[英]should I launch multiple threads if my CPU load suggests otherwise?
I'm making a program in C++ which counts NGS read alignments against a reference annotation. 我正在用C ++编写一个程序,该程序根据参考注释对NGS读取的对齐方式进行计数。 Basically the program reads both the annotation and alignment file into memory, iterates through the annotation, binary searches the alignment file for a probable location, upon finding this location linear searches a frame that is around that probable location.
基本上,程序将注解和对齐文件都读到内存中,遍历注解,对对齐文件进行二进制搜索以查找可能的位置,找到该位置后,线性搜索围绕该可能位置的框架。
Typically I want to keep this frame somewhat large (10000 alignments), so I had the idea to split the frame up and throw parts of it into separate threads. 通常,我想将此框架保持较大(10000个对齐),因此我想到了将框架拆分并将其部分丢入单独线程的想法。
Everything compiles and runs, but it doesn't look like my multithreading is working as intended because my comp is using one core for the job. 一切都可以编译并运行,但是看起来我的多线程没有按预期工作,因为我的comp正在使用一个内核来完成工作。 Would anyone be kind enough to help me figure this out where I implemented the threading wrong.
有人会友好地帮助我弄清楚我在哪里实施了线程错误。
https://sourceforge.net/projects/fast-count/?source=directory https://sourceforge.net/projects/fast-count/?source=directory
#include <iostream>
#include <cstdlib>
#include <vector>
#include <string>
#include <thread>
#include <sstream>
#include <fstream>
#include <math.h>
#include "api/BamReader.h"
using namespace std;
using namespace BamTools;
int hit_count = 0;
struct bam_headers{
string chr;
int start;
};
struct thread_data{
int thread_id;
int total_thread;
int start_gtf;
int stop_gtf;
};
struct gtf_headers{
string chr;
string source;
string feature;
string score;
string strand;
string frame;
string annotation;
int start;
int end;
};
void process(int* start_holder, int size, int gtf_start, int gtf_stop){
//threaded counter process
for (int t = 0; t < size; t++){
if((start_holder[t] >= gtf_start) && (start_holder[t] <= gtf_stop)){
hit_count++;
}
}
}
vector <string> find_index(vector <vector <bam_headers> > bams){
//define vector for bam_index to chromosome
vector <string> compute_holder;
for (int bam_idx = 0; bam_idx < bams.size();bam_idx++){
compute_holder.push_back(bams[bam_idx][0].chr);
}
return compute_holder;
}
vector <gtf_headers> load_gtf(char* filename){
//define matrix to memory holding gtf annotations by assoc. header
vector<gtf_headers> push_matrix;
gtf_headers holder;
ifstream gtf_file(filename);
string line;
cout << "Loading GTF to memory" << "\n";
if (gtf_file.is_open()){
int sub_count = 0;
string transfer_hold[8];
while(getline(gtf_file,line)){
//iterate through file
istringstream iss(line);
string token;
//iterate through line, and tokenize by tab delimitor
while(getline(iss,token,'\t')){
if (sub_count == 8){
//assign to hold struct, and push to vector
holder.chr = transfer_hold[0];
holder.source = transfer_hold[1];
holder.feature = transfer_hold[2];
holder.start = atoi(transfer_hold[3].c_str());
holder.end = atoi(transfer_hold[4].c_str());
holder.score = transfer_hold[5];
holder.strand = transfer_hold[6];
holder.frame = transfer_hold[7];
holder.annotation = token;
push_matrix.push_back(holder);
sub_count = 0;
} else {
//temporarily hold tokens
transfer_hold[sub_count] = token;
++sub_count;
}
}
}
cout << "GTF successfully loaded to memory" << "\n";
gtf_file.close();
return(push_matrix);
}else{
cout << "GTF unsuccessfully loaded to memory. Check path to file, and annotation format. Exiting" << "\n";
exit(-1);
}
}
vector <vector <bam_headers>> load_bam(char* filename){
//parse individual bam file to chromosome bins
vector <vector <bam_headers> > push_matrix;
vector <bam_headers> iter_chr;
int iter_refid = -1;
bam_headers bam_holder;
BamReader reader;
BamAlignment al;
const vector<RefData>& references = reader.GetReferenceData();
cout << "Loading " << filename << " to memory" << "\n";
if (reader.Open(filename)) {
while (reader.GetNextAlignmentCore(al)) {
if (al.IsMapped()){
//bam file must be sorted by chr. otherwise the lookup will segfault
if(al.RefID != iter_refid){
//check if chr. position has advanced in the bam file, if true, push empty vector
iter_refid++;
push_matrix.push_back(iter_chr);
}else{
//if chr. position hasn't advanced push to current index in 2d vector
bam_holder.chr = references[al.RefID].RefName;
bam_holder.start = al.Position;
push_matrix.at(iter_refid).push_back(bam_holder);
}
}
}
reader.Close();
cout << "Successfully loaded " << filename << " to memory" << "\n";
return(push_matrix);
}else{
cout << "Could not open input BAM file. Exiting." << endl;
exit(-1);
}
}
short int find_bin(const string & gtf_chr, const vector <string> mapping){
//determines which chr. bin the gtf line is associated with
int bin_compare = -1;
for (int i = 0; i < mapping.size(); i++){
if(gtf_chr == mapping[i]){
bin_compare = i;
}
}
return(bin_compare);
}
int find_frame(gtf_headers gtf_matrix, vector <bam_headers> bam_file_bin){
//binary search to find alignment index with greater and less than gtf position
