test/bench: add k-nucleotide-parallel

R=rsc
CC=golang-dev
https://golang.org/cl/881042

test/bench/k-nucleotide-parallel.go

+/*
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+    * Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+
+    * Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in the
+    documentation and/or other materials provided with the distribution.
+
+    * Neither the name of "The Computer Language Benchmarks Game" nor the
+    name of "The Computer Language Shootout Benchmarks" nor the names of
+    its contributors may be used to endorse or promote products derived
+    from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/* The Computer Language Benchmarks Game
+ * http://shootout.alioth.debian.org/
+ *
+ * contributed by The Go Authors.
+ */
+
+package main
+
+import (
+	"bufio"
+	"bytes"
+	"fmt"
+	"io/ioutil"
+	"os"
+	"sort"
+)
+
+func count(data string, n int) map[string]int {
+	counts := make(map[string]int)
+	top := len(data) - n
+	for i := 0; i <= top; i++ {
+		s := data[i : i+n]
+		counts[s]++
+	}
+	return counts
+}
+
+func countOne(data string, s string) int {
+	return count(data, len(s))[s]
+}
+
+type kNuc struct {
+	name  string
+	count int
+}
+
+type kNucArray []kNuc
+
+func (kn kNucArray) Len() int      { return len(kn) }
+func (kn kNucArray) Swap(i, j int) { kn[i], kn[j] = kn[j], kn[i] }
+func (kn kNucArray) Less(i, j int) bool {
+	if kn[i].count == kn[j].count {
+		return kn[i].name > kn[j].name // sort down
+	}
+	return kn[i].count > kn[j].count
+}
+
+func sortedArray(m map[string]int) kNucArray {
+	kn := make(kNucArray, len(m))
+	i := 0
+	for k, v := range m {
+		kn[i] = kNuc{k, v}
+		i++
+	}
+	sort.Sort(kn)
+	return kn
+}
+
+func printKnucs(a kNucArray) {
+	sum := 0
+	for _, kn := range a {
+		sum += kn.count
+	}
+	for _, kn := range a {
+		fmt.Printf("%s %.3f\n", kn.name, 100*float64(kn.count)/float64(sum))
+	}
+	fmt.Print("\n")
+}
+
+func main() {
+	in := bufio.NewReader(os.Stdin)
+	three := []byte(">THREE ")
+	for {
+		line, err := in.ReadSlice('\n')
+		if err != nil {
+			fmt.Fprintln(os.Stderr, "ReadLine err:", err)
+			os.Exit(2)
+		}
+		if line[0] == '>' && bytes.Equal(line[0:len(three)], three) {
+			break
+		}
+	}
+	data, err := ioutil.ReadAll(in)
+	if err != nil {
+		fmt.Fprintln(os.Stderr, "ReadAll err:", err)
+		os.Exit(2)
+	}
+	// delete the newlines and convert to upper case
+	j := 0
+	for i := 0; i < len(data); i++ {
+		if data[i] != '\n' {
+			data[j] = data[i] &^ ' ' // upper case
+			j++
+		}
+	}
+	str := string(data[0:j])
+
+	var arr1, arr2 kNucArray
+	countsdone := make(chan bool)
+	go func() {
+		arr1 = sortedArray(count(str, 1))
+		countsdone <- true
+	}()
+	go func() {
+		arr2 = sortedArray(count(str, 2))
+		countsdone <- true
+	}()
+
+	interests := []string{"GGT", "GGTA", "GGTATT", "GGTATTTTAATT", "GGTATTTTAATTTATAGT"}
+	results := make([]chan string, len(interests))
+	for i, s := range interests {
+		ch := make(chan string)
+		results[i] = ch
+		go func(result chan string, ss string) {
+			result <- fmt.Sprintf("%d %s\n", countOne(str, ss), ss)
+		}(ch, s)
+	}
+	<-countsdone
+	<-countsdone
+	printKnucs(arr1)
+	printKnucs(arr2)
+	for _, rc := range results {
+		fmt.Print(<-rc)
+	}
+
+}

test/bench/k-nucleotide-parallel.txt

+T 31.520
+A 29.600
+C 19.480
+G 19.400
+
+AT 9.922
+TT 9.602
+TA 9.402
+AA 8.402
+GA 6.321
+TC 6.301
+TG 6.201
+GT 6.041
+CT 5.961
+AG 5.841
+CA 5.461
+AC 5.441
+CC 4.041
+CG 4.021
+GC 3.701
+GG 3.341
+
+54 GGT
+24 GGTA
+4 GGTATT
+0 GGTATTTTAATT
+0 GGTATTTTAATTTATAGT

test/bench/timing.sh

@@ -140,7 +140,9 @@ knucleotide() {
 	runonly echo 'k-nucleotide 1000000'
 	run 'gcc -O2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include k-nucleotide.c -lglib-2.0' a.out <x
 	run 'gccgo -O2 k-nucleotide.go' a.out <x	# warning: pages badly!
+	run 'gccgo -O2 k-nucleotide-parallel.go' a.out <x	# warning: pages badly!
 	run 'gc k-nucleotide' $O.out <x
+	run 'gc k-nucleotide-parallel' $O.out <x
 	run 'gc_B k-nucleotide' $O.out <x
 	rm x
 }