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dbscan.c
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dbscan.c
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#include<stdlib.h>
#include<string.h>
#include<stdio.h>
#include<unistd.h>
#include<pthread.h>
#if defined(_SCAN_SMITH_WATERMAN_GPU) || defined(_SCAN_SMITH_WATERMAN_MPI_GPU)
#ifdef __APPLE__
#include<OpenCL/OpenCL.h>
#else
#include<CL/opencl.h>
#endif
#include <sys/types.h>
#include <sys/stat.h>
#endif
#if defined(_SCAN_SMITH_WATERMAN_MPI_GPU)
#include<mpi.h>
#include<signal.h>
#endif
#if defined(_SCAN_L1)
#include<math.h>
#endif
#include"binary_array.h"
#include"dataset.h"
#include"cluster.h"
#include"dbscan.h"
#if defined(_SCAN_SMITH_WATERMAN)
#include"smith-waterman.h"
#endif
#if defined(__AVX__)
#include<immintrin.h>
#elif defined(__SSE__)
#include<xmmintrin.h>
#endif
#if defined(_SCAN_SMITH_WATERMAN_MPI_GPU)
typedef struct {
int* split_set_index;
split_set** split_sets;
} kill_handler;
kill_handler kh;
#endif
typedef struct {
#if defined(_SCAN_SMITH_WATERMAN_GPU)
split_set (*dbscanner) (dataset, float, int, opencl_stuff);
opencl_stuff ocl;
#elif defined(_SCAN_SMITH_WATERMAN_MPI_GPU)
split_set (*dbscanner) (dataset, float, int, opencl_stuff, int, int);
opencl_stuff ocl;
int mpi_rank;
int mpi_size;
#else
split_set (*dbscanner) (dataset, float, int);
#endif
dataset ds;
float* epsilon_now;
float epsilon_inc;
int minpts;
int* split_set_index;
pthread_mutex_t* lock_stop;
pthread_mutex_t* lock_eps;
pthread_mutex_t* lock_split_sets;
int* stop;
split_set** split_sets;
int* stopindex;
} thread_handler_adaptive_scan;
#if defined(_SCAN_SMITH_WATERMAN_GPU) || defined(_SCAN_SMITH_WATERMAN_MPI_GPU)
char* load_program_source(const char* filename) {
struct stat statbuf;
FILE *fh;
char *source;
fh = fopen(filename, "r");
if (fh == 0)
return 0;
stat(filename, &statbuf);
source = (char *) malloc(statbuf.st_size + 1);
fread(source, statbuf.st_size, 1, fh);
source[statbuf.st_size] = '\0';
return source;
}
opencl_stuff opencl_initialization(
#if defined (_SCAN_SMITH_WATERMAN_MPI_GPU)
int mpi_stride,
#endif
dataset ds) {
int i;
opencl_stuff ocl;
cl_platform_id* platform;
cl_context_properties* contprop;
cl_program* programs;
cl_uint num_gpus;
cl_uint num_acc;
cl_uint num_cpus;
int num_devs;
cl_int err;
cl_device_id* devices;
char BuildErrorLog[2048];
size_t BuildErrorLength;
char clSourceFile[] = "smith-waterman-gpu.cl";
char* clSource;
size_t acc_distance_size;
int seq_offset = 300;
char* gpu_sequence_dataset_buffer=
(char*)malloc(sizeof(char)*300*ds.n_values);
for(i=0;i<ds.n_values;i++) {
memcpy(gpu_sequence_dataset_buffer+300*i,
ds.sequences[i],ds.sequence_lengths[i]+1);
}
platform = (cl_platform_id*)malloc(sizeof(cl_platform_id));
clGetPlatformIDs(1, platform,NULL);
err = clGetDeviceIDs(platform[0], CL_DEVICE_TYPE_GPU, 0, NULL, &num_gpus);
if (err == CL_DEVICE_NOT_FOUND) num_gpus = 0;
err = clGetDeviceIDs(platform[0], CL_DEVICE_TYPE_CPU, 0, NULL, &num_cpus);
if (err == CL_DEVICE_NOT_FOUND) num_cpus = 0;
