OpenMP in Ubuntu: parallel program works on double core processor in two times slower than single-threaded. Why? - performance

I get the code from wikipedia:
#include <stdio.h>
#include <omp.h>
#define N 100
int main(int argc, char *argv[])
{
float a[N], b[N], c[N];
int i;
omp_set_dynamic(0);
omp_set_num_threads(10);
for (i = 0; i < N; i++)
{
a[i] = i * 1.0;
b[i] = i * 2.0;
}
#pragma omp parallel shared(a, b, c) private(i)
{
#pragma omp for
for (i = 0; i < N; i++)
c[i] = a[i] + b[i];
}
printf ("%f\n", c[10]);
return 0;
}
I tryed to compile and run it in my Ubuntu 11.04 with gcc4.5 (my configuration: Intel C2D T7500M 2.2GHz, 2048Mb RAM) and this program worked in two times slower than single-threaded. Why?

Very simple answer: Increase N. And set the number of threads equal to the number processors you have.
For your machine, 100 is a very low number. Try some orders of magnitudes higher.
Another question is: How are you measuring the computation time? Usually one takes the program time to get comparable results.

I suppose the compiler optimized the for loop in the non-smp case (using SSE instructions, e.g.) and it can't in the OMP variant.
Use gcc -S (or objdump -S) to view the assembly for the different variants.
You might want to watch out with the shared variables anyway, because they need to be synchronized, making things very slow. If you can 'smart' chunks (look at the schedule pragma) you might reduce the contention, but again:
verify the emitted code
profile
don't underestimate the efficiency of singlethreaded code (because of cache locality and lack of context switches)
set the number of threads to the number of CPUs (let openMP decide it for you!); unless your thread-team has a master thread with dedicated tasks, in which case there might be value in allocating ONE extra thread
In all the cases where I tried to apply OMP for parallelization, roughly 70% of the cases are slower. The cases where it is a definite speedup is with
coarse-grained parallellism (your sample is on the fine-grained end of the spectrum)
no shared data

The issue you are facing is false memory sharing. Each thread should have its own private c[i].
Try this: #pragma omp parallel shared(a, b) private(i, c)

Run the code below and see the difference.
1.) OpenMP has an overhead so the runtime has to be more than the overhead to see a benefit.
2.) Don't set the number of threads yourself. In general I use the default threads. However, if your processor has hyper-threading you might get a bit better performance by setting the number of threads equal to the number of cores. With hyper threading the default number of threads will be twice the number of cores. For example on my machine I have four cores and the default number of threads is eight. By setting it to four in some situations I get better results and in other cases I get worse results.
3.) There is some false sharing in c but as long as N is large enough (which it needs to be to overcome the overhead) the false sharing will not cause much of a problem. You can play with the chunk size but I don't think it will be helpful.
4.) Cache issues. You have at least four levels of memory (the values are for my system): L1 (32Kb), L2(256Kb), L3(12Mb), and main memory (>>12Mb). The benefits of parallelism are going to diminish as you move into higher level. However, in the example below I set N to 100 million floats which is 400 million bytes or about 381Mb and it is still significantly faster using multiple threads. Try adjusting N and see what happens. For example try setting N to your cache levels/4 (one float is 4 bytes) (arrays a and b also need to be in the cache so you might need to set N to the cache level/12). However, if N is too small you fight with the OpenMP overhead (which is what the code in your question does).
#include <stdio.h>
#include <omp.h>
#define N 100000000
int main(int argc, char *argv[]) {
float *a = new float[N];
float *b = new float[N];
float *c = new float[N];
int i;
for (i = 0; i < N; i++) {
a[i] = i * 1.0;
b[i] = i * 2.0;
}
double dtime;
dtime = omp_get_wtime();
for (i = 0; i < N; i++) {
c[i] = a[i] + b[i];
}
dtime = omp_get_wtime() - dtime;
printf ("time %f, %f\n", dtime, c[10]);
dtime = omp_get_wtime();
#pragma omp parallel for private(i)
for (i = 0; i < N; i++) {
c[i] = a[i] + b[i];
}
dtime = omp_get_wtime() - dtime;
printf ("time %f, %f\n", dtime, c[10]);
return 0;
}

