Port over k-nucleotide from TCLBG

contains 2 implementatsion. One using Process.fork, the other using
Ractors

Author: eightbitraptor

benchmarks.yml

@@ -71,6 +71,9 @@ graphql:
   ractor: true
 graphql-native:
   desc: GraphQL gem parsing a large file, but using a native parser
+knucleotide:
+  desc: k-nucleotide from the Computer Language Benchmarks Game - counts nucleotide frequencies using hash tables
+  ractor: true
 lee:
   desc: lee is a circuit-board layout solver, deployed in a plausibly reality-like way
 matmul:

benchmarks/knucleotide/benchmark.rb

@@ -0,0 +1,88 @@
+# The Computer Language Benchmarks Game
+# https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
+#
+# k-nucleotide benchmark - Fastest implementation
+# Based on Ruby #1 with byteslice optimization
+
+require_relative '../../harness/loader'
+
+def frequency(seq, length)
+  frequencies = Hash.new(0)
+  last_index = seq.length - length
+
+  i = 0
+  while i <= last_index
+    frequencies[seq.byteslice(i, length)] += 1
+    i += 1
+  end
+
+  [seq.length - length + 1, frequencies]
+end
+
+def sort_by_freq(seq, length)
+  n, table = frequency(seq, length)
+
+  table.sort { |a, b|
+    cmp = b[1] <=> a[1]
+    cmp == 0 ? a[0] <=> b[0] : cmp
+  }.map { |seq, count|
+    "#{seq} #{'%.3f' % ((count * 100.0) / n)}"
+  }.join("\n") + "\n\n"
+end
+
+def find_seq(seq, s)
+  n, table = frequency(seq, s.length)
+  "#{table[s] || 0}\t#{s}\n"
+end
+
+class Worker
+  def initialize(&block)
+    @r, @w = IO.pipe
+    @p = Process.fork do
+      @r.close
+      @w.write yield
+      @w.close
+    end
+    @w.close
+  end
+
+  def result
+    ret = @r.read
+    @r.close
+    Process.wait(@p)
+    ret
+  end
+end
+
+def generate_test_sequence(size)
+  alu = "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCA" +
+        "GGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGG" +
+        "TGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTT" +
+        "GCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA"
+
+  sequence = ""
+  full_copies = size / alu.length
+  remainder = size % alu.length
+
+  full_copies.times { sequence << alu }
+  sequence << alu[0, remainder] if remainder > 0
+
+  sequence.upcase
+end
+
+TEST_SEQUENCE = generate_test_sequence(100_000)
+
+run_benchmark(5) do
+  freqs = [1, 2]
+  nucleos = %w(GGT GGTA GGTATT GGTATTTTAATT GGTATTTTAATTTATAGT)
+
+  # Parallel processing with Process.fork
+  workers = freqs.map { |i| Worker.new { sort_by_freq(TEST_SEQUENCE, i) } }
+  workers += nucleos.map { |s| Worker.new { find_seq(TEST_SEQUENCE, s) } }
+
+  # Collect results
+  results = workers.map(&:result)
+
+  # Process for benchmark harness
+  results
+end

benchmarks/ractor/knucleotide.rb

@@ -0,0 +1,66 @@
+# The Computer Language Benchmarks Game
+# https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
+#
+# k-nucleotide benchmark - Ractor implementation
+# Mirrors the Process.fork version structure as closely as possible
+
+require_relative "../../harness/loader"
+
+def frequency(seq, length)
+  frequencies = Hash.new(0)
+  last_index = seq.length - length
+
+  i = 0
+  while i <= last_index
+    frequencies[seq.byteslice(i, length)] += 1
+    i += 1
+  end
+
+  [seq.length - length + 1, frequencies]
+end
+
+def sort_by_freq(seq, length)
+  n, table = frequency(seq, length)
+
+  table.sort { |a, b|
+    cmp = b[1] <=> a[1]
+    cmp == 0 ? a[0] <=> b[0] : cmp
+  }.map! { |seq, count|
+    "#{seq} #{'%.3f' % ((count * 100.0) / n)}"
+  }.join("\n") << "\n\n"
+end
+
+def find_seq(seq, s)
+  _, table = frequency(seq, s.length)
+  "#{table[s] || 0}\t#{s}\n"
+end
+
+def generate_test_sequence(size)
+  alu = "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCA" +
+        "GGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGG" +
+        "TGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTT" +
+        "GCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA"
+
+  sequence = ""
+  full_copies = size / alu.length
+  remainder = size % alu.length
+
+  full_copies.times { sequence << alu }
+  sequence << alu[0, remainder] if remainder > 0
+
+  sequence.upcase.freeze
+end
+
+# Make sequence shareable for Ractors
+TEST_SEQUENCE = Ractor.make_shareable(generate_test_sequence(100_000))
+
+run_benchmark(5) do |num_ractors, ractor_args|
+  freqs = [1, 2]
+  nucleos = %w(GGT GGTA GGTATT GGTATTTTAATT GGTATTTTAATTTATAGT)
+
+  # Sequential version - mirrors Process version but without Workers
+  results = []
+  freqs.each { |i| results << sort_by_freq(TEST_SEQUENCE, i) }
+  nucleos.each { |s| results << find_seq(TEST_SEQUENCE, s) }
+  results
+end