2D memory alloc, norm refactored as __device__ function

meanshift.c

@@ -1,8 +1,11 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <sys/time.h>
+#include <math.h>
+#include <float.h>
 
 #include "serial_declarations.h"
+#define N       512
 
 int NUMBER_OF_POINTS = 600;
 int DIMENSIONS = 2;
@@ -15,6 +18,19 @@ double seq_time;
 int meanshift(double **original_points, double ***shifted_points, int h
         , parameters *opt, int iteration);
 
+__device__ double norm(double **matrix, int rows, int cols){
+
+    double sum=0, temp_mul=0;
+    for (int i=0; i<rows; i++) {
+        for (int j=0; j<cols; j++) {
+            temp_mul = matrix[i][j] * matrix[i][j];
+            sum = sum + temp_mul;
+        }
+    }
+    double norm = sqrt(sum);
+    return norm;
+}
+
 int main(int argc, char **argv){
     int h = 1;
 
@@ -74,6 +90,8 @@ int main(int argc, char **argv){
     //save_matrix(shifted_points, iterations);
 }
 
+
+
 int meanshift(double **original_points, double ***shifted_points, int h
         , parameters *opt, int iteration){
 
@@ -102,33 +120,40 @@ int meanshift(double **original_points, double ***shifted_points, int h
 
 
     double * d_kernel_matrix;
-    cudaMalloc(&d_kernel_matrix, NUMBER_OF_POINTS * NUMBER_OF_POINTS * sizeof(double));
+    size_t pitch_kernel_matrix;
+    cudaMallocPitch(&d_kernel_matrix, &pitch_kernel_matrix,
+                    NUMBER_OF_POINTS * sizeof(double), NUMBER_OF_POINTS);
+
     double * d_denominator;
     cudaMalloc(&d_denominator, NUMBER_OF_POINTS * sizeof(double));
+
     double * d_new_shift;
-    cudaMalloc(&d_new_shift, NUMBER_OF_POINTS * DIMENSIONS * sizeof(double));
+    size_t pitch_new_shift;
+    cudaMallocPitch(&d_new_shift, &pitch_new_shift,
+                    NUMBER_OF_POINTS * sizeof(double), DIMENSIONS);
 
-//    (*shifted_points) = alloc_2d_double(NUMBER_OF_POINTS, DIMENSIONS);
-//    duplicate(original_points, NUMBER_OF_POINTS, DIMENSIONS, shifted_points);
     double * d_shifted_points;
-    cudaMalloc(&d_shifted_points, NUMBER_OF_POINTS * DIMENSIONS * sizeof(double));
+    size_t pitch_shifted_points;
+    cudaMallocPitch(&d_shifted_points, &pitch_shifted_points,
+                    NUMBER_OF_POINTS * sizeof(double), DIMENSIONS);
 
-//    double **mean_shift_vector;
-//    mean_shift_vector = alloc_2d_double(NUMBER_OF_POINTS, DIMENSIONS);
     double * d_mean_shift_vector;
-    cudaMalloc(&d_mean_shift_vector, NUMBER_OF_POINTS * DIMENSIONS * sizeof(double));
+    size_t pitch_mean_shift_vector;
+    cudaMallocPitch(&d_mean_shift_vector, &pitch_mean_shift_vector,
+                    NUMBER_OF_POINTS * sizeof(double), DIMENSIONS);
+
 
-    //Copy vectors from host memory to device memory
-    cudaMemcpy(d_shifted_points, *shifted_points, NUMBER_OF_POINTS * DIMENSIONS * sizeof(double),
-               cudaMemcpyHostToDevice);
-    // y[i][j] == d_y[COLUMNS*i + j]
-    cudaMemcpy(d_mean_shift_vector, mean_shift_vector, NUMBER_OF_POINTS * DIMENSIONS * sizeof(double),
-               cudaMemcpyHostToDevice);
+    cudaMemcpy2D(d_shifted_points, NUMBER_OF_POINTS * sizeof(double), *shifted_points,
+                 pitch_shifted_points, NUMBER_OF_POINTS * sizeof(double),
+                 DIMENSIONS, cudaMemcpyHostToDevice);
+
+    cudaMemcpy2D(d_mean_shift_vector, NUMBER_OF_POINTS * sizeof(double), *mean_shift_vector,
+                 pitch_mean_shift_vector, NUMBER_OF_POINTS * sizeof(double),
+                 DIMENSIONS, cudaMemcpyHostToDevice);
 
 
     // TODO REFACTOR AS A KERNEL
-    // find pairwise distance matrix (inside radius)
-    // [I, D] = rangesearch(x,y,h);
+
     for (int i=0; i<NUMBER_OF_POINTS; i++){
         double sum = 0;
         for (int j=0; j<NUMBER_OF_POINTS; j++){
@@ -192,3 +217,57 @@ int meanshift(double **original_points, double ***shifted_points, int h
 
     return iteration;
 }
+
+/**
+
+__global__ int iteration(double * kernel_matrix, double * denominator,
+            double * new_shift, double *shifted_points, double mean_shift_vector,
+            int NUMBER_OF_POINTS, int DIMENSIONS, int h){
+
+    int i = threadIdx.x + blockIdx.x * blockDim.x;
+    for (i = 0; i < NUMBER_OF_POINTS; i++) {
+        double sum = 0;
+        for (int j = 0; j < NUMBER_OF_POINTS; j++) {
+            double dist_sum = 0;
+            for (int p = 0; p < DIMENSIONS; p++) {
+                double dif = ((*shifted_points)[i])[p] - (original_points[j])[p];
+                dist_sum += dif * dif;
+            }
+            double dist = sqrt(dist_sum);
+
+            if (dist < h * h) {
+                kernel_matrix[i][j] = dist * dist;
+                // compute kernel matrix
+                double pow = ((-1) * (kernel_matrix[i][j])) / (2 * (h * h));
+                kernel_matrix[i][j] = exp(pow);
+            } else {
+                kernel_matrix[i][j] = 0;
+            }
+            if (i == j) {
+                kernel_matrix[i][j] += 1;
+            }
+            sum = sum + kernel_matrix[i][j];
+        }
+        denominator[i] = sum;
+
+        // build nominator
+        for (int j = 0; j < DIMENSIONS; j++) {
+            new_shift[i][j] = 0;
+            for (int k = 0; k < NUMBER_OF_POINTS; k++) {
+                new_shift[i][j] += kernel_matrix[i][k] * original_points[k][j];
+            }
+            // divide element-wise
+            new_shift[i][j] = new_shift[i][j] / denominator[i];
+            // calculate mean-shift vector at the same time
+            mean_shift_vector[i][j] = new_shift[i][j] - (*shifted_points)[i][j];
+        }
+    }
+
+    // frees previously shifted points, they're now garbage
+    free((*shifted_points)[0]);
+    // updates shifted points pointer to the new array address
+    shifted_points = &new_shift;
+
+}
+
+*/