Re: [deal.II] Re: .msh file triangulation failed

; Dear Bruno, > Thank you for your help! I added physical groups for volume, surfaces, > curves, and points. But the problem remains the same. The modified geo file > is attached below. > Best regards, > Yuesu > > On Tue, Sep 22, 2020 at 7:55 AM Bruno Turcksin > wrot

Re: [deal.II] Re: .msh file triangulation failed

essage remains the same. I tried a few types of > grouping combinations, the error message did not change. > Best regards, > Yuesu > > On Tue, Sep 22, 2020 at 9:30 AM Bruno Turcksin > wrote: >> >> You don't want to set the physical groups for the curves and the >&

Re: [deal.II] Eigenvalues and Eigenvectors of BlockSparse Matrix

Animesh, Yes, the name are reversed. Basically what happens is that ARPACK uses a method called shift inverse which uses the inverse of the operator you care. In practice, this means that ARPACK is not using your matrix A but only A^{-1} because the largest eigenvalue of A^{-1} is related to

[deal.II] Re: Can dealii handle different type of element in a grid

Hi, deal.II only supports quads in 2D and hex in 3D.So if you have triangles you will need to split them. For the quads, you probably want to load order one quads and then, use a manifold to get the higher order. step 49 (https://dealii.org/current/doxygen/deal.II/step_49.html) shows how to

[deal.II] Re: Anistropic refinement DG - saddle point problem

Juan, Basically the problem is that MeshWorker was not design to handle anisotropic refinement. That assert checks that if the faces of two cells "match" then they have been refined the same number of times. This is obviously not true in case of anisotropic refinement. I think that this is

[deal.II] Re: A small question about subdomain renumbering

Yuesu, On Thursday, August 6, 2020 at 12:08:58 AM UTC-4, yuesu jin wrote: > > Dear all, > I have a question about DoFRenumbering::subdomain_wise(dof_handler). In > step-17 tutorial for example, this function doesn't use the argument of > n_mpi_processes, how does it know how many subdomains

[deal.II] Re: Error while installing dealii

Prakash, How did you configure deal.II? Best, Bruno On Friday, July 3, 2020 at 5:54:23 AM UTC-4, ME20S001 Bardawal Prakash wrote: > > Hello, >I got error while installing dealii, can someone help me for > solving this issue? > Here I'm attaching snapshots of that error

[deal.II] Re: Mesh-induced elastic anisotropy and distorting the quad. points as a way to palliate it

David, Unfortunately this is really not my domain of expertise but maybe you can randomize the cells https://dealii.org/current/doxygen/deal.II/namespaceGridTools.html#aec039d544c93a6e810427ad45ba0c84f instead of randomizing the quadrature points (which you cannot easily do). Best, Bruno

[deal.II] Re: An iterator for all nodes (including midside) in the mesh?

Jimmy, Is this https://github.com/dealii/dealii/wiki/Frequently-Asked-Questions#how-to-get-the-mapped-position-of-support-points-of-my-element what you are looking for? Best, Bruno On Monday, June 22, 2020 at 1:32:43 AM UTC-4, Jimmy Ho wrote: > > Dear All, > > I am trying to write a code to

Re: [deal.II] Re: My machine did't manage to run Deal.II

Prasad, Packaging deal.II and dependencies is a lot of work. When we release a new version of deal.II we update the development version of Debian and from there the package goes to other distributions including Ubuntu. So the next release of Ubuntu will probably have the latest version of

Re: [deal.II] Installation stopped

Yuesu Lin, Do you have access to a newer compiler? gcc 4.8.5 is very old. Best, Bruno On Wednesday, July 22, 2020 at 11:26:05 PM UTC-4, yuesu jin wrote: > > Dear Timo, > The configuration in summary.log file is: > > deal.II configuration: > #CMAKE_BUILD_TYPE: DebugRelease > #

[deal.II] Re: PETSc is not compatible with current MPI

Yuesu Jin, You don't need to compile your own PETSc but you need to use the same MPI library than the one that PETSc is using. There are very hard to debug problems that appear when PETSc and deal.II use different MPI libraries. I think that you want to use this MPI library

[deal.II] Re: KDTree implementation error

Heena, You are missing an include. Try adding #include https://dealii.org/current/doxygen/deal.II/kdtree_8h_source.html>> Best, Bruno On Thursday, July 23, 2020 at 2:55:53 PM UTC-4, heena patel wrote: > > > Dear all, > I had tried to implement KDTree in step_1 >

