I believe I am experiencing false sharing using OpenMP. Is there any way to identify it and fix it?
My code is: https://github.com/wchan/libNN/blob/master/ResilientBackpropagation.hpp line 36.
Using a 4 core CPU compared to the single threaded 1 core version yielded only 10% in additional performance. When using a NUMA 32 physical (64 virtual) CPU system, the CPU utilization is stuck at around 1.5 cores, I think this is a direct symptom of false sharing and unable to scale.
I also tried running it with Intel VTune profiler, it stated most of the time is spent on the "f()" and "+=" functions. I believe this is reasonable and doesn't really explain why I am getting such poor scaling...
Any ideas/suggestions?
Thanks.
Use reduction instead of explicitly indexing an array based on the thread ID. That array virtually guarantees false sharing.
i.e. replace this
#pragma omp parallel for
clones[omp_get_thread_num()]->mse() += norm_2(dedy);
for (int i = 0; i < omp_get_max_threads(); i++) {
neural_network->mse() += clones[i]->mse();
with this:
#pragma omp parallel for reduction(+ : mse)
mse += norm_2(dedy);
neural_network->mse() = mse;
One way of knowing for sure is looking at cache statistics with a tool like cachegrind :
valgrind --tool=cachegrind [command]
Related
I'm trying to implement a faster version of the following code fragment:
Eigen::VectorXd dTX = (( (XPSF.array() - x0).square() + (ZPSF.array() - z0).square() ).sqrt() + txShift)*fs/c + t0*fs;
Eigen::VectorXd Zsq = ZPSF.array().square();
Eigen::MatrixXd idxt(XPSF.size(),nc);
for (int i = 0; i < nc; i++) {
idxt.col(i) = ((XPSF.array() - xe(i)).square() + Zsq.array()).sqrt()*fs/c + dTX.array();
idxt.col(i) = (abs(XPSF.array()-xe(i)) <= ZPSF.array()*0.5/fnumber).select(idxt.col(i),-1);
}
The sample array sizes I'm working with right now are:
XPSF: Column Vector of 591*192 coefficients (113,472 total values in the column vector)
ZPSF: Same size as XPSF
xe: RowVector of 192 coefficients
idxt: Matrix of 113,472x192 size
Current runs with gcc and -msse2 and -o3 optimization yield an average time of ~0.08 seconds for the first line of the loop and ~0.03 seconds for the second line of the loop. I know that runtimes are platform dependent, but I believe that this still can be much faster. A commercial software performs the operations I'm trying to do here in ~two orders of magnitude less time. Also, I suspect my code is a bit amateurish right now!
I've tried reading over Eigen documentation to understand how vectorization works, where it is implemented and how much of this code might be "implicitly" parallelized by Eigen, but I've struggled to keep track of the details. I'm also a bit new to C++ in general, but I've seen the documentation and other resources regarding std::thread and have tried to combine it with this code, but without much success.
Any advice would be appreciated.
Update:
Update 2
I would upvote Soleil's answer because it contains helpful information if I had the reputation score for it. However, I should clarify that I would like to first figure out what optimizations I can do without a GPU. I'm convinced (albeit without OpenMP) Eigen's inherent multithreading and vectorization won't speed it up any further (unless there are unnecessary temporaries being generated). How could I use something like std::thread to explicitly parellelize this? I'm struggling to combine both std::thread and Eigen to this end.
OpenMP
If your CPU has enough many cores and threads, usually a simple and quick first step is to invoke OpenMP by adding the pragma:
#pragma omp parallel for
for (int i = 0; i < nc; i++)
and compile with /openmp (cl) or -fopenmp (gcc) or just -ftree-parallelize-loops with gcc in order to auto unroll the loops.
This will do a map reduce and the map will occur over the number of parallel threads your CPU can handle (8 threads with the 7700HQ).
In general you also can set a clause num_threads(n) where n is the desired number of threads:
#pragma omp parallel num_threads(8)
Where I used 8 since the 7700HQ can handle 8 concurrent threads.
