Hi i am new to c++ and i made a code which runs but it is slow because of many nested for loops i want to speed it up by openmp anyone who can guide me. i tried to use '#pragma omp parallel' before ip loop and inside this loop i used '#pragma omp parallel for' before it loop but it does not works
#pragma omp parallel
for(int ip=0; ip !=nparticle; ip++){
inf14>>r>>xp>>yp>>zp;
zp/=sqrt(gamma2);
counter++;
double para[7]={0,0,Vz,x0-xp,y0-yp,z0-zp,0};
if(ip>=0 && ip<=43){
#pragma omp parallel for
for(int it=0;it<NT;it++){
para[6]=PosT[it];
for(int ix=0;ix<NumX;ix++){
para[3]=PosX[ix]-xp;
for(int iy=0;iy<NumY;iy++){
para[4]=PosY[iy]-yp;
for(int iz=0;iz<NumZ;iz++){
para[5]=PosZ[iz]-zp;
int position=it*NumX*NumY*NumZ+ix*NumY*NumZ+iy*NumZ+iz;
rotation(para,&Field[3*position]);
MagX[position] +=chg*Field[3*position];
MagY[position] +=chg*Field[3*position+1];
MagZ[position] +=chg*Field[3*position+2];
}
}
}
}
}
}enter code here
and my rotation function also has infinite integration for loop as given below
for(int i=1;;i++){
gsl_integration_qag(&F, 10*i, 10*i+10, 1.0e-8, 1.0e-8, 100, 2, w, &temp, &error);
result+=temp;
if(abs(temp/result)<ACCURACY){
break;
}
}
i am using gsl libraries as well. so how to speed up this process or how to make openmp?
If you don't have inter-loop dependences, you can use the collapse keyword to parallelize multiple loops altoghether. Example:
void scale( int N, int M, float A[N][M], float B[N][M], float alpha ) {
#pragma omp for collapse(2)
for( int i = 0; i < N; i++ ) {
for( int j = 0; j < M; j++ ) {
A[i][j] = alpha * B[i][j];
}
}
}
I suggest you to check out the OpenMP C/C++ cheat sheet (PDF), which contain all the specifications for loop parallelization.
Do not set parallel pragmas inside another parallel pragma. You might overhead the machine creating more threads than it can handle. I would establish the parallelization in the outter loop (if it is big enough):
#pragma omp parallel for
for(int ip=0; ip !=nparticle; ip++)
Also make sure you do not have any race condition between threads (e.g. RAW).
Advice: if you do not get a great speed-up, a good practice is iterating by chunks and not only by one increment. For instance:
int num_threads = 1;
#pragma omp parallel
{
#pragma omp single
{
num_threads = omp_get_num_threads();
}
}
int chunkSize = 20; //Define your own chunk here
for (int position = 0; position < total; position+=(chunkSize*num_threads)) {
int endOfChunk = position + (chunkSize*num_threads);
#pragma omp parallel for
for(int ip = position; ip < endOfChunk ; ip += chunkSize) {
//Code
}
}
Related
In an openMP framework, suppose I have a series of tasks that should be done by a single task. Each task is different, so I cannot fit into a #pragma omp for construct. Inside the single construct, each task updates a variable shared by all tasks. How can I protect the update of such a variable?
A simplified example:
#include <vector>
struct A {
std::vector<double> x, y, z;
};
int main()
{
A r;
#pragma omp single nowait
{
std::vector<double> res;
for (int i = 0; i < 10; ++i)
res.push_back(i);
// DANGER
r.x = std::move(res);
}
#pragma omp single nowait
{
std::vector<double> res;
for (int i = 0; i < 10; ++i)
res.push_back(i * i);
// DANGER
r.y = std::move(res);
}
#pragma omp single nowait
{
std::vector<double> res;
for (int i = 0; i < 10; ++i)
res.push_back(i * i + 2);
// DANGER
r.z = std::move(res);
}
#pragma omp barrier
return 0;
}
The code lines below // DANGER are problematic because they modify the memory contents of a shared variable.
In the example above, it might be that it still works without issues, because I am effectively modifying different members of r. Still the problem is: how can I make sure that tasks do not simultaineusly update r? Is there a "sort-of" atomic pragma for the single construct?
