[deal.II] Re: Issue with running step-55

Hello, You are not supposed to modify configuration files. You need to reconfigure and reinstall deal.II from scratch. Best, Bruno On Monday, June 23, 2025 at 4:41:06 PM UTC-4 mahmuduli...@gmail.com wrote: > Dear all, > I hope this email finds everyone in this group in good health. Currently,

Re: [deal.II] Re: Issue with running step-55

I reinstall, what should I focus on to run step 55, the parallel code? > > Md Mahmudul Islam > > On Tue, 24 Jun 2025 at 07:54, Bruno Turcksin > wrote: > >> Hello, >> >> You are not supposed to modify configuration files. You need to >> reconfigure and r

[deal.II] Re: tags polluting the title of conversations

Hello, I couldn't find how to change the behavior in the settings. Sorry. Best, Bruno On Tuesday, June 10, 2025 at 8:37:10 AM UTC-4 dwillia...@gmail.com wrote: > If we show conversations by clicking on the Labels in the google Groups > left column, the titles will be very polluted by the tags

[deal.II] Re: Problem with FENothing and DoFTools::map_dofs_to_support_points()

Hello Davit, This does not work because FE_Nothing does not have a support points. I needed something similar so I implemented it in my code, you can take a look at https://github.com/adamantine-sim/adamantine/blob/efde0a1818ae4f2c476aee56c55a187c7b3ece08/source/experimental_data_utils.cc#L21-L

Re: [deal.II] Re: shmem: mmap: shared memory error on Mac OS

I am glad it's fixed! Best, Bruno Le jeu. 13 mars 2025 à 00:02, Nik Markus Leuenberger a écrit : > Dear Bruno, > > Thank you very much for your reply and apologies for my late reply. I > think that was exactly the issue. > After upgrading to open-mpi 5.0.7, the problem seems to be gone. > > Th

[deal.II] Re: Matrix-Free and FE_Nothing

Hello Thomas, If you use FE_Nothing, you don't want to loop over the cell_range. Instead you create a subrange of cells using create_cell_subrange_hp_by_index() and then loop over the cells in t

Re: [deal.II] Re: Parallel computation fails to converge

Hello Junxiang, It looks like the issue happens at a hanging node. In step-40, we show how to see which processor each cell belongs to. I think it would be interesting to output that image and see if the issue happens because the hanging node is shared between different processors. Best, Bruno

Re: [deal.II] Re: Parallel computation fails to converge

What happens if you don't refine the mesh? Is everything still the same? Bruno Le sam. 8 févr. 2025 à 06:26, Junxiang Wang a écrit : > In the first 80 steps, RHS and Stiffness are all the same. After several > step of refine mesh, the RHS then turns to different from the serial one. > > On Satu

[deal.II] Re: Parallel computation fails to converge

Hello Junxiang, It's very hard to know what the issue could be. What you could do is print some information about your matrix and right hand side (for instance, different norms) and check that they are the same in serial and in parallel. By comparing the serial and parallel simulations at diffe

[deal.II] Re: shmem: mmap: shared memory error on Mac OS

Hello Nik, This looks like an OpenMPI issue. I have you tried the suggestions from https://github.com/open-mpi/ompi/issues/12784 Best, Bruno On Friday, January 17, 2025 at 4:06:07 PM UTC-5 nikl...@stanford.edu wrote: > Dear all, > > Thanks to your help earlier, I was able to compile my progra

[deal.II] Re: mpirun failured for step-17 on WSL

Hello Pei-Liang, Do you have the same problem if you use a simple hello_world code that doesn't use deal.II? This will tell us if the problem is with deal.II or with mpi. Best, Bruno On Tuesday, December 3, 2024 at 3:25:30 AM UTC-5 peilia...@gmail.com wrote: > Hello, > > I am now trying to r

[deal.II] Re: Error installing deal.II in the University of Michigan Great Lakes cluster

Hello David, It seems that the error is from TBB. Is TBB part of the intel/2022.1.2 module? Best, Bruno On Sunday, November 24, 2024 at 5:36:15 PM UTC-5 dmon...@umich.edu wrote: > Hello, > > I am attempting to install deal.II using candi in the University of > Michigan Great Lakes cluster (2

