mirror of
https://github.com/golang/go
synced 2024-11-22 00:14:42 -07:00
benchmark checkpoint milestone checkin submission
R=rsc DELTA=311 (311 added, 0 deleted, 0 changed) OCL=32696 CL=32699
This commit is contained in:
Rob Pike
parent
7deeb5bd78
commit
9155bb3345
173
test/bench/fasta.c
Normal file
173
test/bench/fasta.c
Normal file
@ -0,0 +1,173 @@
|
||||
/*
|
||||
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.
|
||||
*/
|
||||
|
||||
/*
|
||||
* http://shootout.alioth.debian.org/u32q/benchmark.php?test=fasta&lang=gcc&id=4
|
||||
*/
|
||||
/* The Computer Language Benchmarks Game
|
||||
* http://shootout.alioth.debian.org/
|
||||
* Contributed by Joern Inge Vestgaarden
|
||||
* Modified by Jorge Peixoto de Morais Neto
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include <err.h>
|
||||
|
||||
#define WIDTH 60
|
||||
#define MIN(a,b) ((a) <= (b) ? (a) : (b))
|
||||
#define NELEMENTS(x) (sizeof (x) / sizeof ((x)[0]))
|
||||
|
||||
typedef struct {
|
||||
float p;
|
||||
char c;
|
||||
} aminoacid_t;
|
||||
|
||||
static inline float myrandom (float max) {
|
||||
unsigned long const IM = 139968;
|
||||
unsigned long const IA = 3877;
|
||||
unsigned long const IC = 29573;
|
||||
static unsigned long last = 42;
|
||||
last = (last * IA + IC) % IM;
|
||||
/*Integer to float conversions are faster if the integer is signed*/
|
||||
return max * (long) last / IM;
|
||||
}
|
||||
|
||||
static inline void accumulate_probabilities (aminoacid_t *genelist, size_t len) {
|
||||
float cp = 0.0;
|
||||
size_t i;
|
||||
for (i = 0; i < len; i++) {
|
||||
cp += genelist[i].p;
|
||||
genelist[i].p = cp;
|
||||
}
|
||||
}
|
||||
|
||||
/* This function prints the characters of the string s. When it */
|
||||
/* reaches the end of the string, it goes back to the beginning */
|
||||
/* It stops when the total number of characters printed is count. */
|
||||
/* Between each WIDTH consecutive characters it prints a newline */
|
||||
/* This function assumes that WIDTH <= strlen (s) + 1 */
|
||||
static void repeat_fasta (char const *s, size_t count) {
|
||||
size_t pos = 0;
|
||||
size_t len = strlen (s);
|
||||
char *s2 = malloc (len + WIDTH);
|
||||
memcpy (s2, s, len);
|
||||
memcpy (s2 + len, s, WIDTH);
|
||||
do {
|
||||
size_t line = MIN(WIDTH, count);
|
||||
fwrite_unlocked (s2 + pos,1,line,stdout);
|
||||
putchar_unlocked ('\n');
|
||||
pos += line;
|
||||
if (pos >= len) pos -= len;
|
||||
count -= line;
|
||||
} while (count);
|
||||
free (s2);
|
||||
}
|
||||
|
||||
/* This function takes a pointer to the first element of an array */
|
||||
/* Each element of the array is a struct with a character and */
|
||||
/* a float number p between 0 and 1. */
|
||||
/* The function generates a random float number r and */
|
||||
/* finds the first array element such that p >= r. */
|
||||
/* This is a weighted random selection. */
|
||||
/* The function then prints the character of the array element. */
|
||||
/* This is done count times. */
|
||||
/* Between each WIDTH consecutive characters, the function prints a newline */
|
||||
static void random_fasta (aminoacid_t const *genelist, size_t count) {
|
||||
do {
|
||||
size_t line = MIN(WIDTH, count);
