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 performance measurements

Each table row shows performance measurements for this Ruby 2.0 program with a particular command-line input value N.

N	CPU secs	Elapsed secs	Memory KB	Code B	≈ CPU Load
50,000	0.36	0.41	50,976	501	0% 0% 5% 100%
500,000	3.15	3.22	36,628	501	0% 0% 0% 100%
5,000,000	30.69	30.72	339,524	501	0% 0% 0% 100%

Read the ↓ make, command line, and program output logs to see how this program was run.

Read regex-dna benchmark to see what this program should do.

 notes

ruby 2.0.0p0 (2013-02-24 revision 39474) [x86_64-linux]

 regex-dna Ruby 2.0 #3 program source code

# The Computer Language Benchmarks Game
# http://benchmarksgame.alioth.debian.org
#
# contributed by jose fco. gonzalez
# optimized & parallelized by Rick Branson

seq = STDIN.readlines.join
ilen = seq.size

seq.gsub!(/>.*\n|\n/,"")
clen = seq.length

MATCHERS = [
  /agggtaaa|tttaccct/,
  /[cgt]gggtaaa|tttaccc[acg]/,
  /a[act]ggtaaa|tttacc[agt]t/,
  /ag[act]gtaaa|tttac[agt]ct/,
  /agg[act]taaa|ttta[agt]cct/,
  /aggg[acg]aaa|ttt[cgt]ccct/,
  /agggt[cgt]aa|tt[acg]accct/,
  /agggta[cgt]a|t[acg]taccct/,
  /agggtaa[cgt]|[acg]ttaccct/
]

if RUBY_PLATFORM == "java"
  threads = MATCHERS.map do |f|
    Thread.new do
      Thread.current[:result] = "#{f.source} #{seq.scan(f).size}"
    end
  end

  threads.each do |t|
    t.join
  end

  threads.each do |t|
    puts t[:result]
  end
else
  children = MATCHERS.map do |f|
    r, w = IO.pipe
    p = Process.fork do
      r.close
      w.write "#{f.source} #{seq.scan(f).size}"
      w.close
    end
  
    w.close
    [p, r, w]
  end

  children.each do |p, r, w|
    puts r.read
    r.close
  end

  Process.waitall
end

{
'B' => '(c|g|t)', 'D' => '(a|g|t)', 'H' => '(a|c|t)', 'K' => '(g|t)',
'M' => '(a|c)', 'N' => '(a|c|g|t)', 'R' => '(a|g)', 'S' => '(c|t)',
'V' => '(a|c|g)', 'W' => '(a|t)', 'Y' => '(c|t)'
}.each { |f,r| seq.gsub!(f,r) }

puts
puts ilen
puts clen
puts seq.length

 make, command-line, and program output logs

Mon, 25 Feb 2013 10:59:32 GMT

COMMAND LINE:
/usr/local/src/ruby-2.0.0-p0/ruby regexdna.yarv-3.yarv 0 < regexdna-input5000000.txt

PROGRAM OUTPUT:
agggtaaa|tttaccct 356
[cgt]gggtaaa|tttaccc[acg] 1250
a[act]ggtaaa|tttacc[agt]t 4252
ag[act]gtaaa|tttac[agt]ct 2894
agg[act]taaa|ttta[agt]cct 5435
aggg[acg]aaa|ttt[cgt]ccct 1537
agggt[cgt]aa|tt[acg]accct 1431
agggta[cgt]a|t[acg]taccct 1608
agggtaa[cgt]|[acg]ttaccct 2178

50833411
50000000
66800214

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