mirror of
https://github.com/golang/go
synced 2024-09-25 15:20:13 -06:00
166dab6993
As discussed on golang-dev, reduce the size of the fasta dataset to make it possible to run the go1 benchmarks on small ARM systems. Also, remove the 25m suffix from fasta data and Revcomp. linux/arm: pandaboard OMAP4 BenchmarkBinaryTree17 1 70892426000 ns/op BenchmarkFannkuch11 1 35712066000 ns/op BenchmarkGobDecode 10 137146000 ns/op 5.60 MB/s BenchmarkGobEncode 50 64953000 ns/op 11.82 MB/s BenchmarkGzip 1 5675690000 ns/op 3.42 MB/s BenchmarkGunzip 1 1207001000 ns/op 16.08 MB/s BenchmarkJSONEncode 5 860424800 ns/op 2.26 MB/s BenchmarkJSONDecode 1 3321839000 ns/op 0.58 MB/s BenchmarkMandelbrot200 50 45893560 ns/op BenchmarkRevcomp 10 135220300 ns/op 18.80 MB/s BenchmarkTemplate 1 6385681000 ns/op 0.30 MB/s R=rsc, minux.ma, dsymonds CC=golang-dev https://golang.org/cl/6278048
86 lines
1.8 KiB
Go
86 lines
1.8 KiB
Go
// Copyright 2011 The Go Authors. All rights reserved.
|
|
// Use of this source code is governed by a BSD-style
|
|
// license that can be found in the LICENSE file.
|
|
|
|
// This benchmark, taken from the shootout, tests array indexing
|
|
// and array bounds elimination performance.
|
|
|
|
package go1
|
|
|
|
import (
|
|
"bufio"
|
|
"bytes"
|
|
"io/ioutil"
|
|
"testing"
|
|
)
|
|
|
|
var revCompTable = [256]uint8{
|
|
'A': 'T', 'a': 'T',
|
|
'C': 'G', 'c': 'G',
|
|
'G': 'C', 'g': 'C',
|
|
'T': 'A', 't': 'A',
|
|
'U': 'A', 'u': 'A',
|
|
'M': 'K', 'm': 'K',
|
|
'R': 'Y', 'r': 'Y',
|
|
'W': 'W', 'w': 'W',
|
|
'S': 'S', 's': 'S',
|
|
'Y': 'R', 'y': 'R',
|
|
'K': 'M', 'k': 'M',
|
|
'V': 'B', 'v': 'B',
|
|
'H': 'D', 'h': 'D',
|
|
'D': 'H', 'd': 'H',
|
|
'B': 'V', 'b': 'V',
|
|
'N': 'N', 'n': 'N',
|
|
}
|
|
|
|
func revcomp(data []byte) {
|
|
in := bufio.NewReader(bytes.NewBuffer(data))
|
|
out := ioutil.Discard
|
|
buf := make([]byte, 1024*1024)
|
|
line, err := in.ReadSlice('\n')
|
|
for err == nil {
|
|
out.Write(line)
|
|
|
|
// Accumulate reversed complement in buf[w:]
|
|
nchar := 0
|
|
w := len(buf)
|
|
for {
|
|
line, err = in.ReadSlice('\n')
|
|
if err != nil || line[0] == '>' {
|
|
break
|
|
}
|
|
line = line[0 : len(line)-1]
|
|
nchar += len(line)
|
|
if len(line)+nchar/60+128 >= w {
|
|
nbuf := make([]byte, len(buf)*5)
|
|
copy(nbuf[len(nbuf)-len(buf):], buf)
|
|
w += len(nbuf) - len(buf)
|
|
buf = nbuf
|
|
}
|
|
|
|
// This loop is the bottleneck.
|
|
for _, c := range line {
|
|
w--
|
|
buf[w] = revCompTable[c]
|
|
}
|
|
}
|
|
|
|
// Copy down to beginning of buffer, inserting newlines.
|
|
// The loop left room for the newlines and 128 bytes of padding.
|
|
i := 0
|
|
for j := w; j < len(buf); j += 60 {
|
|
n := copy(buf[i:i+60], buf[j:])
|
|
buf[i+n] = '\n'
|
|
i += n + 1
|
|
}
|
|
out.Write(buf[0:i])
|
|
}
|
|
}
|
|
|
|
func BenchmarkRevcomp(b *testing.B) {
|
|
b.SetBytes(int64(len(fastabytes)))
|
|
for i := 0; i < b.N; i++ {
|
|
revcomp(fastabytes)
|
|
}
|
|
}
|