Re: [deal.II] Re: Some changes in arpack.h (Functionality to compute only eigenvalues)

Animesh, Sorry for the slow reply. Le lun. 11 janv. 2021 à 12:40, Animesh Rastogi IIT Gandhinagar a écrit : >> Response - I am not using Trilinos vectors. I am using normal BlockVectors >> and BlockSparseMatrix from dealii Linear Algebra class. Is it possible for >> me to convert my

[deal.II] Re: Parallel distributed hp solution transfer with FE_nothing

Hi, Are you sure that your test makes sense? You randomly assign FE indices to cells then you refine and coarsen cells. But what does it mean to coarsen 4 cells together when one of them is FE_Nothing? What would you expect to happen? Best, Bruno On Monday, December 7, 2020 at 5:54:10 PM

[deal.II] Re: Interacting with Python data // external codes

Corbin, deal.II has some limited support for python mainly for mesh manipulation. We have some python notebooks here . I think what you want to do is similar to the step-62 notebook. Right now, the

[deal.II] Re: Error in Compilation

Pushkar, Have you done any modifications to step-26? Best, Bruno On Friday, December 4, 2020 at 5:16:15 AM UTC-5 pushkar...@gmail.com wrote: > Well that was not a problem it was my silly mistake that I for some reason > commented out the main() function in hurry and raninto such an error but

[deal.II] Re: error encountered while using matrix free in GPU with periodic BCs

Vishal, I don't think anyone has ever tried to use periodic boundary conditions with GPU. The way we apply constraints on the GPU is very different than what is done on the CPU. So, I am not surprised that it doesn't work. I'll add that to my todo list but I have no idea when I will be able to

Re: [deal.II] Re: Some changes in arpack.h (Functionality to compute only eigenvalues)

Le mer. 16 déc. 2020 à 04:55, Animesh Rastogi IIT Gandhinagar a écrit : > > Thank you Bruno for your suggestion. I tried in regular mode and it doesn't > seem to improve the accuracy. The results are approximately the same as I was > getting using the shift-invert method. > > One thing that I

Re: [deal.II] Re: Some changes in arpack.h (Functionality to compute only eigenvalues)

Animesh, You need to download the patch to the deal.II directory. If you cloned deal.II, you can simply use git apply 0001-Enable-ARPACK-in-regular-mode.patch. If you didn't use git to get deal.II, I think patch -i 0001-Enable-ARPACK-in-regular-mode.patch should work. I have also noted that

[deal.II] Re: Building on Cluster

Zachary, The Intel compiler does not have its own standard library and instead, it uses the one from gcc. Often, you need to load a newer version of gcc and then load the Intel compiler to have a compiler *and* a standard library that support C++14. Otherwise the compiler supports C++14 but

[deal.II] Re: Post-processing velocities with Trilinos vectors during simulation

Hi, On Wednesday, November 4, 2020 at 2:34:05 PM UTC-5 acdaig...@gmail.com wrote: > Hi everyone! > > I'm working on post-processing velocities with Trilinos solution vectors > during the simulation on Lethe. > Calculating average velocities and pressures (, , and ) works > well using

Re: [deal.II] Use Gmsh to import external grid calculation elasticity problem

Hi, The function print_mesh_info() ends at line 269. It should end at line 107. Best, Bruno On Wednesday, November 4, 2020 at 9:40:57 PM UTC-5 wjs641...@gmail.com wrote: > Okay, I re-run the program I wrote > vs told me that ,what that mean? > > *2>step-8.obj: error LNK2019: Unresolved

[deal.II] Re: Some changes in arpack.h (Functionality to compute only eigenvalues)

Animesh, On Thursday, November 5, 2020 at 1:11:33 PM UTC-5 animesh...@alumni.iitgn.ac.in wrote: > However, I have no way of passing it as a parameter to the solver > > > function. I was

Re: [deal.II] Use Gmsh to import external grid calculation elasticity problem

Nick, You didn't declare print_mesh_info and you need to replace template void print_mesh_info(const Triangulation& triangulation, const std::string& filename) {...} by template void ElasticProblem::print_mesh_info(const Triangulation& triangulation, const std::string& filename) {...} You

