OpenMP program unexpectedly not faster with more threads - multithreading

I am a newbie to OpenMP. I write a code to calculate value of Pi by calculating the area of function f(x) = 4/(1+x^2). I try to examine the efficiency with different threads. Below is my code:
int main() {
long long num_iteration = 100000000;
double pi = 0;
double x_margin = 1.0 / num_iteration;
double start_time, end_time;
int num_threads_main = 0;
int j = NUM_THREAD;
int a;
for(a = 1; a <= j; a++) {
pi = 0.0;
omp_set_num_threads(a);
start_time = omp_get_wtime();
#pragma omp parallel
{
int i;
int ID = omp_get_thread_num();
double sum = 0.0;
int num_threads_local = omp_get_num_threads();
double x_value = 0;
if(ID == 0)
num_threads_main = num_threads_local;
for (i = ID; i < num_iteration; i = i + num_threads_local) {
x_value = x_margin * ( i + 0.5 );
sum = sum + ( 4.0 / (1.0 + x_value * x_value));
}
#pragma critical
pi = pi + sum * x_margin;
}
end_time = omp_get_wtime() - start_time;
printf("pi with 1000000000 steps is %f in %f seconds with threads %d\n", pi, end_time, num_threads_main);
}
return 0;
}
However, when I got a strange result:
pi with 1000000000 steps is 3.141593 in 0.333257 seconds with threads 1
pi with 1000000000 steps is 3.141593 in 0.175574 seconds with threads 2
pi with 1000000000 steps is 3.141593 in 0.177884 seconds with threads 3
pi with 1000000000 steps is 3.141593 in 0.170591 seconds with threads 4
Why my program is not faster when there are more threads? I know there might be some overhead for OpenMP. However, I compare my code with Tim Mattson's code for OpenMP tutorial. I find quite a resemblance between the two. Below is his code:
static long num_steps = 100000000;
double step;
int main ()
{
int i,j;
double pi, full_sum = 0.0;
double start_time, run_time;
double sum[MAX_THREADS];
step = 1.0/(double) num_steps;
for(j=1;j<=MAX_THREADS ;j++){
omp_set_num_threads(j);
full_sum = 0.0;
start_time = omp_get_wtime();
#pragma omp parallel private(i)
{
int id = omp_get_thread_num();
int numthreads = omp_get_num_threads();
double x;
double partial_sum = 0;
#pragma omp single
printf(" num_threads = %d",numthreads);
for (i=id;i< num_steps; i+=numthreads){
x = (i+0.5)*step;
partial_sum += + 4.0/(1.0+x*x);
}
#pragma omp critical
full_sum += partial_sum;
}
pi = step * full_sum;
run_time = omp_get_wtime() - start_time;
printf("\n pi is %f in %f seconds %d threds \n ",pi,run_time,j);
}
}
And this is his result:
num_threads = 1
pi is 3.141593 in 0.483153 seconds 1 threds
num_threads = 2
pi is 3.141593 in 0.305407 seconds 2 threds
num_threads = 3
pi is 3.141593 in 0.246802 seconds 3 threds
num_threads = 4
pi is 3.141593 in 0.204905 seconds 4 threds
I do the experiment on my MacOS 10.15.3 with a 2.3 GHz Dual-Core Intel Core i5. Am I missing something. Thank you.

Related

Multiply matrices using dgemv and multithreads in c

I have a problem in my code. I want to multiply 2 matrices using dgemv from cblas, but I want to share the operations to the threads I have. I have also used dgemv to multiply the matrices in a previous exercise where there was no parallelism needed. Is there any idea of what I should do?
The code:
for (it = 0; it < itime; it++) {
cblas_dgemv(CblasColMajor,CblasNoTrans,n,n, 1 , sigma, n, u , 1, 0.0 , d, 1);
#pragma omp parallel for private(i,j,sum) schedule(static)
for (i = 0; i < n; i++) {
sum = 0.0;
uplus[i] = u[i] + dtmu - dt * u[i];
#pragma omp simd reduction(+:sum)
for (j = 0; j < n; j++) {
sum += sigma[i*n+j]*u[j];
}
sum = sum - u[i]*m[i];
uplus[i] += dtdiv * sum;
if (uplus[i] > uth) {
uplus[i] = 0.0;
if (it >= ttransient) {
omega1[i] += 1.0;
}
}
}
t = u;
u = uplus;
uplus = t;
}
I want to get the dgemv function into the parallel region and share somehow the multiplications to the threads I have.

