Thanks. That makes sense. By the way: How do you handle multithreading at one level of the library interfering with multithreading in another? For instance, blas using its own thread scheduling...
On Wednesday, March 13, 2024 at 9:37:35 AM UTC-7 bruno.t...@gmail.com wrote: > In step-3, the user assembles the matrix by writing its own for loop and > so it's not multithreaded. To use multithreaded assembly, you need to use > mesh_loop like in step-16 for example. > > deal.II own functions are sometimes multithreaded sometimes they aren't. > Usually if someone (most often a developer) will get a significant speedup > by multithreading a function, then the function is multithreaded. Since we > are not keeping track of which functions are multithreaded and which ones > are not, I cannot tell you what's multithreaded in step-3. The solver is > multithreaded, maybe some other functions are multithreaded too, maybe not. > > Le mer. 13 mars 2024 à 11:56, Petr Krysl <krysl...@gmail.com> a écrit : > >> Btw: the assembly does NOT appear to be multithreaded. Only the CG >> solve... >> >> On Wednesday, March 13, 2024 at 8:17:16 AM UTC-7 Petr Krysl wrote: >> >>> Oh, wow! You must be doing a great deal of checking in debug mode!!! >>> >>> All fixed now: >>> >>> pkrysl@firenze:~/dealii-9.5.2/examples/step-3$ time >>> DEAL_II_NUM_THREADS=1 ./step-3 >>> Number of active cells: 1048576 >>> Number of degrees of freedom: 1050625 >>> Sparsity: 0.496119 >>> As!sembly: 0.741549 >>> DEAL:cg::Starting value 0.00390244 >>> DEAL:cg::Failure step 1000 value 4.73155e-07 >>> terminate called after throwing an instance of >>> 'dealii::SolverControl::NoConvergence' >>> >>> But: the sparsity pattern is definitely not negligible compared to the >>> overall assembly time! >>> >>> On Wednesday, March 13, 2024 at 8:03:50 AM UTC-7 bruno.t...@gmail.com >>> wrote: >>> >>>> Yes, something is strange. Are you running in release mode? deal.II is >>>> a lot slower in debug mode because of all the asserts we have. Can you try >>>> >>>> `make release` in the step-3 directory. We actually use step-3 as one of >>>> our performance benchmark using 2 threads. As you can see here >>>> <https://dealii.org/performance_tests/graphs/whistler-gentoo-clang-16/timing-step-3.png>, >>>> >>>> the assembly takes 0.6 second. >>>> >>>> Le mer. 13 mars 2024 à 10:48, Petr Krysl <krysl...@gmail.com> a écrit : >>>> >>>>> Something is very wrong. I checked with my own code on the same >>>>> machine: >>>>> heat equation with 1M quads, the conductivity matrix >>>>> is completely assembled in 1.9 seconds. The dealii mesh is smaller, >>>>> and just the sparsity pattern takes 3x as long. >>>>> And this can't be multithreading, can it? >>>>> >>>>> On Wednesday, March 13, 2024 at 6:56:57 AM UTC-7 bruno.t...@gmail.com >>>>> wrote: >>>>> >>>>>> I agree, in that case it's not negligible. Be aware that by default >>>>>> deal.II is multithreaded, so if you ran deal.II without explicitly >>>>>> disabling multithreading or forcing deal.II to use a single core, the >>>>>> code >>>>>> was using all the cores available when it could. >>>>>> >>>>>> Best, >>>>>> >>>>>> Bruno >>>>>> >>>>>> Le mer. 13 mars 2024 à 00:46, Petr Krysl <krysl...@gmail.com> a >>>>>> écrit : >>>>>> >>>>>>> Here is a data point: >>>>>>> ``` >>>>>>> pkrysl@firenze:~/dealii-9.5.2/examples/step-3$ make >>>>>>> Consolidate compiler generated dependencies of target step-3 >>>>>>> [ 50%] Building CXX object CMakeFiles/step-3.dir/step-3.cc.o >>>>>>> [100%] Linking CXX executable step-3 >>>>>>> [100%] Built target step-3 >>>>>>> pkrysl@firenze:~/dealii-9.5.2/examples/step-3$ time ./step-3 >>>>>>> Number of active cells: 262144 >>>>>>> Number of degrees of freedom: 263169 >>>>>>> Took: 5.520668 >>>>>>> DEAL:cg::Starting value 0.00779724 >>>>>>> DEAL:cg::Convergence step 583 value 7.44264e-09 >>>>>>> >>>>>>> real 1m2.503s >>>>>>> user 4m45.171s >>>>>>> sys 0m2.427s >>>>>>> pkrysl@firenze:~/dealii-9.5.2/examples/step-3$ >>>>>>> >>>>>>> ``` >>>>>>> I measured >>>>>>> ``` >>>>>>> clock_t start, end; >>>>>>> start = clock(); >>>>>>> >>>>>>> DoFTools::make_sparsity_pattern(dof_handler, dsp); >>>>>>> end = clock(); >>>>>>> printf("Took: %f\n", (float)((end - start) / >>>>>>> (float)CLOCKS_PER_SEC)); >>>>>>> ``` >>>>>>> 5.5 seconds of sparsity pattern construction compared to >>>>>>> 62 seconds of total run time is definitely not negligible, wouldn't >>>>>>> you agree? >>>>>>> >>>>>>> On Tuesday, March 12, 2024 at 7:29:49 PM UTC-7 Petr Krysl wrote: >>>>>>> >>>>>>>> Thank you. I have actually no complaints about the performance. >>>>>>>> I just want to know what is going on in deal.ii for a paper I am >>>>>>>> working on. >>>>>>>> >>>>>>>> On Tuesday, March 12, 2024 at 6:59:19 PM UTC-7 bruno.t...@gmail.com >>>>>>>> wrote: >>>>>>>> >>>>>>>>> If building the sparsity pattern is the bottleneck in your code, >>>>>>>>> feel free to open an issue and we can take a look at how we can >>>>>>>>> improve it. >>>>>>>>> Though if the assembly of the matrix is performance critical, using >>>>>>>>> the >>>>>>>>> MatrixFree class is the way to go. >>>>>>>>> >>>>>>>>> Bruno >>>>>>>>> >>>>>>>>> >>>>>>>>> Le mar. 12 mars 2024 à 20:38, Petr Krysl <krysl...@gmail.com> a >>>>>>>>> écrit : >>>>>>>>> >>>>>>>>>> In Matlab calling sparse() is equivalent to building a sparsity >>>>>>>>>> pattern (just forget about the actual values) >>>>>>>>>> from the I, J row and column indices. And that is NOT a >>>>>>>>>> negligible expense. It is a sizeable fraction of >>>>>>>>>> the cost of building a Laplacian matrix on triangles, for >>>>>>>>>> instance. >>>>>>>>>> >>>>>>>>>> On Tuesday, March 12, 2024 at 2:46:07 PM UTC-7 >>>>>>>>>> bruno.t...@gmail.com wrote: >>>>>>>>>> >>>>>>>>>>> I am not sure why but I need to approve all of your messages. >>>>>>>>>>> Usually we only need to approve the first time someone posts. Not >>>>>>>>>>> sure >>>>>>>>>>> what's going on here. >>>>>>>>>>> >>>>>>>>>>> I don't remember how long the computation of the sparsity >>>>>>>>>>> pattern took but it was small. The reason this part is not >>>>>>>>>>> parallelized in >>>>>>>>>>> deal.II is because nobody found out that this was a bottleneck. If >>>>>>>>>>> you fill >>>>>>>>>>> your matrix with ones, you probably want the sparsity pattern >>>>>>>>>>> computation >>>>>>>>>>> to be multithreaded. However, if you are assembling a mass matrix >>>>>>>>>>> on a >>>>>>>>>>> non-uniform mesh, you have so much more work to do that it doesn't >>>>>>>>>>> matter >>>>>>>>>>> if you build your sparsity pattern in serial. In theory, I agree >>>>>>>>>>> everything >>>>>>>>>>> should be multithreaded but in practice, it has not been worth the >>>>>>>>>>> effort >>>>>>>>>>> so far. If the performance of the assembly is really critical, you >>>>>>>>>>> should >>>>>>>>>>> use the MatrixFree class instead of building a matrix. >>>>>>>>>>> >>>>>>>>>>> Bruno >>>>>>>>>>> >>>>>>>>>>> Le mar. 12 mars 2024 à 17:22, Petr Krysl <krysl...@gmail.com> a >>>>>>>>>>> écrit : >>>>>>>>>>> >>>>>>>>>>>> That is a good point about Tpetra: I will check it out. >>>>>>>>>>>> >>>>>>>>>>>> > SparsityPattern is usually extremely fast >>>>>>>>>>>> It can still become a bottleneck, provided everything else runs >>>>>>>>>>>> in parallel. ;-) >>>>>>>>>>>> Which reminds me: I wanted to ask you about the WorkStream >>>>>>>>>>>> paper: The sparsity pattern computation was not reported. >>>>>>>>>>>> Could you tell me how expensive it was compared to the >>>>>>>>>>>> sequential assembly of the matrix? >>>>>>>>>>>> For linear problems, both the sparsity pattern computation and >>>>>>>>>>>> the computation of the entries need to be done. >>>>>>>>>>>> Therefore, It does not really help if the computation of the >>>>>>>>>>>> entries is run in parallel, when the sparsity pattern is done in >>>>>>>>>>>> serial. >>>>>>>>>>>> Isn't that right? >>>>>>>>>>>> >>>>>>>>>>>> On Tuesday, March 12, 2024 at 12:08:29 PM UTC-7 >>>>>>>>>>>> bruno.t...