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vecdb.c
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vecdb.c
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#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <fcntl.h>
#include <unistd.h>
#include <stddef.h>
#include <stdint.h>
#include <sys/mman.h>
#include <sys/stat.h>
#include <math.h> // doesn't need linking
#include <time.h>
#include "json.h"
const char *vecdb = "[\033[1m\x1b[31mv\x1b[32me\x1b[33mc\x1b[34md\x1b[35mb\x1b[0m]";
typedef float number_t;
typedef number_t* vector_t;
typedef struct { // main state type
char *path;
size_t dimensions;
size_t label_size;
// fixed memory allocation space
vector_t input_vector;
vector_t hot_vector;
char *io_buffer;
} state_t;
#define IO_BUFFER_SIZE (1024 * 1024)
#define get_vector_size(state) ((state)->dimensions * sizeof(number_t))
#define get_chunk_size(state) (get_vector_size((state)) + (state)->label_size)
/* io */
// read stdin into io_buffer
void *io_read_stdin(state_t *state) {
assert(fgets(state->io_buffer, IO_BUFFER_SIZE, stdin) != NULL);
}
// parse json from io_buffer and put it in input_vector
void io_parse_json_vector(
state_t *state
) {
struct json_value_s *json = json_parse(
state->io_buffer,
strlen(state->io_buffer)
);
struct json_array_s* array = json_value_as_array(json);
assert(array != NULL);
assert(array->length == state->dimensions);
size_t i = 0;
for(
struct json_array_element_s *element = array->start;
element->next != NULL;
element = element->next
) {
struct json_value_s *value = element->value;
assert(value->type == json_type_number);
struct json_number_s *number = json_value_as_number(value);
assert(number != NULL);
// convert character slice into null terminated c string
char number_str[1024];
assert(number->number_size < sizeof number_str - 1);
strncpy(number_str, number->number, number->number_size);
number_str[number->number_size] = '\0';
state->input_vector[i++] = atof(number_str);
}
}
// write out io_buffer to db file
void io_db_append_chunk(
state_t *state
) {
FILE *file = fopen(state->path, "a");
assert(file != NULL);
assert(
fwrite(
state->io_buffer,
1,
get_chunk_size(state),
file
) == get_chunk_size(state)
);
assert(fclose(file) == 0);
}
// turn vector + label into a serialized chunk
void io_serialize_chunk(state_t *state, char *label) {
// wipe io_buffer
memset(state->io_buffer, 0, get_chunk_size(state));
// copy vector data
memcpy(state->io_buffer, state->input_vector, get_vector_size(state));
// copy vector label
size_t label_len = (size_t) strlen(label);
assert(label_len < state->label_size - 1);
memcpy(state->io_buffer + get_vector_size(state), label, label_len);
}
typedef struct {
char *mapping;
size_t length; // length of database in chunks
} database_t;
// get read-only mapping of database file
database_t io_map_database(state_t *state) {
int fd = open(state->path, O_RDONLY);
assert(fd != -1);
struct stat sb;
assert(fstat(fd, &sb) != -1);
database_t database;
database.length = sb.st_size / get_chunk_size(state);
assert(sb.st_size % get_chunk_size(state) == 0);
database.mapping = mmap(NULL, sb.st_size, PROT_READ, MAP_SHARED, fd, 0);
assert(database.mapping != MAP_FAILED);
return database;
}
// get a pointer to the beginning of a chunk – the vector
static inline vector_t database_get_chunk(
state_t *state,
database_t *database,
size_t i
) {
return (vector_t) (
database->mapping +
(i * get_chunk_size(state))
);
}
// get a pointer to the second part of a chunk – the label
static inline vector_t database_get_chunk_label(
state_t *state,
database_t *database,
size_t i
) {
return (char *) (
database->mapping +
(i * get_chunk_size(state)) +
get_vector_size(state)
);
}
/* non-simd get_distance() */
float get_distance_basic(size_t dimensions, float *a, float *b) {
float sum = 0.0;