Hybrid MPI+OpenMP Vs MPI Performance

I am converting a 3-D Jacobi solver from pure MPI to Hybrid MPI+OpenMP. I have a 192x192x192 array which is divided among 24 processes in Pure MPI in 1-D decomposition i.e. each process has 192/24 x 192 x 192 = 8 x 192 x 192 slab of data. Now I do :
for(i=0 ; i <= 7; i++)
for(j=0; j<= 191; j++)
for(k=0; k<= 191; k++)
{
unew[i][j][k] = 1/6.0 * (u[i+1][j][k]+u[i-1][j][k]+
u[i][j+1][k]+u[i][j-1][k]+
u[i][j][k+1]+u[i][j][k-1]);
}
This update takes around 60 seconds for each process.
Now with Hybrid MPI, I run two processes (1 process per socket --bind-to socket --map-by socket and OMP_PROC_PLACES=coreswith OMP_PROC_BIND=close). I create 12 threads per MPI Process (i.e. 12 threads per socket or processor). Now each MPI process has an array of size : 192/2 x 192 x 192 = 96x192x192 elements. Each thread works on 96/12 x 192 x 192 = 8 x 192 x 192 portion of the array owned by each process. I do the same triple loop update using threads but the time is approximately 76 seconds for each thread. The load balance is perfect in both the problems. What could be the possible causes of performance degradation ? Is is False Sharing because threads could be invalidating the cache lines close to each other's chunk of data ? If yes, then how do I reduce this performance degradation ? (I have purposefully not mentioned ghost data but initially I am NOT overlapping communication with computation.)
In response to the comments below, am posting the code. Apologies for the long MWE but you can very safely ignore (1) Header files declaration (2) Variable Declaration (3) Memory allocation routine (4) Formation of Cartesian Topology (5) Setting boundary conditions in parallel using OpenMP parallel region (6) Declaration of MPI_Type_subarray datatype (7) MPI_Isend() and MPI_Irecv() calls and just concentrate on (a) INDEPENDENT UPDATE OpenMP parallel region (b) independent_update(...) routine being called from here.
/* IGNORE THIS PORTION */
#include<mpi.h>
#include<omp.h>
#include<stdio.h>
#include<stdlib.h>
#include<math.h>
#define MIN(a,b) (a < b ? a : b)
#define Tol 0.00001
/* IGNORE THIS ROUTINE */
void input(int *X, int *Y, int *Z)
{
int a=193, b=193, c=193;
*X = a;
*Y = b;
*Z = c;
}
/* IGNORE THIS ROUTINE */
float*** allocate_mem(int X, int Y, int Z)
{
int i,j;
float ***matrix;
float *arr;
arr = (float*)calloc(X*Y*Z, sizeof(float));
matrix = (float***)calloc(X, sizeof(float**));
for(i = 0 ; i<= X-1; i++)
matrix[i] = (float**)calloc(Y, sizeof(float*));
for(i = 0 ; i <= X-1; i++)
for(j=0; j<= Y-1; j++)
matrix[i][j] = &(arr[i*Y*Z + j*Z]);
return matrix ;
}
/* THIS ROUTINE IS IMPORTANT */
float independent_update(float ***old, float ***new, int NX, int NY, int NZ, int tID, int chunk)
{
int i,j,k, start, end;
float error = 0.0;
float diff;
start = tID * chunk + 1;
end = MIN( (tID+1)*chunk, NX-2 );
for(i = start; i <= end ; i++)
{
for(j = 1; j<= NY-2; j++)
{
#pragma omp simd
for(k = 1; k<= NZ-2; k++)
{
