Multithreaded concurrent file reading/writing, managing container of processes - c++

Wholly new to multithreading.
I am writing a program which takes as input a vector of objects and an integer for the number of threads to dedicate. The nature of the objects isn't important, only that each has several members that are file paths to large text files. Here's a simplified version:
// Not very important. Reads file, writes new version omitting
// some lines
void proc_file(OBJ obj) {
std::string inFileStr(obj.get_path().c_str());
std::string outFileStr(std::string(obj.get_path().replace_extension("new.txt").c_str()));
std::ifstream inFile(inFileStr);
std::ofstream outFile(outFileStr);
std::string currLine;
while (getline(inFile, currLine)) {
if (currLine.size() == 1 ||
currLine.compare(currLine.length()-5, 5, "thing") != 0) {
outFile << currLine << '\n';
}
else {
for (int i = 0; i < 3; i++) {
getline(inFile, currLine);
}
}
}
inFile.close();
outFile.close();
}
// Processes n file concurrently, working way through
// all OBJ in objs
void multi_file_proc(std::vector<OBJ> objs, int n) {
std::vector<std::thread> procVec;
for (int i = 0; i < objs.size(); i++) {
/*
Ensure that n files are always being processed.
Upon completion of one, initiate another, until
all OBJ in objs have had their text files changed.
*/
}
}
I want to loop through each OBJ and write altered versions of their text files in concurrence, the limitation on simultaneous file read/writes being the thread value (n). Ultimately, all the objects' text files must be changed, but in such a way that there are always n files being processed, to maximize efficiency in concurrence.
Note the vector of threads, procVec. I originally approached this by managing a vector of threads, with a file being processed for each thread in procVec. From my reading, it seems a vector for managing these tasks is logical. But how do I always ensure there are n files open until all have been processed, without exiting with an open thread?
Edit: Apologies, my intention was not to ask others to write code for me. I just didn't want my approach to bias anyone's answer if the approach was bad to begin with.
These are some things I've tried (this code would go into the block comment in my function):
1. First approach. Idea is to add to procVec up until the thread limit n was reached, then join, remove a process from the front of the vector upon its completion. This is a summary of several similar iterations, none of which worked:
if (i >= n) {
procVec.front().join();
procVec.erase(procVec.begin());
}
procVec.push_back(std::thread(proc_file, sra[i]));
Problems with this:
Incorrectly assumes front of vector will always finish first
(Possibly?) Invalidates all iterators in procVec after first is erased
2. Using mutexes, I attempt writing a lambda function where the thread would be removed upon its completion. This is my current approach. Unsure why it isn't working, or if it even suits my needs:
// remThread() and lamb() defined above main function, **procVec** and **threadMutex**
//are global variables
void remThread(std::thread::id id) {
std::lock_guard<std::mutex lock(threadMutex);
auto iter = std::find_if(procVec.begin(), procVec.end(), [=](std::thread &t)
{return (t.get_id() == id); });
if (iter != procVec.end()) {
iter->join();
procVec.erase(iter);
}
}
void lamb(SRA sra, std::thread::id id) {
proc_file(sra);
remThread(id);
}
// This is the code contained in the main for loop. called lambda to process file
// and then remove thread
std::lock_guard<std::mutex> lock(threadMutex);
procVec.push_back(std::thread([sras, i]() {
std::thread(lamb, sras[i], std::this_thread::get_id()).detach();
}));
Problems with this:
Program terminates, likely a joinable thread is active, leaves scope

Given that the example you show is fairly simple, a for loop of fixed size, no strange dependencies, a very simple solution could be to use OpenMP which would allow you to do what you describe (providing I understood correctly) by adding a single line
void multi_file_proc(std::vector<OBJ> objs, int n) {
std::vector<std::thread> procVec;
#pragma omp parallel for num_threads(n) schedule(dynamic, 1)
for (int i = 0; i < objs.size(); i++) {
/*
...
*/
}
}
in front of the for loop. Of course you then have to modify your compile command to add openmp support, the precise flag naturally being different from compiler to compiler i.e. -fopenmp for g++, -qopenmp for icpc, etc.
The line above basically instructs the compiler to create code to execute the for loop below in parallel. The important bit here is the last one where we set the schedule. Dynamic simply means that the order is not predetermined, instead threads will get their next iteration when they finish with the last. The integer 1 there defines the number of steps they take at a time, given that each file is large we want something fine grained since we don't expect too much overhead from the scheduling.
A word of caution, OpenMP, like most of C++, will not even try to stop you from shooting yourself in the foot. And with concurrency there are whole new ways to do just that.
Finally, this is by no means guaranteed to be the absolute best solution outright. For instance if your files are of varying lengths then you would probably want to sort the objects from longest to shortest before the loop. This way once the last object is being processed (at some point only a single thread will be working on the final object) that won't take too long.