TBB
You also can unroll your loop with TBB:
#pragma unroll
for (int i = 0; i < nc; i++)
threading integrated with eigen
With Eigen you can add
OMP_NUM_THREADS=n ./my_program
omp_set_num_threads(n);
Eigen::setNbThreads(n);
remarks with multithreading with eigen
However, in the FAQ:
currently Eigen parallelizes only general matrix-matrix products (bench), so it doesn't by itself take much advantage of parallel hardware."
In general, the improvement with OpenMP is not always here, so benchmark the release build. Another way is to make sure that you're using vectorized instructions.
Again, from the FAQ/vectorization:
How can I enable vectorization?
You just need to tell your compiler to enable the corresponding
instruction set, and Eigen will then detect it. If it is enabled by
default, then you don't need to do anything. On GCC and clang you can
simply pass -march=native to let the compiler enables all instruction
set that are supported by your CPU.
On the x86 architecture, SSE is not enabled by default by most
compilers. You need to enable SSE2 (or newer) manually. For example,
with GCC, you would pass the -msse2 command-line option.
On the x86-64 architecture, SSE2 is generally enabled by default, but
you can enable AVX and FMA for better performance
On PowerPC, you have to use the following flags: -maltivec
-mabi=altivec, for AltiVec, or -mvsx for VSX-capable systems.
On 32-bit ARM NEON, the following: -mfpu=neon -mfloat-abi=softfp|hard,
depending if you are on a softfp/hardfp system. Most current
distributions are using a hard floating-point ABI, so go for the
latter, or just leave the default and just pass -mfpu=neon.
On 64-bit ARM, SIMD is enabled by default, you don't have to do
anything extra.
On S390X SIMD (ZVector), you have to use a recent gcc (version >5.2.1)
compiler, and add the following flags: -march=z13 -mzvector.
multithreading with cuda
Given the size of your arrays, you want to try to offload to a GPU to reach the microsecond; in that case you would have (typically) as many threads as the number of elements in your array.
For a simple start, if you have an nvidia card, you want to look at cublas, which also allows you to use the tensor registers (fused multiply add, etc) of the last generations, unlike regular kernel.
Since eigen is a header only library, it makes sense that you could use it in a cuda kernel.
You also may implements everything "by hand" (ie., without eigen) with regular kernels. This is a nonsense in terms of engineering, but common practice in an education/university project, in order to understand everything.
multithreading with OneAPI and Intel GPU
Since you have a skylake architecture, you also can unroll your loop on your CPU's GPU with OneAPI:
// Unroll loop as specified by the unroll factor.
#pragma unroll unroll_factor
for (int i = 0; i < nc; i++)
(from the sample).
I am novice is parallel programming. I running a my own Gibbs sampler written in C++. The overview of program look some thing like this.
for(int iter=0; iter <=itermax; iter++){ //loop1
#pragma omp parallel for schedule(dynamic)
for(int jobs= 0; jobs<=1000; jobs++){ // loop2
small_job();
#pragma omp critical(dataupdate){
data_updates()
}
}
jobs_that_cannot_be_parallelized();
}
I am running in a machine with 64 cores. Since small_job are of variable length and small I was assigning omp_get_max_threads = 128. The number of cores used seems to be correct (see fig load last hour).. Each of peaks belongs to loop2.
However when I look to the actual cpu usage (see fig it seems lot of of cpu is used by system and only 20% is used by user. Is it because I am spawning lots of threads at loop2. What are best practices to decide on omp_get_max_threads? I know I have not given enough information but I will really appreciate any other recommendation to make the program faster.
I wrote classic game "Life" with 4-sided neighbors. When I run it in debug, it says:
Consecutive version: 4.2s
Parallel version: 1.5s
Okey, it's good. But if I run it in release, it says:
Consecutive version: 0.46s
Parallel version: 1.23s
Why? I run it on the computer with 4 kernels. I run 4 threads in parallel section. Answer is correct. But somethere is leak and I don't know that place. Can anybody help me?
I try to run it in Visual Studio 2008 and 2012. The results are same. OMP is enabled in the project settings.
To repeat my problem, you can find defined constant PARALLEL and set it to 1 or 0 to enable and disable OMP correspondingly. Answer will be in the out.txt (out.txt - right answer example). The input must be in in.txt (my input - in.txt). There are some russian symbols, you don't need to understand them, but the first number in in.txt means number of threads to run in parallel section (it's 4 in the example).