Related

omp parallel for loop (reduction to find max) ran slower than serial codes

I am new in using OpenMP.
I think that use max reduction clause to find the max element of an array is not such a bad idea, but in fact the parallel for loop ran much slower than serial one.
int main() {
double sta, end, elapse_t;
int bsize = 46000;
int q = bsize;
int max_val = 0;
double *buffer;
buffer = (double*)malloc(bsize*sizeof(double));
srand(time(NULL));
for(int i=0;i<q;i++)
buffer[i] = rand()%10000;
sta = omp_get_wtime();
//int i;
#pragma omp parallel for reduction(max : max_val)
for(int i=0;i<q; i++)
{
max_val = max_val > buffer[i] ? max_val : buffer[i];
}
end = omp_get_wtime();
printf("parallel maximum time %f\n", end-sta);
sta = omp_get_wtime();
for(int i=0;i<q; i++)
{
max_val = max_val > buffer[i] ? max_val : buffer[i];
}
end = omp_get_wtime();
printf("serial maximum time %f\n", end-sta);
free(buffer);
return 0;}
Compile command
gcc-7 kp_omp.cpp -o kp_omp -fopenmp
Execution results
./kp_omp
parallel maximum time 0.000505
serial maximum time 0.000266
As for the CPU, it is an Intel Core i7-6700 with 8 cores.
Whenever you parallelise a loop openMP needs to perform some operations, for example creating the threads. Those operations result in some overhead and this in turns implies that, for each loop, there is a minimum number of iterations under which it is not convenient to parallelise.
If I execute your code I obtain the same results you have:
./kp_omp
parallel maximum time 0.000570
serial maximum time 0.000253
However if I modify bsize in line 8 such that
int bsize = 100000;
I obtain
./kp_omp
parallel maximum time 0.000323
serial maximum time 0.000552
So the parallelised version got faster than the sequential. Part of the challenges you encounter when you try to speedup the execution of a code is to understand when it is convenient to parallelise and when the overhead of the parallelisation would kill your expected gain in performance.

