void Genome::read ( std::ifstream& input ) {
log("Genome: reading file...");
unsigned int L(1); // line counter
LockFreeQueue<std::vector<std::string>> q;
auto readerTask = [&q,&input]() {
debug("Starting reader thread...");
for (std::string line; getline(input, line);) {
q.push(strsplit(line, "\t"));
}
q.done();
debug("All data read and tokenized, closing reader rhread");
};
auto parserTask = [&q,&L,this]() {
debug("Starting parser thread...");
std::vector<std::string> splits;
while(q.pop(splits)) {
assume(parseDataLine(splits), "Could not parse data in line " + std::to_string(L), false);
L++;
}
debug("All tokens processed, closing parser thread");
};
// read and parse header lines sequentially
for (std::string line; getline(input, line);) {
// std::cout << "Line #" << L << std::endl;
if (line[0] == '@') {
assume(parseHeaderLine(line), "Could not parse header in line " + std::to_string(L), false);
}
else {
break; // header lines parsed, break and begin threaded processing
}
L++;
}
// init and start threads
std::thread readerThread(readerTask);
std::thread parserThread(parserTask);
// wait for threads to finish
readerThread.join();
parserThread.join();
if (multistrand != nullptr) {
log("Found " + std::to_string(multistrand->size()) + " strand switching events");
}
if (circular != nullptr) {
log("Found " + std::to_string(circular->size()) + " circular transcripts");
}
}
void func2(void)
{
for(int i = 100000; i < 200000; i++)
{
queue.push_back(i);
}
}
void func1(void)
{
for(int i = 0; i <100000 ; i++)
{
queue.push_back(i);
}
}
void dequeue(LockFreeQueue<DummyEntry> &the_queue, std::list<DummyEntry*> &enqueued) {
DummyEntry* expected = enqueued.front(); enqueued.pop_front();
SCOPED_TRACE(testing::Message() << "expected=0x" << std::hex <<
reinterpret_cast<uintptr_t>(expected) << std::dec << ", key=" << expected->_key);
EXPECT_TRUE(contains(expected->_key, the_queue));
DummyEntry* ret = the_queue.dequeue();
EXPECT_EQ(expected->_key, ret->_key);
EXPECT_EQ(expected, ret);
EXPECT_FALSE(contains(expected->_key, the_queue));
EXPECT_TRUE(the_queue.unsafe_consistent());
check_size(enqueued.size(), the_queue);
the_queue.unsafe_dump(std::cout);
delete ret;
}
void enqueue(LockFreeQueue<DummyEntry> &the_queue, std::list<DummyEntry*> &enqueued,
uint32_t key) {
DummyEntry* entry = new DummyEntry(key);
SCOPED_TRACE(testing::Message() << "new pointer=0x" << std::hex <<
reinterpret_cast<uintptr_t>(entry) << std::dec << ", key=" << key);
enqueued.push_back(entry);
EXPECT_FALSE(contains(key, the_queue));
the_queue.enqueue(entry);
the_queue.unsafe_dump(std::cout);
EXPECT_TRUE(contains(key, the_queue));
EXPECT_TRUE(the_queue.unsafe_consistent());
check_size(enqueued.size(), the_queue);
the_queue.unsafe_dump(std::cout);
}
void func3(void)
{
for(int i = 0; i < 100004; i++)
{
std::cout<<queue.pop_front()<<" ";
}
std::cout<<std::endl;
}
bool contains(uint32_t key, LockFreeQueue<DummyEntry> &the_queue) {
std::vector<DummyEntry*> out;
the_queue.unsafe_as_vector(out);
for (size_t i = 0; i < out.size(); ++i) {
if (out[i]->_key == key) {
return true;
}
}
return false;
}
TEST(LockFreeQueue, PuthAndPop) {
LockFreeQueue<int, max_size> queue;
std::vector<int> result;
std::thread writer{[&queue]() {
for (auto i = 0; i < 10; ++i) {
queue.push(i);
}
queue.push(done);
}};
std::thread reader{[&queue, &result]() {
for (;;) {
while (queue.size() == 0) {
// busy wait
}
auto element = queue.front();
queue.pop();
if (element == done) {
break;
}
std::cout << "Got: " << element << '\n';
result.push_back(element);
}
}};
writer.join();
reader.join();
ASSERT_EQ(std::vector<int>({0, 1, 2, 3, 4, 5, 6, 7, 8, 9}), result);
}
NodeIterator(LockFreeQueue<T> &queue)
: mLastReturned(queue.fork()),
mCurrent(const_cast<Node*>(mLastReturned->mNext)),
mFreePool(&queue.mFreeNodePool) {
}
int main()
{
bool finished = false;
timestruct begin, end, *diff;
clock_gettime(CLOCK_MONOTONIC, &begin);
unsigned int count = 0;
LockFreeQueue<message> q;
omp_set_num_threads(4);
#pragma omp parallel shared(finished, count)
{
#pragma omp sections
{
#pragma omp section
{
for( unsigned int i = 0; i < 999999 ; ++i )
{
q.push(new message);
}
finished = true;
}
#pragma omp section
{
message* m;
while((m = q.pop()) != NULL || !finished )
{
if(m)
{
__sync_fetch_and_add(&count, 1);
delete m;
}
}
}
#pragma omp section
{
message* m = NULL;
while((m = q.pop()) != NULL || !finished )
{
if(m)
{
__sync_fetch_and_add(&count, 1);
delete m;
}
}
}
#pragma omp section
{
message* m = NULL;
while((m = q.pop()) != NULL || !finished )
{
if(m)
{
__sync_fetch_and_add(&count, 1);
delete m;
}
}
}
}
}
clock_gettime(CLOCK_MONOTONIC, &end);
diff = time_diff(&end, &begin);
std::cout << "=========================" << std::endl;
std::cout << "tv_sec: " << diff->tv_sec << std::endl << "tv_nsec: " << diff->tv_nsec << std::endl;
std::cout << "count: " << count << std::endl;
return 0;
}
void check_size(size_t expected, LockFreeQueue<DummyEntry> &the_queue) {
// at least in single-thread situation, all of them should be correct
EXPECT_EQ(expected, the_queue.unsafe_size());
EXPECT_EQ(expected, the_queue.safe_size());
EXPECT_EQ(expected, the_queue.approximate_size());
}
