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/* @file slow5threads.c
**
** @@
******************************************************************************/
#include <assert.h>
#include <math.h>
#include <pthread.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <slow5/slow5.h>
#include "../src/slow5_extra.h"
#define SLOW5_WORK_STEAL 1 //simple work stealing enabled or not (no work stealing mean no load balancing)
#define SLOW5_STEAL_THRESH 1 //stealing threshold
extern enum slow5_log_level_opt slow5_log_level;
extern enum slow5_exit_condition_opt slow5_exit_condition;
#define SLOW5_MALLOC_CHK_LAZY_EXIT(ret) { \
SLOW5_MALLOC_CHK(ret) \
if (ret == NULL) { \
exit(EXIT_FAILURE); \
} \
}
/* a batch of read data (dynamic data based on the reads) */
typedef struct {
int32_t n_rec;
int32_t capacity_rec;
char **mem_records; //unused in get()
size_t *mem_bytes;
slow5_rec_t **slow5_rec;
char **rid; //only used in get()
} slow5_db_t;
/* core data structure (mostly static data throughout the program lifetime) */
typedef struct {
//slow5
slow5_file_t *sf;
int num_thread;
int batch_size;
} slow5_core_t;
/* argument wrapper for the multithreaded framework used for data processing */
typedef struct {
slow5_core_t* core;
slow5_db_t* db;
int32_t starti;
int32_t endi;
void (*func)(slow5_core_t*,slow5_db_t*,int);
int32_t thread_index;
#ifdef SLOW5_WORK_STEAL
void *all_pthread_args;
#endif
} slow5_pt_arg_t;
/* initialise the core data structure */
static slow5_core_t* slow5_init_core(slow5_file_t *s5p, int batch_size, int num_thread) {
slow5_core_t* core = (slow5_core_t*)malloc(sizeof(slow5_core_t));
SLOW5_MALLOC_CHK_LAZY_EXIT(core);
core->sf = s5p;
core->batch_size = batch_size;
core->num_thread = num_thread;
return core;
}
/* free the core data structure */
static void slow5_free_core(slow5_core_t* core) {
free(core);
}
/* initialise a data batch */
static slow5_db_t* slow5_init_db(slow5_core_t* core) {
slow5_db_t* db = (slow5_db_t*)(malloc(sizeof(slow5_db_t)));
SLOW5_MALLOC_CHK_LAZY_EXIT(db);
db->capacity_rec = core->batch_size;
db->n_rec = 0;
db->mem_records = (char**)(calloc(db->capacity_rec,sizeof(char*)));
SLOW5_MALLOC_CHK_LAZY_EXIT(db->mem_records);
db->mem_bytes = (size_t*)(calloc(db->capacity_rec,sizeof(size_t)));
SLOW5_MALLOC_CHK_LAZY_EXIT(db->mem_bytes);
db->slow5_rec = (slow5_rec_t**)calloc(db->capacity_rec,sizeof(slow5_rec_t*));
SLOW5_MALLOC_CHK_LAZY_EXIT(db->slow5_rec);
return db;
}
/* load a data batch from disk */
static int slow5_load_db(slow5_core_t* core, slow5_db_t* db) {
db->n_rec = 0;
int32_t i = 0;
while (db->n_rec < db->capacity_rec) {
i=db->n_rec;
db->mem_records[i] = (char *)slow5_get_next_mem(&(db->mem_bytes[i]), core->sf);
if (db->mem_records[i] == NULL) {
if (slow5_errno != SLOW5_ERR_EOF) {
SLOW5_ERROR("Error reading from SLOW5 file %d\n", slow5_errno);
exit(EXIT_FAILURE);
}
else {
SLOW5_LOG_DEBUG("%s","Last Batch!\n");
break;
}
}
else {
db->n_rec++;
}
}
return db->n_rec;
}
static int slow5_write_db(slow5_core_t* core, slow5_db_t* db) {
int32_t i = 0;
for(i=0;i<db->n_rec;i++) {
size_t n = fwrite(db->mem_records[i], db->mem_bytes[i], 1, core->sf->fp);