Optimize Cuda Kernel time execution

I'm a learning Cuda student, and I would like to optimize the execution time of my kernel function. As a result, I realized a short program computing the difference between two pictures. So I compared the execution time between a classic CPU execution in C, and a GPU execution in Cuda C.
Here you can find the code I'm talking about:
int *imgresult_data = (int *) malloc(width*height*sizeof(int));
int size = width*height;
switch(computing_type)
{
case GPU:
HANDLE_ERROR(cudaMalloc((void**)&dev_data1, size*sizeof(unsigned char)));
HANDLE_ERROR(cudaMalloc((void**)&dev_data2, size*sizeof(unsigned char)));
HANDLE_ERROR(cudaMalloc((void**)&dev_data_res, size*sizeof(int)));
HANDLE_ERROR(cudaMemcpy(dev_data1, img1_data, size*sizeof(unsigned char), cudaMemcpyHostToDevice));
HANDLE_ERROR(cudaMemcpy(dev_data2, img2_data, size*sizeof(unsigned char), cudaMemcpyHostToDevice));
HANDLE_ERROR(cudaMemcpy(dev_data_res, imgresult_data, size*sizeof(int), cudaMemcpyHostToDevice));
float time;
cudaEvent_t start, stop;
HANDLE_ERROR( cudaEventCreate(&start) );
HANDLE_ERROR( cudaEventCreate(&stop) );
HANDLE_ERROR( cudaEventRecord(start, 0) );
for(int m = 0; m < nb_loops ; m++)
{
diff<<<height, width>>>(dev_data1, dev_data2, dev_data_res);
}
HANDLE_ERROR( cudaEventRecord(stop, 0) );
HANDLE_ERROR( cudaEventSynchronize(stop) );
HANDLE_ERROR( cudaEventElapsedTime(&time, start, stop) );
HANDLE_ERROR(cudaMemcpy(imgresult_data, dev_data_res, size*sizeof(int), cudaMemcpyDeviceToHost));
printf("Time to generate: %4.4f ms \n", time/nb_loops);
break;
case CPU:
clock_t begin = clock(), diff;
for (int z=0; z<nb_loops; z++)
{
// Apply the difference between 2 images
for (int i = 0; i < height; i++)
{
tmp = i*imgresult_pitch;
for (int j = 0; j < width; j++)
{
imgresult_data[j + tmp] = (int) img2_data[j + tmp] - (int) img1_data[j + tmp];
}
}
}
diff = clock() - begin;
float msec = diff*1000/CLOCKS_PER_SEC;
msec = msec/nb_loops;
printf("Time taken %4.4f milliseconds", msec);
break;
}
And here is my kernel function:
__global__ void diff(unsigned char *data1 ,unsigned char *data2, int *data_res)
{
int row = blockIdx.x;
int col = threadIdx.x;
int v = col + row*blockDim.x;
if (row < MAX_H && col < MAX_W)
{
data_res[v] = (int) data2[v] - (int) data1[v];
}
}
I obtained these execution time for each one
CPU: 1,3210ms
GPU: 0,3229ms
I wonder why GPU result is not as lower as it should be. I am a beginner in Cuda so please be comprehensive if there are some classic errors.
EDIT1:
Thank you for your feedback. I tried to delete the 'if' condition from the kernel but it didn't change deeply my program execution time.
However, after having install Cuda profiler, it told me that my threads weren't running concurrently. I don't understand why I have this kind of message, but it seems true because I only have a 5 or 6 times faster application with GPU than with CPU. This ratio should be greater, because each thread is supposed to process one pixel concurrently to all the other ones. If you have an idea of what I am doing wrong, it would be hepful...
Flow.
Here are two things you could do which may improve the performance of your diff kernel:
1. Let each thread do more work
In your kernel, each thread handles just a single element; but having a thread do anything already has a bunch of overhead, at the block and the thread level, including obtaining the parameters, checking the condition and doing address arithmetic. Now, you could say "Oh, but the reads and writes take much more time then that; this overhead is negligible" - but you would be ignoring the fact, that the latency of these reads and writes is hidden by the presence of many other warps which may be scheduled to do their work.
So, let each thread process more than a single element. Say, 4, as each thread can easily read 4 bytes at once into a register. Or even 8 or 16; experiment with it. Of course you'll need to adjust your grid and block parameters accordingly.
2. "Restrict" your pointers
__restrict is not part of C++, but it is supported in CUDA. It tells the compiler that accesses through different pointers passed to the function never overlap. See:
What does the restrict keyword mean in C++?
Realistic usage of the C99 'restrict' keyword?
Using it allows the CUDA compiler to apply additional optimizations, e.g. loading or storing data via non-coherent cache. Indeed, this happens with your kernel although I haven't measured the effects.
3. Consider using a "SIMD" instruction
CUDA offers this intrinsic:
__device__ ​ unsigned int __vsubss4 ( unsigned int a, unsigned int b )
Which subtracts each signed byte value in a from its corresponding one in b. If you can "live" with the result, rather than expecting a larger int variable, that could save you some of work - and go very well with increasing the number of elements per thread. In fact, it might let you increase it even further to get to the optimum.
I don't think you are measuring times correctly, memory copy is a time consuming step in GPU that you should take into account when measuring your time.
I see some details that you can test:
I suppose you are using MAX_H and MAX_H as constants, you may consider doing so using cudaMemcpyToSymbol().
Remember to sync your threads using __syncthreads(), so you don't get issues between each loop iteration.
CUDA works with warps, so block and number of threads per block work better as multiples of 8, but not larger than 512 threads per block unless your hardware supports it. Here is an example using 128 threads per block: <<<(cols*rows+127)/128,128>>>.
Remember as well to free your allocated memory in GPU and destroying your time events created.
In your kernel function you can have a single variable int v = threadIdx.x + blockIdx.x * blockDim.x .
Have you tested, beside the execution time, that your result is correct? I think you should use cudaMallocPitch() and cudaMemcpy2D() while working with arrays due to padding.
Probably there are other issues with the code, but here's what I see. The following lines in __global__ void diff are considered not optimal:
if (row < MAX_H && col < MAX_W)
{
data_res[v] = (int) data2[v] - (int) data1[v];
}
Conditional operators inside a kernel result in warp divergence. It means that if and else parts inside a warp are executed in sequence, not in parallel. Also, as you might have realized, if evaluates to false only at borders. To avoid the divergence and needless computation, split your image in two parts:
Central part where row < MAX_H && col < MAX_W is always true. Create an additional kernel for this area. if is unnecessary here.
Border areas that will use your diff kernel.
Obviously you'll have modify your code that calls the kernels.
And on a separate note:
GPU has throughput-oriented architecture, but not latency-oriented as CPU. It means CPU may be faster then CUDA when it comes to processing small amounts of data. Have you tried using large data sets?
CUDA Profiler is a very handy tool that will tell you're not optimal in the code.