Re: [deal.II] Re: cmake error when building with arbox

gh. > > On Wed, Oct 16, 2024 at 9:58 AM Bruno Turcksin > wrote: > >> Kaushik, >> >> The message you see is the auto-detect trying to find ADOLC. It's OK if >> the auto-detect does not find ADOLC. The real issue is with Kokkos. When >> you install

[deal.II] Re: cmake error when building with arbox

Kaushik, The message you see is the auto-detect trying to find ADOLC. It's OK if the auto-detect does not find ADOLC. The real issue is with Kokkos. When you installed ArborX, did you use the Kokkos library from Trilinos or did you install Kokkos yourself too? Best, Bruno On Tuesday, October

Re: [deal.II] Re: dealii installation error : git clone failed

Guy, In deal.II-toolchain/packages/dealii.package try changing SOURCE= https://github.com/dealii/ to SOURCE=https://dealii.org/downloads/ and PACKING=git to PACKING=.tar.gz I haven't used CANDI in a long time so I am not sure this will work. Best, Bruno Le ven. 13 sept. 2024 à 11:22, Guy Moebs

[deal.II] Re: dealii installation error : git clone failed

Guy, According to this , it might be a network issue. It seems that using `git config --global pack.window 1` might solve the issue. You could also download the release tarball instead of

[deal.II] Re: Lifting a Triangulation<2> to Triangulation<2,3>

Jasper, You don't want to use GridGenerator::hyper_ball. Instead try: Triangulation<2,3> my_triangulation; GridGenerator::hyper_shell(my_triangulation); Note that you need to use a triangulation where dim is different than spacedim. Best, Bruno On Monday, August 19, 2024 at 8:48:54 AM UTC-4

Re: [deal.II] Re: gmsh imported into dealii

Wang, Do you have a geo file that describes the geometry? Can you remove the "Physical Surface" lines in the geo file and regenerate the mesh. Best, Bruno Le mar. 4 juin 2024 à 10:13, 王艺康 a écrit : > Hello, > Thank you very much for your reply. That's what I thought at first, but I > was wron

[deal.II] Re: gmsh imported into dealii

Hello, Deal.II associates the physical group of a face with a boundary id. You need to remove the physical group that are associated with interior faces. Best, Bruno On Tuesday, June 4, 2024 at 3:28:05 AM UTC-4 yikangw...@gmail.com wrote: > I drew the model in gmsh but importing to dealii is

[deal.II] Re: Regarding getting error during "make release"

Hello, What is crystalPlasticity? Is that your own code? Best, Bruno On Saturday, April 13, 2024 at 3:20:56 PM UTC-4 gaura...@gmail.com wrote: > Dear sir, > I am getting the error, when in crystalPlasticity, i use the command > "make release", it is giving error. > > gmake[6]: *** [CMakeFile

[deal.II] Re: Deal.ii installation - make error

Hello, It looks like you installed your own version of Kokkos which requires C++17 but you compiled deal.II using C++14. You need to compile deal.II with C++17. You need to reconfigure deal.II and to use "-DCMAKE_CXX_STANDARD=17". Best, Bruno On Tuesday, March 19, 2024 at 8:19:36 AM UTC-4 mel

Re: [deal.II] Re: Sparsity pattern

This is a difficult problem. We have talked about it before but if I remember correctly, we couldn't find a satisfying solution and we just pretend that there is no problem. It has happened that inside a multithreaded part of deal.II there is a call to blas and you oversubscribe the machine. Since

Re: [deal.II] Re: Sparsity pattern

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 develo

Re: [deal.II] Re: Sparsity pattern

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

Re: [deal.II] Re: Sparsity pattern

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

Re: [deal.II] Re: Sparsity pattern

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

Re: [deal.II] Re: Sparsity pattern

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

Re: [deal.II] Re: Sparsity pattern

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 b

[deal.II] Re: Sparsity pattern

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

[deal.II] Re: Modifying Cmake to have Deal.ii include paths

Hello, You can just set DEAL_II_DIR in your environment. If you are using bash you can do `export DEAL_II_DIR=/path/to/deal.II` in your terminal or put that line you .bashrc if you want to do this permanently. Personally, I just write the cmake line in a file and make the file executable. When

Re: [deal.II] Re: Can't configure with cmake

Sean, If the configuration steps errors out, there is no point in trying to compile the code. You probably want to remove the deal.II files that have been installed and reinstall the library. Best, Bruno Le mar. 6 févr. 2024 à 18:26, Sean Johnson a écrit : > Bruno, > > I apparently spoke to s

Re: [deal.II] Re: Can't configure with cmake

Sean, That's great to hear. We don't mark problems as solved. So there is nothing to do. Best, Bruno Le mar. 6 févr. 2024 à 16:41, Sean Johnson a écrit : > Thanks again! > > The using a newer version of Boost helped me get further and realize I > made another bone headed mistake of compiling

Re: [deal.II] Re: Can't configure with cmake

Sean, I am not sure what's the issue. It's probably not the issue but make sure that mpi is using nvcc_wrapper as the underlying compiler. If you use OpenMPI, you can use export `OMPI_CXX=nvcc_wrapper`. You could also try to use a newer version of Boost. The bundled version is pretty old. Since yo

Re: [deal.II] Re: Can't configure with cmake

Sean, It's possible that you don't have enough RAM and that you are swapping memory which is extremely slow. Try to reinstall using fewer processors. Best, Bruno Le lun. 5 févr. 2024 à 19:01, Sean Johnson a écrit : > Thanks Bruno, > > This was definitely it. > > So I have now gotten to runnin

[deal.II] Re: Can't configure with cmake

Sean, It looks like you are using the wrong compiler. If you want to use CUDA, you should use nvcc_wrapper as your C++ compiler. You want something like `-DCMAKE_CXX_COMPILER=/path/nvcc_wrapper`. You should already have used `nvcc_wrapper` to compiler Kokkos. Best, Bruno On Monday, February

Re: [deal.II] Re: element birth using FE_Nothing and FE_Collection in time-dependent problem with adaptive mesh refinement

In case you are interested in using MPI, there is class that does that work for you: https://www.dealii.org/current/doxygen/deal.II/classparallel_1_1distributed_1_1experimental_1_1FieldTransfer.html and there are examples on how to use it (for example: https://github.com/dealii/dealii/blob/08160c07

[deal.II] Re: element birth using FE_Nothing and FE_Collection in time-dependent problem with adaptive mesh refinement

Hello, This is not how you should activate elements. Instead **before** you call triangulation.prepare_coarsening_and_refinement(), you call your activate_FE function but instead of using set_active_fe_index() you call set_future_fe_index(). Best, Bruno On Wednesday, January 17, 2024 at 4:2

[deal.II] Re: Missing documentation for Tensor class?

Ernesto, Yes, something is wrong with documentation. I don't know why the functions don't show up. I am not sure what happened with double_contract being deprecated. Maybe it was a different version maybe the function was reinstated. Best, Bruno On Tuesday, December 19, 2023 at 1:29:54 AM U

[deal.II] Re: Q: deserialize after updating dealii

Najwa, Are you serializing/deserializing the solution using the same version of deal.II and Boost? If you serialized the solution using the old version of deal.II, I don't think you can deserialize it using a newer version of deal.II Best, Bruno On Monday, November 6, 2023 at 3:03:07 AM UTC-

[deal.II] Re: Utilities::MPI::broadcas doesn't work

Hello, broadcast returns the updated value. tt is unchanged. See the documentation here Best, Bruno On Thursday, November 2, 2023 at 10:26:46 AM UTC-4 ztdep...@gmail.com wrote: > I t

[deal.II] Re: Function to obtain the cell(s) that belong to a certain vertex

Sebastian, Take a look at GridTools::find_cells_adjacent_to_vertex() Best, Bruno On Friday, October 27, 2023 at 11:51:48 AM UTC-4 sebastian...@gmail.com wrote: > Hello, > > I am searchin

[deal.II] Re: dealii installation error-oneapi

ninghui, Can you share /media/ninghui/Aspect/dealii-candi-oneapi/tmp/build/deal.II-v9.5.1/CMakeFiles/CMakeOutput.log and /media/ninghui/Aspect/dealii-candi-oneapi/tmp/build/deal.II-v9.5.1/CMakeFiles/CMakeError.log. Best, Bruno On Tuesday, October 17, 2023 at 8:27:33 PM UTC-4 nh3242...@gmail

[deal.II] Re: what's the good way to use GPU acceleration in matrix-based code under dealii environment

Tim, There is currently no way to do what you want. There is ongoing work to replace the Epetra wrappers with Tpetra (https://github.com/dealii/dealii/pull/16052), this will allow to use GPU in matrix-based code. You will probably get the majority of the speedup using GPU for the solver, so yo

Re: [deal.II] Re: question about hybrid MPI and TBB thread parallelism

Tim, Valgrind is great but it is always slow. Instead you can use the AddressSanitizer from clang or gcc. It's much faster than Valgrind but I find the output is harder to read. Best, Bruno Le lun. 2 oct. 2023 à 02:47, timo Hyvärinen a écrit : > Hi, Kendrick and Wolfgang, > > Thank you for yo

Re: [deal.II] Re: question about hybrid MPI and TBB thread parallelism

st, Bruno Le sam. 16 sept. 2023 à 03:47, timo Hyvärinen a écrit : > Hi Bruno, > > Thank you for your explanations. > > Seemingly, I should compile an optimized lib then do profiling. > > Sincerely, > Timo > > On Fri, Sep 15, 2023 at 11:04 PM Bruno Turcksin >

Re: [deal.II] Re: question about hybrid MPI and TBB thread parallelism

Timo, You will get vastly different results in debug and release modes for two reasons. First, the compiler generates much faster code in release mode compared to debug. Second, there are a lot of checks inside deal.II that are only enabled in debug mode. This is great when you develop your cod

[deal.II] Re: Install deal II with PETSc and MPICH

Giselle, You have multiple versions of MPI installed on your computer. I would strongly advise that you remove the extra MPI libraries and keep only one of them. Anyway to fix your issue, you can use `-DMPI_CXX_COMPILER=/path/to/mpich/mpicxx` to tell CMake which MPI compiler to use. Best, Br

Re: [deal.II] Re: Issue on CUDA code

Giuseppe, Le mar. 22 août 2023 à 13:27, giuseppe orlando a écrit : > >1. For 'additional_data.mapping_update_flags', I need to specify >'update_gradients' even though the resulting matrix for the linear system >is nothing but a mass matrix. If I do not specify 'update_gradients', I g

[deal.II] Re: Simulation Error with PRISMS Plasticity on High Core Counts

Kushagra, It's hard to tell without using a debugger. I wonder if you see the error because some processors have no dofs. What happens if you start with a finer mesh? Best, Bruno On Tuesday, August 22, 2023 at 7:51:07 AM UTC-4 Kush wrote: > Dear Team, > > I am using PRISMS Plasticity for my

Re: [deal.II] Re: Compilation deal.II 9.5

. 20 juil. 2023 à 11:53, Giuseppe Orlando a écrit : > Yes, I’m inside a clean directory. The output of mpicxx is > “/opt/cray/pe/craype/2.7.10/bin/CC”, which is the same that I used to > install all the other versions. The cmake version is 3.17.0. > > > > Best > > &g

Re: [deal.II] Re: Compilation deal.II 9.5

A few questions: are you configuring inside a clean directory? What's the output of mpicxx? Which version of cmake are you using? Le jeu. 20 juil. 2023 à 11:11, giuseppe orlando a écrit : > I agree. I had tried to set -DMPI_CXX_COMPILER flag, but it seems to be > ineffective. It keeps using nvcc

Re: [deal.II] Re: Compilation deal.II 9.5

What's strange is that when deal.II tries to compile an MPI code, it is using `nvcc_wrapper` as the compiler instead of `mpicxx`. Can you try to set `-DMPI_CXX_COMPILER=mpicxx`? Bruno Le jeu. 20 juil. 2023 à 10:21, giuseppe orlando a écrit : > Here, you can find both 'CMakeError.log' and 'CMake

Re: [deal.II] Re: Compilation deal.II 9.5

Giuseppe, CMake should create an error log. Can you post it? Best, Bruno Le jeu. 20 juil. 2023 à 04:51, giuseppe orlando a écrit : > Dear Bruno, > I tried to reinstall Kokkos removing the -DCMAKE_CXX_FLAGS option, but I > get the same error during the creation of the Makefile for deal.II. I w