int bin_size = bam_file_bin.size();
int high_end = bin_size;
int low_end = 0;
int binary_i = bin_size / 2;
int repeat = 0;
int frame_start;
bool found = false;
while (found != true){
if ((bam_file_bin[binary_i].start >= gtf_matrix.start) && (bam_file_bin[binary_i].start <= gtf_matrix.end)){
frame_start = binary_i;
found = true;
}else{
if(repeat != binary_i){
if(bam_file_bin[binary_i].start > gtf_matrix.end){
if(repeat != binary_i){
repeat = binary_i;
high_end = binary_i;
binary_i = ((high_end - low_end) / 2) + low_end;
}
}else{
if(repeat != binary_i){
repeat = binary_i;
low_end = binary_i;
binary_i = ((high_end - low_end) / 2) + low_end;
}
}
}else{
frame_start = low_end;
found = true;
}
}
}
return(frame_start);
}
vector <int > define_frame(int frame_size, int frame_start, int bam_matrix){
//define the frame for the search
vector <int> push_ints;
push_ints.push_back(frame_start - (frame_size / 2));
push_ints.push_back(frame_start + (frame_size / 2));
if(push_ints[0] < 0){
push_ints[0] = 0;
push_ints[1] = frame_size;
if(push_ints[1] > bam_matrix){
push_ints[1] = frame_size;
}
}
if(push_ints[1] > bam_matrix){
push_ints[1] = bam_matrix;
push_ints[0] = bam_matrix - (frame_size / 2);
if(push_ints[0] < 0){
push_ints[0] = 0;
}
}
return(push_ints);
}
void thread_handler(int nthread, vector <int> frame, vector <bam_headers> bam_matrix, gtf_headers gtf_record){
int thread_divide = frame[1]-frame[0];//frame_size / nthread;
int thread_remain = (frame[1]-frame[0]) % nthread;
int* start_holder = new int[thread_divide];
for(int i = 0; i < nthread; i++){
if (i < nthread - 1){
for (int frame_index = 0; frame_index < thread_divide; frame_index++){
start_holder[frame_index] = bam_matrix[frame[0]+frame_index].start;
}
frame[0] = frame[0] + thread_divide;
thread first(process, start_holder,thread_divide,gtf_record.start,gtf_record.end);
first.join();
}else{
for (int frame_index = 0; frame_index < thread_divide + thread_remain; frame_index++){
start_holder[frame_index] = bam_matrix[frame[0]+frame_index].start;
}
thread last(process, start_holder,thread_divide + thread_remain,gtf_record.start,gtf_record.end);
last.join();
}
}
}
int main (int argc, char *argv[])
{
// usage
// ./count threads frame_size gtf_file files
//define matrix to memory holding gtf annotations by assoc. header
vector <gtf_headers> gtf_matrix = load_gtf(argv[3]);
//load bam, perform counts
for(int i = 4;i < argc;i++){
//iterate through filenames in argv, define matrix to memory holding bam alignments chr and bp position
vector <vector <bam_headers> > bam_matrix = load_bam(argv[i]);
//map chromosome to bam matrix index
vector <string> index_mapping = find_index(bam_matrix);
//iterate through gtf matrix, find corresponding bins for chr, set search frames, and count
for(int gtf_i = 0; gtf_i < gtf_i < gtf_matrix.size();gtf_i++){ //gtf_i < gtf_matrix.size()
hit_count = 0;
//find corresponding bins for gtf chr
short int bin_compare = find_bin(gtf_matrix[gtf_i].chr,index_mapping);
if(bin_compare != -1){
//find start of search frame
int frame_start = find_frame(gtf_matrix[gtf_i], bam_matrix[bin_compare]);
//get up lower bounds of search frame;
vector <int> full_frame = define_frame(atoi(argv[2]),frame_start,bam_matrix[bin_compare].size());
//create c array of bam positional data for the frame, and post to thread process
thread_handler(atoi(argv[1]),full_frame,bam_matrix[bin_compare],gtf_matrix[gtf_i]);
}
//counts displayed in STOUT
cout << gtf_matrix[gtf_i].chr << "\t" << gtf_matrix[gtf_i].source << "\t" << gtf_matrix[gtf_i].feature << "\t" << gtf_matrix[gtf_i].start << "\t" << gtf_matrix[gtf_i].end << "\t" << gtf_matrix[gtf_i].score << "\t" << gtf_matrix[gtf_i].strand << "\t" << gtf_matrix[gtf_i].frame << "\t" << gtf_matrix[gtf_i].annotation << "\t" << hit_count << "\n";
}
}
}
The answer to your question is very simple: 您问题的答案非常简单:
thread last(process, start_holder,thread_divide + thread_remain,gtf_record.start,gtf_record.end);
last.join();
Here, the parent task creates a new thread, and ... immediately waits for the thread to finish. 在这里,父任务创建了一个新线程,并且...立即等待线程完成。 That's what join() does, it waits for the thread to terminate.
这就是join()的作用,它等待线程终止。
So, your code starts a new thread, and immediately waits for it to finish, before doing anything else, like starting the next thread. 因此,您的代码将启动一个新线程,并立即等待其完成,然后再执行其他操作,例如启动下一个线程。
You need to rewrite thread_handler() to instantiate all std::thread
instances, and then after instantiating all of them, call join()
on each one, to wait for all of them to finish. 您需要重写thread_handler()以实例化所有
std::thread
实例,然后在实例化所有实例之后,对每个实例调用join()
,以等待它们完成。
The typical approach is to precreate a std::vector
of all thread instances, using std::thread
's default constructor, then loop over them to initialize each one, then loop over them again, calling join
() on each one. 典型的方法是使用
std::thread
的默认构造函数预创建所有线程实例的std::vector
,然后对其进行循环以初始化每个线程实例,然后再次对其进行循环,在每个实例上调用join
()。
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