err = clGetDeviceIDs(platform[0], CL_DEVICE_TYPE_ACCELERATOR, 0, NULL, &num_acc);
if (err == CL_DEVICE_NOT_FOUND) num_acc = 0;
if (num_acc == 0 && num_gpus == 0 && num_cpus == 0) {
printf("No opencl devices found");
_exit(1);
}
if ( num_gpus > 0 ) {
devices = (cl_device_id*)malloc(sizeof(cl_device_id)*num_gpus);
clGetDeviceIDs(platform[0], CL_DEVICE_TYPE_GPU, num_gpus, devices, NULL);
num_devs = num_gpus;
} else if (num_acc > 0) {
devices = (cl_device_id*)malloc(sizeof(cl_device_id)*num_acc);
clGetDeviceIDs(platform[0], CL_DEVICE_TYPE_ACCELERATOR,
num_acc, devices, NULL);
num_devs = num_acc;
} else if (num_cpus > 0 ) {
devices = (cl_device_id*)malloc(sizeof(cl_device_id)*num_cpus);
clGetDeviceIDs(platform[0], CL_DEVICE_TYPE_CPU, num_cpus, devices, NULL);
num_devs = num_cpus;
}
ocl.cmdq = (cl_command_queue*)malloc(sizeof(cl_command_queue)*num_devs);
ocl.contexts = (cl_context*)malloc(sizeof(cl_context)*num_devs);
ocl.kernel = (cl_kernel*)malloc(sizeof(cl_kernel)*num_devs);
programs = (cl_program*)malloc(sizeof(cl_program)*num_devs);
ocl.acc_sequences = (cl_mem*)malloc(sizeof(cl_mem)*num_devs);
ocl.acc_sequence_lengths = (cl_mem*)malloc(sizeof(cl_mem)*num_devs);
ocl.acc_distances = (cl_mem*)malloc(sizeof(cl_mem)*num_devs);
#if defined (_SCAN_SMITH_WATERMAN_MPI_GPU)
ocl.local_distances = (int*)malloc(sizeof(int)*mpi_stride);
#else
ocl.local_distances = (int*)malloc(sizeof(int)*ds.n_values);
#endif
contprop = (cl_context_properties*)malloc(sizeof(cl_context_properties)*3);
contprop[0] = CL_CONTEXT_PLATFORM;
contprop[1] = (cl_context_properties)platform[0];
contprop[2] = 0;
clSource = load_program_source(clSourceFile);
for(i=0;i<num_devs;i++) {
ocl.contexts[i] = clCreateContext(contprop, 1, devices+i, NULL, NULL, &err);
if(err != CL_SUCCESS) {
printf("Context Creation failed! OCL-ERROR-CODE: %i\n", err);
}
ocl.cmdq[i] = clCreateCommandQueue(ocl.contexts[i], devices[i], 0, NULL);
programs[i] = clCreateProgramWithSource(ocl.contexts[i],1,
(const char**)&clSource,NULL,
&err);
if( err != CL_SUCCESS) {
printf("Program creation failed! \n");
}
err = clBuildProgram(programs[i],0,NULL, NULL, NULL, NULL);
if( err != CL_SUCCESS) {
clGetProgramBuildInfo(programs[i],devices[i],CL_PROGRAM_BUILD_LOG,
2048,BuildErrorLog,&BuildErrorLength);
printf("Build Error Log: \n%s\n",BuildErrorLog);
}
//free(clSource);
ocl.kernel[i] = clCreateKernel(programs[i],"gpuwaterman",&err);
ocl.acc_sequence_lengths[i] = clCreateBuffer(ocl.contexts[i],
CL_MEM_READ_WRITE,
sizeof(size_t)*ds.n_values,
NULL,&err);
err = clEnqueueWriteBuffer(ocl.cmdq[i],
ocl.acc_sequence_lengths[i],
CL_TRUE,
0,
sizeof(size_t)*ds.n_values,
ds.sequence_lengths,
0,NULL,NULL);
ocl.acc_sequences[i] = clCreateBuffer(ocl.contexts[i],
CL_MEM_READ_WRITE,
sizeof(char)*300*ds.n_values,
NULL,&err);
err = clEnqueueWriteBuffer(ocl.cmdq[i],
ocl.acc_sequences[i],
CL_TRUE,
0,
sizeof(char)*300*ds.n_values,
gpu_sequence_dataset_buffer,
0,NULL,NULL);
#if defined (_SCAN_SMITH_WATERMAN_MPI_GPU)
if (i == 0) {
acc_distance_size = mpi_stride/num_devs + mpi_stride%num_devs;
} else {
