 819
       2    dict.jl; ht_keyindex; line: 444
         1 dict.jl; int64hash; line: 225
       4    dict.jl; setindex!; line: 523
         1 dict.jl; ht_keyindex2; line: 467
           1 dict.jl; ht_keyindex2; line: 476
             1 dict.jl; ht_keyindex2; line: 467
              1 dict.jl; ht_keyindex2; line: 476
       1    dict.jl; setindex!; line: 526
       7    dict.jl; setindex!; line: 528
        1 dict.jl; _setindex!; line: 503
                   3 dict.jl; _setindex!; line: 503
                   1 dict.jl; _setindex!; line: 508
                   1 dict.jl; _setindex!; line: 510
       1    sparse/csparse.jl; sparse; line: 30
       4    sparse/csparse.jl; sparse; line: 31
       1    sparse/csparse.jl; sparse; line: 45
       1    sparse/csparse.jl; sparse; line: 46
       1    sparse/csparse.jl; sparse; line: 49
       6    sparse/csparse.jl; sparse; line: 50
       3    sparse/csparse.jl; sparse; line: 51
       1    sparse/csparse.jl; sparse; line: 56
       28   string.jl; isequal; line: 521
        1  utf8.jl; endof; line: 32
         1  utf8.jl; endof; line: 32
           3  dict.jl; ht_keyindex2; line: 470
             2 utf8.jl; endof; line: 32
             1 utf8.jl; endof; line: 35
           22 dict.jl; ht_keyindex2; line: 486
             8  utf8.jl; endof; line: 33
             14 utf8.jl; endof; line: 35
       1    string.jl; map; line: 802
           1 dict.jl; hashindex; line: 360
             1 utf8.jl; endof; line: 35
       1    utf8.jl; utf8; line: 161
        39   ... RF\text_proc_2.jl; vocabulary_to_feature_names; line: 163
         1  dict.jl; skip_deleted; line: 639
        5    ... RF\text_proc_2.jl; vocabulary_to_feature_names; line: 164
          1 dict.jl; setindex!; line: 517
          1 dict.jl; setindex!; line: 531
            1 dict.jl; setindex!; line: 517
        2    ... RF\text_proc_2.jl; vocabulary_to_feature_names; line: 166
        2    dict.jl; _setindex!; line: 504
        1    string.jl; isequal; line: 521
        1    string.jl; map; line: 805
         8    dict.jl; _setindex!; line: 505
         1    dict.jl; _setindex!; line: 508
         2    dict.jl; setindex!; line: 517
          1    abstractarray.jl; compute_dims; line: 629
           1 abstractarray.jl; compute_dims; line: 629
            1 abstractarray.jl; compute_dims; line: 622
                            1 ...e/csparse.jl; sparse; line: 72
          10   array.jl; push!; line: 445
          1    array.jl; push!; line: 446
          1    array.jl; shift!; line: 521
           1 array.jl; shift!; line: 519
            1 task.jl; wait; line: 279
                            1 ...e/csparse.jl; sparse; line: 74
          1    base.jl; append_any; line: 139
           1 base.jl; append_any; line: 139
                            1 ...e/csparse.jl; sparse; line: 73
          2    cell.jl; setindex!; line: 32
           2 cell.jl; setindex!; line: 32
            1 inference.jl; anonymous; line: 201
                            1 ...e/csparse.jl; sparse; line: 74
                            1 ...e/csparse.jl; sparse; line: 74
          1    dict.jl; ht_keyindex; line: 460
           1 dict.jl; ht_keyindex; line: 460
            1 dict.jl; ht_keyindex; line: 441
                            1 ...e/csparse.jl; sparse; line: 72
          1    inference.jl; abstract_call; line: 757
           1 inference.jl; abstract_call; line: 757
            1 inference.jl; abstract_call; line: 752
                            1 ...e/csparse.jl; sparse; line: 72
          1    inference.jl; abstract_call; line: 833
           1 inference.jl; abstract_call; line: 833
            1 inference.jl; abstract_call; line: 814
                            1 ...e/csparse.jl; sparse; line: 76
                                1 inference.jl; abstract_call; line: 814
          1    inference.jl; abstract_call_gf; line: 638
           1 inference.jl; abstract_call_gf; line: 638
            1 inference.jl; abstract_call_gf; line: 706
                            1 ...e/csparse.jl; sparse; line: 69
          1    inference.jl; abstract_call_gf; line: 655
           1 inference.jl; abstract_call_gf; line: 655
            1 inference.jl; abstract_call_gf; line: 635
                            1 ...e/csparse.jl; sparse; line: 76
          1    inference.jl; abstract_eval; line: 928
           1 inference.jl; abstract_eval; line: 928
            1 inference.jl; abstract_eval; line: 931
                            1 ...e/csparse.jl; sparse; line: 71
          1    inference.jl; abstract_eval_symbol; line: 1012
           1 inference.jl; abstract_eval_symbol; line: 1012
            1 inference.jl; abstract_eval_arg; line: 852
                            1 ...e/csparse.jl; sparse; line: 73
          1    inference.jl; abstract_eval_symbol; line: 1014
           1 inference.jl; abstract_eval_symbol; line: 1014
            1 inference.jl; abstract_eval_symbol; line: 1012
                            1 ...e/csparse.jl; sparse; line: 74
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                            1 ...e/csparse.jl; sparse; line: 71
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           1 inference.jl; anonymous; line: 277
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                            1 ...e/csparse.jl; sparse; line: 74
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                            1 ...e/csparse.jl; sparse; line: 69
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                            1 ...e/csparse.jl; sparse; line: 76