Re: [deal.II] Re: Compilation deal.II 9.5

Giuseppe, I think the issue is because you set -DCMAKE_CXX_FLAGS=-arch=sm_60 when compiling Kokkos. This is not necessary because Kokkos takes care of that when you use -DKokkos_ARCH_PASCAL60=ON. Since you set that as a CXX flags it might be passed to MPI when it shouldn't. The rest looks good. B

[deal.II] Re: Compilation deal.II 9.5

Giuseppe, Your configuration line looks good. I use the same but I also export OMPI_CXX=/path/kokkos/bin/nvcc_wrapper Best, Bruno On Wednesday, July 19, 2023 at 4:38:07 AM UTC-4 gius...@gmail.com wrote: Hello everyone, I'm writing this post because I'm having some issues to compile the latest

Re: [deal.II] Re: Issue on CUDA code

Giuseppe, We totally rewrote the GPU matrix-free framework on the latest release of deal.II (version 9.5). One of the advantages is that you can now write/debug the code on the CPU and then switch to run the code on the GPU. The new code is not 100% backward compatible but the changes are pretty s

Re: [deal.II] Re: Issue on CUDA code

Giuseppe, The CUDA::Handle needs to live longer than the sparse matrix but in your code it goes out-of-scope at the end of assemble_system(). I know the same code works with assemble_matrix but it only works "by chance" because nothing wrote over the memory. I don't know if that's the only proble

[deal.II] Re: Issue on CUDA code

Giuseppe, It's hard to tell what's wrong without seeing the code. Best, Bruno On Monday, July 17, 2023 at 9:04:42 AM UTC-4 gius...@gmail.com wrote: > Hello everyone, > I'm writing this post to ask some help for a CUDA code. I have implemented > a matrix-based CUDA coda for the so-called solid

[deal.II] Re: Error evaluating derivative of abs() function using symbolic differentiation

Vinayak, The error is pretty explicit, the function is not implemented in SymEngine. Maybe it is fixed in a newer version of SymEngine. If it is not, you will need to change the formulation of your equation. Best, Bruno On Monday, July 17, 2023 at 3:51:24 AM UTC-4 vinay...@gmail.com wrote: >

[deal.II] Re: Finding unconnected regions in a triangulation

Kaushik, You could use get_face_connectivity_of_cells() or get_vertex_connectivity_of_cells()

Re: [deal.II] Re: dealii v 9.2.0 installation difficulty (also posted on spack group)

It looks like the error you get when using cxx=11 is from ginkgo so if you don't need ginkgo, you could try something like spack install dea...@9.2.0 ~ginkgo ^bo...@1.76.0 cxxstd=11 %g...@12.2.0 Bruno Le ven. 23 juin 2023 à 14:47, Andrew Li a écrit : > Unfortunately dealii@9.2.0 seems to be in

Re: [deal.II] Re: dealii v 9.2.0 installation difficulty (also posted on spack group)

The error is from here In file included from ./boost/math/tools/mp.hpp:341, from ./boost/math/policies/policy.hpp:11, from ./boost/math/special_functions/math_fwd.hpp:31, from ./boost/math/special_functions/airy.hpp:11, from ./boo

[deal.II] Re: dealii v 9.2.0 installation difficulty (also posted on spack group)

Andrew, What's the error message that you get when using `spack install dealii@9.2.0 %gcc@12.2.0` ? spack writes the exact error in an output file. I don't think changing the C++ standard is the right fix, instead I would change the version of boost. Best, Bruno On Friday, June 23, 2023 at 1

Re: [deal.II] Re: evaluation FE function outside domain

I do not know if that's reasonable. > > Best, > > Math > > Bruno Turcksin schrieb am Di., 6. Juni 2023, > 21:55: > >> Math, >> >> The basis functions are not defined outside of an element, so you cannot >> extrapolate them outside of the mesh. What

[deal.II] Re: evaluation FE function outside domain

Math, The basis functions are not defined outside of an element, so you cannot extrapolate them outside of the mesh. What are you trying to achieve? Best, Bruno On Monday, June 5, 2023 at 4:59:28 PM UTC-4 Mathieu wrote: > Hello everyone, > > I was wondering if deal.II has built-in functions

