Implementation of Smith-waterman algorithm openmp + mpi

// This Smith-Waterman algorithm can be implemented using mpi and openmp respectively, but there will be various problems during mixed programming, what you want to understand is a clear path... Thank you very much.

# Include
 
  
# Include
  
   
# Include
   
    
# Include
    
     
# Include
     
      
# Include
      
        # Include
       
         /* File pointers */FILE * ptr_file_1, * ptr_file_2, * ptr_file_3; // test file pointers/* Definitions */# define TRUE 1 # define FALSE 0 # define Match 1 # define MissMatch-1 # define GapPenalty 2 # define MAXLEN 20/* Global Variables * /char inputC [5]; // user input characterint inputI; int StrLen1, StrLen2; int intcheck = TRUE; char holder, ch; int filelen1 = 0; int filelen2 = 0; int filelen3 = 0; int I, j, k, l, m, n, lenA, lenB, compv Al, top, left, left_top, rows, columns, contrl; char FASTA1 [MAXLEN], FASTA2 [MAXLEN]; char dash = '-'; char strA [MAXLEN]; // holds 1st string to be aligned in character arraychar strB [MAXLEN]; // holds 2nd string to be aligned in character array int HiScore; // holds value of highest scoring alignment (s ). int HiScorePos [2]; // the position of the HiScoreint SWArray [MAXLEN] [MAXLEN]; // S-W Matrixchar MaxA [MAXLEN]; Char MaxB [MAXLEN]; char OptA [MAXLEN]; char OptB [MAXLEN]; int MaxAcounter = 1; // MaxA counterint MaxBcounter = 1; // MaxB counterint cont = TRUE; int check; int rank, size; MPI_Status status; int buff [3];/* alignment function */int Align (int PosA, int PosB) {/* Function Variables */int relmax =-1; // hold highest value in sub columns and rowsint relmaxpos [2]; // holds position of relmaxif (SWArray [PosA-1] [PosB-1] = 0) {cont = FALSE;} while (cont = TRUE) {// until the diagonal of the current cell has a value of zero/* Find relmax in sub columns and rows */for (I = PosA; I> 0; -- I) {if (relmax <SWArray [I-1] [PosB-1]) {relmax = SWArray [I-1] [PosB-1]; relmaxpos [0] = I-1; relmaxpos [1] = PosB-1 ;}} for (j = PosB; j> 0; -- j) {if (relmax <SWArray [PosA-1] [J-1]) {relmax = SWArray [PosA-1] [J-1]; relmaxpos [0] = PosA-1; relmaxpos [1] = J-1;}/* Al Ign strings to relmax */if (relmaxpos [0] = PosA-1) & (relmaxpos [1] = PosB-1 )) {// if relmax position is diagonal from current position simply align and increment countersMaxA [MaxAcounter] = strA [relmaxpos [0]-1]; ++ MaxAcounter; maxB [MaxBcounter] = strB [relmaxpos [1]-1]; ++ MaxBcounter;} else {if (relmaxpos [1] = PosB-1) & (relmaxpos [0]! = PosA-1) {// maxB needs at least one '-' for (I = PosA-1; I> relmaxpos [0]-1; -- I) {// for all elements of strA between PosA and relmaxpos [0] MaxA [MaxAcounter] = strA [I-1]; ++ MaxAcounter;} for (j = PosA-1; j> relmaxpos [0]; -- j) {// set dashes to MaxB up to relmaxMaxB [MaxBcounter] = dash; ++ MaxBcounter ;} maxB [MaxBcounter] = strB [relmaxpos [1]-1]; // at relmax set pertinent strB value to MaxB ++ MaxBcounter;} if (relmaxpos [0] = PosA-1) & (relmaxpos [1]! = PosB-1) {// MaxA needs at least one '-' for (j = PosB-1; j> relmaxpos [1]-1; -- j) {// for all elements of strB between PosB and relmaxpos [1] MaxB [MaxBcounter] = strB [J-1]; ++ MaxBcounter;} for (I = PosB-1; i> relmaxpos [1]; -- I) {// set dashes to strAMaxA [MaxAcounter] = dash; ++ MaxAcounter ;} maxA [MaxAcounter] = strA [relmaxpos [0]-1]; ++ MaxAcounter ;}// printf ("(% I, % I)", relmaxpos [0], relmaxpos [1]); Align (relmaxpos [0], rel Maxpos [1]);} return (cont);} int SWMax (int num1, int num2, int num3) {int max =-1; if (num1> num2) {max = num1;} else if (num2> num3) {max = num2;} else {max = num3;} return max ;} /* main functions */int main (int argc, char ** argv) {MPI_Init (& argc, & argv); // MPI initializes MPI_Comm_rank (MPI_COMM_WORLD, & rank ); // obtain the current process ID MPI_Comm_size (MPI_COMM_WORLD, & size); // The total number of processes printf ("size = % d \ n", size ); /* open first file */ptr_file_1 = fopen ("d:/mpi /Str1.fa "," r ");/* check to see if it opened okay */if (ptr_file_1 = NULL) {printf (" Error opening 'str1. fa '\ n "); system (" PAUSE "); exit (8);}/* open second file */ptr_file_2 = fopen (" d:/mpi/str2.fa ", "r");/* check to see if it opened okay */if (ptr_file_2 = NULL) {printf ("Error opening 'str2. fa '\ n "); system (" PAUSE "); exit (8);}/* measure file1 length */while (holder! = EOF) {holder = fgetc (ptr_file_1); if (filelen1 <MAXLEN & holder! = EOF) {strA [filelen1] = holder; ++ filelen1 ;}} strA [filelen1] =-1; holder = '0 '; /* measure file2 length */while (holder! = EOF) {holder = fgetc (ptr_file_2); if (filelen2 <MAXLEN & holder! = EOF) {strB [filelen2] = holder; ++ filelen2 ;}} strB [filelen2] =-1; fclose (ptr_file_1); fclose (ptr_file_2 ); lenA = strlen (strA)-1; lenB = strlen (strB)-1; time_t t1 = time (NULL); printf ("t1 = % d \ n", t1 ); /* ---------------------------- problem code ** --------------------------- */for (contrl = 0; contrl
        
          0) {fprintf (ptr_file_3, "% c", strA [I-1]);} for (j = 0; j <= lenB; ++ j) {fprintf (ptr_file_3, "% 3i", SWArray [I] [j]);} fprintf (ptr_file_3, "\ n");} fclose (ptr_file_3 ); /* make alignmentt */for (I = 0; I <= lenA; ++ I) {// find highest score in matrix: this is the starting point of an optimal local alignmentfor (j = 0; j <= lenB; ++ j) {if (SWArray [I] [j]> HiScore) {HiScore = SWArray [I] [j]; HiScorePos [0] = I; HiScorePos [1] = j ;}}} // send Position to alignment functionMaxA [0] = strA [HiScorePos [0]-1]; MaxB [0] = strB [HiScorePos [1]-1]; check = Align (HiScorePos [0], HiScorePos [1]); // in the end reverse Max A and Bk = 0; for (I = strlen (MaxA)-1; i>-1; -- I) {OptA [k] = MaxA [I]; ++ k;} k = 0; for (j = strlen (MaxB)-1; j>-1; -- j) {OptB [k] = MaxB [j]; ++ k;} printf ("% s \ n", OptA, optB); time_t t2 = time (NULL); printf ("t2 = % d \ n", t2); printf ("Time-consuming is: % ds \ n ", (t2-t1); MPI_Finalize (); return (0 );}