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 the Google Groups "deal.II User Group" group. 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