[deal.II] Re: Tips on writing "versatile" assembly function

Bruno, If you are worry about the cost of looking up though the vtable, I think that you are stuck using template. So either use 2 or 3 and CRTP. But first of all, I think that you should profile your code and verify that this is a problem. There is no point in spending time refactoring your

[deal.II] Re: issue in installing dealii@9.2 on ubuntu through spack

Alberto, Do not use the master branch in spack. The last commit from the master branch on spack is from 2018. I'm guessing you want to use develop. develop for spack is the equivalent of master in deal.II Best, Bruno On Thursday, January 14, 2021 at 1:20:09 PM UTC-5 Alberto Salvadori wrote:

Re: [deal.II] Re: Parallel distributed hp solution transfer with FE_nothing

Kaushik, I am working on the exact same problem for the same application :-) PETSc Vector do not support compress(min) You need to use a dealii::LinearAlgebra::distributed::Vector instead. Best, Bruno Le sam. 2 janv. 2021 à 18:38, Kaushik Das a écrit : > > Hi Marc, > I tried using cell data

Re: [deal.II] Re: Parallel distributed hp solution transfer with FE_nothing

ink I have to copy the solution from a PETSc vector to a > dealii vector after the solution in every time step. > thanks, > Kaushik > > On Sun, Jan 3, 2021 at 8:35 PM Bruno Turcksin > wrote: >> >> Kaushik, >> >> I am working on the exact same problem for the same

[deal.II] Re: How to construct p::d::Triangulation from a locally refined Triangulation?

Ce, If you don't have hanging nodes, you can flatten the triangulation (C++ , python )

[deal.II] Re: Deal.II site appears to be down

Alex, I think it's because we are preparing for the release of deal.II 9.3.0 If you use the direct link to the 9.2 documentation https://dealii.org/9.2.0/doxygen/deal.II/index.html it works fine. It's the "current" link which seems to be broken. Best, Bruno On Monday, June 14, 2021 at

Re: [deal.II] Compiling deal.II with GCC version 9.3.0 results in missing C++11 features error

Alex, This is really strange. I've never seen that error before. Can you try to install deal.II 9.3 https://github.com/dealii/dealii/releases/tag/v9.3.0 and see if you get the same error? Best, Bruno Le lun. 7 juin 2021 à 05:54, Alex Cumberworth a écrit : > > Hello, > > I recompiled trilinos

Re: [deal.II] Compiling deal.II with GCC version 9.3.0 results in missing C++11 features error

Alex, I am glad it is finally working. To answer your question, when using Trilinos MPI is required. We just merged a fix that makes this clear: https://github.com/dealii/dealii/pull/12381 Best, Bruno Le mer. 9 juin 2021 à 11:18, Alex Cumberworth a écrit : > > Hello, > > I finally managed to

[deal.II] Re: Do docker container support cuda

Chengjiang, On Saturday, June 19, 2021 at 2:38:24 PM UTC-4 richard...@gmail.com wrote: > > So is there a possible way to enable the flag without rebuild and install > the whole library or does the dealii team has any plans to release an extra > version based on nvidia/cuda image? To enable

[deal.II] Re: writing values in the solution vector for constrained dofs

Simon, Yes, you should be able to skip the constrained hanging nodes. Like you said the value will be overwritten when you call distribute(). Let us know if you get something unexpected but that should work. Best, Bruno On Wednesday, June 23, 2021 at 5:00:06 AM UTC-4 Simon wrote: > Dear

[deal.II] Re: adaptive mesh refinement for Navier Stokes

Hello, The error message is pretty clear: you are calling the function setup_system() but you didn't define it. I am guessing the function exists in Step 26 but not in Step 35. Best, Bruno On Thursday, June 24, 2021 at 2:40:56 AM UTC-4 jack urombo wrote: > I am working on a adaptive finite

[deal.II] Re: problem with quik_tests when install dealii by spack: make -jn test causes to error "bad file descriptor"

It looks like I clicked on the wrong button and I didn't sent the message to the mailing list :( There are two solutions to this problem: 1. Compile everything using a single processor, i.e. using spack install -j1 ... This works but it will be very slow 2. Do not run quicktest when using spack.