Related

Why the following program does not mix the output when mutex is not used?

I have made multiple runs of the program. I do not see that the output is incorrect, even though I do not use the mutex. My goal is to demonstrate the need of a mutex. My thinking is that different threads with different "num" values will be mixed.
Is it because the objects are different?
using VecI = std::vector<int>;
class UseMutexInClassMethod {
mutex m;
public:
VecI compute(int num, VecI veci)
{
VecI v;
num = 2 * num -1;
for (auto &x:veci) {
v.emplace_back(pow(x,num));
std::this_thread::sleep_for(std::chrono::seconds(1));
}
return v;
}
};
void TestUseMutexInClassMethodUsingAsync()
{
const int nthreads = 5;
UseMutexInClassMethod useMutexInClassMethod;
VecI vec{ 1,2,3,4,5 };
std::vector<std::future<VecI>> futures(nthreads);
std::vector<VecI> outputs(nthreads);
for (decltype(futures)::size_type i = 0; i < nthreads; ++i) {
futures[i] = std::async(&UseMutexInClassMethod::compute,
&useMutexInClassMethod,
i,vec
);
}
for (decltype(futures)::size_type i = 0; i < nthreads; ++i) {
outputs[i] = futures[i].get();
for (auto& x : outputs[i])
cout << x << " ";
cout << endl;
}
}
If you want an example that does fail with a high degree of certainty you can look at the below. It sets up a variable called accumulator to be shared by reference to all the futures. This is what is missing in your example. You are not actually sharing any memory. Make sure you understand the difference between passing by reference and passing by value.
#include <vector>
#include <memory>
#include <thread>
#include <future>
#include <iostream>
#include <cmath>
#include <mutex>
struct UseMutex{
int compute(std::mutex & m, int & num)
{
for(size_t j = 0;j<1000;j++)
{
///////////////////////
// CRITICAL SECTIION //
///////////////////////
// this code currently doesn't trigger the exception
// because of the lock on the mutex. If you comment
// out the single line below then the exception *may*
// get called.
std::scoped_lock lock{m};
num++;
std::this_thread::sleep_for(std::chrono::nanoseconds(1));
num++;
if(num%2!=0)
throw std::runtime_error("bad things happened");
}
return 0;
}
};
template <typename T> struct F;
void TestUseMutexInClassMethodUsingAsync()
{
const int nthreads = 16;
int accumulator=0;
std::mutex m;
std::vector<UseMutex> vs{nthreads};
std::vector<std::future<int>> futures(nthreads);
for (auto i = 0; i < nthreads; ++i) {
futures[i]= std::async([&,i](){return vs[i].compute(m,accumulator);});
}
for(auto i = 0; i < nthreads; ++i){
futures[i].get();
}
}
int main(){
TestUseMutexInClassMethodUsingAsync();
}
You can comment / uncomment the line
std::scoped_lock lock{m};
which protects the increment of the shared variable num. The rule for this mini program is that at the line
if(num%2!=0)
throw std::runtime_error("bad things happened");
num should be a multiple of two. But as multiple threads are accessing this variable without a lock you can't guarantee this. However if you add a lock around the double increment and test then you can be sure no other thread is accessing this memory during the duration of the increment and test.
Failing
https://godbolt.org/z/sojcs1WK9
Passing
https://godbolt.org/z/sGdx3x3q3
Of course the failing one is not guaranteed to fail but I've set it up so that it has a high probability of failing.
Notes
[&,i](){return vs[i].compute(m,accumulator);};
is a lambda or inline function. The notation [&,i] means it captures everything by reference except i which it captures by value. This is important because i changes on each loop iteration and we want each future to get a unique value of i
Is it because the objects are different?
Yes.
Your code is actually perfectly thread safe, no need for mutex here. You never share any state between threads except for copying vec from TestUseMutexInClassMethodUsingAsync to compute by std::async (and copying is thread-safe) and moving computation result from compute's return value to futures[i].get()'s return value. .get() is also thread-safe: it blocks until the compute() method terminates and then returns its computation result.
It's actually nice to see that even a deliberate attempt to get a race condition failed :)
You probably have to fully redo your example to demonstrate is how simultaneous* access to a shared object breaks things. Get rid of std::async and std::future, use simple std::thread with capture-by-reference, remove sleep_for (so both threads do a lot of operations instead of one per second), significantly increase number of operations and you will get a visible race. It may look like a crash, though.
* - yes, I'm aware that "wall-clock simulateneous access" does not exist in multithreaded systems, strictly speaking. However, it helps getting a rough idea of where to look for visible race conditions for demonstration purposes.
Comments have called out the fact that just not protecting a critical section does not guarantee that the risked behavior actually occurs.
That also applies for multiple runs, because while you are not allowed to test a few times and then rely on the repeatedly observed behavior, it is likely that optimization mechanisms cause a likely enough reoccurring observation as to be perceived has reproducible.
If you intend to demonstrate the need for synchronization you need to employ synchronization to poise things to a near guaranteed misbehavior of observable lack of protection.
Allow me to only outline a sequence for that, with a few assumptions on scheduling mechanisms (this is based on a rather simple, single core, priority based scheduling environment I have encountered in an embedded environment I was using professionally), just to give an insight with a simplified example:
start a lower priority context.
optionally set up proper protection before entering the critical section
start critical section, e.g. by outputting the first half of to-be-continuous output
asynchronously trigger a higher priority context, which is doing that which can violate your critical section, e.g. outputs something which should not be in the middle of the two-part output of the critical section
(in protected case the other context is not executed, in spite of being higher priority)
(in unprotected case the other context is now executed, because of being higher priority)
end critical section, e.g. by outputting the second half of the to-be-continuous output
optionally remove the protection after leaving the critical section
(in protected case the other context is now executed, now that it is allowed)
(in unprotected case the other context was already executed)
Note:
I am using the term "critical section" with the meaning of a piece of code which is vulnerable to being interrupted/preempted/descheduled by another piece of code or another execution of the same code. Specifically for me a critical section can exist without applied protection, though that is not a good thing. I state this explicitly because I am aware of the term being used with the meaning "piece of code inside applied protection/synchronization". I disagree but I accept that the term is used differently and requires clarification in case of potential conflicts.