if (n != 1) {
SLOW5_ERROR("Writing failed for read id %s!\n", db->slow5_rec[i]->read_id);
}
}
return i;
}
static void slow5_parse_single(slow5_core_t* core,slow5_db_t* db, int32_t i){
assert(db->mem_bytes[i]>0);
assert(db->mem_records[i]!=NULL);
int ret=slow5_rec_depress_parse(&db->mem_records[i], &db->mem_bytes[i], NULL, &db->slow5_rec[i], core->sf);
if(ret!=0){
SLOW5_ERROR("Error parsing the record %s",db->slow5_rec[i]->read_id);
exit(EXIT_FAILURE);
}
}
static void slow5_work_per_single_read(slow5_core_t* core,slow5_db_t* db, int32_t i){
slow5_parse_single(core,db,i);
}
static void slow5_work_per_single_read2(slow5_core_t* core,slow5_db_t* db, int32_t i){
assert(db->rid[i]!=NULL);
int ret = slow5_get(db->rid[i],&db->slow5_rec[i], core->sf);
if(ret<0){
SLOW5_ERROR("Error when fetching the read %s\n",db->rid[i]);
exit(EXIT_FAILURE);
}
db->mem_bytes[i]=ret;
}
static void slow5_work_per_single_read3(slow5_core_t* core,slow5_db_t* db, int32_t i){
assert(db->slow5_rec[i]!=NULL);
slow5_file_t *sf = core->sf;
//fprintf(stderr,"Here %d\n",i);
slow5_press_method_t press_out = {SLOW5_COMPRESS_ZLIB, SLOW5_COMPRESS_SVB_ZD};
slow5_press_t *press_ptr = slow5_press_init(press_out);
if(!press_ptr){
SLOW5_ERROR("Could not initialize the slow5 compression method%s","");
exit(EXIT_FAILURE);
}
db->mem_records[i] = slow5_rec_to_mem(db->slow5_rec[i], sf->header->aux_meta, sf->format, press_ptr, &(db->mem_bytes[i]));
//fprintf(stderr,"Here 2 %d\n",i);
slow5_press_free(press_ptr);
if(db->mem_records[i] == NULL){
SLOW5_ERROR("Error when converting the read %d to memory\n",i);
exit(EXIT_FAILURE);
}
}
/* partially free a data batch - only the read dependent allocations are freed */
static void slow5_free_db_tmp(slow5_db_t* db) {
int32_t i = 0;
for (i = 0; i < db->n_rec; ++i) {
free(db->mem_records[i]);
}
}
/* completely free a data batch */
static void slow5_free_db(slow5_db_t* db) {
free(db->mem_records);
free(db->mem_bytes);;
free(db);
}
static inline int32_t steal_work(slow5_pt_arg_t* all_args, int32_t num_thread) {
int32_t i, c_i = -1;
int32_t k;
for (i = 0; i < num_thread; ++i){
slow5_pt_arg_t args = all_args[i];
//fprintf(stderr,"endi : %d, starti : %d\n",args.endi,args.starti);
if (args.endi-args.starti > SLOW5_STEAL_THRESH) {
//fprintf(stderr,"gap : %d\n",args.endi-args.starti);
c_i = i;
break;
}
}
if(c_i<0){
return -1;
}
k = __sync_fetch_and_add(&(all_args[c_i].starti), 1);
//fprintf(stderr,"k : %d, end %d, start %d\n",k,all_args[c_i].endi,all_args[c_i].starti);
return k >= all_args[c_i].endi ? -1 : k;
}
static void* slow5_pthread_single(void* voidargs) {
int32_t i;
slow5_pt_arg_t* args = (slow5_pt_arg_t*)voidargs;
slow5_db_t* db = args->db;
slow5_core_t* core = args->core;
#ifndef SLOW5_WORK_STEAL
for (i = args->starti; i < args->endi; i++) {
args->func(core,db,i);
}
#else
slow5_pt_arg_t* all_args = (slow5_pt_arg_t*)(args->all_pthread_args);
//adapted from kthread.c in minimap2
for (;;) {
i = __sync_fetch_and_add(&args->starti, 1);
if (i >= args->endi) {
break;
}
args->func(core,db,i);
}
while ((i = steal_work(all_args,core->num_thread)) >= 0){
args->func(core,db,i);
}
#endif