new[i][j][k] = (1/6.0) *(old[i-1][j][k] + old[i+1][j][k] + old[i][j-1][k] + old[i][j+1][k] + old[i][j][k-1] + old[i][j][k+1] );
diff = 1.0 - new[i][j][k];
diff = (diff > 0 ? diff : -1.0 * diff );
if(diff > error)
error = diff;
}
}
}
return error;
}
int main(int argc, char *argv[])
{
/* IGNORE VARIABLE DECLARATION */
int size, rank; //Size of old_comm and rank of process
int i, j, k,l; //General loop variables
MPI_Comm old_comm, new_comm; //MPI_COMM_WORLD handle and for MPI_Cart_create()
int N[3]; //For taking input of size of matrix from user
int P; //Represent number of processes i.e. same as size
int dims[3]; //For dimensions of Cartesian topology
int PX, PY, PZ; //X dim, Y dim, Z dim of each process
float ***old, ***new, ***temp; //Matrices for results dimensions is (Px+2)*(PY+2)*(PZ+2)
int period[3]; //Periodicity for each dimension
int reorder; //Whether processes should be reordered in new cartesian topology
int ndims; //Number of dimensions (which is 3)
int Z_TOWARDS_U, Z_AWAY_U; //Z neighbour towards you and away from you (Z const)
int X_DOWN, X_UP; //Below plane and above plane (X const)
int Y_LEFT, Y_RIGHT; //Left plane and right plane (Y const)
int coords[3]; //Finding coordinates of processes
int dimension; //Used in MPI_Cart_shift() , values = 0, 1,2
int displacement; //Used in MPI_Cart_shift(), values will be +1 to find immediate neighbours
float l_max_err; //Local maximum error on process
float l_max_err_new; //For dependent faces.
float G_max_err = 1.0; //Maximum error for stopping criterion
int iterations = 0 ; //Counting number of iterations
MPI_Request send[6], recv[6]; //For MPI_Isend and MPI_Irecv
int start[3]; //Start will be defined in MPI_Isend() and MPI_Irecv()
int gsize[3]; //Defining global size of subarray
MPI_Datatype x_subarray; //For sending X_UP and X_DOWN
int local_x[3]; //Defining local plane size for X_UP/X_DOWN
MPI_Datatype y_subarray; //For sending Y_LEFT and Y_RIGHT
int local_y[3]; //Defining local plane for Y_LEFT/Y_RIGHT
MPI_Datatype z_subarray; //For sending Z_TOWARDS_U and Z_AWAY_U
int local_z[3]; //Defining local plan size for XY plane i.e. where Z=0
double strt, end; //For measuring time
double strt1, end1, delta1; //For measuring trivial time 1
double strt2, end2, delta2; //For measuring trivial time 2
double t_i_strt, t_i_end, t_i_sum=0; //Time for independent computational kernel
double t_up_strt, t_up_end, t_up_sum=0; //Time for X_UP
double t_down_strt, t_down_end, t_down_sum=0; //Time for X_DOWN
double t_left_strt, t_left_end, t_left_sum=0; //Time for Y_LEFT
double t_right_strt, t_right_end, t_right_sum=0; //Time for Y_RIGHT
double t_towards_strt, t_towards_end, t_towards_sum=0; //For Z_TOWARDS_U
double t_away_strt, t_away_end, t_away_sum=0; //For Z_AWAY_U
double t_comm_strt, t_comm_end, t_comm_sum=0; //Time comm + independent update (need to subtract to get comm time)
double t_setup_strt,t_setup_end; //Set-up start and end time
double t_allred_strt,t_allred_end,t_allred_total=0.0; //Measuring Allreduce time separately.