Re: [deal.II] Regarding using Boost library functions with deal.II

/libk5crypto.so.3 > (0x7f0ab3aa) > libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2 (0x7f0ab3a99000) > libkrb5support.so.0 => /lib/x86_64-linux-gnu/libkrb5support.so.0 > (0x7f0ab3a8a000) > libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x000

Re: [deal.II] Regarding using Boost library functions with deal.II

Kishore, Can you show the result of the command ldd, i.e. what do you see when you type ldd ./my_code Best, Bruno On Friday, May 14, 2021 at 9:32:26 AM UTC-4 kishore...@gmail.com wrote: > Just an update: The code gives the above errors even before the execution > of the code starts. The

Re: [deal.II] Regarding using Boost library functions with deal.II

shes, > > Kishore > > On Friday, May 14, 2021 at 9:49:52 PM UTC+5:30 Kishore Nori wrote: >> >> Dear Prof. Bangerth, >> >> Thank you for the reply, yes I was having some doubt on this. I removed the >> FIND_PACKAGE(Boost REQUIRED) in CMakeLists.txt but I still g

Re: [deal.II] Compiling deal.II with GCC version 9.3.0 results in missing C++11 features error

Alex, How did you install your compiler? You should not need to set these paths yourself. Best, Bruno Le mer. 26 mai 2021 à 13:17, Alex Cumberworth a écrit : > > It seems that the issues stem from not setting the include directories > properly. Even with CPATH, C_INCLUDE_PATH, and

[deal.II] Re:

Shahin, I think this does what you want https://dealii.org/current/doxygen/deal.II/namespaceGridTools.html#addb822f0e3068e48640ecc981ee6c1e6 I am not sure I understand what's your question about lumping. Best, Bruno On Thursday, May 20, 2021 at 4:11:47 AM UTC-4 sh1990@gmail.com wrote:

[deal.II] Re: Compiling deal.II with GCC version 9.3.0 results in missing C++11 features error

Alex, Can you check that deal.II pick up the right compiler? It should be printed on your screen. You don't need to specify DEAL_II_CXX_VERSION_FLAG when using gcc. Best, Bruno On Friday, May 21, 2021 at 1:03:13 PM UTC-4 alexanderc...@gmail.com wrote: > Hello, > > I am trying to compile

Re: [deal.II] Re: Compiling deal.II with GCC version 9.3.0 results in missing C++11 features error

Alex, I think that deal.II picks the compiler correctly but it looks like the stl library is too old. What version of libstdc++ is installed on the system? Best, Bruno Le ven. 21 mai 2021 à 13:41, Alex Cumberworth a écrit : > > Hi Bruno, > > From the output when I run a fresh configuration: >

Re: [deal.II] Re:

s.JxW(q_index) ; > > else > > 0; > > } > but I am not sure if it always works, what if I want to use Q2, I feel > like it's not correct. I would be happy to hear your opinion or advice. > > Regards > Shahin > > > On Thu, May 20, 2021, 14:49 Bruno Turcksin > w

[deal.II] Re: solution of linear system using LAPACKFullMatrix - problems with singular matrix

Simon, Unfortunately, there is no such thing as a preconditioner for direct solver. The best way to fix your problem is to try to scale x and y so that they have the same order of magnitude. Another way is to try SVD

Re: [deal.II] About installation

Le mer. 30 juin 2021 à 09:11, Hyun-Geun Shin a écrit : > > Ah ok. > So, I need to type "cmake -DCMAKE_INSTALL_PREFIX=/usr/local ..". Then, I type > "make -j1 install". > Is it correct? I think you need to be root/use sudo to write in /usr/local. So you can use "make -j1" but to install the

Re: [deal.II] About installation

Hyungeun, It looks like you are trying to install the library in /path/usr/local/share/ but I guess you meant to install it in /usr/local/share/. You need to reconfigure the library to install it at the correct place. Best, Bruno On Tuesday, June 29, 2021 at 6:32:45 PM UTC-4 shg...@gmail.com

[deal.II] Re: Compile Error: no type named ‘active_cell_iterator’

Yes, it looks like DataOut used to have DataOut::active_cell_iterator. I looked back at an old version of deal.II and DataOut::active_cell_iterator was just a typedef for Triangulation::cell_iterator. Bruno On Monday, July 12, 2021 at 9:28:50 AM UTC-4 mjri...@gmail.com wrote: > OK, > > At one

[deal.II] Re: Compile Error: no type named ‘active_cell_iterator’

