performance measurements
Each table row shows performance measurements for this C CINT program with a particular command-line input value N.
| N | CPU secs | Elapsed secs | Memory KB | Code B | ≈ CPU Load |
|---|---|---|---|---|---|
| 250,000 | 1,135.90 | 1,136.23 | 20,252 | 1224 | 0% 0% 0% 100% |
| 2,500,000 | Timed Out | 1224 |
Read the ↓ make, command line, and program output logs to see how this program was run.
Read k-nucleotide benchmark to see what this program should do.
notes
cint 5.18.00, July 2, 2010
k-nucleotide C CINT program source code
/* The Computer Language Benchmarks Game * http://benchmarksgame.alioth.debian.org/ Contributed by Josh Goldfoot */ #include <stdio.h> #include <string.h> #include <ctype.h> #include <stdlib.h> // missing in CINT char* strdup(const char* in) { char* out = malloc(strlen(in) + 1); strcpy(out, in); return out; } #include "Include/simple_hash.h" long hash_table_size (int fl, long buflen) { long maxsize1, maxsize2; maxsize1 = buflen - fl; maxsize2 = 4; while (--fl > 0 && maxsize2 < maxsize1) maxsize2 = maxsize2 * 4; if (maxsize1 < maxsize2) return maxsize1; return maxsize2; } struct ht_ht * generate_frequencies (int fl, char *buffer, long buflen) { struct ht_ht *ht; char *reader; long i; char nulled; if (fl > buflen) return NULL; ht = ht_create (hash_table_size (fl, buflen)); for (i = 0; i < buflen - fl + 1; i++) { reader = &(buffer[i]); nulled = reader[fl]; reader[fl] = 0x00; ht_find_new (ht, reader)->val++; reader[fl] = nulled; } return ht; } typedef struct ssorter { char *string; int num; } sorter; void write_frequencies (int fl, char *buffer, long buflen) { struct ht_ht *ht; long total, i, j, size; struct ht_node *nd; sorter *s; sorter tmp; ht = generate_frequencies (fl, buffer, buflen); total = 0; size = 0; for (nd = ht_first (ht); nd != NULL; nd = ht_next (ht)) { total = total + nd->val; size++; } s = calloc (size, sizeof (sorter)); i = 0; for (nd = ht_first (ht); nd != NULL; nd = ht_next (ht)) { s[i].string = nd->key; s[i++].num = nd->val; } for (i = 0; i < size - 1; i++) for (j = i + 1; j < size; j++) if (s[i].num < s[j].num) { memcpy (&tmp, &(s[i]), sizeof (sorter)); memcpy (&(s[i]), &(s[j]), sizeof (sorter)); memcpy (&(s[j]), &tmp, sizeof (sorter)); } for (i = 0; i < size; i++) printf ("%s %.3f\n", s[i].string, 100 * (float) s[i].num / total); printf ("\n"); ht_destroy (ht); free (s); } void write_count (char *searchFor, char *buffer, long buflen) { struct ht_ht *ht; ht = generate_frequencies (strlen (searchFor), buffer, buflen); printf ("%d\t%s\n", ht_find_new (ht, searchFor)->val, searchFor); ht_destroy (ht); } int main () { char c; char *line, *buffer, *tmp, *x; int i, linelen, nothree; long buflen, seqlen; line = malloc (256); if (!line) return -1; seqlen = 0; nothree = 1; while (nothree && fgets (line, 255, stdin)) if (line[0] == '>' && line[1] == 'T' && line[2] == 'H') nothree = 0; free (line); buflen = 10240; buffer = malloc (buflen + 1); if (!buffer) return -1; x = buffer; while (fgets (x, 255, stdin)) { linelen = strlen (x); if (linelen) { if (x[linelen - 1] == '\n') linelen--; c = x[0]; if (c == '>') break; else if (c != ';') { seqlen = seqlen + linelen; if (seqlen + 512 >= buflen) { buflen = buflen + 10240; tmp = realloc (buffer, buflen + 1); if (tmp == NULL) return -1; buffer = tmp; x = &(buffer[seqlen]); } else x = &(x[linelen]); x[0] = 0; } } } for (i = 0; i < seqlen; i++) buffer[i] = toupper (buffer[i]); write_frequencies (1, buffer, seqlen); write_frequencies (2, buffer, seqlen); write_count ("GGT", buffer, seqlen); write_count ("GGTA", buffer, seqlen); write_count ("GGTATT", buffer, seqlen); write_count ("GGTATTTTAATT", buffer, seqlen); write_count ("GGTATTTTAATTTATAGT", buffer, seqlen); free (buffer); return 0; }
make, command-line, and program output logs
Fri, 22 Apr 2011 01:59:52 GMT COMMAND LINE: /usr/local/src/cint/bin/cint -K -p -E -E -J0 -I Include/simple_hash.h knucleotide.cint 0 < knucleotide-input2500000.txt TIMED OUT after 3600s PROGRAM OUTPUT: