Single memory allocations in GPU, Move new_shift and mean_shift_vector calculations in kernel

mean_shift_cuda/meanshift_kernels.cu

@@ -1,24 +1,8 @@
 #include "meanshift_kernels.h"
 #include <stdio.h>
 
-__global__ void multiply_kernel(Matrix matrix1, Matrix matrix2, Matrix output){
-    // Each thread computes one element of output
-    // by accumulating results into cell_value
-    double cell_value = 0;
-    int row = blockIdx.x * blockDim.x + threadIdx.x;
-    int col = blockIdx.y * blockDim.y + threadIdx.y;
-
-    if (row + col < output.height * output.width){
-        for (int element_index = 0; element_index < matrix1.width; ++element_index){
-            cell_value += matrix1.elements[row * matrix1.width + element_index]
-                * matrix2.elements[element_index * matrix2.width + col];
-        }
-        output.elements[row * output.width + col] = cell_value;
-    }
-}
-
-__global__ void calculate_kernel_matrix_kernel(Matrix shifted_points, Matrix original_points
-    , double deviation, Matrix kernel_matrix){
+__global__ void calculate_kernel_matrix_kernel(Matrix shifted_points, Matrix original_points,
+    double deviation, Matrix kernel_matrix){
     // Each thread calculates one element of kernel_matrix
     int row = blockIdx.x * blockDim.x + threadIdx.x;
     int col = blockIdx.y * blockDim.y + threadIdx.y;
@@ -48,17 +32,43 @@ __global__ void calculate_kernel_matrix_kernel(Matrix shifted_points, Matrix ori
     }
 }
 
+__global__ void shift_points_kernel(Matrix original_points, Matrix kernel_matrix, Matrix shifted_points,
+    Matrix new_shift, Matrix denominator, Matrix mean_shift_vector){
+    // Each thread computes one element of new_shift
+    // by accumulating results into cell_value
+    double cell_value = 0;
+    int row = blockIdx.x * blockDim.x + threadIdx.x;
+    int col = blockIdx.y * blockDim.y + threadIdx.y;
+
+    // performs calculations only if indexes are within matrix bounds
+    //if (row + col < new_shift.height * new_shift.width){
+    if (row < new_shift.height){
+        // calculates new_shift
+        // builds nominator by multiplying kernel_matrix and original_points
+        for (int element_index = 0; element_index < kernel_matrix.width; ++element_index){
+            cell_value += kernel_matrix.elements[row * kernel_matrix.width + element_index]
+                * original_points.elements[element_index * original_points.width + col];
+        }
+        // new_shift elements are calculated by dividing with the denominator
+        new_shift.elements[row * new_shift.width + col] =
+            cell_value / denominator.elements[row];
+
+        // calculates mean-shift vector
+        mean_shift_vector.elements[row * new_shift.width + col] =
+            new_shift.elements[row * new_shift.width + col] -
+            shifted_points.elements[row * new_shift.width + col];
+    }
+}
+
 __global__ void denominator_kernel(Matrix denominator, Matrix kernel_matrix){
 
     int row = blockIdx.x * blockDim.x + threadIdx.x;
     int col = blockIdx.y * blockDim.y + threadIdx.y;
 
-
     if (row * denominator.width + col > denominator.width * denominator.height){
         return;
     }
 
     denominator.elements[col]=0;
     denominator.elements[row] += kernel_matrix.elements[row*denominator.width + col];
-
 }

mean_shift_cuda/meanshift_kernels.h

@@ -1,17 +1,18 @@
 #ifndef SERIAL_KERNELS_H    /*    Include guard    */
 #define SERIAL_KERNELS_H
 
-typedef struct{
+typedef struct {
     int width;
     int height;
     double *elements;
 } Matrix;
 
-//Function multiply_kernel calculates the product of matrices 1 and 2 into output.
-__global__ void multiply_kernel(Matrix matrix1, Matrix matrix2, Matrix output);
+__global__ void calculate_kernel_matrix_kernel(Matrix shifted_points, Matrix original_points,
+    double deviation, Matrix kernel_matrix);
 
-__global__ void calculate_kernel_matrix_kernel(Matrix shifted_points, Matrix original_points
-    , double deviation, Matrix kernel_matrix);
+//Function multiply_kernel calculates the product of matrices 1 and 2 into output.
+__global__ void shift_points_kernel(Matrix original_points, Matrix kernel_matrix, Matrix shifted_points,
+    Matrix new_shift, Matrix denominator, Matrix mean_shift_vector);
 
 __global__ void denominator_kernel(Matrix denominator, Matrix kernel_matrix);
 

mean_shift_cuda/meanshift_utils.cu

@@ -5,7 +5,6 @@
 #include <string.h>
 
 #include "meanshift_utils.h"
-#include "meanshift_kernels.h"
 
 #define OUTPUT_PREFIX "../output/output_"
 
@@ -61,7 +60,7 @@ void get_args(int argc, char **argv, parameters *params){
 void init(double ***vectors, char **labels){
     int bytes_read = 0;
 
-    set_Gpu();
+    set_GPU();
 
     if (params.verbose){
         printf("Reading dataset and labels...\n");
@@ -127,7 +126,7 @@ void init(double ***vectors, char **labels){
 
 //Based on https://stackoverflow.com/a/28113186
 //Poio psagmeno link https://www.cs.virginia.edu/~csadmin/wiki/index.php/CUDA_Support/Choosing_a_GPU
-void set_Gpu(){
+void set_GPU(){
     int devices_count = 0, max_multiprocessors = 0, max_device = 0;
 
     // gets devices count checking for errors like no devices or no drivers to check for
@@ -162,11 +161,20 @@ void set_Gpu(){
 
 int meanshift(double **original_points, double ***shifted_points, int deviation
     , parameters *opt){
+    // host variables
+    int size = 0;
     static int iteration = 0;
-    static double **mean_shift_vector, **kernel_matrix, *denominator;
+    static double **kernel_matrix, *denominator, **mean_shift_vector;
+    double **new_shift;
+
+    // device variables
+    static Matrix d_original_points, d_shifted_points, d_kernel_matrix, d_denominator,
+        d_mean_shift_vector;
+    Matrix d_new_shift;
 
     // allocates memory and copies original points on first iteration
     if (iteration == 0 || (*shifted_points) == NULL){
+        // allocates memory for shifted points array and copies original points into it
         (*shifted_points) = alloc_2d_double(NUMBER_OF_POINTS, DIMENSIONS);
         duplicate(original_points, NUMBER_OF_POINTS, DIMENSIONS, shifted_points);
 
@@ -182,42 +190,49 @@ int meanshift(double **original_points, double ***shifted_points, int deviation
         // allocates memory for other arrays needed
         kernel_matrix = alloc_2d_double(NUMBER_OF_POINTS, NUMBER_OF_POINTS);
         denominator = (double *)malloc(NUMBER_OF_POINTS * sizeof(double));
+
+        // allocates corresponding memory in device
+        init_device_memory(original_points, *shifted_points, &d_original_points, &d_shifted_points,
+            &d_kernel_matrix, &d_denominator, &d_mean_shift_vector);
     }
-    // TODO move arrays to device and create global kernel for the iteration
 
     // finds pairwise distance matrix (inside radius)
     // [I, D] = rangesearch(x,y,h);
-    calculate_kernel_matrix((*shifted_points), original_points, deviation, &kernel_matrix);
-
-//    // calculate denominator
-//    for (int i=0; i<NUMBER_OF_POINTS; i++){
-//        double sum = 0;
-//        for (int j=0; j<NUMBER_OF_POINTS; j++){
-//            sum = sum + kernel_matrix[i][j];
-//        }
-//        denominator[i] = sum;
-//    }
-    denominator = calculate_denominator(kernel_matrix);
-
-    // creates new y vector
-    double **new_shift = alloc_2d_double(NUMBER_OF_POINTS, DIMENSIONS);
+    calculate_kernel_matrix(d_shifted_points, d_original_points, d_kernel_matrix, deviation,
+        &kernel_matrix);
 
-    // builds nominator
-    multiply(kernel_matrix, original_points, &new_shift);
-
-    // divides element-wise
+    // calculates denominator
     for (int i=0; i<NUMBER_OF_POINTS; i++){
-        for (int j=0; j<DIMENSIONS; j++){
-            new_shift[i][j] = new_shift[i][j] / denominator[i];
-            // calculates mean-shift vector at the same time
-            mean_shift_vector[i][j] = new_shift[i][j] - (*shifted_points)[i][j];
+        double sum = 0;
+        for (int j=0; j<NUMBER_OF_POINTS; j++){
+            sum = sum + kernel_matrix[i][j];
         }
+        denominator[i] = sum;
     }
 
+    //calculate_denominator(kernel_matrix);
+
+    size = NUMBER_OF_POINTS * sizeof(double);
+    gpuErrchk( cudaMemcpy(d_denominator.elements, &(denominator[0])
+        , size, cudaMemcpyHostToDevice) );
+
+    // creates new y vector
+    // allocates memory in every recursion
+    new_shift = alloc_2d_double(NUMBER_OF_POINTS, DIMENSIONS);
+    // allocates corresponding memory in device
+    d_new_shift.width = DIMENSIONS;
+    d_new_shift.height = NUMBER_OF_POINTS;
+    size = NUMBER_OF_POINTS * DIMENSIONS * sizeof(double);
+    gpuErrchk( cudaMalloc(&(d_new_shift.elements), size) );
+
+    shift_points(d_kernel_matrix, d_original_points, d_shifted_points, d_new_shift, d_denominator,
+        d_mean_shift_vector, kernel_matrix, original_points, &new_shift, &mean_shift_vector);
+
     // 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;
+    d_shifted_points.elements = d_new_shift.elements;
 
     if (params.display){
         save_matrix((*shifted_points), iteration);
@@ -242,12 +257,14 @@ int meanshift(double **original_points, double ***shifted_points, int deviation
         free(kernel_matrix[0]);
         free(kernel_matrix);
         free(denominator);
+
+        free_device_memory(d_original_points, d_kernel_matrix, d_denominator, d_new_shift);
     }
 
     return iteration;
 }
 
-
+// TODO check why there's is a difference in the norm calculate in matlab
 double norm(double **matrix, int rows, int cols){
     double sum=0, temp_mul=0;
     for (int i=0; i<rows; i++) {
@@ -260,43 +277,57 @@ double norm(double **matrix, int rows, int cols){
     return norm;
 }
 
-void calculate_kernel_matrix(double **shifted_points, double **original_points, double deviation
-    , double ***kernel_matrix){
-    static bool first_iter = true;
-
-    // allocates memory for shifted_points in GPU and copies the array
-    Matrix d_shifted_points;
-    d_shifted_points.width = DIMENSIONS;
-    d_shifted_points.height = NUMBER_OF_POINTS;
-    int size = DIMENSIONS * NUMBER_OF_POINTS * sizeof(double);
-    gpuErrchk( cudaMalloc(&d_shifted_points.elements, size) );
-    gpuErrchk( cudaMemcpy(d_shifted_points.elements, &(shifted_points[0][0])
-        , size, cudaMemcpyHostToDevice) );
+void init_device_memory(double **original_points, double **shifted_points,
+    Matrix *d_original_points, Matrix *d_shifted_points, Matrix *d_kernel_matrix,
+    Matrix *d_denominator, Matrix *d_mean_shift_vector){
+    int size;
 
     // allocates memory for original_points in GPU and copies the array
-    Matrix d_original_points;
-    d_original_points.width = DIMENSIONS;
-    d_original_points.height = NUMBER_OF_POINTS;
+    d_original_points->width = DIMENSIONS;
+    d_original_points->height = NUMBER_OF_POINTS;
     size = NUMBER_OF_POINTS * DIMENSIONS * sizeof(double);
-    gpuErrchk( cudaMalloc(&d_original_points.elements, size) );
-    gpuErrchk( cudaMemcpy(d_original_points.elements, &(original_points[0][0])
+    gpuErrchk( cudaMalloc(&(d_original_points->elements), size) );
+    gpuErrchk( cudaMemcpy(d_original_points->elements, &(original_points[0][0])
+        , size, cudaMemcpyHostToDevice) );
+
+    // allocates memory for shifted_points in GPU and copies the array
+    d_shifted_points->width = DIMENSIONS;
+    d_shifted_points->height = NUMBER_OF_POINTS;
+    size = DIMENSIONS * NUMBER_OF_POINTS * sizeof(double);
+    gpuErrchk( cudaMalloc(&(d_shifted_points->elements), size) );
+    gpuErrchk( cudaMemcpy(d_shifted_points->elements, &(shifted_points[0][0])
         , size, cudaMemcpyHostToDevice) );
 
     // allocates memory for kernel_matrix in GPU
-    Matrix d_kernel_matrix;
-    d_kernel_matrix.width = NUMBER_OF_POINTS;
-    d_kernel_matrix.height = NUMBER_OF_POINTS;
+    d_kernel_matrix->width = NUMBER_OF_POINTS;
+    d_kernel_matrix->height = NUMBER_OF_POINTS;
     size = NUMBER_OF_POINTS * NUMBER_OF_POINTS * sizeof(double);
-    gpuErrchk( cudaMalloc(&d_kernel_matrix.elements, size) );
+    gpuErrchk( cudaMalloc(&(d_kernel_matrix->elements), size) );
 
-    // get max sizes supported from the device
-    int max_block_size = (int)sqrt(device_properties.maxThreadsPerBlock);
-    int requested_block_size = max_block_size;
+    // allocates memory for denominator in GPU
+    d_denominator->width = 1;
+    d_denominator->height = NUMBER_OF_POINTS;
+    size = NUMBER_OF_POINTS * sizeof(double);
+    gpuErrchk( cudaMalloc(&(d_denominator->elements), size) );
+
+    // allocates memory for mean_shift_vector in GPU
+    d_mean_shift_vector->width = DIMENSIONS;
+    d_mean_shift_vector->height = NUMBER_OF_POINTS;
+    size = NUMBER_OF_POINTS * DIMENSIONS * sizeof(double);
+    gpuErrchk( cudaMalloc(&(d_mean_shift_vector->elements), size) );
+}
+
+void calculate_kernel_matrix(Matrix d_shifted_points, Matrix d_original_points,
+    Matrix d_kernel_matrix, double deviation, double ***kernel_matrix){
+    int size;
+    static bool first_iter = true;
+    // gets max block size supported from the device
+    int max_block_size = device_properties.maxThreadsPerBlock;
+    int requested_block_size = (int)sqrt(max_block_size);
     bool block_size_too_big = true;
 
     dim3 dimBlock;
     dim3 dimGrid;
-
     do {
         dimBlock.x = requested_block_size;
         dimBlock.y = requested_block_size;
@@ -323,65 +354,106 @@ void calculate_kernel_matrix(double **shifted_points, double **original_points,
     size = NUMBER_OF_POINTS * NUMBER_OF_POINTS * sizeof(double);
     gpuErrchk( cudaMemcpy(&((*kernel_matrix)[0][0]), d_kernel_matrix.elements
         , size, cudaMemcpyDeviceToHost) );
-
-    gpuErrchk( cudaFree(d_shifted_points.elements) );
-    gpuErrchk( cudaFree(d_original_points.elements) );
-    gpuErrchk( cudaFree(d_kernel_matrix.elements) );
 }
 
-
-void multiply(double **kernel_matrix, double **original_points, double ***new_shift){
+double * calculate_denominator(double **kernel_matrix){
     static bool first_iter = true;
 