for (size_t i = 0; i < dimensions; i++) {
sum += (a[i] - b[i]) * (a[i] - b[i]);
}
return __builtin_sqrtf(sum);
}
#define VECDB_SIMD "generic"
#define get_distance get_distance_basic
/* arm neon 128-bit get_distance() */
#ifdef __ARM_NEON
#include <arm_neon.h>
float get_distance_arm_128(size_t dimensions, float *a, float *b) {
assert(dimensions % 4 == 0);
float sum = 0.0;
for (int i = 0; i < dimensions; i += 4) {
float32x4_t va = vld1q_f32(&a[i]);
float32x4_t vb = vld1q_f32(&b[i]);
// vc = va - vb
float32x4_t vc = vsubq_f32(va, vb);
// vc = vc * vc
vc = vmulq_f32(vc, vc);
// vd = sum(vc)
float32x2_t vd = vadd_f32(vget_low_f32(vc), vget_high_f32(vc));
vd = vpadd_f32(vd, vd);
sum += vget_lane_f32(vd, 0);
}
return __builtin_sqrtf(sum);
}
#define get_distance get_distance_arm_128
#define VECDB_SIMD "neon-128"
#endif
/* x86 avr 256-bit get_distance() */
#ifdef __AVX__
#include <immintrin.h>
static inline float get_distance_avx_256(size_t dimensions, float *a, float *b) {
assert(dimensions % 8 == 0); // AVX processes 8 floats at a time
__m256 sum_vec = _mm256_setzero_ps(); // Initialize sum vector to zero
for (size_t i = 0; i < dimensions; i += 8) {
__m256 va = _mm256_loadu_ps(&a[i]); // Load 8 floats from array a
__m256 vb = _mm256_loadu_ps(&b[i]); // Load 8 floats from array b
// vc = va - vb
__m256 vc = _mm256_sub_ps(va, vb);
// vc = vc * vc
vc = _mm256_mul_ps(vc, vc);
// Accumulate the sum of squares
sum_vec = _mm256_add_ps(sum_vec, vc);
}
// Sum the elements of sum_vec
__m128 vlow = _mm256_castps256_ps128(sum_vec);
__m128 vhigh = _mm256_extractf128_ps(sum_vec, 1);
vlow = _mm_add_ps(vlow, vhigh);
__m128 sum128 = _mm_hadd_ps(vlow, vlow);
sum128 = _mm_hadd_ps(sum128, sum128);
float sum = _mm_cvtss_f32(sum128);
return sqrtf(sum);
}
#undef get_distance
#define get_distance get_distance_avx_256
#undef VECDB_SIMD
#define VECDB_SIMD "avx-256"
#endif
/* commands */
void command_add(state_t *state, int argc, char *argv[]) {
io_read_stdin(state);
// read stdin into state->io_buffer
io_parse_json_vector(state);
// parse state->io_buffer as json into state->input_vector
char *label = argv[2];
printf("Writing vector '%s'...\n", label);
io_serialize_chunk( // turn state->input_vector into serialized state->io_buffer
state,
label
);
io_db_append_chunk( // state->io_buffer to file
state
);
}
void command_list(state_t *state, int argc, char *argv[]) {
database_t db = io_map_database(state);
for(size_t i = 0; i < db.length; i++) {
printf("%s\n", database_get_chunk_label(state, &db, i));
}
}
struct search_result_s {
number_t distance;
char *label;
};
/*
inline void search_insert_contender(
struct search_result_s *results,
size_t results_length,
struct search_result_s *contender
) {
if (contender->distance < results[results_length - 1].distance) {
// replace the worst result with the new result
results[results_length - 1] = *contender;
// Sort the results array to keep the lowest distances in order
for (
size_t j = results_length - 1;
j > 0 && results[j].distance < results[j - 1].distance;
j--
) {
// Swap the results
struct search_result_s temp = results[j];
results[j] = results[j - 1];
results[j - 1] = temp;
}
}
}
*/
static inline void search_insert_contender(
struct search_result_s *results,
size_t results_length,
struct search_result_s *contender
) {
// Only proceed if the contender is better than the worst result
if (contender->distance < results[results_length - 1].distance) {
// Perform a binary search to find the correct position for the new contender
size_t low = 0;
size_t high = results_length - 1;
while (low < high) {
size_t mid = (low + high) / 2;
if (results[mid].distance > contender->distance) {
high = mid;
} else {
low = mid + 1;
}
}
// Shift elements to the right to make room for the new contender
for (size_t j = results_length - 1; j > low; j--) {
results[j] = results[j - 1];
