spectral-norm

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

test/bench/regex-dna.go

@@ -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));
 }

test/bench/spectral-norm.c

+/*
+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;
+}

test/bench/spectral-norm.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.
+ * 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));
+}

test/bench/spectral-norm.txt

+1.274224152

test/bench/timing.log

@@ -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]
+

test/bench/timing.sh

@@ -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 $# in
 0)
-	run="fasta revcom nbody binarytree fannkuch regexdna"
+	run="fasta revcom nbody binarytree fannkuch regexdna spectralnorm"
 	;;
 *)
 	run=$*