int threadID; //ID of a thread
int nthreads; //Total threads in OpenMP region
int chunk; //chunk - used to calculate iterations of a thread
/* IGNORE MPI STARTUP ETC */
MPI_Init(&argc, &argv);
t_setup_strt = MPI_Wtime();
old_comm = MPI_COMM_WORLD;
MPI_Comm_size(old_comm, &size);
MPI_Comm_rank(old_comm, &rank);
P = size;
if(rank == 0)
{
input(&N[0], &N[1], &N[2]);
}
MPI_Bcast(N, 3, MPI_INT, 0, old_comm);
dims[0] = 0;
dims[1] = 0;
dims[2] = 0;
period[0] = period[1] = period[2] = 0; //All dimensions aperiodic
reorder = 0 ; //No reordering of ranks in new_comm
ndims = 3;
MPI_Dims_create(P,ndims,dims);
MPI_Cart_create(old_comm, ndims, dims, period, reorder, &new_comm);
if( (N[0]-1) % dims[0] == 0 && (N[1]-1) % dims[1] == 0 && (N[2]-1) % dims[2] == 0 )
{
PX = (N[0]-1)/dims[0]; //Rows of unknowns each process gets
PY = (N[1]-1)/dims[1]; //Columns of unknowns each process gets
PZ = (N[2]-1)/dims[2]; //Depth of unknowns each process gets
}
old = allocate_mem(PX+2, PY+2, PZ+2); //3D arrays with ghost points
new = allocate_mem(PX+2, PY+2, PZ+2); //3D arrays with ghost points
dimension = 0;
displacement = 1;
MPI_Cart_shift(new_comm, dimension, displacement, &X_UP, &X_DOWN); //Find UP and DOWN neighbours
dimension = 1;
MPI_Cart_shift(new_comm, dimension, displacement, &Y_LEFT, &Y_RIGHT); //Find UP and DOWN neighbours
dimension = 2;
MPI_Cart_shift(new_comm, dimension, displacement, &Z_TOWARDS_U, &Z_AWAY_U); //Find UP and DOWN neighbours
/* IGNORE BOUNDARY SETUPS FOR PDE */
#pragma omp parallel for default(none) shared(old,new,PX,PY,PZ) private(i,j,k) schedule(static)
for(i = 0; i <= PX+1; i++)
{
for(j = 0; j <= PY+1; j++)
{
for(k = 0; k <= PZ+1; k++)
{
old[i][j][k] = 0.0;
new[i][j][k] = 0.0;
}
}
}
#pragma omp parallel default(none) shared(X_DOWN,X_UP,Y_LEFT,Y_RIGHT,Z_TOWARDS_U,Z_AWAY_U,old,new,PX,PY,PZ) private(i,j,k,threadID,nthreads)
{
threadID = omp_get_thread_num();
nthreads = omp_get_num_threads();
if(threadID == 0)
{
if(X_DOWN == MPI_PROC_NULL) //X is constant here, this is YZ upper plane
{
for(j = 1 ; j<= PY ; j++)
for(k = 1 ; k<= PZ ; k++)
{
old[0][j][k] = 1;
new[0][j][k] = 1; //Set boundaries in new also
}
}
}
if(threadID == (nthreads-1))
{
if(X_UP == MPI_PROC_NULL) //YZ lower plane
{
for(j = 1 ; j<= PY ; j++)
for(k = 1; k<= PZ ; k++)
{
old[PX+1][j][k] = 1;
new[PX+1][j][k] = 1;
}
}
}
if(Y_LEFT == MPI_PROC_NULL) //Y is constant, this is left XZ plane, possibly can use collapse(2)
{
#pragma omp for schedule(static)
for(i = 1 ; i<= PX ; i++)
for(k = 1; k<= PZ; k++)
{
old[i][0][k] = 1;
new[i][0][k] = 1;
}
}
if(Y_RIGHT == MPI_PROC_NULL) //XZ right plane, again collapse(2) potential
{
#pragma omp for schedule(static)
for(i = 1 ; i<= PX; i++)
for(k = 1; k<= PZ ; k++)
{
old[i][PY+1][k] = 1;
new[i][PY+1][k] = 1;
}
}
if(Z_TOWARDS_U == MPI_PROC_NULL) //Z is constant here, towards you XY plane, collapse(2)
{
#pragma omp for schedule(static)
for(i = 1 ; i<= PX ; i++)
for(j = 1; j<= PY ; j++)
{
old[i][j][0] = 1;
new[i][j][0] = 1;
}
}
if(Z_AWAY_U == MPI_PROC_NULL) //Away from you XY plane, collapse(2)
{
#pragma omp for schedule(static)
for(i = 1 ; i<= PX; i++)
for(j = 1; j<= PY ; j++)
{
old[i][j][PZ+1] = 1;
new[i][j][PZ+1] = 1;
}
}
}
/* IGNORE SUBARRAY DECLARATION */
gsize[0] = PX+2; //Global sizes of 3-D cubes for each process
gsize[1] = PY+2;
gsize[2] = PZ+2;
start[0] = 0; //Will specify starting location while sending/receiving