use std::thread and join for parallelism

I'm making a script that iterates through all chromosomes of a fasta file and splitting it into pieces of 10 bp, the function is called chrdata and i am saving these fragments into a single file. This fragmentation can occur on each chromosome individually completely separate for the other chromosomes, as such i'm trying threads.
chrdata(faidx_t *seq_ref ,int chr_no,FILE *fp)
My goal is wish to make this process faster. To achieve this i have tried multi-threading with the std::thread function.
I have tried different things.
First i tried to create a thread for the first chromosome and then thread.join() then the next thread for next chromosome and so on.
Then i tried to create multiple threads at once, like explained in Simultaneous Threads in C++ using <thread>
This is the example below.
However as far as I understand and that I can read, I always need to use join otherwise I'll end up with "terminate called without an active exception". The issue is there is no time execution difference between example (1) and (2).
Based on my understanding its becuase despite of creating a vector with thread object they still have to join and thus wait for all the threads to execute. This means this would be concurrent execution and not parallele.
So my question is: Would anyone be able to give me suggestions to the function below where i might change to make the execution faster by using parallele execution?
Or is my understanding of join and concurrent wrong in this instance? I'm not completely sure why we cannot just skip the whole join part, if all the threads are done, why cant we just use detach()?
void function(const char* fastafile,FILE *fp,int thread_no) {
std::vector<std::thread> threads;
//extracting the chromosome file
faidx_t *seq_ref = NULL;
seq_ref = fai_load(fastafile);
assert(seq_ref!=NULL);
int chr_total = 10; //just the first 10 chromosomes
int chr_idx = 0;
int chr_no = 0;
while(chr_idx < chr_total){
for (chr_no; chr_no < std::min(chr_idx+thread_no,chr_total);chr_no++){
threads.push_back(std::thread(chrdata,seq_ref,chr_no,fp));
}
for (auto &th : threads) { th.join(); }
threads.clear();
chr_idx = chr_idx + thread_no;
}
}
I havent attacked main() or chrdata() to make the code and question more clear.
pastebin.com/iY6u9CbH