Using both GPU device of CUDA and zero copy pinned memory

I am using the CUSP library for sparse matrix-multiplication on CUDA a machine. My current code is
#include <cusp/coo_matrix.h>
#include <cusp/multiply.h>
#include <cusp/print.h>
#include <cusp/transpose.h>
#include<stdio.h>
#define CATAGORY_PER_SCAN 1000
#define TOTAL_CATAGORY 100000
#define MAX_SIZE 1000000
#define ELEMENTS_PER_CATAGORY 10000
#define ELEMENTS_PER_TEST_CATAGORY 1000
#define INPUT_VECTOR 1000
#define TOTAL_ELEMENTS ELEMENTS_PER_CATAGORY * CATAGORY_PER_SCAN
#define TOTAL_TEST_ELEMENTS ELEMENTS_PER_TEST_CATAGORY * INPUT_VECTOR
int main(void)
{
cudaEvent_t start, stop;
cudaEventCreate(&start);
cudaEventCreate(&stop);
cudaEventRecord(start, 0);
cusp::coo_matrix<long long int, double, cusp::host_memory> A(CATAGORY_PER_SCAN,MAX_SIZE,TOTAL_ELEMENTS);
cusp::coo_matrix<long long int, double, cusp::host_memory> B(MAX_SIZE,INPUT_VECTOR,TOTAL_TEST_ELEMENTS);
for(int i=0; i< ELEMENTS_PER_TEST_CATAGORY;i++){
for(int j = 0;j< INPUT_VECTOR ; j++){
int index = i * INPUT_VECTOR + j ;
B.row_indices[index] = i; B.column_indices[ index ] = j; B.values[index ] = i;
}
}
for(int i = 0;i < CATAGORY_PER_SCAN; i++){
for(int j=0; j< ELEMENTS_PER_CATAGORY;j++){
int index = i * ELEMENTS_PER_CATAGORY + j ;
A.row_indices[index] = i; A.column_indices[ index ] = j; A.values[index ] = i;
}
}
/*cusp::print(A);
cusp::print(B); */
//test vector
cusp::coo_matrix<long int, double, cusp::device_memory> A_d = A;
cusp::coo_matrix<long int, double, cusp::device_memory> B_d = B;
// allocate output vector
cusp::coo_matrix<int, double, cusp::device_memory> y_d(CATAGORY_PER_SCAN, INPUT_VECTOR ,CATAGORY_PER_SCAN * INPUT_VECTOR);
cusp::multiply(A_d, B_d, y_d);
cusp::coo_matrix<int, double, cusp::host_memory> y=y_d;
cudaEventRecord(stop, 0);
cudaEventSynchronize(stop);
float elapsedTime;
cudaEventElapsedTime(&elapsedTime, start, stop); // that's our time!
printf("time elaplsed %f ms\n",elapsedTime);
return 0;
}
cusp::multiply function uses 1 GPU only (as of my understanding).
How can I use setDevice() to run same program on both the GPU(one cusp::multiply per GPU) .
Measure the total time accurately.
How can I use zero-copy pinned memory with this library as I can use malloc myself.
1 How can I use setDevice() to run same program on both the GPU
If you mean "How can I perform a single cusp::multiply operation using two GPUs", the answer is you can't.
EDIT:
For the case where you want to run two separate CUSP sparse matrix-matrix products on different GPUs, it is possible to simply wrap the operation in a loop and call cudaSetDevice before the transfers and the cusp::multiply call. You will probably not, however get any speed up by doing so. I think I am correct in saying that both the memory transfers and cusp::multiply operations are blocking calls, so the host CPU will stall until they are finished. Because of this, the calls for different GPUs cannot overlap and there will be no speed up over performing the same operation on a single GPU twice. If you were willing to use a multithreaded application and have a host CPU with multiple cores, you could probably still run them in parallel, but it won't be as straightforward host code as it seems you are hoping for.
2 Measure the total time accurately
The cuda_event approach you have now is the most accurate way of measuring the execution time of a single kernel. If you had a hypthetical multi-gpu scheme, then the sum of the events from each GPU context would be the total execution time of the kernels. If, by total time, you mean the "wallclock" time to complete the operation, then you would need to either use a host timer around the whole multigpu segment of your code. I vaguely recall that it might be possible in the latest versions of CUDA to synchronize between events in streams from different contexts in some circumstances, so a CUDA event based timer might still be usable in such a scenario.
3 How can I use zero-copy pinned memory with this library as I can use malloc myself.
To the best of my knowledge that isn't possible. The underlying thrust library CUSP uses can support containers using zero copy memory, but CUSP doesn't expose the necessary mechanisms in the standard matrix constructors to be able to use allocate a CUSP sparse matrix in zero copy memory.