The main part is placed in the StartSimulation function. If you run the program, you will see some russian text with running time in the console.
The program code is big enough, so I add it with file hosting - main.cpp (l2 means "lab 2" for me)
Some comments about StartSimulation function. I cuts 2D surface with cells into small rectangles. It is done by AdjustKernelsParameters function.
I do not find the ratio so strange. Having multiple threads co-operate is a complex business and has overheads.
Access to shared memory needs to be serialized which normally involves some form of locking mechanism and contention between threads where they have to wait for the lock to be released.
Such shared variables need to be synchronized between the processor cores which can give significant slowdowns. Also the compiler needs to treat these critical areas differently as a "sequence point".
All this reduces the scope for per thread optimization both in the processor hardware and the compiler for each thread when it is working with the shared variable.
It seems that in this case the overheads of parallelization outweigh the optimization possibilities for the single threaded case.
If there were more work for each thread to do independently before needed to access a shared variable then these overheads would be less significant.
You are using guided loop schedule. This is a very bad choice given that you are dealing with a regular problem where each task can easily do exactly the same amount of work as any other if the domain is simply divided into chunks of equal size.
Replace schedule(guided) with schedule(static). Also employ sum reduction over livingCount instead of using locked increments:
#if PARALLEL == 1
#pragma omp parallel for schedule(static) num_threads(kernelsCount) \
reduction(+:livingCount)
#endif
for (int offsetI = 0; offsetI < n; offsetI += kernelPartSizeN)
{
for (int offsetJ = 0; offsetJ < m; offsetJ += kernelPartSizeM)
{
int boundsN = min(kernelPartSizeN, n - offsetI),
boundsM = min(kernelPartSizeM, m - offsetJ);
for (int kernelOffsetI = 0; kernelOffsetI < boundsN; ++kernelOffsetI)
{
for (int kernelOffsetJ = 0; kernelOffsetJ < boundsM; ++kernelOffsetJ)
{
if(BirthCell(offsetI + kernelOffsetI, offsetJ + kernelOffsetJ))
{
++livingCount;
}
}
}
}
}
I have a c++ program with multiple For loops; each one runs about 5 million iterations. Is there any command I can use with g++ to make the resulting .exe will use multiple cores; i.e. make the first For loop run on the first core and the second For loop run on the second core at the same time? I've tried -O3 and -O3 -ftree-vectorize, but in both cases, my cpu usage still only hovers at around 25%.
EDIT:
Here is my code, in case in helps. I'm basically just making a program to test the speed capabilities of my computer.
#include <iostream>
using namespace std;
#include <math.h>
int main()
{
float *bob = new float[50102133];
float *jim = new float[50102133];
float *joe = new float[50102133];
int i,j,k,l;
//cout << "Starting test...";
for (i=0;i<50102133;i++)
bob[i] = sin(i);
for (j=0;j<50102133;j++)
bob[j] = sin(j*j);
for (k=0;k<50102133;k++)
bob[k] = sin(sqrt(k));
for (l=0;l<50102133;l++)
bob[l] = cos(l*l);
cout << "finished test.";
cout << "the 100120 element is," << bob[1001200];
return 0;
}
The most obviously choice would be to use OpenMP. Assuming your loop is one that's really easy to execute multiple iterations in parallel, you might be able to just add:
#pragma openmp parallel for
...immediately before the loop, and get it to execute in parallel. You'll also have to add -fopenmp when you compile.
Depending on the content of the loop, that may give anywhere from a nearly-linear speedup to slowing the code down somewhat. In the latter cases (slowdown or minimal speedup) there may be other things you can do with OpenMP to help speed it up, but without knowing at least a little about the code itself, it's hard to guess what to do or what improvement you may be able to expect at maximum.
The other advice you're getting ("Use threads") may be suitable. OpenMP is basically an automated way of putting threads to use for specific types of parallel code. For a situation such as you describe (executing multiple iterations of a loop in parallel) OpenMP is generally preferred--it's quite a bit simpler to implement, and may well give better performance unless you know multithreading quite well and/or expend a great deal of effort on parallelizing the code.