|
||||
size_t pos = 0;
|
||||
char buf[WIDTH + 1];
|
||||
do {
|
||||
float r = myrandom (1.0);
|
||||
size_t i = 0;
|
||||
while (genelist[i].p < r)
|
||||
++i; /* Linear search */
|
||||
buf[pos++] = genelist[i].c;
|
||||
} while (pos < line);
|
||||
buf[line] = '\n';
|
||||
fwrite_unlocked (buf, 1, line + 1, stdout);
|
||||
count -= line;
|
||||
} while (count);
|
||||
}
|
||||
|
||||
int main (int argc, char **argv) {
|
||||
size_t n;
|
||||
if (argc > 1) {
|
||||
char const *arg = argv[1];
|
||||
char *tail;
|
||||
n = strtoul (arg, &tail, 0);
|
||||
if (tail == arg)
|
||||
errx (1, "Could not convert \"%s\" to an unsigned long integer", arg);
|
||||
} else n = 1000;
|
||||
|
||||
static aminoacid_t iub[] = {
|
||||
{ 0.27, 'a' },
|
||||
{ 0.12, 'c' },
|
||||
{ 0.12, 'g' },
|
||||
{ 0.27, 't' },
|
||||
{ 0.02, 'B' },
|
||||
{ 0.02, 'D' },
|
||||
{ 0.02, 'H' },
|
||||
{ 0.02, 'K' },
|
||||
{ 0.02, 'M' },
|
||||
{ 0.02, 'N' },
|
||||
{ 0.02, 'R' },
|
||||
{ 0.02, 'S' },
|
||||
{ 0.02, 'V' },
|
||||
{ 0.02, 'W' },
|
||||
{ 0.02, 'Y' }};
|
||||
|
||||
static aminoacid_t homosapiens[] = {
|
||||
{ 0.3029549426680, 'a' },
|
||||
{ 0.1979883004921, 'c' },
|
||||
{ 0.1975473066391, 'g' },
|
||||
{ 0.3015094502008, 't' }};
|
||||
|
||||
accumulate_probabilities (iub, NELEMENTS(iub));
|
||||
accumulate_probabilities (homosapiens, NELEMENTS(homosapiens));
|
||||
|
||||
static char const *const alu ="\
|
||||
GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG\
|
||||
GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA\
|
||||
CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT\
|
||||
ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA\
|
||||
GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG\
|
||||
AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC\
|
||||
AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
|
||||
|
||||
fputs_unlocked (">ONE Homo sapiens alu\n", stdout);
|
||||
repeat_fasta (alu, 2 * n);
|
||||
fputs_unlocked (">TWO IUB ambiguity codes\n", stdout);
|
||||
random_fasta (iub, 3 * n);
|
||||
fputs_unlocked (">THREE Homo sapiens frequency\n", stdout);
|
||||
random_fasta (homosapiens, 5 * n);
|
||||
return 0;
|
||||
}
|
||||
198
test/bench/fasta.go
Normal file
198
test/bench/fasta.go
Normal file
@ -0,0 +1,198 @@
|
||||
/*
|
||||
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 C program by Joern Inge Vestgaarden
|
||||
* and Jorge Peixoto de Morais Neto.
|
||||
*/
|
||||
|
||||
package main
|
||||
|
||||
import (
|
||||
"bufio";
|
||||
"bytes";
|
||||
"flag";
|
||||
"os";
|
||||
"strings";
|
||||
)
|
||||
|
||||
var out *bufio.Writer
|
||||
|
||||
var n = flag.Int("n", 1000, "length of result")
|
||||
|
||||
const WIDTH = 60
|
||||
|
||||
func min(a, b int) int {
|
||||
if a < b {
|
||||
return a
|
||||
}
|
||||
return b
|
||||
}
|
||||
|
||||
type AminoAcid struct {
|
||||
p float;
|
||||
c byte;
|
||||
}
|
||||
|
||||
var lastrandom uint32 = 42
|
||||
|
||||
func myrandom() float {
|
||||
const (
|
||||
IM = 139968;
|
||||
IA = 3877;
|
||||
IC = 29573;
|
||||
)
|
||||
lastrandom = (lastrandom * IA + IC) % IM;
|
||||
// Integer to float conversions are faster if the integer is signed.