+    // allocates memory for denominator_matrix in GPU
+    Matrix d_denominator_matrix;
+    d_denominator_matrix.width = NUMBER_OF_POINTS;
+    d_denominator_matrix.height = 1;
+    int size = NUMBER_OF_POINTS * sizeof(double);
+    gpuErrchk( cudaMalloc(&d_denominator_matrix.elements, size) );
+
     // allocates memory for kernel_matrix in GPU and copies the array
     Matrix d_kernel_matrix;
     d_kernel_matrix.width = NUMBER_OF_POINTS;
     d_kernel_matrix.height = NUMBER_OF_POINTS;
-    int size = NUMBER_OF_POINTS * NUMBER_OF_POINTS * sizeof(double);
+    size = NUMBER_OF_POINTS * NUMBER_OF_POINTS * sizeof(double);
     gpuErrchk( cudaMalloc(&d_kernel_matrix.elements, size) );
     gpuErrchk( cudaMemcpy(d_kernel_matrix.elements, &(kernel_matrix[0][0])
-        , size, cudaMemcpyHostToDevice) );
-
-    // allocates memory for original_points in GPU and copies the array
-    Matrix d_original_points;
-    d_original_points.width = DIMENSIONS;
-    d_original_points.height = NUMBER_OF_POINTS;
-    size = NUMBER_OF_POINTS * DIMENSIONS * sizeof(double);
-    gpuErrchk( cudaMalloc(&d_original_points.elements, size) );
-    gpuErrchk( cudaMemcpy(d_original_points.elements, &(original_points[0][0])
-        , size, cudaMemcpyHostToDevice) );
-
-    // allocates memory for new_shift in GPU
-    Matrix d_new_shift;
-    d_new_shift.width = DIMENSIONS;
-    d_new_shift.height = NUMBER_OF_POINTS;
-    size = NUMBER_OF_POINTS * DIMENSIONS * sizeof(double);
-    gpuErrchk( cudaMalloc(&d_new_shift.elements, size) );
+            , size, cudaMemcpyHostToDevice) );
 
     // get max sizes supported from the device
     int max_block_size = device_properties.maxThreadsPerBlock;
-    dim3 dimBlock((d_new_shift.height < sqrt(max_block_size)) ? d_new_shift.height : sqrt(max_block_size)
-        , (d_new_shift.width < sqrt(max_block_size)) ? d_new_shift.width : sqrt(max_block_size));
-    dim3 dimGrid((d_new_shift.height + dimBlock.x - 1) / dimBlock.x
-        , (d_new_shift.width + dimBlock.y - 1) / dimBlock.y);
+    dim3 dimBlock((d_denominator_matrix.height < sqrt(max_block_size)) ? d_denominator_matrix.height : sqrt(max_block_size)
+            , (d_denominator_matrix.width < sqrt(max_block_size)) ? d_denominator_matrix.width : sqrt(max_block_size));
+    dim3 dimGrid((d_denominator_matrix.height + dimBlock.x - 1) / dimBlock.x
+            , (d_denominator_matrix.width + dimBlock.y - 1) / dimBlock.y);
 
     if (first_iter && params.verbose){
-        printf("multiply_kernel called with:\n");
+        printf("calculate_denominator called with:\n");
         printf("dimBlock.x = %d, dimBlock.y = %d\n", dimBlock.x, dimBlock.y);
         printf("dimGrid.x = %d, dimGrid.y = %d\n\n", dimGrid.x, dimGrid.y);
         first_iter = false;
     }
 
-    multiply_kernel<<<dimGrid, dimBlock>>>(d_kernel_matrix, d_original_points, d_new_shift);
+    denominator_kernel<<<dimGrid, dimBlock>>>(d_denominator_matrix, d_kernel_matrix);
     gpuErrchk( cudaPeekAtLastError() );
     gpuErrchk( cudaDeviceSynchronize() );
 
