added ElementSet, Sequence, skeleton maximum-parsimony.cc, updated Makefile

git-svn-id: svn://anubis/gvsu@298 45c1a28c-8058-47b2-ae61-ca45b979098e

cs677/pa4/ElementSet.cc

@@ -0,0 +1,12 @@
+
+#include "ElementSet.h"
+using namespace std;
+
+ElementSet::ElementSet()
+{
+}
+
+ElementSet::ElementSet(char initial)
+{
+    mySet.insert(initial);
+}

cs677/pa4/ElementSet.h

@@ -0,0 +1,17 @@
+
+#ifndef ELEMENTSET_H
+#define ELEMENTSET_H ELEMENTSET_H
+
+#include <set>
+
+class ElementSet
+{
+private:
+    std::set<char> mySet;
+
+public:
+    ElementSet();
+    ElementSet(char initial);
+};
+
+#endif

cs677/pa4/Makefile

@@ -1,11 +1,17 @@
 
-FILE := maximum-parsimony
+CXX := mpiCC
-TARGET := $(FILE)
+TARGET := maximum-parsimony
+OBJS := Sequence.o
+OBJS += ElementSet.o
+OBJS += maximum-parsimony.o
 
 all: $(TARGET)
 
-$(TARGET): $(FILE).cc
+$(TARGET): $(OBJS)
-	mpiCC -o $@ $<
+	mpiCC -o $@ $^
+
+%.o: %.cc
+	$(CXX) -c -o $@ $<
 
 clean:
 	-rm -f *.o *~ $(TARGET)

cs677/pa4/Sequence.cc

@@ -0,0 +1,21 @@
+
+#include <cstring>
+#include "Sequence.h"
+#include "ElementSet.h"
+using namespace std;
+
+Sequence::Sequence()
+{
+    myMutationCount = 0;
+}
+
+Sequence::Sequence(char * initializer)
+{
+    myMutationCount = 0;
+    int len = strlen(initializer);
+    myElements = vector<ElementSet>(len);
+    for (int i = 0; i < len; i++)
+    {
+        myElements[i] = ElementSet(initializer[i]);
+    }
+}

cs677/pa4/Sequence.h

@@ -0,0 +1,19 @@
+
+#ifndef SEQUENCE_H
+#define SEQUENCE_H SEQUENCE_H
+
+#include <vector>
+#include "ElementSet.h"
+
+class Sequence
+{
+private:
+    int myMutationCount;
+    std::vector<ElementSet> myElements;
+
+public:
+    Sequence();
+    Sequence(char * initializer);
+};
+
+#endif

cs677/pa4/maximum-parsimony.cc

@@ -2,144 +2,16 @@
 #include <iostream>
 #include <sys/time.h>
 #include <mpi.h>
-#include <unistd.h>     /* usleep() */
 using namespace std;
 
-/*
- * taskAllocate() will divide a set of total_tasks tasks into
- * total_workers groups, as evenly as possible
- * Parameters:
- *   total_tasks   : IN  : the total number of tasks to divide up
- *   total_workers : IN  : the total number of workers to allocate tasks to (>0)
- *   this_id       : IN  : the id (0-based) of the task calling us for work
- *   first_task_id : OUT : the id (0-based) of the first task for this worker
- *   num           : OUT : the number of tasks assigned to this worker
- */
-void taskAllocate(int total_tasks, int total_workers, int this_id,
-                         int * first_task_id, int * num)
-{
-    int l_num;
-    int leftovers = total_tasks % total_workers; /* num of "leftover" tasks */
-    if (this_id < leftovers)
-    {
-        l_num = total_tasks / total_workers + 1; /* do one of the leftovers */
-        *first_task_id = l_num * this_id;
-    }
-    else
-    {
-        l_num = total_tasks / total_workers;
-        *first_task_id = l_num * this_id + leftovers;
-    }
-    *num = l_num;
-}
-
-void printMatrix(int * matrix, int width, int height)
-{
-    for (int i = 0; i < height; i++)
-    {
-        for (int j = 0; j < width; j++)
-        {
-            cout << *matrix++ << " ";
-        }
-        cout << endl;
-    }
-}
-
 int main(int argc, char * argv[])
 {
     int my_rank;
-    int p;          /* the number of processes */
+    int world_size;          /* the number of processes */
-    int n = 10;     /* the size of the matrix */
 
     MPI_Init(&argc, &argv);
     MPI_Comm_rank(MPI_COMM_WORLD, &my_rank);
-    MPI_Comm_size(MPI_COMM_WORLD, &p);
+    MPI_Comm_size(MPI_COMM_WORLD, &world_size);
-
-    /* Initialize the matrices */
-    int matrix[n][n];
-    int recvmatrix[n][n];
-    for (int i = 0; i < n; i++)
-    {
-        for (int j = 0; j < n; j++)
-        {
-            matrix[i][j] = 0;           /* zero the matrices for prettier */
-            recvmatrix[i][j] = 0;       /* printing */
-        }
-    }
-
-    /* Determine which rows I am responsible for and initialize them */
-    int my_first_row;
-    int my_num_rows;
-    taskAllocate(n, p, my_rank, &my_first_row, &my_num_rows);
-    for (int row = my_first_row; row < my_first_row + my_num_rows; row++)
-    {
-        for (int j = 0; j < n; j++)
-        {
-            matrix[row][j] = 100 * (row + 1) + (j + 1);
-        }
-    }
-
-    /* Print the initial matrices */
-    if (my_rank == 0)
-        cout << " *** Initial Matrices ***" << endl;
-    for (int i = 0; i < p; i++)
-    {
-        if (my_rank == i)
-        {
-            cout << "Process " << i << " matrix:" << endl;
-            printMatrix(&matrix[0][0], n, n);
-            cout << endl;
-        }
-        MPI_Barrier(MPI_COMM_WORLD);      /* just for printing coherently */
-        usleep(100000);
-        MPI_Barrier(MPI_COMM_WORLD);
-    }
-
-    /* Populate the displacements array */
-    int displs[p];
-    int counts[p];
-    for (int i = 0, total = 0; i < p; i++)
-    {
-        int first;
-        int count;
-        taskAllocate(n, p, i, &first, &count);
-        displs[i] = total;
-        counts[i] = count;
-        total += count;
-    }
-
-    /* Transpose the matrix with n gather operations */
-    for (int i = 0, toproc = 0, proccount = counts[0]; i < n; i++)
-    {
-        int my_col_i_vals[my_num_rows];
-        for (int row_offset = 0; row_offset < my_num_rows; row_offset++)
-            my_col_i_vals[row_offset] = matrix[my_first_row + row_offset][i];
-        MPI_Gatherv(&my_col_i_vals[0], my_num_rows, MPI_INT,
-                    &recvmatrix[i][0], &counts[0], &displs[0],
-                    MPI_INT, toproc, MPI_COMM_WORLD);
-        proccount--;
-        if (proccount <= 0)
-        {
-            toproc++;
-            proccount = counts[toproc];
-        }
-    }
-
-    /* Print the transposed matrices */
-    if (my_rank == 0)
-        cout << " *** Final Transposed Matrices ***" << endl;
-    for (int i = 0; i < p; i++)
-    {
-        if (my_rank == i)
-        {
-            cout << "Process " << i << " matrix:" << endl;
-            printMatrix(&recvmatrix[0][0], n, n);
-            cout << endl;
-        }
-        MPI_Barrier(MPI_COMM_WORLD);      /* just for printing coherently */
-        usleep(100000);
-        MPI_Barrier(MPI_COMM_WORLD);
-    }
 
     MPI_Finalize();