start[1] = 0;
start[2] = 0;
local_x[0] = 1;
local_x[1] = PY;
local_x[2] = PZ;
MPI_Type_create_subarray(ndims, gsize, local_x, start, MPI_ORDER_C, MPI_FLOAT, &x_subarray);
MPI_Type_commit(&x_subarray);
local_y[0] = PX;
local_y[1] = 1;
local_y[2] = PZ;
MPI_Type_create_subarray(ndims, gsize, local_y, start, MPI_ORDER_C, MPI_FLOAT, &y_subarray);
MPI_Type_commit(&y_subarray);
local_z[0] = PX;
local_z[1] = PY;
local_z[2] = 1;
MPI_Type_create_subarray(ndims, gsize, local_z, start, MPI_ORDER_C, MPI_FLOAT, &z_subarray);
MPI_Type_commit(&z_subarray);
t_setup_end = MPI_Wtime();
strt = MPI_Wtime();
while(G_max_err > Tol) //iterations < ITERATIONS)
{
iterations++ ;
t_comm_strt = MPI_Wtime();
/* IGNORE MPI COMMUNICATION */
MPI_Irecv(&old[0][1][1], 1, x_subarray, X_DOWN, 10, new_comm, &recv[0]);
MPI_Irecv(&old[PX+1][1][1], 1, x_subarray, X_UP, 20, new_comm, &recv[1]);
MPI_Irecv(&old[1][PY+1][1], 1, y_subarray, Y_RIGHT, 30, new_comm, &recv[2]);
MPI_Irecv(&old[1][0][1], 1, y_subarray, Y_LEFT, 40, new_comm, &recv[3]);
MPI_Irecv(&old[1][1][PZ+1], 1, z_subarray, Z_AWAY_U, 50, new_comm, &recv[4]);
MPI_Irecv(&old[1][1][0], 1, z_subarray, Z_TOWARDS_U, 60, new_comm, &recv[5]);
MPI_Isend(&old[PX][1][1], 1, x_subarray, X_UP, 10, new_comm, &send[0]);
MPI_Isend(&old[1][1][1], 1, x_subarray, X_DOWN, 20, new_comm, &send[1]);
MPI_Isend(&old[1][1][1], 1, y_subarray, Y_LEFT, 30, new_comm, &send[2]);
MPI_Isend(&old[1][PY][1], 1, y_subarray, Y_RIGHT, 40, new_comm, &send[3]);
MPI_Isend(&old[1][1][1], 1, z_subarray, Z_TOWARDS_U, 50, new_comm, &send[4]);
MPI_Isend(&old[1][1][PZ], 1, z_subarray, Z_AWAY_U, 60, new_comm, &send[5]);
MPI_Waitall(6, send, MPI_STATUSES_IGNORE);
MPI_Waitall(6, recv, MPI_STATUSES_IGNORE);
t_comm_end = MPI_Wtime();
t_comm_sum = t_comm_sum + (t_comm_end - t_comm_strt);
/* Use threads in Independent update */
t_i_strt = MPI_Wtime();
l_max_err = 0.0; //Very important, Reduction result is combined with this !
/* THIS IS THE IMPORTANT REGION */
#pragma omp parallel default(none) shared(old,new,PX,PY,PZ,chunk) private(threadID,nthreads) reduction(max:l_max_err)
{
nthreads = omp_get_num_threads();
threadID = omp_get_thread_num();
chunk = (PX-1+1) / nthreads ;
l_max_err = independent_update(old, new, PX+2, PY+2, PZ+2, threadID, chunk);
}
t_i_end = MPI_Wtime();
t_i_sum = t_i_sum + (t_i_end - t_i_strt) ;
/* IGNORE THE REMAINING CODE */
t_allred_strt = MPI_Wtime();
MPI_Allreduce(&l_max_err, &G_max_err, 1, MPI_FLOAT, MPI_MAX, new_comm);
t_allred_end = MPI_Wtime();
t_allred_total = t_allred_total + (t_allred_end - t_allred_strt);
temp = new ;
new = old;
old = temp;
}
MPI_Barrier(new_comm);
end = MPI_Wtime();
if( rank == 0)
{
printf("\nIterations = %d, G_max_err = %f", iterations, G_max_err);
printf("\nThe total SET-UP time for MPI and boundary conditions is %lf", (t_setup_end-t_setup_strt));
printf("\nThe total time for SOLVING is %lf", (end-strt));
printf("\nThe total time for INDEPENDENT COMPUTE %lf", t_i_sum);
printf("\nThe total time for COMMUNICATION OVERHEAD is %lf", t_comm_sum);
printf("\nThe total time for MPI_ALLREDUCE() is %lf", t_allred_total);
}
MPI_Type_free(&x_subarray);
MPI_Type_free(&y_subarray);
MPI_Type_free(&z_subarray);
free(&old[0][0][0]);
free(&new[0][0][0]);
MPI_Finalize();
return 0;
}
P.S. : I am almost sure that the cost of spawning/waking the threads is not the reason for such a huge difference in the timing.
