performance measurements

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

 N  CPU secs Elapsed secs Memory KB Code B ≈ CPU Load
50,0005.905.9393,236442  1% 0% 2% 100%
500,00011.4411.46196,136442  1% 1% 1% 100%
5,000,00059.8259.86932,816442  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

jruby 1.7.11 (1.9.3p392) 2014-02-24 86339bb on Java HotSpot(TM) Server VM 1.8.0-b132 +indy [linux-i386]

 regex-dna Ruby JRuby #6 program source code

# The Computer Language Benchmarks Game
# http://benchmarksgame.alioth.debian.org
#
# contributed by jose fco. gonzalez
# optimized & parallelized by Rick Branson
# optimized for ruby2 by Aaron Tavistock

require 'fiber'

seq = $stdin.read.force_encoding("ASCII-8BIT")
origin_len = seq.size

seq.gsub!(/>.*\n|\n/,'')
clean_len = seq.size

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'
]

results = matchers.map do |matcher|
  Fiber.new do
    count = seq.scan( Regexp.new(matcher) ).size
    Fiber.yield "#{matcher} #{count}"
  end.resume
end

replacements = {
  '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)'
}
seq.gsub!(Regexp.new(replacements.keys.join('|')), replacements)

puts "#{results.join("\n")}\n\n#{origin_len}\n#{clean_len}\n#{seq.size}"

 make, command-line, and program output logs

Sat, 29 Mar 2014 22:16:08 GMT

MAKE:
mv regexdna.jruby-6.jruby regexdna.rb
0.01s to complete and log all make actions

COMMAND LINE:
/usr/local/src/jruby-1.7.11/bin/jruby -Xcompile.invokedynamic=true -J-server -J-Xmn512m -J-Xms2048m -J-Xmx2048m regexdna.rb 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

Revised BSD license

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