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           1 inference.jl; anonymous; line: 2538
            1 inference.jl; anonymous; line: 2538
                            1 ...e/csparse.jl; sparse; line: 73
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           1 inference.jl; eval_annotate; line: 1586
            1 inference.jl; eval_annotate; line: 1582
                            1 ...e/csparse.jl; sparse; line: 72
          1    inference.jl; find_sa_vars; line: 2572
           1 inference.jl; find_sa_vars; line: 2572
                            1 ...e/csparse.jl; sparse; line: 73
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           2 inference.jl; inlineable; line: 2035
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                            1 ...e/csparse.jl; sparse; line: 71
                            1 ...e/csparse.jl; sparse; line: 72
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           1 inference.jl; inlineable; line: 2153
            1 inference.jl; inlineable; line: 2151
                            1 ...e/csparse.jl; sparse; line: 76
                                1 inference.jl; inlineable; line: 2151
                                    1 int.jl; +; line: 33
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           1 inference.jl; inlineable; line: 2173
            1 inference.jl; inlineable; line: 2197
                            1 ...e/csparse.jl; sparse; line: 73
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           1 inference.jl; inlining_pass; line: 2429
            1 inference.jl; inlining_pass; line: 2418
                            1 ...e/csparse.jl; sparse; line: 72
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            1 inference.jl; is_known_call; line: 2515
                            1 ...e/csparse.jl; sparse; line: 69
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           1 inference.jl; typeinf; line: 1214
            1 inference.jl; typeinf; line: 1395
                            1 ...e/csparse.jl; sparse; line: 73
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           1 inference.jl; typeinf_ext; line: 1185
            1 array.jl; reinterpret; line: 81
                            1 ...e/csparse.jl; sparse; line: 69
          1    inference.jl; unique_names; line: 2490
           1 inference.jl; unique_names; line: 2490
            1 expr.jl; copy; line: 30
                            1 ...e/csparse.jl; sparse; line: 73
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           1 multi.jl; call_on_owner; line: 743
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                            1 ...e/csparse.jl; sparse; line: 69
          1    path.jl; joinpath; line: 58
           1 path.jl; joinpath; line: 58
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                            1 ...e/csparse.jl; sparse; line: 73
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                            1 ...e/csparse.jl; sparse; line: 69
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                            1 ...e/csparse.jl; sparse; line: 71
                                1 pcre.jl; exec; line: 126
                                     1 array.jl; setindex!; line: 298
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                            1 ...e/csparse.jl; sparse; line: 73
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           1 range.jl; StepRange; line: 49
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                            1 ...e/csparse.jl; sparse; line: 74
          1    show.jl; show_unquoted; line: 456
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                            1 ...e/csparse.jl; sparse; line: 69
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                            1 ...e/csparse.jl; sparse; line: 71
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                            1 ...e/csparse.jl; sparse; line: 72
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                            1 ...e/csparse.jl; sparse; line: 71
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                            1 ...e/csparse.jl; sparse; line: 76
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                            1 ...e/csparse.jl; sparse; line: 73
          1    string.jl; print; line: 623
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                            1 ...e/csparse.jl; sparse; line: 71
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                            1 ...e/csparse.jl; sparse; line: 74
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                            1 ...e/csparse.jl; sparse; line: 71
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                            1 ...e/csparse.jl; sparse; line: 73
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                            1 ...e/csparse.jl; sparse; line: 72
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                            1 ...e/csparse.jl; sparse; line: 71
              1    sparse/csparse.jl; sparse; line: 71
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                                      1   ...oc_2.jl; tokenize; line: 22
                                     +3 211 ...c_2.jl; tokenize; line: 22
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                                     +7 1   ...c_2.jl; ngramize; line: 116