Please find attached Scalasca snapshot for INDEPENDENT COMPUTE of the Hybrid Program.
Using loop simd construct
#pragma omp parallel default(none) shared(old,new,PX,PY,PZ,l_max_err) private(i,j,k,diff)
{
#pragma omp for simd schedule(static) reduction(max:l_max_err)
for(i = 1; i <= PX ; i++)
{
for(j = 1; j<= PY; j++)
{
for(k = 1; k<= PZ; k++)
{
new[i][j][k] = (1/6.0) *(old[i-1][j][k] + old[i+1][j][k] + old[i][j-1][k] + old[i][j+1][k] + old[i][j][k-1] + old[i][j][k+1] );
diff = 1.0 - new[i][j][k];
diff = (diff > 0 ? diff : -1.0 * diff );
if(diff > l_max_err)
l_max_err = diff;
}
}
}
}
You frequently get memory access and cache issues when you just do one MPI process per socket on a CPU with multiple memory controllers. It can be on either the read or the write side, so you can't really say which. This is especially an issue when doing thread-parallel execution with lightweight compute tasks (e.g. math on arrays). One MPI process per socket in this case tends to fare significantly worse than pure MPI.
In your BIOS, set up whatever the maximal NUMA per socket option is
Use one MPI process per NUMA node.
Try some different parameter values in schedule(static). I've rarely found the default to be best.
Essentially what this will do is ensure each bundle of threads only works on a single pool of memory.

Errors with repeated FFTW calls

I'm having a strange issue that I can't resolve. I made this as a simple example that demonstrates the problem. I have a sine wave defined between [0, 2*pi]. I take the Fourier transform using FFTW. Then I have a for loop where I repeatedly take the inverse Fourier transform. In each iteration, I take the average of my solution and print the results. I expect that the average stays the same with each iteration because there is no change to solution, y. However, when I pick N = 256 and other even values of N, I note that the average grows as if there are numerical errors. However, if I choose, say, N = 255 or N = 257, this is not the case and I get what is expect (avg = 0.0 for each iteration).