acc_distance_size = mpi_stride/num_devs;
}
#else
if (i == 0) {
acc_distance_size = ds.n_values/num_devs + ds.n_values%num_devs;
} else {
acc_distance_size = ds.n_values/num_devs;
}
#endif
ocl.acc_distances[i] = clCreateBuffer(ocl.contexts[i],
CL_MEM_READ_WRITE,
(sizeof(int)*acc_distance_size),
NULL,&err);
err = clSetKernelArg(ocl.kernel[i],
0,sizeof(cl_mem),ocl.acc_sequences+i);
err = clSetKernelArg(ocl.kernel[i],
1,sizeof(cl_mem),ocl.acc_sequence_lengths+i);
err = clSetKernelArg(ocl.kernel[i],
2,sizeof(cl_mem),ocl.acc_distances+i);
err = clSetKernelArg(ocl.kernel[i],
3,sizeof(int),&seq_offset);
}
free(gpu_sequence_dataset_buffer);
ocl.num_devs =num_devs;
ocl.devices = devices;
ocl.platform = platform;
ocl.contprop = contprop;
ocl.programs = programs;
//free(devices);
//free(programs);
return(ocl);
}
void opencl_destroy(opencl_stuff ocl) {
free(ocl.cmdq);
free(ocl.kernel);
free(ocl.contexts);
free(ocl.acc_sequences);
free(ocl.acc_sequence_lengths);
free(ocl.acc_distances);
free(ocl.local_distances);
free(ocl.programs);
free(ocl.devices);
free(ocl.contprop);
free(ocl.platform);
}
#endif
static inline int compare(const void* a , const void* b) {
int na = *(int*)a;
int nb = *(int*)b;
return (na-nb);
}
#if defined(_SCAN_SMITH_WATERMAN_MPI_GPU)
int adaptive_dbscan_mpi_client(dataset ds,
int mpi_rank,
int mpi_size) {
int i;
cl_int err;
size_t mpi_stride = ds.n_values / mpi_size;
size_t mpi_stride_rest = ds.n_values % mpi_size;
size_t acc_distance_size;
size_t mpi_offset = mpi_stride_rest+mpi_rank*mpi_stride;
opencl_stuff ocl = opencl_initialization(mpi_stride,ds);
size_t pointer_offset;
int current_point;
size_t recovery_offset;
mpi_client_loop:
// printf("Client %i",mpi_rank);
MPI_Recv(¤t_point,1,MPI_INT,0,0,MPI_COMM_WORLD,MPI_STATUS_IGNORE);
pointer_offset = mpi_offset;
if (current_point == -1) {
goto finish;
}
recovery_offset = 0;
for(i=0;i<ocl.num_devs;i++) {
if (i == 0) {
acc_distance_size = mpi_stride/ocl.num_devs + mpi_stride%ocl.num_devs;
} else {
acc_distance_size = mpi_stride/ocl.num_devs;
}
err = clSetKernelArg(ocl.kernel[i],4,sizeof(int),¤t_point);
err = clSetKernelArg(ocl.kernel[i],5,sizeof(int),&pointer_offset);
err = clEnqueueNDRangeKernel(ocl.cmdq[i],ocl.kernel[i],1,
NULL,
&acc_distance_size,
NULL,
0,NULL,NULL);
err = clEnqueueReadBuffer(ocl.cmdq[i], ocl.acc_distances[i],
CL_FALSE, 0,
acc_distance_size*sizeof(int),
ocl.local_distances+recovery_offset,
0,NULL,NULL);
recovery_offset+=acc_distance_size;
pointer_offset+=acc_distance_size;
}
for(i=0;i<ocl.num_devs;i++) {
clFinish(ocl.cmdq[i]);
}
MPI_Send(ocl.local_distances,
mpi_stride,
MPI_INT,
0,
0,
MPI_COMM_WORLD);
goto mpi_client_loop;
finish:
return(0);
}
static inline neighbors region_query(int point, float epsilon, dataset ds,
opencl_stuff ocl,
int mpi_rank,
int mpi_size) {
int i,j,k;
neighbors nb;
cl_int err;
size_t mpi_stride = ds.n_values / mpi_size;
size_t mpi_stride_rest = ds.n_values % mpi_size;
int* mpi_comm_buffer=(int*)malloc(sizeof(int)*mpi_stride);
int pointer_offset = 0;
size_t acc_distance_size;
nb.members=(int*)malloc(sizeof(int)*ds.n_values);