//fprintf(stderr,"Thread %d done\n",(myargs->position)/THREADS);
pthread_exit(0);
}
static void slow5_pthread_db(slow5_core_t* core, slow5_db_t* db, void (*func)(slow5_core_t*,slow5_db_t*,int)){
//create threads
pthread_t tids[core->num_thread];
slow5_pt_arg_t pt_args[core->num_thread];
int32_t t, ret;
int32_t i = 0;
int32_t num_thread = core->num_thread;
int32_t step = (db->n_rec + num_thread - 1) / num_thread;
//todo : check for higher num of threads than the data
//current works but many threads are created despite
SLOW5_LOG_DEBUG("Creating %d threads\n",num_thread);
//set the data structures
for (t = 0; t < num_thread; t++) {
pt_args[t].core = core;
pt_args[t].db = db;
pt_args[t].starti = i;
i += step;
if (i > db->n_rec) {
pt_args[t].endi = db->n_rec;
} else {
pt_args[t].endi = i;
}
pt_args[t].func=func;
#ifdef SLOW5_WORK_STEAL
pt_args[t].all_pthread_args = (void *)pt_args;
#endif
//fprintf(stderr,"t%d : %d-%d\n",t,pt_args[t].starti,pt_args[t].endi);
}
//create threads
for(t = 0; t < core->num_thread; t++){
ret = pthread_create(&tids[t], NULL, slow5_pthread_single,
(void*)(&pt_args[t]));
if(ret < 0){
SLOW5_ERROR("Error creating thread %d\n",t);
exit(EXIT_FAILURE);
}
}
//pthread joining
for (t = 0; t < core->num_thread; t++) {
int ret = pthread_join(tids[t], NULL);
if(ret < 0){
SLOW5_ERROR("Error creating thread %d\n",t);
exit(EXIT_FAILURE);
}
}
}
/* process all reads in the given batch db */
static void slow5_work_db(slow5_core_t* core, slow5_db_t* db, void (*func)(slow5_core_t*,slow5_db_t*,int)){
if (core->num_thread == 1) {
int32_t i=0;
for (i = 0; i < db->n_rec; i++) {
func(core,db,i);
}
}
else {
slow5_pthread_db(core,db,func);
}
}
int slow5_get_batch(slow5_rec_t ***read, slow5_file_t *s5p, char **rid, int num_rid, int num_threads){
slow5_core_t *core = slow5_init_core(s5p,num_rid,num_threads);
slow5_db_t* db = slow5_init_db(core);
db->rid = rid;
db->n_rec = num_rid;
slow5_work_db(core,db,slow5_work_per_single_read2);
SLOW5_LOG_DEBUG("loaded and parsed %d recs\n",num_rid);
*read = db->slow5_rec;
slow5_free_db_tmp(db);
slow5_free_db(db);
slow5_free_core(core);
return num_rid;
}
int slow5_get_next_batch(slow5_rec_t ***read, slow5_file_t *s5p, int batch_size, int num_threads){
slow5_core_t *core = slow5_init_core(s5p,batch_size,num_threads);
slow5_db_t* db = slow5_init_db(core);
int num_read=slow5_load_db(core,db);
SLOW5_LOG_DEBUG("Loaded %d recs\n",num_read);
slow5_work_db(core,db,slow5_work_per_single_read);
SLOW5_LOG_DEBUG("Parsed %d recs\n",num_read);
*read = db->slow5_rec;
slow5_free_db_tmp(db);
slow5_free_db(db);
slow5_free_core(core);
return num_read;
}
int slow5_write_batch(slow5_rec_t **read, slow5_file_t *s5p, int batch_size, int num_threads){
slow5_core_t *core = slow5_init_core(s5p,batch_size,num_threads);
slow5_db_t* db = slow5_init_db(core);
db->n_rec = batch_size;
free(db->slow5_rec); //stupid lazy for now
db->slow5_rec = read;
slow5_work_db(core,db,slow5_work_per_single_read3);
SLOW5_LOG_DEBUG("Processed %d recs\n",batch_size);
int num_wr=slow5_write_db(core,db);
SLOW5_LOG_DEBUG("Written %d recs\n",num_wr);
db->slow5_rec = NULL;
slow5_free_db_tmp(db);
