Commit edcd70e0 authored by Kyle Consalus's avatar Kyle Consalus Committed by Russ Cox

test/bench: add k-nucleotide-parallel

R=rsc
CC=golang-dev
https://golang.org/cl/881042
parent 2e90f66e
/*
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)
}
}
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
...@@ -140,7 +140,9 @@ knucleotide() { ...@@ -140,7 +140,9 @@ knucleotide() {
runonly echo 'k-nucleotide 1000000' 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 '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.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' $O.out <x
run 'gc k-nucleotide-parallel' $O.out <x
run 'gc_B k-nucleotide' $O.out <x run 'gc_B k-nucleotide' $O.out <x
rm x rm x
} }
......
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