Code:
#include <stdio.h>
#include <stdlib.h>
#include <fftw3.h>
#include <math.h>
int main(void)
{
int N = 256;
double dx = 2.0 * M_PI / (double)N, dt = 1.0e-3;
double *x, *y;
x = (double *) malloc (sizeof (double) * N);
y = (double *) malloc (sizeof (double) * N);
// initial conditions
for (int i = 0; i < N; i++) {
x[i] = (double)i * dx;
y[i] = sin(x[i]);
}
fftw_complex yhat[N/2 + 1];
fftw_plan fftwplan, fftwplan2;
// forward plan
fftwplan = fftw_plan_dft_r2c_1d(N, y, yhat, FFTW_ESTIMATE);
fftw_execute(fftwplan);
// set N/2th mode to zero if N is even
if (N % 2 < 1.0e-13) {
yhat[N/2][0] = 0.0;
yhat[N/2][1] = 0.0;
}
// backward plan
fftwplan2 = fftw_plan_dft_c2r_1d(N, yhat, y, FFTW_ESTIMATE);
for (int i = 0; i < 50; i++) {
// yhat to y
fftw_execute(fftwplan2);
// rescale
for (int j = 0; j < N; j++) {
y[j] = y[j] / (double)N;
}
double avg = 0.0;
for (int j = 0; j < N; j++) {
avg += y[j];
}
printf("%.15f\n", avg/N);
}
fftw_destroy_plan(fftwplan);
fftw_destroy_plan(fftwplan2);
void fftw_cleanup(void);
free(x);
free(y);
return 0;
}
Output for N = 256:
0.000000000000000
0.000000000000000
0.000000000000000
-0.000000000000000
0.000000000000000
0.000000000000022
-0.000000000000007
-0.000000000000039
0.000000000000161
-0.000000000000314
0.000000000000369
0.000000000004775
-0.000000000007390
-0.000000000079126
-0.000000000009457
-0.000000000462023
0.000000000900855
-0.000000000196451
0.000000000931323
-0.000000009895302
0.000000039348379
0.000000133179128
0.000000260770321
-0.000003233551979
0.000008285045624
-0.000016331672668
0.000067450106144
-0.000166893005371
0.001059055328369
-0.002521514892578
0.005493164062500
-0.029907226562500
0.093383789062500
-0.339111328125000
1.208251953125000
-3.937500000000000
13.654296875000000
-43.812500000000000
161.109375000000000
-479.250000000000000
1785.500000000000000
-5369.000000000000000
19376.000000000000000
-66372.000000000000000
221104.000000000000000
-753792.000000000000000
2387712.000000000000000
-8603776.000000000000000
29706240.000000000000000
-96833536.000000000000000
Any ideas?
libfftw has the odious habit of modifying its inputs. Back up yhat if you want to do repeated inverse transforms.
OTOH, it's perverse, but why are you repeating the same operation if you don't expect it give different results? (Despite this being the case)
As indicated in comments: "if you want to keep the input data unchanged, use the FFTW_PRESERVE_INPUT flag. Per http://www.fftw.org/doc/Planner-Flags.html"
For example:
// backward plan
fftwplan2 = fftw_plan_dft_c2r_1d(N, yhat, y, FFTW_ESTIMATE | FFTW_PRESERVE_INPUT);

increase number of threads decrease time

I'm newbie in openmp. Beginning with a tutorial from the official page of openmp
https://www.youtube.com/playlist?list=PLLX-Q6B8xqZ8n8bwjGdzBJ25X2utwnoEG
In that page there is a hello world program to calculate pi by an approximation of integral.
I simply wrote the code below following the instructions but the time-speed of it increase as I increase the number of threads changing the NUM_THREADS. In the video, the speed goes down.
I'm executing the program in a remote server with 64 cpus having 8 cores each.
#include <stdio.h>
#include <omp.h>
static long num_steps = 100000;
double step;
#define NUM_THREADS 2
int main()
{
int i, nthreads; double pi, sum[NUM_THREADS];
double start_t;
step = 1.0 / (double) num_steps;
omp_set_num_threads(NUM_THREADS);
start_t = omp_get_wtime();
#pragma omp parallel
{
int i, id, nthrds;
double x;
id = omp_get_thread_num();
nthrds = omp_get_num_threads();
if (id == 0) nthreads = nthrds;
for (i = id, sum[id] = 0.0; i < num_steps; i = i + nthrds) {
x = (i + 0.5) * step;
sum[id] += 4.0 / (1.0 + x*x);
}
}
for (i = 0, pi = 0.0; i < nthreads; i++) {
pi += sum[i] * step;
}
printf("%f\n", omp_get_wtime() - start_t);
}
This is a bad approach to implementing reduction using shared arrays. The successive elements of sum are too close to each other and therefore reside in the same cache line. On cache-coherent architectures like x86/x64, this leads to a problem known as false sharing. The following simple modification will get rid of it:
double sum[8*NUM_THREADS];
#pragma omp parallel
{
...
for (i = id, sum[id] = 0.0; i < num_steps; i = i + nthrds) {
...
sum[8*id] += 4.0 / (1.0 + x*x);
}
}
for (i = 0, pi = 0.0; i < nthreads; i++) {
pi += sum[8*i] * step;
}
Only the relevant changes are shown. The idea is simple: instead of having threads access successive elements of sum, make them access every 8-th element. Thus it is guaranteed that threads do not share the same cache line as on most modern CPUs a cache line is 64 bytes long and that corresponds to 64 / sizeof(double) = 8 array elements.