There is no data race in your original code, because x,y, and z are different vectors in struct A (as already emphasized by #463035818_is_not_a_number), so in this respect you do not have to change anything in your code.
However, a #pragma omp parallel directive is missing in your code, so at the moment it is a serial program. So, it should look like this:
#pragma omp parallel num_threads(3)
{
#pragma omp single nowait
{
std::vector<double> res;
for (int i = 0; i < 10; ++i)
res.push_back(i);
// DANGER
r.x = std::move(res);
}
#pragma omp single nowait
{
std::vector<double> res;
for (int i = 0; i < 10; ++i)
res.push_back(i * i);
// DANGER
r.y = std::move(res);
}
#pragma omp single nowait
{
std::vector<double> res;
for (int i = 0; i < 10; ++i)
res.push_back(i * i + 2);
// DANGER
r.z = std::move(res);
}
}
In this case #pragma omp barrier is not necessary as there is an implied barrier at the end of parallel region. Note that I have used num_threads(3) clause to make sure that only 3 threads are assigned to this parallel region. If you skip this clause then all other threads just wait at the barrier.
In the case of an actual data race (i.e. more than one single region/section changes the same struct member), you can use #pragma omp critical (name) to rectify this. But keep in mind that this kind of serialization can negate the benefits of multithreading when there is not enough real parallel work beside the critical section.
Note that, a much better solution is to use #pragma omp sections (as suggested by #PaulG). If the number of tasks to run parallel is known at compile time sections are the typical choice in OpenMP:
#pragma omp parallel sections
{
#pragma omp section
{
//Task 1 here
}
#pragma omp section
{
//Task 2
}
#pragma omp section
{
// Task 3
}
}
For the record, I would like to show that it is easy to do it by #pragma omp for as well:
#pragma omp parallel for
for(int i=0;i<3;i++)
{
if (i==0)
{
// Task 1
} else if (i==1)
{
// Task 2
}
else if (i==2)
{
// Task 3
}
}
each task updates a variable shared by all tasks.
Actually they don't. Consider you rewrite the code like this (you don't need the temporary vectors):
void foo( std::vector<double>& x, std::vector<double>& y, std::vector<double>& z) {
#pragma omp single nowait
{
for (int i = 0; i < 10; ++i)
x.push_back(i);
}
#pragma omp single nowait
{
for (int i = 0; i < 10; ++i)
y.push_back(i * i);
}
#pragma omp single nowait
{
for (int i = 0; i < 10; ++i)
z.push_back(i * i + 2);
}
#pragma omp barrier
}
As long as the caller can ensure that x, y and z do not refer to the same object, there is no data race. Each part of the code modifies a seperate vector. No synchronization needed.
Now, it does not matter where those vectors come from. You can call the function like this:
A r;
foo(r.x, r.y, r.z);
PS: I am not familiar with omp anymore, I assumed the annotations correctly do what you want them to do.
So I started using OpenMP (multithreading) to increase the speed of my matrix multiplication and I witnessed weird things: when I turn off OpenMP Support (in Visual Studio 2019) my nested for-loop completes 2x faster. So I removed "#pragma omp critical" to test if it slows down the proccess significantly and the proccess went 4x faster than before (with OpenMP Support On).
Here's my question: is "#pragma omp critical" important in nested loop? Can't I just skip it?
#pragma omp parallel for collapse(3)
for (int i = 0; i < this->I; i++)
{
for (int j = 0; j < A.J; j++)
{
m.matrix[i][j] = 0;
for (int k = 0; k < A.I; k++)
{
#pragma omp critical
m.matrix[i][j] += this->matrix[i][k] * A.matrix[k][j];
}
}
}
Here's my question: is "#pragma omp critical" important in nested
loop? Can't I just skip it?
If the matrices m, this and A are different you do not need any critical region. Instead, you need to ensure that each thread will write to a different position of the matrix m as follows:
#pragma omp parallel for collapse(2)
for (int i = 0; i < this->I; i++)
{
for (int j = 0; j < A.J; j++)
{
m.matrix[i][j] = 0;
for (int k = 0; k < A.I; k++)
{
m.matrix[i][j] += this->matrix[i][k] * A.matrix[k][j];
}
}
}
The collapse clause will assign to each thread a different pair (i, j) therefore there will not be multiple threads writing to the same position of the matrix m (i.e., race-condition).