How to parallelize an array shift with OpenMP?

How can I parallelize an array shift with OpenMP?
I've tryed a few things but didn't get any accurate results for the following example (which rotates the elements of an array of Carteira objects, for a permutation algorithm):
void rotaciona(int i)
{
Carteira aux = this->carteira[i];
for(int c = i; c < this->size - 1; c++)
{
this->carteira[c] = this->carteira[c+1];
}
this->carteira[this->size-1] = aux;
}
Thank you very much!
This is an example of a loop with loop-carried dependencies, and so can't be easily parallelized as written because the tasks (each iteration of the loop) aren't independent. Breaking the dependency can vary from a trivial modification to the completely impossible
(eg, an iteration loop).
Here, the case is somewhat in between. The issue with doing this in parallel is that you need to find out what your rightmost value is going to be before your neighbour changes the value. The OMP for construct doesn't expose to you which loop iterations values will be "yours", so I don't think you can use the OpenMP for worksharing construct to break up the loop. However, you can do it yourself; but it requires a lot more code, and it won't nicely reduce to the serial case any more.
But still, an example of how to do this is shown below. You have to break the loop up yourself, and then get your rightmost value. An OpenMP barrier ensures that no one starts modifying values until all the threads have cached their new rightmost value.
#include <stdio.h>
#include <stdlib.h>
#include <omp.h>
int main(int argc, char **argv) {
int i;
char *array;
const int n=27;
array = malloc(n * sizeof(char) );
for (i=0; i<n-1; i++)
array[i] = 'A'+i;
array[n-1] = '\0';
printf("Array pre-shift = <%s>\n",array);
#pragma omp parallel default(none) shared(array) private(i)
{
int nthreads = omp_get_num_threads();
int tid = omp_get_thread_num();
int blocksize = (n-2)/nthreads;
int start = tid*blocksize;
int end = start + blocksize - 1;
if (tid == nthreads-1) end = n-2;
/* we are responsible for values start...end */
char rightval = array[end+1];
#pragma omp barrier
for (i=start; i<end; i++)
array[i] = array[i+1];
array[end] = rightval;
}
printf("Array post-shift = <%s>\n",array);
return 0;
}
Though your sample doesn't show any explicit openmp pragma's, I don't think it could work easily:
you are doing an in-place operation with overlapping regions.
If you split the loop in chunks, you'll have race conditions at the boundaries (because el[n] gets copied from el[n+1], which might already have been updated in another thread).
I suggest that you do manual chunking (which can be done), but I suspect that openmp parallel for is not flexible enough (haven't tried), so you could just have a parallell region that does the work in chunks, and fixup the boundary elements after a thread barrier/end of parallel block
Other thoughts:
if your values are POD, you can use memmove instead
if you can, simply switch to a list
.
std::list<Carteira> items(3000);
// rotation is now simply:
items.push_back(items.front());
items.erase(items.begin());