                                     +7 109 ...c_2.jl; ngramize; line: 123
                                     +9 1  utf8.jl; string; line: 134
                                    +11 1  utf8.jl; string; line: 134
                                    +11 1  utf8.jl; string; line: 135
                                    +11 4  utf8.jl; string; line: 138
                                    +14 1 utf8.jl; string; line: 135
                                    +17 1 utf8.jl; string; line: 134
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                                    +11 1  array.jl; push!; line: 447
                                    +15 24 string.jl; bytestring; line: 653
                                    +19 22 array.jl; push!; line: 445
                                    +19 2  array.jl; push!; line: 446
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                          1   array.jl; push!; line: 447
                             328 array.jl; push!; line: 445
                                 1   array.jl; push!; line: 440
                                 299 array.jl; push!; line: 444
                                    +14 1 io.jl; close; line: 260
                                 18  array.jl; push!; line: 445
                                 10  array.jl; push!; line: 446
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                         1 dict.jl; get!; line: 535
                     40  ...ext_proc_2.jl; dtm; line: 154
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                             31 array.jl; push!; line: 445
                                 1  array.jl; push!; line: 440
                                 5  array.jl; push!; line: 444
                                 19 array.jl; push!; line: 445
                                 6  array.jl; push!; line: 446
                      3   dict.jl; rehash; line: 387
                      4   dict.jl; rehash; line: 388
                      207 dict.jl; rehash; line: 391
                        1   dict.jl; int64hash; line: 223
                           202 dict.jl; hashindex; line: 360
                      5   dict.jl; rehash; line: 392
                      1   dict.jl; rehash; line: 393
                      7   dict.jl; rehash; line: 396
                      4   dict.jl; rehash; line: 397
                      3   dict.jl; rehash; line: 398
                         2   ...xt_proc_2.jl; dtm; line: 157
                               1 reduce.jl; maximum_rgn; line: 396
                               1 reduce.jl; maximum_rgn; line: 397
                         1   ...e/csparse.jl; sparse; line: 73
                          1   ...e/csparse.jl; sparse; line: 72
                            1   .../csparse.jl; sparse; line: 63
                            1   .../csparse.jl; sparse; line: 65
                            1   .../csparse.jl; sparse; line: 66
                            6   .../csparse.jl; sparse; line: 67
                            55  .../csparse.jl; sparse; line: 69
                                     1 int.jl; +; line: 20
                            53  .../csparse.jl; sparse; line: 71
                                     1  array.jl; setindex!; line: 298
                                        1 array.jl; setindex!; line: 298
                            40  .../csparse.jl; sparse; line: 72
                            62  .../csparse.jl; sparse; line: 73
                                        2 array.jl; setindex!; line: 298
                            36  .../csparse.jl; sparse; line: 74
                                        1 array.jl; setindex!; line: 298
                            39  .../csparse.jl; sparse; line: 76
                            5   .../csparse.jl; sparse; line: 80
                            4   .../csparse.jl; sparse; line: 81
                            1   .../csparse.jl; sparse; line: 85
                              49 ..._proc_2.jl; dtm; line: 157
                                     +7 1  ...arse.jl; sparse; line: 69
                                     +7 1  ...arse.jl; sparse; line: 74
                                    +15 1  ...arse.jl; sparse; line: 69
                                    +17 1  ...arse.jl; sparse; line: 69
                                    +21 1  ...arse.jl; sparse; line: 69
                                    +36 1  ...rse.jl; sparse; line: 101
                                    +36 1  ...rse.jl; sparse; line: 107
                                    +36 2  ...rse.jl; sparse; line: 108
                                    +36 26 ...rse.jl; sparse; line: 109
                                    +36 14 ...rse.jl; sparse; line: 110
                              1  ...csparse.jl; sparse; line: 90
                              8  ...csparse.jl; sparse; line: 95
                                     53 ...oc_2.jl; dtm; line: 157
                                    +21 53 ...c_2.jl; ...ature_names; line: 166
                                    +23 1  dict.jl; ht_keyindex; line: 441
                                    +37 4  dict.jl; ht_keyindex; line: 441
                                    +37 1  dict.jl; ht_keyindex; line: 443
                                    +37 22 dict.jl; ht_keyindex; line: 448
                                    +37 6  dict.jl; ht_keyindex; line: 451
                                    +37 1  dict.jl; ht_keyindex; line: 452
                                    +37 6  dict.jl; ht_keyindex; line: 460
                                     +5 1 ...arse.jl; sparse; line: 71