List Iterator from STL library malfunctioning

The following is a snippet of a larger program and is done using Pthreads.
The UpdateFunction reads from a text file. The FunctionMap is just used to output (key,1). Here essentially UpdateFunction and FunctionMap run on different threads.
queue <list<string>::iterator> mapperpool;
void *UpdaterFunction(void* fn) {
std::string *x = static_cast<std::string*>(fn);
string filename = *x;
ifstream file (filename.c_str());
string word;
list <string> letterwords[50];
char alphabet = '0';
bool times = true;
int charno=0;
while(file >> word) {
if(times) {
alphabet = *(word.begin());
times = false;
}
if (alphabet != *(word.begin())) {
alphabet = *(word.begin());
mapperpool.push(letterwords[charno].begin());
letterwords[charno].push_back("xyzzyspoon");
charno++;
}
letterwords[charno].push_back(word);
}
file.close();
cout << "UPDATER DONE!!" << endl;
pthread_exit(NULL);
}
void *FunctionMap(void *i) {
long num = (long)i;
stringstream updaterword;
string toQ;
int charno = 0;
fprintf(stderr, "Print me %ld\n", num);
sleep(1);
while (!mapperpool.empty()) {
list<string>::iterator it = mapperpool.front();
while(*it != "xyzzyspoon") {
cout << "(" << *it << ",1)" << "\n";
cout << *it << "\n";
it++;
}
mapperpool.pop();
}
pthread_exit(NULL);
}
If I add the while(!mapperpool.empty()) in the UpdateFunction then it gives me the perfect output. But when I move it back to the FunctionMap then it gives me a weird out and Segfaults later.
Output when used in UpdateFunction:
Print me 0
course
cap
class
culture
class
cap
course
course
cap
culture
concurrency
.....
[Each word in separate line]
Output when used in FunctionMap (snippet shown above):
Print me 0
UPDATER DONE!!
(course%0+�0#+�0�+�05P+�0����cap%�+�0�+�0,�05�+�0����class5P?�0
����xyzzyspoon%�+�0�+�0(+�0%P,�0,�0�,�05+�0����class%p,�0�,�0-�05�,�0����cap%�,�0�,�0X-�05�,�0����course%-�0 -�0�-�050-�0����course%-�0p-�0�-�05�-�0����cap%�-�0�-�0H.�05�-�0����culture%.�0.�0�.�05 .�0
����concurrency%P.�0`.�0�.�05p.�0����course%�.�0�.�08/�05�.�0����cap%�.�0/�0�/�05/�0Segmentation fault (core dumped)
How do I fix this issue?
list <string> letterwords[50] is local to UpdaterFunction. When UpdaterFunction finishes, all its local variables got destroyed. When FunctionMap inspects iterator, that iterator already points to deleted memory.
When you insert while(!mapperpool.empty()) UpdaterFunction waits for FunctionMap completion and letterwords stays 'alive'.
Here essentially UpdateFunction and FunctionMap run on different threads.
And since they both manipulate the same object (mapperpool) and neither of them uses either pthread_mutex nor std::mutex (C++11), you have a data race. If you have a data race, you have Undefined Behaviour and the program might do whatever it wants. Most likely it will write garbage all over memory until eventually crashing, exactly as you see.
How do I fix this issue?
By locking the mapperpool object.
Why is list not thread-safe?
Well, in vast majority of use-cases, a single list (or any other collection) won't be used by more than one thread. In significant part of the rest the lock will have to extend over more than one operation on the collection, so the client will have to do its own locking anyway. The remaining tiny percentage of cases where locking in the operations themselves would help is not worth adding the overhead for everyone; C++ key design principle is that you only pay for what you use.
The collections are only reentrant, meaning that using different instances in parallel is safe.
Note on pthreads
C++11 introduced threading library that integrates well with the language. Most notably, it uses RAII for locking of std::mutex via std::lock_guard, std::unique_lock and std::shared_lock (for reader-writer locking). Consistently using these can eliminate large class of locking bugs that otherwise take considerable time to debug.
If you can't use C++11 yet (on desktop you can, but some embedded platforms did not get a compiler update yet), you should first consider Boost.Thread as it provides the same benefits.
If you can't use even then, still try to find, or write, a simple RAII wrapper for locking like the C++11/Boost do. The basic wrapper is just a couple of lines, but it will save you a lot of debugging.
Note that C++11 and Boost also have atomic operations library that pthreads sorely miss.

