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/*
@copyright 2016-2021 Clarity Genomics BVBA
@copyright 2012-2016 Bonsai Bioinformatics Research Group
@copyright 2014-2016 Knight Lab, Department of Pediatrics, UCSD, La Jolla
@parblock
SortMeRNA - next-generation reads filter for metatranscriptomic or total RNA
This is a free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
SortMeRNA is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License
along with SortMeRNA. If not, see <http://www.gnu.org/licenses/>.
@endparblock
@contributors Jenya Kopylova jenya.kopylov@gmail.com
Laurent No laurent.noe@lifl.fr
Pierre Pericard pierre.pericard@lifl.fr
Daniel McDonald wasade@gmail.com
Mikal Salson mikael.salson@lifl.fr
Hlne Touzet helene.touzet@lifl.fr
Rob Knight robknight@ucsd.edu
*/
/**
* file: ThreadPool.hpp
* created: 20170810 Thu
*
* https://stackoverflow.com/questions/26516683/reusing-thread-in-loop-c
*/
#pragma once
#include <iostream>
#include <sstream>
#include <thread>
#include <mutex>
#include <condition_variable>
#include <queue>
#include <functional>
#include <chrono>
#include <atomic>
#include "common.hpp"
/**
* all the pool threads are initially in a waiting state until jobs are available for execution.
*/
class ThreadPool
{
protected:
std::mutex job_queue_mx; // lock for pop/push on jobs_
std::mutex job_done_mx; // lock for checking jobs_.empty and shutdown
std::condition_variable cv_jobs;
std::condition_variable cv_done;
std::atomic_bool shutdown_;
std::atomic_uint running_threads; // counter of running threads
std::vector <std::thread> threads_;
std::queue <std::function <void(void)>> jobs_;
public:
ThreadPool(int numThreads) : shutdown_(false), running_threads(0)
{
// Create the specified number of threads
threads_.reserve(numThreads);
for (int i = 0; i < numThreads; ++i) {
threads_.emplace_back(std::bind(&ThreadPool::threadEntry, this, i));
}
INFO("initialized Pool with [", numThreads, "] threads\n");
}
~ThreadPool()
{
{
// Unblock any threads and tell them to stop
std::lock_guard <std::mutex> lk(job_queue_mx);
shutdown_ = true;
cv_jobs.notify_all();
}
joinAll();
PRN_MEM("ThreadPool destructor done.");
}
protected:
void threadEntry(int i)
{
std::function<void(void)> job;
for (;;)
{
{
std::unique_lock<std::mutex> lk(job_queue_mx);
// Sleep until there is a job to execute or a shutdown flag set
while (!shutdown_.load() && jobs_.empty())
cv_jobs.wait(lk); // works
//cv_jobs.wait(lk, [this] { return !shutdown_.load() && jobs_.empty(); });
if (jobs_.empty()) // No jobs to do and shutting down
{
INFO("Thread ", std::this_thread::get_id(), " job done");
return;
}
job = std::move(jobs_.front());
jobs_.pop();
++running_threads;
}
// mutex 'job_queue_mx' released here
job(); // Do the job without holding any locks
--running_threads;
INFO("number of running_threads= ", running_threads.load(), " jobs queue is empty= ", jobs_.empty());
cv_done.notify_one(); // wake up the main thread waiting in 'waitAll'. Keep it here for multi-reference cases.
} // ~for
} // ~threadEntry
public:
/**
* lock the jobs queue and add a job
*/
void addJob(std::function <void()> func)
{
std::lock_guard<std::mutex> lk(job_queue_mx);
jobs_.emplace(std::move(func));
cv_jobs.notify_one();
}
// wait till no jobs running
void waitAll()
{
std::unique_lock<std::mutex> lk(job_done_mx);
cv_done.wait(lk, [this] { return running_threads.load() == 0 && jobs_.empty(); });
}
// Wait for all threads to stop
void joinAll()
{
for (auto& thread : threads_)
thread.join();
}
}; // ~class ThreadPool
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