slow5_free_db(db);
slow5_free_core(core);
return num_wr;
}
void slow5_free_batch(slow5_rec_t ***read, int num_rec){
slow5_rec_t **reads = *read;
for(int i=0;i<num_rec;i++){
slow5_rec_free(reads[i]);
}
free(reads);
*read = NULL;
}
#ifdef PYSLOW5_DEBUG_THREAD
#define FILE_PATH "test.blow5" //for reading
#define FILE_PATH_WRITE "test.blow5"
//#define FILE_PATH "/home/jamfer/Data/SK/multi_fast5/s5/FAK40634_d1cc054609fe2c5fcdeac358864f9dc81c8bb793_95.blow5"
int read_func(){
slow5_file_t *sp = slow5_open(FILE_PATH,"r");
if(sp==NULL){
fprintf(stderr,"Error in opening file\n");
exit(EXIT_FAILURE);
}
slow5_rec_t **rec = NULL;
int ret=0;
int batch_size = 4096;
int num_thread = 8;
while((ret = slow5_get_next_batch(&rec,sp,batch_size,num_thread)) > 0){
for(int i=0;i<ret;i++){
uint64_t len_raw_signal = rec[i]->len_raw_signal;
printf("%s\t%ld\n",rec[i]->read_id,len_raw_signal);
}
slow5_free_batch(&rec,ret);
if(ret<batch_size){ //this indicates nothing left to read //need to handle errors
break;
}
}
slow5_close(sp);
//now random read fun
sp = slow5_open(FILE_PATH,"r");
if(sp==NULL){
fprintf(stderr,"Error in opening file\n");
exit(EXIT_FAILURE);
}
rec = NULL;
ret = slow5_idx_load(sp);
if(ret<0){
fprintf(stderr,"Error in loading index\n");
exit(EXIT_FAILURE);
}
int num_rid = 4;
num_thread = 2;
char *rid[num_rid];
rid[0]="read_id_50";
rid[1]="read_id_3999",
rid[2]="read_id_0";
rid[3]="read_id_4";
ret = slow5_get_batch(&rec, sp, rid, num_rid, num_thread);
assert(ret==num_rid);
for(int i=0;i<ret;i++){
uint64_t len_raw_signal = rec[i]->len_raw_signal;
printf("%s\t%ld\n",rec[i]->read_id,len_raw_signal);
}
slow5_free_batch(&rec,ret);
slow5_idx_unload(sp);
slow5_close(sp);
return 0;
}
int write_func(){
slow5_file_t *sf = slow5_open(FILE_PATH_WRITE,"w");
if(sf==NULL){
fprintf(stderr,"Error in opening file\n");
exit(EXIT_FAILURE);
}
/*********************** Header ******************/
slow5_hdr_t *header=sf->header;
//add a header group attribute called run_id
if (slow5_hdr_add_attr("run_id", header) != 0){
fprintf(stderr,"Error adding run_id attribute\n");
exit(EXIT_FAILURE);
}
//add another header group attribute called asic_id
if (slow5_hdr_add_attr("asic_id", header) != 0){
fprintf(stderr,"Error adding asic_id attribute\n");
exit(EXIT_FAILURE);
}
//set the run_id attribute to "run_0" for read group 0
if (slow5_hdr_set("run_id", "run_0", 0, header) != 0){
fprintf(stderr,"Error setting run_id attribute in read group 0\n");
exit(EXIT_FAILURE);
}
//set the asic_id attribute to "asic_0" for read group 1
if (slow5_hdr_set("asic_id", "asic_id_0", 0, header) != 0){
fprintf(stderr,"Error setting asic_id attribute in read group 0\n");
exit(EXIT_FAILURE);
}
//add auxilliary field: channel number
if (slow5_aux_add("channel_number", SLOW5_STRING, sf->header)!=0){
fprintf(stderr,"Error adding channel_number auxilliary field\n");
exit(EXIT_FAILURE);
}
//add axuilliary field: median_before
if (slow5_aux_add("median_before", SLOW5_DOUBLE, sf->header)!=0){
fprintf(stderr,"Error adding median_before auxilliary field\n");
exit(EXIT_FAILURE);
}
//add axuilliary field: read_number
if(slow5_aux_add("read_number", SLOW5_INT32_T, sf->header)!=0){
