Re: [deal.II] Re: Issue regarding higher order element
Thanks a lot Bruno. I did find the issue following your suggestion!
On Tuesday, 16 July 2019 15:10:40 UTC-5, Bruno Turcksin wrote:
>
> Krishanu
>
> Le mar. 16 juil. 2019 à 16:00, Krishanu Sen > a écrit :
> >
> > I am using deal.ii for a nonlinear elasticity problem. And the change in
> the code that is causing this error message is:
> >
> >
> > template
> > ElasticProblem::ElasticProblem ()
> > :
> > dof_handler (triangulation),
> > fe (FE_Q(3), dim)
> > {}
> No it's not where the error comes from. It is from somewhere in
> Step8::ElasticProblem<1>::assemble_system_matrix() You need to find
> which line produces the error.
>
> Best,
>
> Bruno
>
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Re: [deal.II] Re: Issue regarding higher order element
Thanks Prof. Bangerth for the suggestion. I will definitely learn about the debugger as it seems like a great tool. Thanks, Krishanu On Thursday, 18 July 2019 03:42:54 UTC-5, Wolfga ng Bangerth wrote: > > On 7/16/19 2:10 PM, Bruno Turcksin wrote: > > No it's not where the error comes from. It is from somewhere in > > Step8::ElasticProblem<1>::assemble_system_matrix() You need to find > > which line produces the error. > > Krishanu, > indeed, Bruno knows this because he is looking at the backtrace shown in > the > error message you posted: > > #0 ./nodal_growth_dyn_full: > Step8::ElasticProblem<1>::assemble_system_matrix() > #1 ./nodal_growth_dyn_full: Step8::ElasticProblem<1>::run() > #2 ./nodal_growth_dyn_full: main > > The easiest way to find these errors is to run the program in a debugger. > It > will stop in exactly the place where the problem is, and allow you to > inspect > all local variables. It's a tool so worth learning how to use! (There are > also > video lectures showing how to do that in eclipse.) > > Best > W. > > -- > > Wolfgang Bangerth email: bang...@colostate.edu > > www: http://www.math.colostate.edu/~bangerth/ > > -- 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/102a6b2e-50cc-4d09-86b4-a3195fbf6c06%40googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Re: Porting tutorials to PETSc from Trilinos
Franco, Le jeu. 18 juil. 2019 à 10:27, Franco Milicchio a écrit : > Thanks for your answer. By the way, would a wrapper for the Eigen library be > appealing to anyone? I am sure it would be useful! > > An error occurred in line <382> of file > > in function > T *dealii::SmartPointer dealii::SparseMatrix >::operator->() const [T = const > dealii::SparsityPattern, P = dealii::SparseMatrix] > The violated condition was: > pointed_to_object_is_alive > Additional information: > The object pointed to is not valid anymore. It looks like the sparsity pattern does not exist anymore. The matrix object does not keep a copy of the sparsity pattern, so the sparsity pattern needs to exist as long as the matrix that uses it is alive. Best, Bruno -- 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/CAGVt9eNGQNQt9qe389vk8ZWm2e02z_T8_cQ53_d%2B5KQ9%3DdX-jw%40mail.gmail.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Porting tutorials to PETSc from Trilinos
Thanks for your answer. By the way, would a wrapper for the Eigen library be appealing to anyone? And back to my lowly question :) I was able to port the Step 31 code to plain deal.II without PETSc, but I have an error at runtime. At the moment I removed the preconditioners and just used a PreconditionIdentity to make it compile and link, I will deal with the right preconditioner later. Apparently I have initialized something wrong, as the assignment to the matrix if (rebuild_stokes_matrix == true) stokes_matrix = 0; makes the program die. Number of active cells: 256 (on 5 levels) Number of degrees of freedom: 3556 (n_u 2178 + n_p 289 + n_T 1089) Timestep 0: t=0 Assembling...stokes_matrix 2467 x 2467 blocks 2 x 2 An error occurred in line <382> of file in function T *dealii::SmartPointer >::operator->() const [T = const dealii::SparsityPattern, P = dealii::SparseMatrix] The violated condition was: pointed_to_object_is_alive Additional information: The object pointed to is not valid anymore. Stacktrace: --- #0 2 libdeal_II.g.9.1.0.dylib0x0001174e003e _ZNK6dealii12SmartPointerIKNS_15SparsityPatternENS_12SparseMatrixIdEEEptEv + 206: 2 libdeal_II.g.9.1.0.dylib0x0001174e003e _ZNK6dealii12SmartPointerIKNS_15SparsityPatternENS_12SparseMatrixIdEEEptEv #1 3 libdeal_II.g.9.1.0.dylib0x00011abc65e5 _ZN6dealii12SparseMatrixIdEaSEd + 69: 3 libdeal_II.g.9.1.0.dylib 0x00011abc65e5 _ZN6dealii12SparseMatrixIdEaSEd #2 4 step-31 0x00010ada5f3a _ZN6dealii17BlockSparseMatrixIdEaSEd + 90: 4 step-31 0x00010ada5f3a _ZN6dealii17BlockSparseMatrixIdEaSEd #3 5 step-31 0x00010ada0e77 _ZN6Step3121BoussinesqFlowProblemILi2EE22assemble_stokes_systemEv + 247: 5 step-31 0x00010ada0e77 _ZN6Step3121BoussinesqFlowProblemILi2EE22assemble_stokes_systemEv #4 6 step-31 0x00010ad944b8 _ZN6Step3121BoussinesqFlowProblemILi2EE3runEv + 504: 6 step-31 0x00010ad944b8 _ZN6Step3121BoussinesqFlowProblemILi2EE3runEv #5 7 step-31 0x00010ad93ebd main + 125: 7 step-31 0x00010ad93ebd main #6 8 libdyld.dylib 0x7fff6bbd93d5 start + 1: 8 libdyld.dylib 0x7fff6bbd93d5 start