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5 x decrease in performance with new Julia build #7000

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jfrolich opened this issue May 27, 2014 · 10 comments
Closed

5 x decrease in performance with new Julia build #7000

jfrolich opened this issue May 27, 2014 · 10 comments
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performance Must go faster regression Regression in behavior compared to a previous version

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@jfrolich
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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
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Contributor

Can you do git bisect to pin down the culprit?

@jfrolich
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Author

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

@JeffBezanson
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Member

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

@jfrolich
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Author

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
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Author

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 ...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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                            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: 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 ...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 ...e/csparse.jl; sparse; line: 69
          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 ...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: 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
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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: 73
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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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                                     +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
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                                    +19 2  array.jl; push!; line: 446
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                             328 array.jl; push!; line: 445
                                 1   array.jl; push!; line: 440
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                                    +14 1 io.jl; close; line: 260
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                             31 array.jl; push!; line: 445
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                                 5  array.jl; push!; line: 444
                                 19 array.jl; push!; line: 445
                                 6  array.jl; push!; line: 446
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                      207 dict.jl; rehash; line: 391
                        1   dict.jl; int64hash; line: 223
                           202 dict.jl; hashindex; line: 360
                      5   dict.jl; rehash; line: 392
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                      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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   1  ...lia RF\text_proc_2.jl; ngramize; line: 121
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   94 ...lia RF\text_proc_2.jl; ngramize; line: 123
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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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230  ...lia RF\text_proc_2.jl; tokenize; line: 22
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 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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3    dict.jl; ht_keyindex2; line: 426
1    dict.jl; ht_keyindex; line: 368
86   dict.jl; isslotempty; line: 289
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14   utf8.jl; string; line: 142

@JeffBezanson
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Seems likely to be Dict and hash related.

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

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

@JeffBezanson
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Please try again. Reopen if not fixed.

@ivarne
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ivarne commented May 28, 2014

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

@jrevels jrevels mentioned this issue Nov 6, 2015
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