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spectral-norm

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make regexp-dna use bytes not strings (no significant timing change)

R=rsc
DELTA=149  (138 added, 1 deleted, 10 changed)
OCL=32804
CL=32807
This commit is contained in:
Rob Pike 2009-08-05 17:25:38 -07:00
parent a288095813
commit 8764ebee95
6 changed files with 205 additions and 11 deletions
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20
test/bench/regex-dna.go
View File

@ -40,6 +40,7 @@ import (
"io";
"os";
"regexp";
"strings";
)
func compile(s string) *regexp.Regexp {
@ -81,17 +82,17 @@ var substs = [] Subst {
Subst {"Y", "(c|t)"},
}
func countMatches(pat, str string) int {
func countMatches(pat string, bytes []byte) int {
re := compile(pat);
n := 0;
pos := 0;
for {
e := re.Execute(str);
e := re.Execute(bytes);
if len(e) == 0 {
break;
}
n++;
str = str[e[1]:len(str)];
bytes = bytes[e[1]:len(bytes)];
}
return n;
}
@ -102,16 +103,15 @@ func main() {
fmt.Fprintf(os.Stderr, "can't read input: %s\n", err);
os.Exit(2);
}
str := string(bytes);
ilen := len(str);
ilen := len(bytes);
// Delete the comment lines and newlines
str = compile("(>[^\n]+)?\n").ReplaceAll(str, "");
clen := len(str);
bytes = compile("(>[^\n]+)?\n").ReplaceAll(bytes, []byte{});
clen := len(bytes);
for i, s := range variants {
fmt.Printf("%s %d\n", s, countMatches(s, str));
fmt.Printf("%s %d\n", s, countMatches(s, bytes));
}
for i, sub := range substs {
str = compile(sub.pat).ReplaceAll(str, sub.repl);
bytes = compile(sub.pat).ReplaceAll(bytes, strings.Bytes(sub.repl));
}
fmt.Printf("\n%d\n%d\n%d\n", ilen, clen, len(str));
fmt.Printf("\n%d\n%d\n%d\n", ilen, clen, len(bytes));
}

82
test/bench/spectral-norm.c Normal file
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@ -0,0 +1,82 @@
/*
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.
*/
/* -*- mode: c -*-
*
* The Great Computer Language Shootout
* http://shootout.alioth.debian.org/
*
* Contributed by Sebastien Loisel
*/
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
double eval_A(int i, int j) { return 1.0/((i+j)*(i+j+1)/2+i+1); }
void eval_A_times_u(int N, const double u[], double Au[])
{
int i,j;
for(i=0;i<N;i++)
{
Au[i]=0;
for(j=0;j<N;j++) Au[i]+=eval_A(i,j)*u[j];
}
}
void eval_At_times_u(int N, const double u[], double Au[])
{
int i,j;
for(i=0;i<N;i++)
{
Au[i]=0;
for(j=0;j<N;j++) Au[i]+=eval_A(j,i)*u[j];
}
}
void eval_AtA_times_u(int N, const double u[], double AtAu[])
{ double v[N]; eval_A_times_u(N,u,v); eval_At_times_u(N,v,AtAu); }
int main(int argc, char *argv[])
{
int i;
int N = ((argc == 2) ? atoi(argv[1]) : 2000);
double u[N],v[N],vBv,vv;
for(i=0;i<N;i++) u[i]=1;
for(i=0;i<10;i++)
{
eval_AtA_times_u(N,u,v);
eval_AtA_times_u(N,v,u);
}
vBv=vv=0;
for(i=0;i<N;i++) { vBv+=u[i]*v[i]; vv+=v[i]*v[i]; }
printf("%0.9f\n",sqrt(vBv/vv));
return 0;
}

95
test/bench/spectral-norm.go Normal file
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@ -0,0 +1,95 @@
/*
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.
* Based on spectral-norm.c by Sebastien Loisel
*/
package main
import (
"flag";
"fmt";
"math";
)
var n = flag.Int("n", 2000, "count")
func evalA(i, j int) float64 {
return 1 / float64(((i + j)*(i + j + 1)/2+ i + 1));
}
type Vec []float64
func (v Vec) Times(u Vec) {
for i := 0; i < len(v); i++ {
v[i] = 0;
for j := 0; j < len(u); j++ {
v[i] += evalA(i, j)*u[j];
}
}
}
func (v Vec) TimesTransp(u Vec) {
for i := 0; i < len(v); i++ {
v[i] = 0;
for j := 0; j < len(u); j++ {
v[i] += evalA(j, i)*u[j];
}
}
}
func (v Vec) ATimesTransp(u Vec) {
x := make(Vec, len(u));
x.Times(u);
v.TimesTransp(x);
}
func main() {
flag.Parse();
N := *n;
u := make(Vec, N);
for i := 0; i < N; i++ {
u[i] = 1;
}
v := make(Vec, N);
for i := 0; i < 10; i++ {
v.ATimesTransp(u);
u.ATimesTransp(v);
}
var vBv, vv float64;
for i := 0; i < N; i++ {
vBv += u[i]*v[i];
vv += v[i]*v[i];
}
fmt.Printf("%0.9f\n", math.Sqrt(vBv/vv));
}

1
test/bench/spectral-norm.txt Normal file
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@ -0,0 +1 @@
1.274224152

8
test/bench/timing.log
View File

@ -58,3 +58,11 @@ regex-dna 100000
gcc -O2 regex-dna.c -lpcre 0.92u 0.00s 0.99r
gc regexp-dna 26.94u 0.18s 28.75r
gc_B regexp-dna 26.51u 0.09s 26.75r
spectral-norm 5500
gcc -O2 spectral-norm.c -lm 11.54u 0.00s 11.55r
gccgo -O2 spectral-norm.go 12.20u 0.00s 12.23r
gc spectral-norm 50.23u 0.00s 50.36r
gc_B spectral-norm 49.69u 0.01s 49.83r
[using >>1 instead of /2 : gc gives 24.33u 0.00s 24.33r]

10
test/bench/timing.sh
View File

@ -76,9 +76,17 @@ regexdna() {
rm x
}
spectralnorm() {
echo 'spectral-norm 5500'
run 'gcc -O2 spectral-norm.c -lm' a.out 5500
run 'gccgo -O2 spectral-norm.go' a.out -n 5500
run 'gc spectral-norm' $O.out -n 5500
run 'gc_B spectral-norm' $O.out -n 5500
}
case $# in
0)
run="fasta revcom nbody binarytree fannkuch regexdna"
run="fasta revcom nbody binarytree fannkuch regexdna spectralnorm"
;;
*)
run=$*