Hi, On Monday, July 12, 2021 at 5:40:40 AM UTC-4 mjri...@gmail.com wrote: > > Should I just change active_cell_iterator to cell_iterator? I am worried > that they wont work the same creating problems downstream. > Only cell_iterator is accessible not active_cell_iterator. So yes,

Re: [deal.II] Re: Do docker container support cuda

cluster production environment and I've > already trying to set it up on the HPC. Though I still prefer to docker while > doing test and dev considering its convenience. Updates would be posted here > if any one of them works. > > Regards, > Chengjiang Yin > > Bruno Tu

[deal.II] Re:

Chenyi, Unless you have measured that this is a bottleneck in you code, you should use what's the more readable. If there is a difference between these two codes, it would need to be in a hot loop to matter. My advice is to write easy to understand code and once you have made sure that the

[deal.II] Re: Segfault upon printing Point in GDB

Corbin, Take a look at https://dealii.org/developer/users/gdb.html This should help. Note that gdb should not segfault. It probably means that there is a problem with your code. Best, Bruno On Saturday, May 1, 2021 at 12:07:49 AM UTC-4 corbin@gmail.com wrote: > And the file is here. > >

[deal.II] Re: make install fails with ld signal 9

Vachan, On Tuesday, May 4, 2021 at 2:45:30 AM UTC-4 vachanpo...@gmail.com wrote: > Dear all, > > I am trying to do a new installation of dealii. `make install` exits while > compiling libdeal_II.g.so with ld signal 9. I had a look at this question >

[deal.II] Re: Problem related to make_hanging_nodes_constraints in the hp cases

Chong Liu, On Tuesday, May 4, 2021 at 12:06:39 PM UTC-4 liuch...@gmail.com wrote: > > Question: > > *How can I only constrain the hanging nodes for fe_type_1*? > Why do you want to do that? If you don't constrain fe_type_2, the solution won't be continuous. If you have more dofs in one side

[deal.II] Re: Step-8 Extension : Unable to modify BCs with face iterator

Pushkar, Which version of deal.II are you using? That function was introduced in version 9.1. Here is the documentation to the constructor of the Bessel functio: https://dealii.org/current/doxygen/deal.II/classFunctions_1_1Bessel1.html#ac102d190a35cfc17f1876c82bab41004 Is the documentation

[deal.II] Re: CUDA without nVidia

Michal, Support for AMD through HIP is very high on my todo list but the compiler is not that great right now, i.e. the compiler can (and will) generate buggy code. I've tried to hipify the code a few months ago but it didn't go too well. My plan is to work on support for AMD after we branch

[deal.II] Re: Error in p4est installation using deal.II suggested script

Kishore, Can you try the following command: $ bash ./p4est-setup.sh p4est-2.2.tar.gz /home/kishore/bin Best, Bruno On Friday, March 12, 2021 at 11:41:21 AM UTC-5 kishore...@gmail.com wrote: > Hi everyone, > > Hope you are doing well! > > I am new to deal.II and I am trying to install p4est

Re: [deal.II] Re: Error in p4est installation using deal.II suggested script

Best wishes, > > Kishore > > On Sat, Mar 13, 2021 at 12:43 AM Bruno Turcksin > wrote: >> >> Kishore, >> >> Can you check that /home/kishore/p4est-2.2 exists and that there are >> files in the directory. According to google this error usually if >&g

Re: [deal.II] Re: Issue with Boost 1.75.0

17:47, Ed Read a écrit : > > I have attached it. > > Thank you for your help > > On Mon, Mar 1, 2021 at 2:43 PM Bruno Turcksin > wrote: >> >> >> Hi, >> >> Can you post the detailed.log file. It should be in you build directory. >> >> B

[deal.II] Re: Issue with Boost 1.75.0

Hi, Can you post the detailed.log file. It should be in you build directory. Best, Bruno On Monday, March 1, 2021 at 12:30:58 PM UTC-5 tr...@rrwkk.net wrote: > > Hello Everyone, > > I am working on installing Deal.II on my linux box and am now receiving > the following: > > [ 79%] Built

[deal.II] Re: dealii::SolverControl::NoConvergence with Bicgstab

Hi, Bicgstab is not guaranteed to converge especially when using a bad preconditioner. You are using Jacobi as preconditioner which is a simple but not very good preconditioner. As you can see from the error message, you performed 1959 bicgstab iterations. That's a lot and it probably