Bad:

223  ...lia RF\text_proc_2.jl; dtm; line: 150
 223 ...ulia RF\text_proc_2.jl; tokenize; line: 22
  203 string.jl; bytestring; line: 652
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   6  ...lia RF\text_proc_2.jl; ngramize; line: 119
   1  ...lia RF\text_proc_2.jl; ngramize; line: 121
   2  ...lia RF\text_proc_2.jl; ngramize; line: 122
   94 ...lia RF\text_proc_2.jl; ngramize; line: 123
    5 utf8.jl; string; line: 134
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   35 ...lia RF\text_proc_2.jl; ngramize; line: 124
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179  ...lia RF\text_proc_2.jl; dtm; line: 153
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110  ...lia RF\text_proc_2.jl; dtm; line: 157
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 28 sparse/csparse.jl; sparse; line: 109
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230  ...lia RF\text_proc_2.jl; tokenize; line: 22
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  10 ...lia RF\text_proc_2.jl; ngramize; line: 124
   10 string.jl; bytestring; line: 652
    10 array.jl; push!; line: 452
 31 string.jl; map; line: 803
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  2 utf8.jl; getindex; line: 77
 84 string.jl; map; line: 804
  11 string.jl; lowercase; line: 786
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370  ...lia RF\text_proc_2.jl; vocabulary_to_feature_names; line: 163
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80   array.jl; getindex; line: 244
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116  array.jl; push!; line: 452
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 52 string.jl; ==; line: 523
  3  utf8.jl; endof; line: 32
  23 utf8.jl; endof; line: 33
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  18 utf8.jl; endof; line: 35
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 36  dict.jl; ht_keyindex2; line: 402
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189  dict.jl; get!; line: 470
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293  dict.jl; ht_keyindex2; line: 397
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313  dict.jl; rehash; line: 310
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JeffBezanson commented 10 years ago

Seems likely to be Dict and hash related.

JeffBezanson commented 10 years ago

Is the dataset available so I can try to reproduce this?

JeffBezanson commented 10 years ago

The shootout benchmark k_nucleotide also uses Dicts, and regressed 4x within the same time window.

JeffBezanson commented 10 years ago

Please try again. Reopen if not fixed.

ivarne commented 10 years ago

Note that if you can't reopen, you can just comment and someone will reopen it for you.