From edcd70e07a803b13bff09b950be80a23261f7f89 Mon Sep 17 00:00:00 2001 From: Kyle Consalus Date: Mon, 5 Apr 2010 22:32:36 -0700 Subject: [PATCH] test/bench: add k-nucleotide-parallel R=rsc CC=golang-dev https://golang.org/cl/881042 --- test/bench/k-nucleotide-parallel.go | 155 +++++++++++++++++++++++++++ test/bench/k-nucleotide-parallel.txt | 27 +++++ test/bench/timing.sh | 2 + 3 files changed, 184 insertions(+) create mode 100644 test/bench/k-nucleotide-parallel.go create mode 100644 test/bench/k-nucleotide-parallel.txt diff --git a/test/bench/k-nucleotide-parallel.go b/test/bench/k-nucleotide-parallel.go new file mode 100644 index 00000000000..0234f33d113 --- /dev/null +++ b/test/bench/k-nucleotide-parallel.go @@ -0,0 +1,155 @@ +/* +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) + } + +} diff --git a/test/bench/k-nucleotide-parallel.txt b/test/bench/k-nucleotide-parallel.txt new file mode 100644 index 00000000000..84169b8ec36 --- /dev/null +++ b/test/bench/k-nucleotide-parallel.txt @@ -0,0 +1,27 @@ +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 diff --git a/test/bench/timing.sh b/test/bench/timing.sh index 5a53bf024cb..5e3a066f61a 100755 --- a/test/bench/timing.sh +++ b/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