[deal.II] Re: LineMinimization and p-Laplace

Julie, There is a tutorial in progress https://github.com/dealii/dealii/pull/11953 that is based on step-15 but uses KINSOL . KINSOL is a package dedicated to non-linear solve. It's probably worth using it in

Re: [deal.II] Re: dealii::SolverControl::NoConvergence with Bicgstab

Le jeu. 15 avr. 2021 à 11:57, bunel...@gmail.com a écrit : > Hi, > > thank you very much for your answer. > I have actually tried to solve using GMRES like this : > > SolverControl > solver_control(phi_system_rhs.size()*2,1e-10); > PreconditionJacobi<> preconditioner; >

[deal.II] Re: deai.II module on Stampede2

David, It looks like you have two modules that provides metis */opt/apps/intel18/metis/5.0.2/lib and /home1/apps/intel18/impi18_0/petsc/3.11/skylake/lib *This creates a conflict because the cmake see the symbols twice Which modules are you loading? Are you loading both yourself? Best,

Re: [deal.II] Re: deai.II module on Stampede2

alii/9.2.0* > > Out of those modules, the ones I marked with an asterisk are automatically > added when I load the dealii module. The rest are the default modules that > are loaded when I login. > > David > > > > > On Tue, Feb 16, 2021 at 8:32 AM Bruno Turc

[deal.II] Re: Configuring deal.II with LAPACK

Giselle, Instead of setting the library yourself can you try: -DBLAS_LIBRARY_NAMES:STRING='mkl_core;mkl_sequential' -DLAPACK_LIBRARY_NAMES:STRING=mkl_intel_lp64 Don't set BLAS/LAPACK_FOUND/LIBRARIES/LINKER_FLAGS. Let CMake find the libraries and the flags it needs to use. Best, Bruno

Re: [deal.II] Re: Configuring deal.II with LAPACK

ere. Do you happen to have any other > suggestions? Maybe it is an issue with Intel mkl? > > Thanks again. > > Best, > Giselle > > On Fri, 19 Feb 2021 at 14:11, Bruno Turcksin wrote: >> >> Giselle, >> >> Instead of setting the library yourself can

[deal.II] Re: MPI error while running inside a Docker container

David, Have you try to create a new file and save it inside docker? What is your user name in docker? Are you root? It could be a problem with your permission. Best, Bruno On Saturday, August 7, 2021 at 3:07:56 PM UTC-4 dmon...@umich.edu wrote: > Sorry in my original email I wrote "This

Re: [deal.II] Re: MPI error while running inside a Docker container

a écrit : > > Hello, Bruno. > > Thank you, I will check. I assumed that was not the issue because when I > compile inside docker files are created. > > David > > > On Tue, Aug 17, 2021, 4:30 AM Bruno Turcksin wrote: >> >> David, >> >> Have

[deal.II] Re: Question on TimeStepping methods

Praveen, On Thursday, August 26, 2021 at 12:22:47 PM UTC-4 Praveen C wrote: > ExplicitRungeKutta and EmbeddedExplicitRungeKutta are derived from > RungeKutta but there is no virtual function with these arguments in > RungeKutta. > > Is it possible to declare such a virtual function in the

[deal.II] Re: Problem using EmbeddedRungeKutta

Praveen, Good catch. When you split the initialization part there is flag that is not initialized. I guess in debug, the flag is correctly set to false (0) while in release mode the flag is undetermined and you may get true. I'll fix this. Best, Bruno On Thursday, August 26, 2021 at

[deal.II] Re: step-29 & step-40

Hermes, The following line is wrong: *DynamicSparsityPattern dsp(locally_relevant_dofs.n_elements(), locally_relevant_dofs.n_elements());* This constructor says that you want a sparsity pattern that has *locally_relevant_dofs.n_elements() *elements. This is not the case. You want a sparsity

[deal.II] Re: step-4: Neumann boundary conditions

Morris, How to implement Neumann boundary conditions is explained in step-7. Best, Bruno On Thursday, September 9, 2021 at 1:37:56 PM UTC-4 Morris Jowas wrote: > Hello all, > > Has anyone implemented Neumann boundary conditions as a way to extend > step-4? > Please let me know or point me to

Re: [deal.II] Re: step-29 & step-40

ut_results(myfile) *takes care of writing the > solution of a single point in a plain .txt file for each frequency. > > > Step-40 shows a way to write .vtu files format when using MPI, but I did > not find any function to write the plain solution. > > I would appreciate any suggest