mpi_stride += mpi_stride_rest;
for(i=1;i<mpi_size;i++) {
MPI_Send(&point,1,MPI_INT,i,0,MPI_COMM_WORLD);
}
for(i=0;i<ocl.num_devs;i++) {
if (i == 0) {
acc_distance_size = mpi_stride/ocl.num_devs + mpi_stride%ocl.num_devs;
} else {
acc_distance_size = mpi_stride/ocl.num_devs;
}
err = clSetKernelArg(ocl.kernel[i],4,sizeof(int),&point);
err = clSetKernelArg(ocl.kernel[i],5,sizeof(int),&pointer_offset);
err = clEnqueueNDRangeKernel(ocl.cmdq[i],ocl.kernel[i],1,
NULL,
&acc_distance_size,
NULL,
0,NULL,NULL);
err = clEnqueueReadBuffer(ocl.cmdq[i], ocl.acc_distances[i],
CL_FALSE, 0,
acc_distance_size*sizeof(int),
ocl.local_distances+pointer_offset,
0,NULL,NULL);
pointer_offset+=acc_distance_size;
}
for(i=0;i<ocl.num_devs;i++) {
clFinish(ocl.cmdq[i]);
}
nb.n_members = 0;
for(i=0;i<mpi_stride;i++) {
if(ocl.local_distances[i] <= epsilon) {
nb.members[nb.n_members++] = i;
}
}
mpi_stride -= mpi_stride_rest;
for(j=1;j<mpi_size;j++) {
MPI_Recv(mpi_comm_buffer,mpi_stride,
MPI_INT,j,0,MPI_COMM_WORLD,MPI_STATUS_IGNORE);
for(i=0;i<mpi_stride;i++) {
if(mpi_comm_buffer[i] <= epsilon) {
nb.members[nb.n_members++] =
mpi_stride+mpi_stride_rest+(j-1)*mpi_stride+i;
}
}
}
free(mpi_comm_buffer);
return(nb);
}
#elif defined(_SCAN_SMITH_WATERMAN_GPU)
static inline neighbors region_query(int point, float epsilon, dataset ds,
opencl_stuff ocl) {
int i,j,k;
neighbors nb;
cl_int err;
size_t pointer_offset = 0;
size_t acc_distance_size;
nb.members=(int*)malloc(sizeof(int)*ds.n_values);
for(i=0;i<ocl.num_devs;i++) {
if (i == 0) {
acc_distance_size = ds.n_values/ocl.num_devs + ds.n_values%ocl.num_devs;
} else {
acc_distance_size = ds.n_values/ocl.num_devs;
}
err = clSetKernelArg(ocl.kernel[i],4,sizeof(int),&point);
err = clSetKernelArg(ocl.kernel[i],5,sizeof(int),&pointer_offset);
err = clEnqueueNDRangeKernel(ocl.cmdq[i],ocl.kernel[i],1,
NULL,
&acc_distance_size,
NULL,
0,NULL,NULL);
err = clEnqueueReadBuffer(ocl.cmdq[i], ocl.acc_distances[i],
CL_FALSE, 0,
acc_distance_size*sizeof(int),
ocl.local_distances+pointer_offset,
0,NULL,NULL);
pointer_offset+=acc_distance_size;
}
for(i=0;i<ocl.num_devs;i++) {
clFinish(ocl.cmdq[i]);
}
nb.n_members = 0;
for(i =0;i<ds.n_values;i++) {
if(ocl.local_distances[i] <= epsilon) {
nb.members[nb.n_members++] = i;
}
}
return(nb);
}
#elif defined(_SCAN_SMITH_WATERMAN)
static inline neighbors region_query(int point, float epsilon, dataset ds) {
int i,j,k;
neighbors nb;
float* a_point;
float* b_point;
float distance;
float a_minus_b;
int* work;
nb.members = (int*)malloc(sizeof(int)*ds.n_values);
nb.n_members = 0;
work =
(int*)malloc(sizeof(int)
*(ds.max_sequence_length+1)*(ds.max_sequence_length+1));
for(i=0;i<ds.n_values;i++) {
distance = (float)score(ds.sequences[i],ds.sequences[point],
ds.sequence_lengths[i],ds.sequence_lengths[point],
work);
if(distance <= epsilon) {
nb.members[nb.n_members]=i;
nb.n_members++;
}
}
/* nb.members = (int*)realloc((void*)nb.members,sizeof(int)*nb.n_members); */
free(work);
return(nb);
}
#elif defined(_SCAN_L2) || defined(_SCAN_L1)
#if defined(_SCAN_L1)