@gmail.com wrote: >>>>>>>>>>>> >>>>>>>>>>>>> In Trilinos, the Tpetra library has Graph which is basically a >>>>>>>>>>>>> SparsityPattern. Tpetra uses Kokkos (which abstracts >>>>>>>>>>>>> multithreading and GPU >>>>>>>>>>>>> support) everywhere so I would expect that they use Kokkos to >>>>>>>>>>>>> build the >>>>>>>>>>>>> Graph too. Multithreading for dealii's SparsityPattern is not >>>>>>>>>>>>> planned so >>>>>>>>>>>>> far. It could be done but building the SparsityPattern is usually >>>>>>>>>>>>> extremely >>>>>>>>>>>>> fast compared to the rest of the code and so, it's not worth >>>>>>>>>>>>> doing. >>>>>>>>>>>>> >>>>>>>>>>>>> Bruno >>>>>>>>>>>>> >>>>>>>>>>>>> Le mar. 12 mars 2024 à 14:17, Petr Krysl <krysl...@gmail.com> >>>>>>>>>>>>> a écrit : >>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks, that is a helpful confirmation. >>>>>>>>>>>>>> Would you know if there is any multithreading sparsity >>>>>>>>>>>>>> pattern computation available anywhere? >>>>>>>>>>>>>> Is something like this planned for dealii? >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Tuesday, March 12, 2024 at 10:39:22 AM UTC-7 >>>>>>>>>>>>>> bruno.t...@gmail.com wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hello, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> SparsityPattern is used for deal.II own matrices which do >>>>>>>>>>>>>>> not support MPI. As far as I can tell, SparsityPattern does not >>>>>>>>>>>>>>> use >>>>>>>>>>>>>>> multithreading and I don't think adding elements is threadsafe. >>>>>>>>>>>>>>> So you are >>>>>>>>>>>>>>> right. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Bruno >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Tuesday, March 12, 2024 at 12:58:37 PM UTC-4 >>>>>>>>>>>>>>> krysl...@gmail.com wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> It would appear that the sparsity pattern is not (and >>>>>>>>>>>>>>>> cannot be) computed in parallel. That is my reading of the >>>>>>>>>>>>>>>> code. Am I wrong? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>> The deal.II project is located at http://www.dealii.org/ >>>>>>>>>>>>>> For mailing list/forum options, see >>>>>>>>>>>>>> https://groups.google.com/d/forum/dealii?hl=en >>>>>>>>>>>>>> --- >>>>>>>>>>>>>> You received this message because you are subscribed to a >>>>>>>>>>>>>> topic in the Google Groups "deal.II User Group" group. >>>>>>>>>>>>>> To unsubscribe from this topic, visit >>>>>>>>>>>>>> https://groups.google.com/d/topic/dealii/hq6L0-qgpbE/unsubscribe >>>>>>>>>>>>>> . >>>>>>>>>>>>>> To unsubscribe from this group and all its topics, send an >>>>>>>>>>>>>> email to dealii+un...@googlegroups.com. >>>>>>>>>>>>>> To view this discussion on the web visit >>>>>>>>>>>>>> https://groups.google.com/d/msgid/dealii/d9905f95-ef78-4564-a605-e10c2c19d981n%40googlegroups.com >>>>>>>>>>>>>> >>>>>>>>>>>>>> <https://groups.google.com/d/msgid/dealii/d9905f95-ef78-4564-a605-e10c2c19d981n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>>>>>>>>>>> . >>>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>> The deal.II project is located at http://www.dealii.org/ >>>>>>>>>>>> For mailing list/forum options, see >>>>>>>>>>>> https://groups.google.com/d/forum/dealii?hl=en >>>>>>>>>>>> --- >>>>>>>>>>>> You received this message because you are subscribed to a topic >>>>>>>>>>>> in the Google Groups "deal.II User Group" group. >>>>>>>>>>>> To unsubscribe from this topic, visit >>>>>>>>>>>> https://groups.google.com/d/topic/dealii/hq6L0-qgpbE/unsubscribe >>>>>>>>>>>> . >>>>>>>>>>>> To unsubscribe from this group and all its topics, send an >>>>>>>>>>>> email to dealii+un...