nussinov.c

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/* nussinov.c: this file is part of PolyBench/C */

#include <stdio.h>
#include <unistd.h>
#include <string.h>
#include <math.h>

/* Include polybench common header. */
#include <polybench.h>

/* Include benchmark-specific header. */
#include "nussinov.h"

/* RNA bases represented as chars, range is [0,3] */
typedef char base;

#define match(b1, b2) (((b1)+(b2)) == 3 ? 1 : 0)
#define max_score(s1, s2) ((s1 >= s2) ? s1 : s2)

/* Array initialization. */
static
void init_array (int n,
                 base POLYBENCH_1D(seq,N,n),
                 DATA_TYPE POLYBENCH_2D(table,N,N,n,n))
{
  int i, j;

  //base is AGCT/0..3
  for (i=0; i <n; i++) {
     seq[i] = (base)((i+1)%4);
  }

  for (i=0; i <n; i++)
     for (j=0; j <n; j++)
       table[i][j] = 0;
}


/* DCE code. Must scan the entire live-out data.
   Can be used also to check the correctness of the output. */
static
void print_array(int n,
                 DATA_TYPE POLYBENCH_2D(table,N,N,n,n))

{
  int i, j;
  int t = 0;

  POLYBENCH_DUMP_START;
  POLYBENCH_DUMP_BEGIN("table");
  for (i = 0; i < n; i++) {
    for (j = i; j < n; j++) {
      if (t % 20 == 0) fprintf (POLYBENCH_DUMP_TARGET, "\n");
      fprintf (POLYBENCH_DUMP_TARGET, DATA_PRINTF_MODIFIER, table[i][j]);
      t++;
    }
  }
  POLYBENCH_DUMP_END("table");
  POLYBENCH_DUMP_FINISH;
}


/* Main computational kernel. The whole function will be timed,
   including the call and return. */
/*
  Original version by Dave Wonnacott at Haverford College <davew@cs.haverford.edu>,
  with help from Allison Lake, Ting Zhou, and Tian Jin,
  based on algorithm by Nussinov, described in Allison Lake's senior thesis.
*/
__attribute__((noinline))
void kernel_nussinov(int n, base POLYBENCH_1D(seq,N,n),
                           DATA_TYPE POLYBENCH_2D(table,N,N,n,n))
{
  int i, j, k;

#pragma scop
 for (i = _PB_N-1; i >= 0; i--) {
  for (j=i+1; j<_PB_N; j++) {

   if (j-1>=0)
      table[i][j] = max_score(table[i][j], table[i][j-1]);
   if (i+1<_PB_N)
      table[i][j] = max_score(table[i][j], table[i+1][j]);

   if (j-1>=0 && i+1<_PB_N) {
     /* don't allow adjacent elements to bond */
     if (i<j-1)
        table[i][j] = max_score(table[i][j], table[i+1][j-1]+match(seq[i], seq[j]));
     else
        table[i][j] = max_score(table[i][j], table[i+1][j-1]);
   }

   for (k=i+1; k<j; k++) {
      table[i][j] = max_score(table[i][j], table[i][k] + table[k+1][j]);
   }
  }
 }
#pragma endscop

}


int main(int argc, char** argv)
{
  /* Retrieve problem size. */
  int n = N;

  /* Variable declaration/allocation. */
  POLYBENCH_1D_ARRAY_DECL(seq, base, N, n);
  POLYBENCH_2D_ARRAY_DECL(table, DATA_TYPE, N, N, n, n);

  /* Initialize array(s). */
  init_array (n, POLYBENCH_ARRAY(seq), POLYBENCH_ARRAY(table));

  /* Start timer. */
  polybench_start_instruments;

  /* Run kernel. */
  kernel_nussinov (n, POLYBENCH_ARRAY(seq), POLYBENCH_ARRAY(table));

  /* Stop and print timer. */
  polybench_stop_instruments;
  polybench_print_instruments;

  /* Prevent dead-code elimination. All live-out data must be printed
     by the function call in argument. */
  polybench_prevent_dce(print_array(n, POLYBENCH_ARRAY(table)));

  /* Be clean. */
  POLYBENCH_FREE_ARRAY(seq);
  POLYBENCH_FREE_ARRAY(table);

  return 0;
}