static int abs_sign_i = 0x7fffffff;
#endif
static inline neighbors region_query(int point, float epsilon, dataset ds) {
int i,j,k;
neighbors nb;
float* a_point;
float* b_point;
float epsilon_square = epsilon*epsilon;
float distance;
float a_minus_b;
a_point = (float*)malloc(sizeof(float)*ds.n_dimensions);
b_point = (float*)malloc(sizeof(float)*ds.n_dimensions);
#if defined(__AVX__)
__m256* point_v;
__m256 current_v;
__m256 a_minus_b_v;
__m256 dist_squared;
__m256 cmp_v;
int i_eight;
float result[8] __attribute__((aligned(32)));
int end;
#if defined(_SCAN_L1)
__m256 abs_sign;
float* abs_sign_f = (float*)&abs_sign_i;
abs_sign = _mm256_set1_ps(abs_sign_f[0]);
#endif
posix_memalign((void**)&point_v,32,32*ds.n_dimensions);
#elif defined(__SSE__)
__m128* point_v;
__m128 current_v;
__m128 a_minus_b_v;
__m128 dist_squared;
__m128 cmp_v;
int i_four;
float result[4] __attribute__((aligned(16)));
int end;
#if defined(_SCAN_L1)
__m128 abs_sign;
float* abs_sign_f = (float*)&abs_sign_i;
abs_sign = _mm_set1_ps(abs_sign_f[0]);
#endif
posix_memalign((void**)&point_v,16,16*ds.n_dimensions);
#endif
nb.members = (int*)malloc(sizeof(int)*ds.n_values);
nb.n_members = 0;
#if defined(__AVX__)
for(k = 0;k < ds.n_dimensions; k++) {
point_v[k] = _mm256_set1_ps(ds.values[k][point]);
}
for(i=0;i<ds.n_values/8+(ds.n_values%8 != 0);i++) {
i_eight = i*8;
dist_squared = _mm256_setzero_ps();
for(k = 0; k < ds.n_dimensions; k++) {
current_v = _mm256_load_ps(ds.values[k]+i_eight);
a_minus_b_v = _mm256_sub_ps(point_v[k], current_v);
#if defined(_SCAN_L2)
#ifdef __FMA__
dist_squared = _mm256_fmadd_ps(a_minus_b_v,
a_minus_b_v,
dist_squared);
#else
dist_squared = _mm256_add_ps(_mm256_mul_ps(a_minus_b_v,
a_minus_b_v),
dist_squared);
#endif
#elif defined(_SCAN_L1)
dist_squared = _mm256_add_ps(_mm256_and_ps(a_minus_b_v,
abs_sign),
dist_squared);
#endif
}
_mm256_store_ps(result,dist_squared);
if (__builtin_expect(i != ds.n_values/8,1)) {
end = 8;
} else {
end = ds.n_values%8;
}
for(j=0;j<end;j++) {
if (
#if defined(_SCAN_L2)
result[j] <= epsilon_square
#elif defined(_SCAN_L1)
result[j] <= epsilon
#endif
) {
nb.members[nb.n_members]=i_eight+j;
nb.n_members++;
}
}
}
#elif defined(__SSE__)
for(k = 0; k < ds.n_dimensions; k++) {
point_v[k] = _mm_set1_ps(ds.values[k][point]);
}
for(i=0;i<ds.n_values/4+(ds.n_values%4 != 0);i++) {
i_four = i*4;
dist_squared = _mm_setzero_ps();
for(k = 0; k < ds.n_dimensions; k ++) {
current_v = _mm_load_ps(ds.values[k]+i_four);
a_minus_b_v = _mm_sub_ps(point_v[k],current_v);
#if defined(_SCAN_L2)
dist_squared = _mm_add_ps(_mm_mul_ps(a_minus_b_v,a_minus_b_v),
dist_squared);
#elif defined(_SCAN_L1)
dist_squared = _mm_add_ps(_mm_and_ps(a_minus_b_v,
abs_sign),
dist_squared);
#endif
}
_mm_store_ps(result,dist_squared);
if (__builtin_expect(i != ds.n_values/4,1)) {
end = 4;
} else {
end = ds.n_values%4;
}
for(j=0;j<end;j++) {
if(
#if defined (_SCAN_L2)
result[j] <= epsilon_square
#elif defined (_SCAN_L1)
result[j] <= epsilon
#endif
) {
nb.members[nb.n_members]=i_four+j;
nb.n_members++;
}
}
}
#else