Re: [deal.II] Re: CUDA facilities

Kokkos keywords’, but I cannot figure out from a rapid glance if it > can be already executed with a version of deal.II installed with > ‘DEAL_II_WITH_KOKKOS’ flag on or one has to wait the new release. > > > > Best > > > > Giuseppe > > > > *Da: *Bruno

[deal.II] Re: CUDA facilities

Giuseppe, I am not sure if google sent my previous message, so I will send it again. I apologize if you get it twice. We are currently replacing the CUDA code with Kokkos. These will allow us to support Nvidia, AMD, and Intel GPUs. It will also make it easier to add new functionalities. Unfor

[deal.II] Re: Poor parallel efficiency of FEValues::reinit() with Workstream

Jonas, What you are seeing is expected. There is an overhead associated with using multiple threads. Since the overhead is constant it looks like it disappears when you do more work. You probably want to give more work do to your threads to amortize the constant cost. Best, Bruno On Thursday

Re: [deal.II] Re: Problem compiling deal.II with CUDA

No, there is nothing to do. Best, Bruno Le mer. 3 mai 2023 à 14:37, Sean Johnson a écrit : > Thanks! No problem with the documentation not being changed on the compute > capability. With all the changes being made this is really just the > smallest thing. Do I need to mark this solved or anyth

[deal.II] Re: Problem compiling deal.II with CUDA

Hello, It looks like the documentation is not up to date. We do not support GPU your GPU, deal.II requires compute capability of at least 6.0. Sorry about that. Best, Bruno On Saturday, April 29, 2023 at 1:46:44 PM UTC-4 sljoh...@gmail.com wrote: > Hey everyone, > > Sorry I have been workin

Re: [deal.II] Re: How can I visit a face exactly once when running with MPI?

Right, it won't clear it everywhere. You would need to use MPI to clear the flag on the other processor. If you would do that you would create a huge amount of messages and your code would be extremely slow. Best, Bruno Le jeu. 27 avr. 2023 à 10:09, Abbas Ballout a écrit : > This works!! Thank

[deal.II] Re: How can I visit a face exactly once when running with MPI?

Hello, On Thursday, April 27, 2023 at 7:56:50 AM UTC-4 abbas.b...@gmail.com wrote: This works with a single MPI but not for more. Is it because the cell->face( face)->clear_user_flag() doesn't clear the user flag in the other distributed meshes? That's correct. The flag is only cleared locall

[deal.II] Re: How can I get the jump in my solution if my solution vector is distributed?

Hello, You are using a non-ghosted vector. You need to created a ghosted vector and they assign the non-ghosted vector to the ghosted one. Best, Bruno On Thursday, April 20, 2023 at 7:07:09 AM UTC-4 Abbas wrote: > I am trying to querry for the jump in my solution with > "get_jump_in_functio

Re: [deal.II] writing data to a file changes program output although this file is never used

Simon, Le ven. 31 mars 2023 à 08:58, Simon Wiesheier a écrit : > > > Given that it works fine in debug mode, there are likely no out-of-bound > violations. I just use std::vector and Vector as data structures > which would be detected in debug mode. > > That's optimistic :) It's not because you

[deal.II] Re: Linking error when compiling examples: error: cannot find -lhdf5-shared

Amit, Did you load the hdf5 package? You can check using `spack find --loaded`. Best, Bruno On Friday, March 31, 2023 at 4:51:02 AM UTC-4 amitshar...@gmail.com wrote: > Hello everyone, > > I installed dealii using spack manager. I started learning dealii using > examples but I am getting a li

Re: [deal.II] writing data to a file changes program output although this file is never used

Hello, Usually when I have this kind of bug, there are two possibilities: 1. I am using an un-initialized value 2. I am writing out of bound What I do is using valgrind with my code in Debug mode and without TBB enabled otherwise you get difficult to understand backtrace like here. However,

[deal.II] Re: Status of hybrid shared/distributed parallelism

Lucas, Why are you interested in hybrid parallelism? Are you hoping to improve the performance of your code or is it simply something you want to try? If the solver is the bottleneck in your code, you should focus on finding a better preconditioner. With that being said, matrix-free methods ten

Re: [deal.II] Re: trying to install dealii 9.1.1 using candi.