Multihreading recursive program c++

I am working on a recursive algorithm which we want to parallelize to improve the performance.
I implemented multithreading using Visual c++ 12.0 and < thread > library . However I dont see any performance improvements. The time taken either less by a few milliseconds or is more than the time with single thread.
Kindly let me know if am doing something wrong and what corrections should I make to the code.
Here is my code
void nonRecursiveFoo(<className> &data, int first, int last)
{
//process the data between first and last index and set its value to true based on some condition
//no threads are created here
}
void recursiveFoo(<className> &data, int first, int last)
{
int partitionIndex = -1;
data[first]=true;
data[last]=true;
for (int i = first + 1; i < last; i++)
{
//some logic setting the index
If ( some condition is true)
partitionIndex = i;
}
//no dependency of partitions on one another and so can be parallelized
if( partitionIndex != -1)
{
data[partitionIndex]=true;
//assume some threadlimit
if (Commons::GetCurrentThreadCount() < Commons::GetThreadLimit())
{
std::thread t1(recursiveFoo, std::ref(data), first, index);
Commons::IncrementCurrentThreadCount();
recursiveFoo(data, partitionIndex , last);
t1.join();
}
else
{
nonRecursiveFoo(data, first, partitionIndex );
nonRecursiveFoo(data, partitionIndex , last);
}
}
}
//main
int main()
{
recursiveFoo(data,0,data.size-1);
}
//commons
std::mutex threadCountMutex;
static void Commons::IncrementCurrentThreadCount()
{
threadCountMutex.lock();
CurrentThreadCount++;
threadCountMutex.unlock();
}
static int GetCurrentThreadCount()
{
return CurrentThreadCount;
}
static void SetThreadLimit(int count)
{
ThreadLimit = count;
}
static int GetThreadLimit()
{
return ThreadLimit;
}
static int GetMinPointsPerThread()
{
return MinimumPointsPerThread;
}
Without further information (see comments) this is mostly guesswork, but there are a few things you should watch out for:
First of all, make sure that your partitioning logic is very short and fast compared to the processing. Otherwise, you are just creating more work than you gain processing power.
Make sure, there is enough work to begin with or the speedup might be not enough to pay for the additional overhead of thread creation.
Check that your work gets evenly distributed among the different threads and don't spawn more threads than you have cores on your computer (print the number of total threads at the end - don't rely on your ThreadLimit).
Don't let your partitions get too small, (especially no less than 64 Bytes) or you end up with false sharing.
It would be MUCH more efficient, to implement CurrentThreadCount as a std::atomic<int> in which case you don't need a mutex.
Put the increment of the counter before the creation of the thread. Otherwise, the newly created thread might read the counter before it is incremented and spawn a new thread again, even if the max number of threads is already reached (This is still not a perfect solution, but I would only invest more time on this if you have verified, that overcommitting is your actual problem)
If you really must use a mutex (for reasons outside of the example code) you have to use it for every access to CurrentThreadCount (read and write access). Otherwise this is - strictly speaking - a race condition and thus UB.
By using t1.join you're basically waiting for the other thread to finish - i.e. not doing anything in parallel.
By looking at your algorithm I don't see how it can be parallelized(thus improved) by using threads - you have to wait for a single recursive call to end.
First of all, you are not doing anything in parallel, as every thread creation blocks, until the created thread has finished. Hence, your multithreaded code will always be slower than the non multithreaded version.
In order to parallelize you could spawn threads for that part, where the non-recursive function is called, put the thread ID into a vector and join on the highest level of the recursion, by walking through the vector. (Although there are more elegant ways to do that, but for a first should this would be OK, I think).
Thus, all non recursive calls will run in parallel. But you should use another condition than the max number of threads, but the size of the problem, e.g. last-first<threshold.