|
||||
return float(lastrandom) / IM;
|
||||
}
|
||||
|
||||
func AccumulateProbabilities(genelist []AminoAcid) {
|
||||
cp := 0.0;
|
||||
for i := 0; i < len(genelist); i++ {
|
||||
cp += genelist[i].p;
|
||||
genelist[i].p = cp;
|
||||
}
|
||||
}
|
||||
|
||||
/* This function prints the characters of the string s. When it */
|
||||
/* reaches the end of the string, it goes back to the beginning */
|
||||
/* It stops when the total number of characters printed is count. */
|
||||
/* Between each WIDTH consecutive characters it prints a newline */
|
||||
/* This function assumes that WIDTH <= strlen (s) + 1 */
|
||||
func RepeatFasta(s []byte, count int) {
|
||||
pos := 0;
|
||||
s2 := make([]byte, len(s) + WIDTH);
|
||||
bytes.Copy(s2, s);
|
||||
bytes.Copy(s2[len(s):len(s2)], s);
|
||||
for {
|
||||
line := min(WIDTH, count);
|
||||
out.Write(s2[pos:pos+line]);
|
||||
out.WriteByte('\n');
|
||||
pos += line;
|
||||
if pos >= len(s) {
|
||||
pos -= len(s);
|
||||
}
|
||||
count -= line;
|
||||
if count <= 0 {
|
||||
break
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* This function takes a pointer to the first element of an array */
|
||||
/* Each element of the array is a struct with a character and */
|
||||
/* a float number p between 0 and 1. */
|
||||
/* The function generates a random float number r and */
|
||||
/* finds the first array element such that p >= r. */
|
||||
/* This is a weighted random selection. */
|
||||
/* The function then prints the character of the array element. */
|
||||
/* This is done count times. */
|
||||
/* Between each WIDTH consecutive characters, the function prints a newline */
|
||||
func RandomFasta(genelist []AminoAcid, count int) {
|
||||
buf := make([]byte, WIDTH + 1);
|
||||
for {
|
||||
line := min(WIDTH, count);
|
||||
pos := 0;
|
||||
for {
|
||||
r := myrandom();
|
||||
var i int;
|
||||
for i = 0; genelist[i].p < r; i++ {
|
||||
}
|
||||
buf[pos] = genelist[i].c;
|
||||
pos++;
|
||||
if pos >= line {
|
||||
break
|
||||
}
|
||||
}
|
||||
buf[line] = '\n';
|
||||
out.Write(buf[0:line + 1]);
|
||||
count -= line;
|
||||
if count <= 0 {
|
||||
break
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
func main() {
|
||||
out = bufio.NewWriter(os.Stdout);
|
||||
defer out.Flush();
|
||||
|
||||
flag.Parse();
|
||||
|
||||
iub := []AminoAcid {
|
||||
AminoAcid{ 0.27, 'a' },
|
||||
AminoAcid{ 0.12, 'c' },
|
||||
AminoAcid{ 0.12, 'g' },
|
||||
AminoAcid{ 0.27, 't' },
|
||||
AminoAcid{ 0.02, 'B' },
|
||||
AminoAcid{ 0.02, 'D' },
|
||||
AminoAcid{ 0.02, 'H' },
|
||||
AminoAcid{ 0.02, 'K' },
|
||||
AminoAcid{ 0.02, 'M' },
|
||||
AminoAcid{ 0.02, 'N' },
|
||||
AminoAcid{ 0.02, 'R' },
|
||||
AminoAcid{ 0.02, 'S' },
|
||||
AminoAcid{ 0.02, 'V' },
|
||||
AminoAcid{ 0.02, 'W' },
|
||||
AminoAcid{ 0.02, 'Y' }
|
||||
};
|
||||
|
||||
homosapiens := []AminoAcid {
|
||||
AminoAcid{ 0.3029549426680, 'a' },
|
||||
AminoAcid{ 0.1979883004921, 'c' },
|
||||
AminoAcid{ 0.1975473066391, 'g' },
|
||||
AminoAcid{ 0.3015094502008, 't' }
|
||||
};
|
||||
|
||||
AccumulateProbabilities(iub);
|
||||
AccumulateProbabilities(homosapiens);
|
||||
|
||||
alu := strings.Bytes(""
|
||||
"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG"
|
||||
"GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA"
|
||||
"CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT"
|
||||
"ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA"
|
||||
"GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG"
|
||||
"AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC"
|
||||
"AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA");
|
||||
|
||||
out.WriteString(">ONE Homo sapiens alu\n");
|
||||
RepeatFasta(alu, 2 * *n);
|
||||
out.Flush();
|
||||
out.WriteString(">TWO IUB ambiguity codes\n");
|
||||
RandomFasta(iub, 3 * *n);
|
||||
out.Flush();
|
||||
out.WriteString(">THREE Homo sapiens frequency\n");
|
||||
RandomFasta(homosapiens, 5 * *n);
|
||||
out.Flush();
|
||||
}
|
||||
Loading…
Reference in New Issue
Block a user