Do you need to use Boost in your own project? If you don't, try adding -DDEAL_II_FORCE_BUNDLED_BOOST=ON to your configuration. Best, Bruno Le mer. 8 mars 2023 à 00:02, ME20D503 NEWTON a écrit : > Dear Bruno, > i am using ubuntu 22.04.1 and g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0. > > Thank y

[deal.II] Re: trying to install dealii 9.1.1 using candi.

Hello, It looks like the error is from boost. Which version are you using? What's your compiler? Best, Bruno On Tuesday, March 7, 2023 at 12:58:10 AM UTC-5 me20...@iittp.ac.in wrote: > Dear Sir/Ma'am, > trying to install dealii-9.1.1 version using candi command. i just change > the version i

[deal.II] Re: Spack error with cgal and arbox

Hi, Don't set any variable when using spack. Please post the exact spack command you are using to install deal.II with spack. In general, you want to let spack picks the dependencies for you. I would also advise that you restart from a clean state and remove the configuration files created by

[deal.II] Re: Creating a plot in dealii

Hello, DataOut is made to add data to a mesh. It cannot be used to do what you want. The easiest way to do what you want is to write the vectors to a file using print() and then do the plot using matlab or python. Best, Bruno On Saturday, February 11, 2023 at 9:27:06 AM UTC-5 ce21...@smail.ii

[deal.II] Re: facing problem in deal.ii Installation

Hello, It looks like you are trying to install deal.II in /usr/local and you need to be sudo to do it. If you do "ccmake ." in the directory where you configured deal.II you should be able to see what's the path in CMAKE_INSTALL_PREFIX. Make sure that it's what you expect. Best, Bruno On Fri

[deal.II] Re: Monitor memory usage of the program

Hello, Personally, I prefer to use profilers when monitoring the memory usage. This is because what really matters is how much memory the operating system is allocating for you code. For multiple reasons this can be different than what your code require. Best, Bruno On Tuesday, February 7, 2

Re: [deal.II] Extracting all the nodes on a particular boundary

Nice, I looked for such a function in GridTools but I forgot about DoFTools. Bruno Le jeu. 19 janv. 2023 à 11:44, Wolfgang Bangerth a écrit : > On 1/19/23 02:43, Wasim Niyaz Munshi ce21d400 wrote: > > I am trying to extract all the nodes present on a boundary with a > > particular id. > > Would

[deal.II] Re: Extracting all the nodes on a particular boundary

Wasim, You need to loop over the cells. That's the only way to get the information that you want. Best, Bruno On Thursday, January 19, 2023 at 4:43:34 AM UTC-5 ce21...@smail.iitm.ac.in wrote: > Hello everyone. > I am trying to extract all the nodes present on a boundary with a > particular

[deal.II] Re: Running non-cuda code when dealii and petsc are compiled with cuda support

Stefano, Currently in deal.II we always assume that the PETSc vector is on the CPU but I don't know what PETSc does internally when it is compiled with GPU support. I don't think that the deal.II developers who use PETSc, use GPU so it's not tested. If you can, compile deal.II with GPU support

[deal.II] Re: Regarding deal ii installation with PETSC

Anupama, The error message tells you that PETSc was compiled with MPI support but deal.II was configured without MPI support. Either recompile PETSc without MPI or reconfigure deal.II with MPI support using -DDEAL_II_WITH_MPI=ON Best, Bruno On Tuesday, December 27, 2022 at 3:30:49 AM UTC-5 an

[deal.II] Re: Error in Reading Gmsh File in Dealii

Deepika, Can you try using a linear mesh instead of curvilinear one? Does that work? Best, Bruno On Thursday, December 22, 2022 at 1:47:32 AM UTC-5 deepika...@iitgoa.ac.in wrote: > Hello Everyone, > > I have successfully read a gmsh file for one material in my code. Now I am > trying to read

[deal.II] Re: Helmholtz solve on GPUs with multicomponent vector

Gourab, Multicomponent vector is currently not supported. Part of the infrastructure is already present as you saw but you cannot use MatrixFree on GPU with multicomponent vectors at the moment. Best, Bruno On Wednesday, December 14, 2022 at 1:19:19 AM UTC-5 pgo...@iisc.ac.in wrote: > I am t

