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/*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Bowtie 2 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef THREADING_H_
#define THREADING_H_
#include <iostream>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#ifdef WITH_TBB
# include <tbb/mutex.h>
# include <tbb/spin_mutex.h>
# include <tbb/queuing_mutex.h>
# ifdef WITH_AFFINITY
# include <sched.h>
# include <tbb/task_group.h>
# include <tbb/task_scheduler_observer.h>
# include <tbb/atomic.h>
# include <tbb/task_scheduler_init.h>
# endif
#else
# include "tinythread.h"
# include "fast_mutex.h"
#endif
#ifdef NO_SPINLOCK
# ifdef WITH_TBB
# ifdef WITH_QUEUELOCK
# define MUTEX_T tbb::queuing_mutex
# else
# define MUTEX_T tbb::mutex
# endif
# else
# define MUTEX_T tthread::mutex
# endif
#else
# ifdef WITH_TBB
# define MUTEX_T tbb::spin_mutex
# else
# define MUTEX_T tthread::fast_mutex
# endif
#endif /* NO_SPINLOCK */
/**
* Wrap a lock; obtain lock upon construction, release upon destruction.
*/
class ThreadSafe {
public:
ThreadSafe() : ptr_mutex(NULL) { }
ThreadSafe(MUTEX_T* ptr_mutex, bool locked = true) : ptr_mutex(NULL) {
if(locked) {
#if WITH_TBB && NO_SPINLOCK && WITH_QUEUELOCK
//have to use the heap as we can't copy
//the scoped lock
this->ptr_mutex = new MUTEX_T::scoped_lock(*ptr_mutex);
#else
this->ptr_mutex = ptr_mutex;
ptr_mutex->lock();
#endif
}
}
~ThreadSafe() {
if (ptr_mutex != NULL)
#if WITH_TBB && NO_SPINLOCK && WITH_QUEUELOCK
delete ptr_mutex;
#else
ptr_mutex->unlock();
#endif
}
private:
#if WITH_TBB && NO_SPINLOCK && WITH_QUEUELOCK
MUTEX_T::scoped_lock* ptr_mutex;
#else
MUTEX_T *ptr_mutex;
#endif
};
#ifdef WITH_TBB
#ifdef WITH_AFFINITY
//ripped entirely from;
//https://software.intel.com/en-us/blogs/2013/10/31/applying-intel-threading-building-blocks-observers-for-thread-affinity-on-intel
class concurrency_tracker: public tbb::task_scheduler_observer {
tbb::atomic<int> num_threads;
public:
concurrency_tracker() : num_threads() { observe(true); }
/*override*/ void on_scheduler_entry( bool ) { ++num_threads; }
/*override*/ void on_scheduler_exit( bool ) { --num_threads; }
int get_concurrency() { return num_threads; }
};
class pinning_observer: public tbb::task_scheduler_observer {
cpu_set_t *mask;
int ncpus;
const int pinning_step;
tbb::atomic<int> thread_index;
public:
pinning_observer( int pinning_step=1 ) : pinning_step(pinning_step), thread_index() {
for ( ncpus = sizeof(cpu_set_t)/CHAR_BIT; ncpus < 16*1024 /* some reasonable limit */; ncpus <<= 1 ) {
mask = CPU_ALLOC( ncpus );
if ( !mask ) break;
const size_t size = CPU_ALLOC_SIZE( ncpus );
CPU_ZERO_S( size, mask );
const int err = sched_getaffinity( 0, size, mask );
if ( !err ) break;
CPU_FREE( mask );
mask = NULL;
if ( errno != EINVAL ) break;
}
if ( !mask )
std::cout << "Warning: Failed to obtain process affinity mask. Thread affinitization is disabled." << std::endl;
}
/*override*/ void on_scheduler_entry( bool ) {
if ( !mask ) return;
const size_t size = CPU_ALLOC_SIZE( ncpus );
const int num_cpus = CPU_COUNT_S( size, mask );
int thr_idx =
//cwilks: we're one interface version lower than what
//is required for task arena (7000 vs. 7001)
#if USE_TASK_ARENA_CURRENT_SLOT
tbb::task_arena::current_slot();
#else
thread_index++;
#endif
#if __MIC__
thr_idx += 1; // To avoid logical thread zero for the master thread on Intel(R) Xeon Phi(tm)
#endif
thr_idx %= num_cpus; // To limit unique number in [0; num_cpus-1] range
// Place threads with specified step
int cpu_idx = 0;
for ( int i = 0, offset = 0; i<thr_idx; ++i ) {
cpu_idx += pinning_step;
if ( cpu_idx >= num_cpus )
cpu_idx = ++offset;
}
// Find index of 'cpu_idx'-th bit equal to 1
int mapped_idx = -1;
while ( cpu_idx >= 0 ) {
if ( CPU_ISSET_S( ++mapped_idx, size, mask ) )
--cpu_idx;
}
cpu_set_t *target_mask = CPU_ALLOC( ncpus );
CPU_ZERO_S( size, target_mask );
CPU_SET_S( mapped_idx, size, target_mask );
const int err = sched_setaffinity( 0, size, target_mask );
//std::cout << "Just set affinity for thread " << thr_idx << "\n";
if ( err ) {
std::cout << "Failed to set thread affinity!n";
exit( EXIT_FAILURE );
}
#if LOG_PINNING
else {
std::stringstream ss;
ss << "Set thread affinity: Thread " << thr_idx << ": CPU " << mapped_idx << std::endl;
std::cerr << ss.str();
}
#endif
CPU_FREE( target_mask );
}
~pinning_observer() {
if ( mask )
CPU_FREE( mask );
}
};
#endif
#endif
#endif
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