+
+    size = NUMBER_OF_POINTS * sizeof(double);
+    double ** denominator = (double**)malloc(size);
+    gpuErrchk( cudaMemcpy(&((*denominator)[0]), d_denominator_matrix.elements
+            ,size, cudaMemcpyDeviceToHost) );
+
+    gpuErrchk( cudaFree(d_kernel_matrix.elements) );
+    gpuErrchk( cudaFree(d_denominator_matrix.elements) );
+
+    return (*denominator);
+}
+
+void shift_points(Matrix d_kernel_matrix, Matrix d_original_points, Matrix d_shifted_points,
+    Matrix d_new_shift, Matrix d_denominator, Matrix d_mean_shift_vector, double **kernel_matrix,
+    double **original_points, double ***new_shift, double ***mean_shift_vector){
+    int size;
+    static bool first_iter = true;
+    // gets max block size supported from the device
+    int max_block_size = device_properties.maxThreadsPerBlock;
+    int requested_block_size = (int)sqrt(max_block_size);
+    bool block_size_too_big = true;
+
+    dim3 dimBlock;
+    dim3 dimGrid;
+    do {
+        dimBlock.x = requested_block_size;
+        dimBlock.y = 2;
+        dimGrid.x = (d_kernel_matrix.height + dimBlock.x - 1) / dimBlock.x;
+        dimGrid.y = 1;
+
+        shift_points_kernel<<<dimGrid, dimBlock>>>(d_original_points, d_kernel_matrix, d_shifted_points,
+            d_new_shift, d_denominator, d_mean_shift_vector);
+        if (cudaGetLastError() != cudaSuccess){
+            --requested_block_size;
+        } else {
+            block_size_too_big = false;
+            gpuErrchk( cudaDeviceSynchronize() );
+        }
+    } while(block_size_too_big);
+
+    if (first_iter && params.verbose){
+        printf("shift_points_kernel called with:\n");
+        printf("dimBlock.x = %d, dimBlock.y = %d\n", dimBlock.x, dimBlock.y);
+        printf("dimGrid.x = %d, dimGrid.y = %d\n\n", dimGrid.x, dimGrid.y);
+        first_iter = false;
+    }
+
     size = NUMBER_OF_POINTS * DIMENSIONS * sizeof(double);
     gpuErrchk( cudaMemcpy(&((*new_shift)[0][0]), d_new_shift.elements
         , size, cudaMemcpyDeviceToHost) );
+    gpuErrchk( cudaMemcpy(&((*mean_shift_vector)[0][0]), d_mean_shift_vector.elements
+        , size, cudaMemcpyDeviceToHost) );
+}
 
-    gpuErrchk( cudaFree(d_kernel_matrix.elements) );
+void free_device_memory(Matrix d_original_points, Matrix d_kernel_matrix, Matrix d_denominator,
+    Matrix d_new_shift){
+    // frees all memory previously allocated in device
     gpuErrchk( cudaFree(d_original_points.elements) );
+    gpuErrchk( cudaFree(d_kernel_matrix.elements) );
+    //gpuErrchk( cudaFree(d_shifted_points.elements) );
+    gpuErrchk( cudaFree(d_denominator.elements) );
     gpuErrchk( cudaFree(d_new_shift.elements) );
 }
 