Re: [deal.II] Re: Importing .msh file from CUBIT

.inp format file and used read_ucd here. I was actually > trying to import a .msh file. However, the same error occurs for the > read_msh function as well. > > Himal. > > > On Tue, Dec 6, 2022 at 9:41 PM Bruno Turcksin > wrote: > >> Himal, >> >> It lo

[deal.II] Re: Importing .msh file from CUBIT

Himal, It looks like there is a problem opening the file. How did you export the mesh? Are you using read_ucd or read_abaqus? Best, Bruno On Tuesday, December 6, 2022 at 10:36:30 AM UTC-5 075bme0...@pcampus.edu.np wrote: > Warm Greetings!, > I am trying to import .msh file that I have create

[deal.II] Re: How to solve 2d elasticity problem for two different materials.

Deepika, You can take a look at step-28. We use material_id to represent different materials. Best, Bruno On Monday, November 28, 2022 at 1:56:22 AM UTC-5 deepika...@iitgoa.ac.in wrote: > Hello Everyone, > > I have solved the 2d elasticity problem for DBCs and NBCs for a single > material.

Re: [deal.II] Re: Solving elasticity and laplace(damage) equation, one after the other.

all boundaries might have same bcs but for elasticity different bcs > exist at different faces of the square domain). > > On Tue, Nov 22, 2022 at 2:25 AM Bruno Turcksin > wrote: > >> Wasim, >> >> Why do you have two different triangulations? Can you have single >

Re: [deal.II] Re: Solving elasticity and laplace(damage) equation, one after the other.

g to me, comes in this line in H function : > fe_values_elastic.reinit(cell);* > I need to *reinit *the fe_values_elasticity for each cell, but the > problem is that the *cell *I am passing as an argument lives on the > traingulation_damage while fe_values_elasticity lives on > triangulation_elasticity

Re: [deal.II] Re: Solving elasticity and laplace(damage) equation, one after the other.

Wasim, Before the line that errors out can you do std::cout<get_fe().get_name()< a écrit : > I am working with 2 DoFHandlers. I checked my code. I am using the correct > DoFHandlers for the 2 equations. > > On Mon, Nov 21, 2022 at 6:58 PM Bruno Turcksin > wrote: > >

[deal.II] Re: Solving elasticity and laplace(damage) equation, one after the other.

Wasim, It's hard to say without seeing any code. Are you working with one or two DoFHandler? If you are working with two DoFHandler, are you sure that you are using the correct one? Best, Bruno On Monday, November 21, 2022 at 5:54:22 AM UTC-5 ce21...@smail.iitm.ac.in wrote: > Hello everyone

[deal.II] Re: MacOS Installation - Monterey - M1 - spack

Francesco, You can do spack spec dealii%clang to see what spack will install. You can then check which package requires OpenGL (it is not deal.II) and then remove support for this package if you don't need it. For instance, let's say that it's trilinos that's pulling OpenGL and you don't nee

Re: [deal.II] Re: measuring cpu and wall time for assembly routine

Simon, Le mer. 19 oct. 2022 à 09:33, Simon Wiesheier a écrit : > Thank you for your answer! > > " Did you set DEAL_II_NUM_THREADS=1?" > > How can I double-check that? > ccmake . > only shows my the variables CMAKE_BUILD_TYPE and deal.II_DIR . > But I do do knot if this is the right place to loo

[deal.II] Re: measuring cpu and wall time for assembly routine

Simon, The best way to profile a code is to use a profiler. It can give a lot more information than what simple timers can do. You say that your code is not parallelized but by default deal.II is multithreaded . Did you set DEAL_II_NUM_THREADS=1? That could explain why CPU and Wall time are di

[deal.II] Re: MUMPS solver with Trilinos

Rahul, On Sunday, October 16, 2022 at 11:42:50 AM UTC-4 grrah...@gmail.com wrote: > > 1. Does mumps has to be any specific version to compile with amesos. > Trilinos documentation available on net suggest 4.7.3. However, this is > fairly old version. > I don't know the answer to this question

  1   2   3   4   5   6   7   8   >