Edit: my mistake, should have watched the video in the first place. False sharing is explained just after the results from running the code are shown. If you don't get any speedup in your case, that's probably because newer CPU generations handle false sharing better.

Not able to set processor affinity

I'm trying to implement this code on a 8 core cluster. It has 2 sockets each with 4 cores. I am trying to create 8 threads and set affinity using pthread_attr_setaffinity_np function. But when I look at my performance in VTunes , it shows me that 3969 odd threads are being created. I don't understand why and how! Above all, my performance is exactly the same as it was when no affinity was set (OS thread scheduling). Can someone please help me debug this problem? My code is running perfectly fine but I have no control over the threads! Thanks in advance.
--------------------------------------CODE-------------------------------------------
const int num_thrd=8;
bool RCTAlgorithmBackprojection(RabbitCtGlobalData* r)
{
float O_L = r->O_L;
float R_L = r->R_L;
double* A_n = r->A_n;
float* I_n = r->I_n;
float* f_L = r->f_L;*/
cpu_set_t cpu[num_thrd];
pthread_t thread[num_thrd];
pthread_attr_t attr[num_thrd];
for(int i =0; i< num_thrd; i++)
{
threadCopy[i].L = r->L;
threadCopy[i].O_L = r->O_L;
threadCopy[i].R_L = r->R_L;
threadCopy[i].A_n = r->A_n;
threadCopy[i].I_n = r->I_n;
threadCopy[i].f_L = r->f_L;
threadCopy[i].slice= i;
threadCopy[i].S_x = r->S_x;
threadCopy[i].S_y = r->S_y;
pthread_attr_init(&attr[i]);
CPU_ZERO(&cpu[i]);
CPU_SET(i, &cpu[i]);
pthread_attr_setaffinity_np(&attr[i], CPU_SETSIZE, &cpu[i]);
int rc=pthread_create(&thread[i], &attr[i], backProject, (void*)&threadCopy[i]);
if (rc!=0)
{
cout<<"Can't create thread\n"<<endl;
return -1;
}
// sleep(1);
}
for (int i = 0; i < num_thrd; i++) {
pthread_join(thread[i], NULL);
}
//s_rcgd = r;
return true;
}
void* backProject (void* parm)
{
copyStruct* s = (copyStruct*)parm; // retrive the slice info
unsigned int L = s->L;
float O_L = s->O_L;
float R_L = s->R_L;
double* A_n = s->A_n;
float* I_n = s->I_n;
float* f_L = s->f_L;
int slice1 = s->slice;
//cout<<"The size of volume is L= "<<L<<endl;
int from = (slice1 * L) / num_thrd; // note that this 'slicing' works fine
int to = ((slice1+1) * L) / num_thrd; // even if SIZE is not divisible by num_thrd
//cout<<"computing slice " << slice1<< " from row " << from<< " to " << to-1<<endl;
for (unsigned int k=from; k<to; k++)
{
double z = O_L + (double)k * R_L;
for (unsigned int j=0; j<L; j++)
{
double y = O_L + (double)j * R_L;
for (unsigned int i=0; i<L; i++)
{
double x = O_L + (double)i * R_L;
double w_n = A_n[2] * x + A_n[5] * y + A_n[8] * z + A_n[11];
double u_n = (A_n[0] * x + A_n[3] * y + A_n[6] * z + A_n[9] ) / w_n;
double v_n = (A_n[1] * x + A_n[4] * y + A_n[7] * z + A_n[10]) / w_n;
f_L[k * L * L + j * L + i] += (float)(1.0 / (w_n * w_n) * p_hat_n(u_n, v_n));
}
}
}
//cout<<" finished slice "<<slice1<<endl;
return NULL;
}
Alright, so I found out the reason was because of CPU_SETSIZE that I was using as an argument in pthread_attr_setaffinity_np. I replaced it with num_thrd . Apparently CPU_SETSIZE which will be declared inside #define __USE_GNU was not included in my file.!! Sorry if I bothered any of y'all who were trying to debug this thanks again!

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