I have checked the sizes as you can see, and they seem to be properly initialized. So my guess is that I am doing something wrong with sparsity patterns, but I don't know how: BlockSparsityPattern sp(2, 2); sp.copy_from(dsp); stokes_matrix.reinit(sp); //stokes_matrix.reinit(dsp); // ... SparsityPattern sp(n_T, n_T); sp.copy_from(dsp); temperature_matrix.reinit(sp); //temperature_matrix.reinit(dsp); temperature_mass_matrix.reinit(sp); //temperature_mass_matrix.reinit(temperature_matrix); temperature_stiffness_matrix.reinit(sp); //temperature_stiffness_matrix.reinit(temperature_matrix); The code I've modified is available in full here: https://gist.github.com/fmilicchio/2dac430d7c071f98b4f66d79d2101b04 Any hints? Thank you very much for your help! Franco -- 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/49a9517b-cb68-4dfd-96fb-0e1ed53ec1e7%40googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Setting up system matrix fails
On 7/18/19 3:41 AM, Gabriel Peters wrote: > > Thanks a lot for the hint, now I found an error in my coupling for the > make_sparsity_pattern function. > So indeed the space was not allocated. Great, glad to help. It's easier to point people at the likely problem once you've made every mistake yourself once (or even more often than that)... ;-) Cheers W. -- Wolfgang Bangerth email: bange...@colostate.edu www: http://www.math.colostate.edu/~bangerth/ -- 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/d801189d-d676-f9c8-6a83-9e5d00f12e7d%40colostate.edu. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Setting up system matrix fails
Am Donnerstag, 18. Juli 2019 10:52:46 UTC+2 schrieb Wolfgang Bangerth: > > On 7/9/19 9:01 AM, Gabriel Peters wrote: > > > > After some debugging I found out that the term /(-1)* > sol_p[i]*div_sol_u[j]/ > > makes this trouble. Can somebody tell me why? > > My suspicion would be that you are writing into an element of the matrix > for > which you have not allocated space in the sparsity pattern. Could that be > the > case? > > Thanks a lot for the hint, now I found an error in my coupling for the make_sparsity_pattern function. So indeed the space was not allocated. Thanks a lot Gabriel Best > W. > > -- > > Wolfgang Bangerth email: bang...@colostate.edu > > www: http://www.math.colostate.edu/~bangerth/ > > -- 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/1b940cdf-8252-49c8-8b0a-f59faa2b73dd%40googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Setting up system matrix fails
On 7/9/19 9:01 AM, Gabriel Peters wrote: > > After some debugging I found out that the term /(-1)* sol_p[i]*div_sol_u[j]/ > makes this trouble. Can somebody tell me why? My suspicion would be that you are writing into an element of the matrix for which you have not allocated space in the sparsity pattern. Could that be the case? Best W. -- Wolfgang Bangerth email: bange...@colostate.edu www: http://www.math.colostate.edu/~bangerth/ -- 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/835a0843-815a-28fc-b976-43e209af3ebc%40colostate.edu. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] How to set material id with MPI
On 7/17/19 7:46 PM, Phạm Ngọc Kiên wrote: > I am trying to write codes to find a subset of cells that I want to set their > material id. > The codes run well with 1 processor. > However, when testing with more than 1 processor, the codes did wrong things. > This is because each processor only owns a subset of cells with distributed > triangulation. > Do we have a way to address this issue in deal.II? In addition to Daniel's questions, take a look at the documentation of the parallel::distributed::Triangulation class documentation. It talks about similar issues with boundary ids. I would imagine that setting material ids poses similar challenges, and has similar solutions. Best W. -- Wolfgang Bangerth email: bange...@colostate.edu www: http://www.math.colostate.edu/~bangerth/ -- 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/9afe5b13-a5db-ba22-81d1-acd9eb952d7d%40colostate.edu. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Re: Issue regarding higher order element
On 7/16/19 2:10 PM, Bruno Turcksin wrote: > No it's not where the error comes from. It is from somewhere in > Step8::ElasticProblem<1>::assemble_system_matrix() You need to find > which line produces the error. Krishanu, indeed, Bruno knows this because he is looking at the backtrace shown in the error message you posted: #0 ./nodal_growth_dyn_full: Step8::ElasticProblem<1>::assemble_system_matrix() #1 ./nodal_growth_dyn_full: Step8::ElasticProblem<1>::run() #2 ./nodal_growth_dyn_full: main The easiest way to find these errors is to run the program in a debugger. It will stop in exactly the place where the problem is, and allow you to inspect all local variables. It's a tool so worth learning how to use! (There are also video lectures showing how to do that in eclipse.) Best W. -- Wolfgang Bangerth email: bange...@colostate.edu www: http://www.math.colostate.edu/~bangerth/ -- 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/165fa819-3baf-0faf-cabc-5206b54fb1bf%40colostate.edu. For more options, visit https://groups.google.com/d/optout.