}
// Insert the new contender at the found position
results[low] = *contender;
}
}
#ifdef VECDB_USE_OPENMP
#include <omp.h>
#endif
void command_search(state_t *state, int argc, char*argv[]) {
io_read_stdin(state);
// read stdin into state->io_buffer
io_parse_json_vector(state);
// parse state->io_buffer as json into state->input_vector
database_t db = io_map_database(state);
const size_t results_length = 20;
struct search_result_s global_results[results_length];
// initialise results to infinity
for(size_t i = 0; i < results_length; i++) {
global_results[i].distance = INFINITY;
}
int start_time = clock();
#ifdef VECDB_USE_OPENMP
omp_set_num_threads(8);
#pragma omp parallel
#endif
{
// database_t db = io_map_database(state);
#ifdef VECDB_USE_OPENMP
int total_threads = omp_get_num_threads();
int thread_id = omp_get_thread_num();
#else
int total_threads = 1;
int thread_id = 1;
#endif
struct search_result_s local_results[results_length];
// initialise results to infinity
for(size_t i = 0; i < results_length; i++) {
local_results[i].distance = INFINITY;
}
for(size_t i = thread_id; i < db.length; i += total_threads) {
number_t hot_vector[state->dimensions];
// copy vector from database into the aligned space for comparison
memcpy(
hot_vector,
database_get_chunk(state, &db, i),
get_vector_size(state)
);
struct search_result_s contender;
contender.distance = get_distance(
state->dimensions,
state->input_vector,
hot_vector
);
contender.label = database_get_chunk_label(state, &db, i);
search_insert_contender(
local_results,
results_length,
&contender
);
if(i % 10000 == 0) {
double cpu_time_used = ((double) (clock() - start_time)) / CLOCKS_PER_SEC;
double mbs = ((i * get_vector_size(state)) / 1e+6) / cpu_time_used;
fprintf(stderr, "\r%s searching at \033[4m%.2f\033[0m MB/s", vecdb, mbs);
}
}
#ifdef VECDB_USE_OPENMP
#pragma omp critical
#endif
{
for(size_t i = 0; i < results_length; i++) {
search_insert_contender(
global_results,
results_length,
&local_results[i]
);
}
}
}
for(size_t i = 0; i < results_length; i++) {
if(global_results[i].label != NULL) {
printf("%s\n", global_results[i].label);
}
}
}
int main(int argc, char *argv[]) {
assert(sizeof(number_t) == 4); // better be fp32
// set state params
state_t state;
state.path = getenv("VECDB_PATH");
assert(state.path != NULL);
char *dimensions_string = getenv("VECDB_DIMENSIONS");
assert(state.path != NULL);
state.dimensions = strtoul(dimensions_string, 0, 10);
assert(state.dimensions > 0 && state.dimensions < UINT32_MAX);
char *label_size_string = getenv("VECDB_LABEL_SIZE");
assert(label_size_string != NULL);
state.label_size = strtoul(label_size_string, 0, 10);
assert(state.label_size > 0 && state.label_size < UINT32_MAX);
fprintf(stderr, "%s float type = fp%d\n", vecdb, sizeof(number_t) * 8);
fprintf(stderr, "%s simd = %s\n", vecdb, VECDB_SIMD);
fprintf(stderr, "%s state.path = '%s'\n", vecdb, state.path);
fprintf(stderr, "%s state.dimensions = '%d'\n", vecdb, state.dimensions);
fprintf(stderr, "%s state.label_size = '%d'\n", vecdb, state.label_size);
fprintf(stderr, "\n");
size_t total_allocation =
get_vector_size(&state) + // input vec
get_vector_size(&state) + // hot vec
IO_BUFFER_SIZE;
// allocate single fixed-size block of memory
char *memory = malloc(total_allocation);
assert(memory != NULL);
memset(memory, 0, total_allocation);
// slice up
state.input_vector = memory;
state.hot_vector = memory + get_vector_size(&state);
state.io_buffer = memory + get_vector_size(&state) + get_vector_size(&state);
if(strcmp(argv[1], "add") == 0) {
command_add(&state, argc, argv);
} else if(strcmp(argv[1], "list") == 0) {
command_list(&state, argc, argv);
} else if(strcmp(argv[1], "search") == 0) {
command_search(&state, argc, argv);
} else {
printf("Unknown subcommand '%s'!\n", argv[1]);
}
return 0;
}