Low performance in a OpenMP program

I am trying to understand an openmp code from here. You can see the code below.
In order to measure the speedup, difference between the serial and omp version, I use time.h, do you find right this approach?
The program runs on a 4 core machine. I specify export OMP_NUM_THREADS="4" but can not see substantially speedup, usually I get 1.2 - 1.7. Which problems am I facing in this parallelization?
Which debug/performace tool could I use to see the loss of performace?
code (for compilation I use xlc_r -qsmp=omp omp_workshare1.c -o omp_workshare1.exe)
#include <omp.h>
#include <stdio.h>
#include <stdlib.h>
#include <sys/time.h>
#define CHUNKSIZE 1000000
#define N 100000000
int main (int argc, char *argv[])
{
int nthreads, tid, i, chunk;
float a[N], b[N], c[N];
unsigned long elapsed;
unsigned long elapsed_serial;
unsigned long elapsed_omp;
struct timeval start;
struct timeval stop;
chunk = CHUNKSIZE;
// ================= SERIAL start =======================
/* Some initializations */
for (i=0; i < N; i++)
a[i] = b[i] = i * 1.0;
gettimeofday(&start,NULL);
for (i=0; i<N; i++)
{
c[i] = a[i] + b[i];
//printf("Thread %d: c[%d]= %f\n",tid,i,c[i]);
}
gettimeofday(&stop,NULL);
elapsed = 1000000 * (stop.tv_sec - start.tv_sec);
elapsed += stop.tv_usec - start.tv_usec;
elapsed_serial = elapsed ;
printf (" \n Time SEQ= %lu microsecs\n", elapsed_serial);
// ================= SERIAL end =======================
// ================= OMP start =======================
/* Some initializations */
for (i=0; i < N; i++)
a[i] = b[i] = i * 1.0;
gettimeofday(&start,NULL);
#pragma omp parallel shared(a,b,c,nthreads,chunk) private(i,tid)
{
tid = omp_get_thread_num();
if (tid == 0)
{
nthreads = omp_get_num_threads();
printf("Number of threads = %d\n", nthreads);
}
//printf("Thread %d starting...\n",tid);
#pragma omp for schedule(static,chunk)
for (i=0; i<N; i++)
{
c[i] = a[i] + b[i];
//printf("Thread %d: c[%d]= %f\n",tid,i,c[i]);
}
} /* end of parallel section */
gettimeofday(&stop,NULL);
elapsed = 1000000 * (stop.tv_sec - start.tv_sec);
elapsed += stop.tv_usec - start.tv_usec;
elapsed_omp = elapsed ;
printf (" \n Time OMP= %lu microsecs\n", elapsed_omp);
// ================= OMP end =======================
printf (" \n speedup= %f \n\n", ((float) elapsed_serial) / ((float) elapsed_omp)) ;
}
There's nothing really wrong with the code as above, but your speedup is going to be limited by the fact that the main loop, c=a+b, has very little work -- the time required to do the computation (a single addition) is going to be dominated by memory access time (2 loads and one store), and there's more contention for memory bandwidth with more threads acting on the array.
We can test this by making the work inside the loop more compute-intensive:
c[i] = exp(sin(a[i])) + exp(cos(b[i]));
And then we get
$ ./apb
Time SEQ= 17678571 microsecs
Number of threads = 4
Time OMP= 4703485 microsecs
speedup= 3.758611
which is obviously a lot closer to the 4x speedup one would expect.
Update: Oh, and to the other questions -- gettimeofday() is probably fine for timing, and on a system where you're using xlc - is this AIX? In that case, peekperf is a good overall performance tool, and the hardware performance monitors will give you access to to memory access times. On x86 platforms, free tools for performance monitoring of threaded code include cachegrind/valgrind for cache performance debugging (not the problem here), scalasca for general OpenMP issues, and OpenSpeedShop is pretty useful, too.

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