Edit:
The code you gave in the question probably won't benefit from multiple threads. The problem is that it does very little computation on each data item before writing the result out to memory. Even a single core can probably do the computation fast enough that the overall speed will be limited by the bandwidth to memory.
To stand a decent chance of getting some real benefit from multiple threads, you probably want to write some code that does more computation and less just reading and writing memory. For example, if we collapse your computations together, and do all of them on a single item, then sum the results:
double total = 0;
for (int i = 0; i < size; i++)
total += sin(i) + sin(i*i) + sin(sqrt(i)) + cos(i*i);
By adding a pragma:
#pragma omp parallel for reduction(+:total)
...just before the for loop, we stand a good chance of seeing a substantial improvement in execution speed. Without OpenMP, I get a time like this:
Real 16.0399
User 15.9589
Sys 0.0156001
...but with the #pragma and OpenMP enabled when I compile, I get a time like this:
Real 8.96051
User 17.5033
Sys 0.0468003
So, on my (dual core) processor, time has dropped from 16 to 9 seconds--not quite twice as fast, but pretty close. Of course, a lot of the improvement you get will depend on exactly how many cores you have available. For example, on my other computer (with an Intel i7 CPU), I get a rather larger improvement because it has more cores.
Without OpenMP:
Real 15.339
User 15.3281
Sys 0.015625
...and with OpenMP:
Real 3.09105
User 23.7813
Sys 0.171875
For completeness, here's the final code I used:
#include <math.h>
#include <iostream>
static const int size = 1024 * 1024 * 128;
int main(){
double total = 0;
#pragma omp parallel for reduction(+:total)
for (int i = 0; i < size; i++)
total += sin(i) + sin(i*i) + sin(sqrt(i)) + cos(i*i);
std::cout << total << "\n";
}
The compiler has no way to tell if your code inside the loop can be safely executed on multiple cores. If you want to use all your cores, use threads.
Use Threads or Processes, you may want to look to OpenMp
C++11 got support for threading but c++ compilers won't/can't do any threading on their own.
As others have pointed out, you can manually use threads to achieve this. You might look at libraries such as libdispatch (aka. GCD) or Intel's TBB to help you do this with the least pain.
The -ftree-vectorize option you mention is for targeting SIMD vector processor units on CPUs such as ARM's NEON or Intel's SSE. The code produced is not thread-parallel, but rather operation parallel using a single thread.
The code example posted above is highly amenable to parallelism on SIMD systems as the body of each loop very obviously has no dependancies on the previous iteration, and the operations in the loop are linear.
On some ARM Cortex A series systems at least, you may need to accept slightly reduced accuracy to get the full benefits.
I am working on parallel algorithms using OpenMP. Judging from the CPU usage, much of the "sequential" code I write is actually executed in parallel.
For example:
#pragma omp parallel for if (par == "parallel")
for (int64_t u = 1; u <= n; ++u) {
for (int64_t v = u + 1; v <= n; ++v) {
....
}
}
This is conditionally parallel if a flag is set. With the flag set, I see CPU usages of 1500% on a 16 core machine. With the flag not set, I still see 250% CPU usage.
I suppose this is due to some autoparallelization going on. Correct? Does GCC do this?
Since I need to compare sequential and parallel running times, I would like code not annotated with (#pragma omp parallel... etc.) to run on one CPU only. Can I achieve this easily? Is there a GCC flag by which I can switch of autoparallelization and have parallelism where I explicitly annotate with OpenMP?
Note that the OpenMP if clause exerts run-time rather than compile-time control over the concurrency. It means that while the condition inside the if clause might evaluate to false when the program is executed, which deactivates the parallel region by setting the number of threads in its team to 1, the region would still expand to several runtime calls and a separate function for its body, although this would not lead to parallel execution. The OpenMP runtime might also keep a running pool of OpenMP threads busy-waiting for tasks.
The only way to guarantee that your OpenMP code would compile as a clearly serial executable (given that you do not link to parallel libraries) is to compile with OpenMP support disabled. In your case that would mean no -fopenmp option given to GCC while the code is being compiled.