Re: [deal.II] Re: step-29 & step-40

Hermes, Le mar. 14 sept. 2021 à 05:19, Hermes Sampedro a écrit : > > Should I use dealii::PETScWrappers::MPI::SparseMatrix system_matrix instead? > If so could ou please help me to with the reinit() function? I do not fully > understand how to call it. That's right, you need the matrix to be

Re: [deal.II] Re: step-29 & step-40

update_system() to update the system matrix as it change due to the > frequency. I need to do system_matrix .reinit before the update to clean > the matrix which I realize is time comsuming. I would like to ask if there > is another efficient way to update the matrix. > > Thank you >

[deal.II] Re: Grid deformation after load-balancing

Shahab. You can loop over the cells, get the vertices (see https://dealii.org/current/doxygen/deal.II/classTriaAccessor.html#a3dd6518eb0cf5fccc5926470128415d9) and print the Point associated to each vertex. Then you can compare the vertices before and after load balancing. Best, Bruno On

[deal.II] Re: Grid deformation after load-balancing

Shahab, Can you quantify the deformation? It would be useful if you could output the coordinates of the vertices of the deformed cells before and after load balancing. It is possible that's a rendering issue but it's hard to tell without having numbers. Best, Bruno On Wednesday, July 28,

Re: [deal.II] Re: issue in installing dealii 9.2 and .3 on centos

; tel 030 3715426 > > e-mail: > alberto@unibs.it > web-page: > http://m4lab.unibs.it/faculty.html > > > > On Fri, Jul 30, 2021 at 4:12 PM Bruno Turcksin > wrote: > >> Alberto, >> >> I have no clue what med is, so it's not a basic dependency of deal

[deal.II] Re: issue in installing dealii 9.2 and .3 on centos

Alberto, I have no clue what med is, so it's not a basic dependency of deal.II. Which version of spack are you using? I don't see a dependency on med when I do `spack speck dealii` You can tell spack not to install med but you need to know which package pulled it. Best, Bruno On Friday,

Re: [deal.II] Re: issue in installing dealii 9.2 and .3 on centos

aly > tel 030 3715426 > > e-mail: > alberto@unibs.it > web-page: > http://m4lab.unibs.it/faculty.html > > > On Fri, Jul 30, 2021 at 5:01 PM Bruno Turcksin > wrote: > >> Alberto, >> >> My experience with spack is to use a release

[deal.II] Re: profiling and parallel performance of deal.II user codes

Richard, On Tuesday, August 3, 2021 at 9:58:07 AM UTC-4 richard@gmail.com wrote: > a) which (free) profiling tools can you recommend? I watched the video > lecture of Wolfgang about that topic, but was looking for more opinions! I > want to see which parts of the code take time apart from

[deal.II] Re: dealii not compiling because of boost geometry problem

Lucas, There are problems with Boost 1.77.0 (see https://github.com/dealii/dealii/issues/12817). The problems are in Boost itself and there is nothing we can do about it. Use Boost 1.76 instead. Best, Bruno On Wednesday, October 20, 2021 at 3:18:03 PM UTC-4 lucasm...@gmail.com wrote: > Hi

[deal.II] Re: Assigning anisotropic thermal conductivities in the assemble loop

MJ, fe_values.shape_grad() returns a Tensor<1,dim> so you can do something like this Tensor<1,dim> k_grad; for (int d=0; d Hello everyone, > > > > I am solving the heat equation with the Laplacian expressed in terms of > spatially varying thermal conductivities (k_x, k_y and k_z) as shown

[deal.II] Re: Problem using EmbeddedRungeKutta

Praveen, I have a fix here: https://github.com/dealii/dealii/pull/12725 Best, Bruno On Friday, August 27, 2021 at 12:12:36 PM UTC-4 Bruno Turcksin wrote: > Praveen, > > Good catch. When you split the initialization part there is flag that is > not initialized. I guess in deb

[deal.II] Re: Interlacing update ghost and assemble

Praveen, We do something like that in CUDA MatrixFree. It is slightly more complicated because we need to update the ghost values on both the source vector and the destination vector. The idea is to first loop over the mesh and store all the vertices that are ghosted then you loop over the

Re: [deal.II] Problems installing dealii-9.3.2 (AVX)

Daniel, There is something strange with Trilinos configuration. Somehow only Kokkos was found, I don't see Epetra or AztecOO. These libraries are required when using Trilinos, I bet if you look carefully when the configuration happens you will see an error message when Trilinos is detected.

