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
250,0007.543.33317,068449  74% 68% 53% 33%
2,500,00017.0911.61584,860449  27% 38% 17% 67%
25,000,00097.4489.931,952,044449  58% 5% 14% 33%

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

Read k-nucleotide 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]

 k-nucleotide Ruby JRuby #4 program source code

# The Computer Language Benchmarks Game
# http://benchmarksgame.alioth.debian.org
#
# contributed by Aaron Tavistock

def frequency(seq, keys)
  counts = Hash.new(0)
  keys.each do |key|
    last_index = 0
    while last_index = seq.index(key, last_index+1)
      counts[key] += 1
    end
  end
  counts
end

def percentage(seq, keys)
  frequency(seq, keys).sort { |a,b| b[1] <=> a[1] }.map do |key, value|
    "%s %.3f" % [ key.upcase, ( (value*100).to_f / seq.size) ]
  end
end

def count(seq, keys)
  frequency(seq, keys).map do |key, value|
    "#{value.to_s}\t#{key.upcase}"
  end
end

_, seq = STDIN.read.scan(/(\n>THREE[^\n]*\n)([^>]*)\n/).flatten
seq.force_encoding('ASCII-8BIT')
seq.gsub!(/\s/, '')

singles = %w(a t c g)
doubles = singles.map { |a| singles.map { |b| "#{a}#{b}" }}.flatten
chains  = %w(ggt ggta ggtatt ggtattttaatt ggtattttaatttatagt)

print "#{percentage(seq, singles).join("\n")}\n\n"
print "#{percentage(seq, doubles).join("\n")}\n\n"
print "#{count(seq, chains).join("\n")}\n"

 make, command-line, and program output logs

Sat, 29 Mar 2014 17:51:55 GMT

MAKE:
mv knucleotide.jruby-4.jruby knucleotide.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 knucleotide.rb 0 < knucleotide-input25000000.txt

PROGRAM OUTPUT:
A 30.295
T 30.151
C 19.800
G 19.754

AA 9.177
TA 9.132
AT 9.131
TT 9.091
CA 6.002
AC 6.001
AG 5.987
GA 5.984
CT 5.971
TC 5.971
GT 5.957
TG 5.956
CC 3.917
GC 3.911
CG 3.909
GG 3.902

1471758	GGT
446535	GGTA
47336	GGTATT
893	GGTATTTTAATT
893	GGTATTTTAATTTATAGT

Revised BSD license

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