@@ -434,53 +506,4 @@ void save_matrix(double **matrix, int iteration){
         }
         fprintf(file, "\n");
     }
-}
-
-double * calculate_denominator(double **kernel_matrix){
-    static bool first_iter = true;
-
-    // allocates memory for denominator_matrix in GPU
-    Matrix d_denominator_matrix;
-    d_denominator_matrix.width = NUMBER_OF_POINTS;
-    d_denominator_matrix.height = 1;
-    int size = NUMBER_OF_POINTS * sizeof(double);
-    gpuErrchk( cudaMalloc(&d_denominator_matrix.elements, size) );
-
-    // allocates memory for kernel_matrix in GPU and copies the array
-    Matrix d_kernel_matrix;
-    d_kernel_matrix.width = NUMBER_OF_POINTS;
-    d_kernel_matrix.height = NUMBER_OF_POINTS;
-    size = NUMBER_OF_POINTS * NUMBER_OF_POINTS * sizeof(double);
-    gpuErrchk( cudaMalloc(&d_kernel_matrix.elements, size) );
-    gpuErrchk( cudaMemcpy(d_kernel_matrix.elements, &(kernel_matrix[0][0])
-            , size, cudaMemcpyHostToDevice) );
-
-    // get max sizes supported from the device
-    int max_block_size = device_properties.maxThreadsPerBlock;
-    dim3 dimBlock((d_denominator_matrix.height < sqrt(max_block_size)) ? d_denominator_matrix.height : sqrt(max_block_size)
-            , (d_denominator_matrix.width < sqrt(max_block_size)) ? d_denominator_matrix.width : sqrt(max_block_size));
-    dim3 dimGrid((d_denominator_matrix.height + dimBlock.x - 1) / dimBlock.x
-            , (d_denominator_matrix.width + dimBlock.y - 1) / dimBlock.y);
-
-    if (first_iter && params.verbose){
-        printf("calculate_denominator called with:\n");
-        printf("dimBlock.x = %d, dimBlock.y = %d\n", dimBlock.x, dimBlock.y);
-        printf("dimGrid.x = %d, dimGrid.y = %d\n\n", dimGrid.x, dimGrid.y);
-        first_iter = false;
-    }
-
-    denominator_kernel<<<dimGrid, dimBlock>>>(d_denominator_matrix, d_kernel_matrix);
-    gpuErrchk( cudaPeekAtLastError() );
-    gpuErrchk( cudaDeviceSynchronize() );
-
-
-    size = NUMBER_OF_POINTS * sizeof(double);
-    double ** denominator = (double**)malloc(size);
-    gpuErrchk( cudaMemcpy(&((*denominator)[0]), d_denominator_matrix.elements
-            ,size, cudaMemcpyDeviceToHost) );
-
-    gpuErrchk( cudaFree(d_kernel_matrix.elements) );
-    gpuErrchk( cudaFree(d_denominator_matrix.elements) );
-
-    return (*denominator);
 }

mean_shift_cuda/meanshift_utils.h

@@ -2,6 +2,7 @@
 #define SERIAL_UTILS_H
 
 #include <stdbool.h>
+#include "meanshift_kernels.h"
 
 //GPU error check snippet taken from:
 //https://stackoverflow.com/a/14038590
@@ -35,7 +36,7 @@ void get_args(int argc, char **argv, parameters *params);
 //Function init reads the dataset and label arrays from the corresponding files.
 void init(double ***vectors, char **labels);
 
-void set_Gpu();
+void set_GPU();
 
 //Function meanshift recursively shifts original points according to th
 //mean-shift algorithm saving the result to shiftedPoints. Struct opt has user
@@ -43,16 +44,24 @@ void set_Gpu();
 int meanshift(double **original_points, double ***shifted_points, int h
     , parameters *opt);
 
+void init_device_memory(double **original_points, double **shifted_points,
+    Matrix *d_original_points, Matrix *d_shifted_points,
+    Matrix *d_kernel_matrix, Matrix *d_denominator, Matrix *d_new_shift);
+
 //Function norm returns the second norm of matrix of dimensions rowsXcols.
 double norm(double **matrix, int rows, int cols);
 
-void calculate_kernel_matrix(double **shifted_points, double **original_points, double deviation
-    , double ***kernel_matrix);
+void calculate_kernel_matrix(Matrix d_shifted_points, Matrix d_original_points,
+    Matrix d_kernel_matrix, double deviation, double ***kernel_matrix);
 
 //Function multiply allocates memory in GPU, sends the data and calls the 
 //multiply kernel function.
-void multiply(double **kernel_matrix, double **original_points
-    , double ***new_shift);
+void shift_points(Matrix d_kernel_matrix, Matrix d_original_points, Matrix d_shifted_points,
+    Matrix d_new_shift, Matrix d_denominator, Matrix d_mean_shift_vector, double **kernel_matrix,
+    double **original_points, double ***new_shift, double ***mean_shift_vector);
+
+void free_device_memory(Matrix d_original_points, Matrix d_kernel_matrix, Matrix d_denominator,
+    Matrix d_new_shift);
 
 //Function calculateDistance returns the distance between x and y vectors.
 double calculateDistance(double *y, double *x);