for(k = 0; k< ds.n_dimensions; k++) {
a_point[k] = ds.values[k][point];
}
nb.n_members = 0;
for(i=0;i<ds.n_values;i++) {
for(k = 0; k < ds.n_dimensions; k++) {
b_point[k] = ds.values[k][i];
}
distance = 0;
for(j=0;j< ds.n_dimensions;j++) {
a_minus_b=(a_point[j]-b_point[j]);
#if defined (_SCAN_L2)
distance += a_minus_b*a_minus_b;
#elif defined (_SCAN_L1)
distance += fabsf(a_minus_b);
#endif
}
if(
#if defined (_SCAN_L2)
distance <= epsilon_square
#elif defined(_SCAN_L1)
distance <= epsilon
#endif
) {
nb.members[nb.n_members]=i;
nb.n_members++;
}
}
#endif
#if defined(__AVX__) || defined (__SSE__)
free(point_v);
#endif
free(a_point);
free(b_point);
/* nb.members = (int*)realloc((void*)nb.members,sizeof(int)*nb.n_members); */
//qsort(nb.members,nb.n_members,sizeof(int),compare);
return(nb);
}
#endif
static inline void expand_cluster(int point,
neighbors nb,
cluster* cl,
float epsilon,
int minpts,
char* visited,
int* cluster_member,
#if defined (_SCAN_SMITH_WATERMAN_GPU)
dataset ds,
opencl_stuff ocl
#elif defined (_SCAN_SMITH_WATERMAN_MPI_GPU)
int mpi_rank, int mpi_size,
dataset ds,
opencl_stuff ocl
#else
dataset ds
#endif
) {
int i,j;
neighbors nb_of_nb;
int * merge;
int * right_in_left;
int n_right_in_left;
int merge_counter;
int current_point;
int add_to_unsorted_counter;
int right_in_left_counter;
int max_members_nb_nb_of_nb;
int left;
int right;
int n_left;
int n_right;
neighbors nb_unsorted;
nb_unsorted.members = (int*)malloc(sizeof(int)*ds.n_values);
memset(nb_unsorted.members,0,sizeof(int)*ds.n_values);
merge = (int*)malloc(ds.n_values*sizeof(int));
memcpy(nb_unsorted.members,nb.members,sizeof(int)*nb.n_members);
nb_unsorted.n_members = nb.n_members;
cl->members = (int*)malloc(sizeof(int)*ds.n_values);
cl->members[cl->n_members] = point;
cluster_member[point] = 1;
cl->n_members++;
for(i=0;i < nb_unsorted.n_members;i++) {
if(!get_value_in_binary_array_at_index(visited,
(size_t)nb_unsorted.members[i])) {
set_value_in_binary_array_at_index(visited,
(size_t)nb_unsorted.members[i]);
#if defined (_SCAN_SMITH_WATERMAN_GPU)
nb_of_nb = region_query(nb_unsorted.members[i], epsilon, ds, ocl);
#elif defined (_SCAN_SMITH_WATERMAN_MPI_GPU)
nb_of_nb = region_query(nb_unsorted.members[i], epsilon, ds, ocl,
mpi_rank, mpi_size);
#else
nb_of_nb = region_query(nb_unsorted.members[i], epsilon, ds);
#endif
if (nb_of_nb.n_members >= minpts) {
/*merge = (int*)malloc((nb.n_members+nb_of_nb.n_members)
*sizeof(int));*/
right_in_left = (int*)malloc(nb_of_nb.n_members*sizeof(int));
n_left = n_right = merge_counter = 0;
n_right_in_left = 0;
while(n_left < nb.n_members && n_right < nb_of_nb.n_members) {
left = nb.members[n_left];
right = nb_of_nb.members[n_right];
if( left < right ) {
merge[merge_counter] = left;
merge_counter++;
n_left++;
}
if( right < left ) {
merge[merge_counter] = right;
merge_counter++;
n_right++;
}
if( right == left ) {
merge[merge_counter] = left;
n_left++;
n_right++;
merge_counter++;
right_in_left[n_right_in_left] = left;
n_right_in_left++;
}
}
if(n_left != nb.n_members || n_right != nb_of_nb.n_members) {