C++ - Threads without coordinating mechanism like mutex_Lock

I attended one interview two days back. The interviewed guy was good in C++, but not in multithreading. When he asked me to write a code for multithreading of two threads, where one thread prints 1,3,5,.. and the other prints 2,4,6,.. . But, the output should be 1,2,3,4,5,.... So, I gave the below code(sudo code)
mutex_Lock LOCK;
int last=2;
int last_Value = 0;
void function_Thread_1()
{
while(1)
{
mutex_Lock(&LOCK);
if(last == 2)
{
cout << ++last_Value << endl;
last = 1;
}
mutex_Unlock(&LOCK);
}
}
void function_Thread_2()
{
while(1)
{
mutex_Lock(&LOCK);
if(last == 1)
{
cout << ++last_Value << endl;
last = 2;
}
mutex_Unlock(&LOCK);
}
}
After this, he said "these threads will work correctly even without those locks. Those locks will reduce the efficiency". My point was without the lock there will be a situation where one thread will check for(last == 1 or 2) at the same time the other thread will try to change the value to 2 or 1. So, My conclusion is that it will work without that lock, but that is not a correct/standard way. Now, I want to know who is correct and in which basis?
Without the lock, running the two functions concurrently would be undefined behaviour because there's a data race in the access of last and last_Value Moreover (though not causing UB) the printing would be unpredictable.
With the lock, the program becomes essentially single-threaded, and is probably slower than the naive single-threaded code. But that's just in the nature of the problem (i.e. to produce a serialized sequence of events).
I think the interviewer might have thought about using atomic variables.
Each instantiation and full specialization of the std::atomic template defines an atomic type. Objects of atomic types are the only C++ objects that are free from data races; that is, if one thread writes to an atomic object while another thread reads from it, the behavior is well-defined.
In addition, accesses to atomic objects may establish inter-thread synchronization and order non-atomic memory accesses as specified by std::memory_order.
[Source]
By this I mean the only thing you should change is remove the locks and change the lastvariable to std::atomic<int> last = 2; instead of int last = 2;
This should make it safe to access the last variable concurrently.
Out of curiosity I have edited your code a bit, and ran it on my Windows machine:
#include <iostream>
#include <atomic>
#include <thread>
#include <Windows.h>
std::atomic<int> last=2;
std::atomic<int> last_Value = 0;
std::atomic<bool> running = true;
void function_Thread_1()
{
while(running)
{
if(last == 2)
{
last_Value = last_Value + 1;
std::cout << last_Value << std::endl;
last = 1;
}
}
}
void function_Thread_2()
{
while(running)
{
if(last == 1)
{
last_Value = last_Value + 1;
std::cout << last_Value << std::endl;
last = 2;
}
}
}
int main()
{
std::thread a(function_Thread_1);
std::thread b(function_Thread_2);
while(last_Value != 6){}//we want to print 1 to 6
running = false;//inform threads we are about to stop
a.join();
b.join();//join
while(!GetAsyncKeyState('Q')){}//wait for 'Q' press
return 0;
}
and the output is always:
1
2
3
4
5
6
Ideone refuses to run this code (compilation errors)..
Edit: But here is a working linux version :) (thanks to soon)
The interviewer doesn't know what he is talking about. Without the locks you get races on both last and last_value. The compiler could for example reorder the assignment to last before the print and increment of last_value, which could lead to the other thread executing on stale data. Furthermore you could get interleaved output, meaning things like two numbers not being seperated by a linebreak.
Another thing, which could go wrong is that the compiler might decide not to reload last and (less importantly) last_value each iteration, since it can't (safely) change between those iterations anyways (since data races are illegal by the C++11 standard and aren't acknowledged in previous standards). This means that the code suggested by the interviewer actually has a good chance of creating infinite loops of doing absoulutely doing nothing.
While it is possible to make that code correct without mutices, that absolutely needs atomic operations with appropriate ordering constraints (release-semantics on the assignment to last and acquire on the load of last inside the if statement).
Of course your solution does lower efficiency due to effectivly serializing the whole execution. However since the runtime is almost completely spent inside the streamout operation, which is almost certainly internally synchronized by the use of locks, your solution doesn't lower the efficiency anymore then it already is. Waiting on the lock in your code might actually be faster then busy waiting for it, depending on the availible resources (the nonlocking version using atomics would absolutely tank when executed on a single core machine)