fprintf(stderr,"Error adding read_number auxilliary field\n");
exit(EXIT_FAILURE);
}
//add axuilliary field: start_mux
if(slow5_aux_add("start_mux", SLOW5_UINT8_T, sf->header)!=0){
fprintf(stderr,"Error adding start_mux auxilliary field\n");
exit(EXIT_FAILURE);
}
//add auxilliary field: start_time
if(slow5_aux_add("start_time", SLOW5_UINT64_T, sf->header)!=0){
fprintf(stderr,"Error adding start_time auxilliary field\n");
exit(EXIT_FAILURE);
}
if(slow5_hdr_write(sf) < 0){
fprintf(stderr,"Error writing header!\n");
exit(EXIT_FAILURE);
}
slow5_rec_t *rec[4000];
int ret=0;
int batch_size = 4000;
int num_thread = 8;
/******************* SLOW5 records ************************/
for(int i=0;i<batch_size;i++){
slow5_rec_t *slow5_record = rec[i] = slow5_rec_init();
if(slow5_record == NULL){
fprintf(stderr,"Could not allocate space for a slow5 record.");
exit(EXIT_FAILURE);
}
//primary fields
char tmp_read_id[100];
sprintf(tmp_read_id,"read_id_%d",i);
slow5_record -> read_id = strdup(tmp_read_id);
if(slow5_record->read_id == NULL){
fprintf(stderr,"Could not allocate space for strdup.");
exit(EXIT_FAILURE);
}
slow5_record -> read_id_len = strlen(slow5_record -> read_id);
slow5_record -> read_group = 0;
slow5_record -> digitisation = 4096.0;
slow5_record -> offset = 3.0+i;
slow5_record -> range = 10.0+i;
slow5_record -> sampling_rate = 4000.0;
slow5_record -> len_raw_signal = 10+i;
slow5_record -> raw_signal = malloc(sizeof(int16_t)*(10+i));
if(slow5_record->raw_signal == NULL){
fprintf(stderr,"Could not allocate space for raw signal.");
exit(EXIT_FAILURE);
}
for(int j=0;j<10+i;j++){
slow5_record->raw_signal[j] = j+i;
}
//auxiliary fileds
char *channel_number = "channel_number";
double median_before = 0.1+i;
int32_t read_number = 10+i;
uint8_t start_mux = (1+i)%4;
uint64_t start_time = 100+i;
if(slow5_aux_set_string(slow5_record, "channel_number", channel_number, sf->header)!=0){
fprintf(stderr,"Error setting channel_number auxilliary field\n");
exit(EXIT_FAILURE);
}
if(slow5_aux_set(slow5_record, "median_before", &median_before, sf->header)!=0){
fprintf(stderr,"Error setting median_before auxilliary field\n");
exit(EXIT_FAILURE);
}
if(slow5_aux_set(slow5_record, "read_number", &read_number, sf->header)!=0){
fprintf(stderr,"Error setting read_number auxilliary field\n");
exit(EXIT_FAILURE);
}
if(slow5_aux_set(slow5_record, "start_mux", &start_mux, sf->header)!=0){
fprintf(stderr,"Error setting start_mux auxilliary field\n");
exit(EXIT_FAILURE);
}
if(slow5_aux_set(slow5_record, "start_time", &start_time, sf->header)!=0){
fprintf(stderr,"Error setting start_time auxilliary field\n");
exit(EXIT_FAILURE);
}
}
//end of record setup
ret = slow5_write_batch(rec,sf,batch_size,num_thread);
if(ret<batch_size){
fprintf(stderr,"Writing failed\n");
exit(EXIT_FAILURE);
}
slow5_close(sf);
for(int i=0;i<batch_size;i++){
slow5_rec_free(rec[i]);
}
return 0;
}
int main(){
write_func();
read_func();
return 0;
}
//gcc -Wall python/slow5threads.c -I include/ lib/libslow5.a -lpthread -lz -DPYSLOW5_DEBUG_THREAD=1 -O2 -g
#endif
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