if(n_left == nb.n_members) { /* Hit the left wall */
for(j=n_right;j<nb_of_nb.n_members;j++) {
merge[merge_counter] = nb_of_nb.members[j];
merge_counter++;
}
}
if(n_right == nb_of_nb.n_members) { /*Hit the right wall */
for(j=n_left;j<nb.n_members;j++) {
merge[merge_counter] = nb.members[j];
merge_counter++;
}
}
}
/* nb_unsorted.members = (int*)realloc((void*)nb_unsorted.members,
merge_counter*sizeof(int));*/
add_to_unsorted_counter = 0;
right_in_left_counter = 0;
/* if there are rights in left */
if (n_right_in_left) {
for(j=0;j<nb_of_nb.n_members;j++) {
if(right_in_left[right_in_left_counter] != nb_of_nb.members[j]) {
nb_unsorted.members[nb_unsorted.n_members
+add_to_unsorted_counter] =
nb_of_nb.members[j];
add_to_unsorted_counter++;
} else {
right_in_left_counter++;
}
}
/* if there are no rights in left */
} else {
for(j=0;j<nb_of_nb.n_members;j++) {
nb_unsorted.members[nb_unsorted.n_members+j] = nb_of_nb.members[j];
}
}
free(right_in_left);
free(nb_of_nb.members);
nb_unsorted.n_members = merge_counter;
/*merge = (int*)realloc((void*)merge,merge_counter*sizeof(int));*/
memcpy(nb.members,merge,sizeof(int)*merge_counter);
//nb.members = merge;
nb.n_members = merge_counter;
/*
nb.members = (int*)realloc((void*)nb.members,
merge_counter*sizeof(int));
*/
} else {
free(nb_of_nb.members);
}
}
if(!cluster_member[nb_unsorted.members[i]]) {
/* cl->members = (int*)realloc((void*)(cl->members)
,sizeof(int)*(cl->n_members+1));*/
cl->members[cl->n_members] = nb_unsorted.members[i];
cl->n_members++;
cluster_member[nb_unsorted.members[i]] = 1;
}
}
cl->members=(int*)realloc((void*)(cl->members),sizeof(int)*(cl->n_members));
free(nb_unsorted.members);
free(nb.members);
free(merge);
}
split_set
#if defined (_SCAN_L1)
dbscan_L1
#elif defined (_SCAN_L2)
dbscan_L2
#elif defined (_SCAN_SMITH_WATERMAN)
dbscan_SW
#elif defined (_SCAN_SMITH_WATERMAN_GPU)
dbscan_SW_GPU
#elif defined (_SCAN_SMITH_WATERMAN_MPI_GPU)
dbscan_SW_GPU_MPI
#endif
#if defined (_SCAN_SMITH_WATERMAN_GPU)
(dataset ds, float epsilon, int minpts, opencl_stuff ocl)
#elif defined (_SCAN_SMITH_WATERMAN_MPI_GPU)
(dataset ds, float epsilon, int minpts, opencl_stuff ocl, int mpi_rank,
int mpi_size)
#else
(dataset ds, float epsilon, int minpts)
#endif
{
int i;
neighbors nb;
split_set ret_val;
cluster* clusters = (cluster*)malloc(sizeof(cluster)*ds.n_values);
char* visited = alloc_and_set_zero_binary_array(ds.n_values);
int n_clusters = 0;
int* cluster_member = (int*)malloc(sizeof(int)*ds.n_values);
if (epsilon == -1) {
printf("Warning @dbscan: epsilon value is: %f\n", epsilon);
epsilon = 0.015;
printf("Warning @dbscan: epsilon was changed to: %f\n", epsilon);
}
if (minpts == -1) {
printf("Warning @dbscan: minpts value is: %i\n", minpts);
minpts = 5;
printf("Warning @dbscan: minpts was changed to: %i\n", minpts);
}
ret_val.clusters = (cluster*)malloc(sizeof(cluster)*ds.n_values);
memset(cluster_member,0,sizeof(int)*ds.n_values);
for(i=0;i<ds.n_values;i++) {
// clusters[i].members = NULL;
clusters[i].n_members = 0;
clusters[i].id = i;
}