#pragma omp critical is necessary here, as there is a (remote) chance that two threads could write to a particular m.matrix[i][j] value. It hurts performance because only one thread at a time can access that protected assignment statement.
This would likely be better without the collapse part (then you can remove the #pragma omp critical). Accumulate the sums to a temporary local variable, then store it in m.matrix[i][j] after the k loop finishes.
I'm trying to make my serial programm parallel with openMP. Here is the code where I have a big parallel region with a number of internal "#pragma omp for" sections. In serial version I have a function fftw_shift() which has "for" loops inside it too.
The question is how to rewrite the fftw_shift() function properly in order to already existed threads in the external parallel region could split "for" loops inside with no nested threads.
I'm not sure that my realisation works correctly. There is the way to inline the whole function in parallel region but I'm trying to realise how to deal with it in the described situation.
int fftw_shift(fftw_complex *pulse, fftw_complex *shift_buf, int
array_size)
{
int j = 0; //counter
if ((pulse != nullptr) || (shift_buf != nullptr)){
if (omp_in_parallel()) {
//shift the array
#pragma omp for private(j) //shedule(dynamic)
for (j = 0; j < array_size / 2; j++) {
//left to right
shift_buf[(array_size / 2) + j][REAL] = pulse[j][REAL]; //real
shift_buf[(array_size / 2) + j][IMAG] = pulse[j][IMAG]; //imaginary
//right to left
shift_buf[j][REAL] = pulse[(array_size / 2) + j][REAL]; //real
shift_buf[j][IMAG] = pulse[(array_size / 2) + j][IMAG]; //imaginary
}
//rewrite the array
#pragma omp for private(j) //shedule(dynamic)
for (j = 0; j < array_size; j++) {
pulse[j][REAL] = shift_buf[j][REAL]; //real
pulse[j][IMAG] = shift_buf[j][IMAG]; //imaginary
}
return 0;
}
}
....
#pragma omp parallel firstprivate(x, phase) if(array_size >=
OMP_THREASHOLD)
{
// First half-step
#pragma omp for schedule(dynamic)
for (x = 0; x < array_size; x++) {
..
}
// Forward FTW
fftw_shift(pulse_x, shift_buf, array_size);
#pragma omp master
{
fftw_execute(dft);
}
#pragma omp barrier
fftw_shift(pulse_kx, shift_buf, array_size);
...
}
If you call fftw_shift from a parallel region - but not a work-sharing construct (i.e. not in a parallel for), then you can just use omp for just as if you were inside a parallel region. This is called an orphaned directive.
However, your loops just copy data, so don't expect a perfect speedup depending on your system.
I am doing some very simple tests with OpenMP in C++ and I encounter a problem that is probably silly, but I can't find out what's wrong. In the following MWE:
#include <iostream>
#include <ctime>
#include <vector>
#include <omp.h>
int main()
{
int nthreads=1, threadid=0;
clock_t tstart, tend;
const int nx=10, ny=10, nz=10;
int i, j, k;
std::vector<std::vector<std::vector<long long int> > > arr_par;
arr_par.resize(nx);
for (i=0; i<nx; i++) {
arr_par[i].resize(ny);
for (j = 0; j<ny; j++) {
arr_par[i][j].resize(nz);
}
}
tstart = clock();
#pragma omp parallel default(shared) private(threadid)
{
#ifdef _OPENMP
nthreads = omp_get_num_threads();
threadid = omp_get_thread_num();
#endif
#pragma omp master
std::cout<<"OpenMP execution with "<<nthreads<<" threads"<<std::endl;
#pragma omp end master
#pragma omp barrier
#pragma omp critical
{
std::cout<<"Thread id: "<<threadid<<std::endl;
}
#pragma omp for
for (i=0; i<nx; i++) {
for (j=0; j<ny; j++) {
for (k=0; k<nz; k++) {
arr_par[i][j][k] = i*j + k;
}
}
}
}
tend = clock();
std::cout<<"Elapsed time: "<<(tend - tstart)/double(CLOCKS_PER_SEC)<<" s"<<std::endl;
return 0;
}
if nx, ny and nz are equal to 10, the code is running smoothly. If I increase these numbers to 20, I get a segfault. It runs without problem sequentially or with OMP_NUM_THREADS=1, whatever the number of elements.