@googlegroups.com. >>>>>>>>>>>> >>>>>>>>>>> To view this discussion on the web visit >>>>>>>>>>>> https://groups.google.com/d/msgid/dealii/5f66ea8c-1725-4dab-b026-fb7e19e92e14n%40googlegroups.com >>>>>>>>>>>> >>>>>>>>>>>> <https://groups.google.com/d/msgid/dealii/5f66ea8c-1725-4dab-b026-fb7e19e92e14n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>>>>>>>>> . >>>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>> The deal.II project is located at http://www.dealii.org/ >>>>>>>>>> For mailing list/forum options, see >>>>>>>>>> https://groups.google.com/d/forum/dealii?hl=en >>>>>>>>>> --- >>>>>>>>>> You received this message because you are subscribed to a topic >>>>>>>>>> in the Google Groups "deal.II User Group" group. >>>>>>>>>> To unsubscribe from this topic, visit >>>>>>>>>> https://groups.google.com/d/topic/dealii/hq6L0-qgpbE/unsubscribe. >>>>>>>>>> To unsubscribe from this group and all its topics, send an email >>>>>>>>>> to dealii+un...@googlegroups.com. >>>>>>>>>> >>>>>>>>> To view this discussion on the web visit >>>>>>>>>> https://groups.google.com/d/msgid/dealii/a5277543-bc58-4af6-a2c1-3930c5100553n%40googlegroups.com >>>>>>>>>> >>>>>>>>>> <https://groups.google.com/d/msgid/dealii/a5277543-bc58-4af6-a2c1-3930c5100553n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>>>>>>> . >>>>>>>>>> >>>>>>>>> -- >>>>>>> The deal.II project is located at http://www.dealii.org/ >>>>>>> For mailing list/forum options, see >>>>>>> https://groups.google.com/d/forum/dealii?hl=en >>>>>>> --- >>>>>>> You received this message because you are subscribed to a topic in >>>>>>> the Google Groups "deal.II User Group" group. >>>>>>> To unsubscribe from this topic, visit >>>>>>> https://groups.google.com/d/topic/dealii/hq6L0-qgpbE/unsubscribe. >>>>>>> To unsubscribe from this group and all its topics, send an email to >>>>>>> dealii+un...@googlegroups.com. >>>>>>> >>>>>> To view this discussion on the web visit >>>>>>> https://groups.google.com/d/msgid/dealii/444f9972-91ef-43f9-8019-14d9784dd3c4n%40googlegroups.com >>>>>>> >>>>>>> <https://groups.google.com/d/msgid/dealii/444f9972-91ef-43f9-8019-14d9784dd3c4n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>>>> . >>>>>>> >>>>>> -- >>>>> The deal.II project is located at http://www.dealii.org/ >>>>> For mailing list/forum options, see >>>>> https://groups.google.com/d/forum/dealii?hl=en >>>>> --- >>>>> You received this message because you are subscribed to a topic in the >>>>> Google Groups "deal.II User Group" group. >>>>> To unsubscribe from this topic, visit >>>>> https://groups.google.com/d/topic/dealii/hq6L0-qgpbE/unsubscribe. >>>>> To unsubscribe from this group and all its topics, send an email to >>>>> dealii+un...@googlegroups.com. >>>>> >>>> To view this discussion on the web visit >>>>> https://groups.google.com/d/msgid/dealii/c4ec7935-a079-4074-bad5-9e05066df645n%40googlegroups.com >>>>> >>>>> <https://groups.google.com/d/msgid/dealii/c4ec7935-a079-4074-bad5-9e05066df645n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>> . >>>>> >>>> -- >> The deal.II project is located at http://www.dealii.org/ >> For mailing list/forum options, see >> https://groups.google.com/d/forum/dealii?hl=en >> --- >> You received this message because you are subscribed to a topic in the >> Google Groups "deal.II User Group" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/dealii/hq6L0-qgpbE/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to >> dealii+un...@googlegroups.com. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/dealii/3a42fdec-2d75-4b3e-816b-ea0b32073377n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/dealii/3a42fdec-2d75-4b3e-816b-ea0b32073377n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/02762c37-4345-4cab-9a4a-fb152e744a3cn%40googlegroups.com.