[deal.II] Re: parallel SolutionTransfer and LinearAlgebra::distributed::Vector

Hello, Which line triggers the error? Is it the zero_out_ghost() line? This line should not be there, the ghost elements are set to zero when you do =0 Best, Bruno On Tuesday, November 16, 2021 at 3:13:23 AM UTC-5 SALMAN wrote: > Dear all, > > I am developing a time dependent code which

Re: [deal.II] Are there known issue between Trilinos 13.0.1 and deal.II?

Bruno, It looks like you are not the only one to have this problem: https://github.com/trilinos/Trilinos/issues/8299 https://github.com/trilinos/Trilinos/issues/9426 Possible solution from the second issue: use `-DBUILD_SHARED_LIBS:BOOL=OFF` or add -undefined dynamic_lookup to CMAKE_CXX_FLAGS

[deal.II] Re: GPU implementation

Hi, The data is moved when you call import. This is done using cudaMemcopy, so there is no need to use __device__ You only need __device__ for functions that are executed on the device. The best place to look for examples is to look at the tests:

[deal.II] Re: Consideration about the number of parallel processors

Toddy, This is just a rule of thumb, there is no formula to choose the number of processors. The documentation says that you need at least 4 dofs per process so people don't run a problem with 1000 dofs on 100 processors and expect their code to be fast. The "best" number of processors to

[deal.II] Re: 2 questions on hanging nodes

Niall, Both statements are correct. Hanging nodes can only be introduced by refining a cell and there can only be one hanging node per face. Best, Bruno On Friday, December 10, 2021 at 7:29:45 AM UTC-5 nialls...@gmail.com wrote: > Hello, > I'm quite new to deal.ii, so I appologise if these

[deal.II] Re: Deal.II programming environment

Martin, You can use whatever you like, there is no such thing as a typical environment. With that being said, we do have documentation and videos to help you setup Eclipse. See https://github.com/dealii/dealii/wiki/Eclipse https://www.math.colostate.edu/~bangerth/videos.676.7.html

[deal.II] Re: dealii in spack - approach to upgrade to latest version 9.3.3 via local git clone of spack

Simon, On Wednesday, July 21, 2021 at 5:17:05 PM UTC-4 Simon wrote: > > In my local working copy of the spack repository, I only have one master > branch so far. I guess I first to need to upgrade spack somehow, in order > to be able to install newer versions of a package, since > 'spack info

Re: [deal.II] Calculate cell center distance from a boundary

Vachan, On Friday, February 11, 2022 at 12:51:49 AM UTC-5 vachanpo...@gmail.com wrote: > Dear Dr. Wolfgang, > > Thank you very much for the kind reply. > > >> This is a very difficult operation to do even in sequential computations >> unless you have an analytical description of the boundary.

Re: [deal.II] Re: Assemble function, long time

Hermes, The problem is that you are using a direct solver. Direct solvers require a lot of memory because the inverse of a sparse matrix is generally not sparse. If you use a LU decomposition, which I think MUMPS does, you need a dense matrix to store the LU decomposition. That's a lot of memory!

[deal.II] Re: Issue with corner value using adaptive mesh

David, Hard to tell what's the problem here. Might be a problem with the AffineConstraints. Are they correct? Do you distribute them when you should? Best, Bruno On Monday, February 28, 2022 at 4:12:16 PM UTC-5 dmon...@umich.edu wrote: > Hello, > > I am working on PRISMS-PF (which is

Re: [deal.II] Re: Assemble function, long time

Hermes, Sorry, I don't use petsc. Maybe someone else can help you. Best, Bruno Le lun. 14 mars 2022 à 05:42, Hermes Sampedro a écrit : > Dear Bruno, > > I have been reading the examples and documents you pointed out. I tried to > use SolvereGREMS with PreconditionILU. However, I am getting a

[deal.II] Re: Error while installing dealii

Hello, Did you configure Trilinos with MPI support? Best, Bruno On Tuesday, March 15, 2022 at 7:09:55 AM UTC-4 punith...@gmail.com wrote: > I've compiled a deal.ii using CMake with the below options > > cmake -DCMAKE_INSTALL_PREFIX=/apps/codes/deal_II/9.3.3 >

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