I compiled the damn thing with
g++ -std=c++0x -fopenmp -gstabs+ -O0 test.cpp -o test
using GCC 4.6.3.
Any thought would be appreciated!
You have a data race in your loop counters:
#pragma omp for
for (i=0; i<nx; i++) {
for (j=0; j<ny; j++) { // <--- data race
for (k=0; k<nz; k++) { // <--- data race
arr_par[i][j][k] = i*j + k;
}
}
}
Since neither j nor k are given the private data-sharing class, their values might exceed the corresponding limits when several threads try to increase them at once, resulting in out-of-bound access to arr_par. The chance to have several threads increase j or k at the same time increases with the number of iterations.
The best way to treat those cases is to simply declare the loop variables inside the loop operator itself:
#pragma omp for
for (int i=0; i<nx; i++) {
for (int j=0; j<ny; j++) {
for (int k=0; k<nz; k++) {
arr_par[i][j][k] = i*j + k;
}
}
}
The other way is to add the private(j,k) clause to the head of the parallel region:
#pragma omp parallel default(shared) private(threadid) private(j,k)
It is not strictly necessary to make i private in your case since the loop variable of parallel loops are implicitly made private. Still, if i is used somewhere else in the code, it might make sense to make it private to prevent other data races.
Also, don't use clock() to measure the time for parallel applications since on most Unix OSes it returns the total CPU time for all threads. Use omp_get_wtime() instead.
At the start of #pragma omp parallel a bunch of threads are created, then when we get to #pragma omp for the workload is distributed. What happens if this for loop has a for loop inside it, and I place a #pragma omp for before it as well? Does each thread create new threads? If not, which threads are assigned this task? What exactly happens in this situation?
By default, no threads are spawned for the inner loop. It is done sequentially using the thread that reaches it.
This is because nesting is disabled by default. However, if you enable nesting via omp_set_nested(), then a new set of threads will be spawned.
However, if you aren't careful, this will result in p^2 number of threads (since each of the original p threads will spawn another p threads.) Therefore nesting is disabled by default.
In a situation like the following:
#pragma omp parallel
{
#pragma omp for
for(int ii = 0; ii < n; ii++) {
/* ... */
#pragma omp for
for(int jj = 0; jj < m; jj++) {
/* ... */
}
}
}
what happens is that you trigger an undefined behavior as you violate the OpenMP standard. More precisely you violate the restrictions appearing in section 2.5 (worksharing constructs):
The following restrictions apply to worksharing constructs:
Each worksharing region must be encountered by all threads in a team or by none at all.
The sequence of worksharing regions and barrier regions encountered must be the same for every thread in a team.
This is clearly shown in the examples A.39.1c and A.40.1c:
Example A.39.1c: The following example of loop construct nesting is conforming because the inner and outer loop regions bind to different parallel
regions:
void work(int i, int j) {}
void good_nesting(int n)
{
int i, j;
#pragma omp parallel default(shared)
{
#pragma omp for
for (i=0; i<n; i++) {
#pragma omp parallel shared(i, n)
{
#pragma omp for
for (j=0; j < n; j++)
work(i, j);
}
}
}
}
Example A.40.1c: The following example is non-conforming because the inner and outer loop regions are closely nested
void work(int i, int j) {}
void wrong1(int n)
{
#pragma omp parallel default(shared)
{
int i, j;
#pragma omp for
for (i=0; i<n; i++) {
/* incorrect nesting of loop regions */
#pragma omp for
for (j=0; j<n; j++)
work(i, j);
}
}
}
Notice that this is different from:
#pragma omp parallel for
for(int ii = 0; ii < n; ii++) {
/* ... */
#pragma omp parallel for
for(int jj = 0; jj < m; jj++) {
/* ... */
}
}
in which you try to spawn a nested parallel region. Only in this case the discussion of Mysticial answer holds.