[deal.II] Re: Adaptive Time Increment Algorithm

2020-10-15 Thread Bruno Turcksin
James, On Tuesday, October 13, 2020 at 8:39:42 PM UTC-4 James Gorman wrote: > > I am, however, at a loss for how to efficiently make it so that Step-44 > (or any other script) will automatically decrease a time-step. The only > idea I had at the moment was to use a ``for'' loop and run a

Re: [deal.II] Re: APPLY BOUNDARY CONDTION ON INTERNAL FACE

2020-10-13 Thread Bruno Turcksin
Xiang, Here is an example on how to do it: https://github.com/geodynamics/aspect/blob/master/cookbooks/prescribed_velocity/prescribed_velocity.cc#L297-L303 As you can see, you need to know which dof you need to constrain Best, Bruno Le mar. 13 oct. 2020 à 11:02, 孙翔 a écrit : > > > Hi, Bruno,

[deal.II] Re: APPLY BOUNDARY CONDTION ON INTERNAL FACE

2020-10-12 Thread Bruno Turcksin
Xiang, You cannot apply a boundary condition on an internal face. You need to use the AffineConstraint class to impose the constraints yourself. This is what we use internally to apply Dirichlet boundary condition.

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

2020-09-28 Thread Bruno Turcksin
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: install problems with clang@12.0.0 and Xcode12.0 from spack

2020-09-25 Thread Bruno Turcksin
Alex, Try using less processors. Something like: spack install -j2 dealii~scalapack ^openblas@develop ^arpack-ng@develop ^trilinos~mumps Best, Bruno On Friday, September 25, 2020 at 11:21:52 AM UTC-4 alexande...@icloud.com wrote: > Update: > I managed to came as far as spack at least tries

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

2020-09-22 Thread Bruno Turcksin
ved after I removed the 'SetFactory("OpenCASCADE")'. > Here are two mesh files with and without 'SetFactory("OpenCASCADE")'. Could > you tell me why this command made the system unable to work? Thank you very > much for your help! > Best regards, > Yuesu > > &

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

2020-09-22 Thread Bruno Turcksin
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] Re: .msh file triangulation failed

2020-09-22 Thread Bruno Turcksin
; 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

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

2020-09-22 Thread Bruno Turcksin
Yuesu, I had the same problem recently. Our gmsh reader assumes that the user has set boundary id and material id to the mesh. It looks like you don't have those and so the file is read incorrectly. Best, Bruno On Tuesday, September 22, 2020 at 2:04:17 AM UTC-4 jinyu...@gmail.com wrote: >

[deal.II] Re: Thermal Modelling of Additive Manufacturing Process

2020-09-02 Thread Bruno Turcksin
Pushkar, What do you want to know? There is no question, so it's hard to help you. Best, Bruno On Wednesday, September 2, 2020 at 8:52:59 AM UTC-4 pushkar...@gmail.com wrote: > Greetings Deal.II Community, > > I wish to simulate the thermal profile in additive manufacturing process > using

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

2020-08-11 Thread Bruno Turcksin
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

2020-08-06 Thread Bruno Turcksin
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: PETSc is not compatible with current MPI

2020-07-23 Thread Bruno Turcksin
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

2020-07-23 Thread Bruno Turcksin
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] Installation stopped

2020-07-23 Thread Bruno Turcksin
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: Mesh-induced elastic anisotropy and distorting the quad. points as a way to palliate it

2020-07-07 Thread Bruno Turcksin
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: Error while installing dealii

2020-07-06 Thread Bruno Turcksin
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: An iterator for all nodes (including midside) in the mesh?

2020-06-22 Thread Bruno Turcksin
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

2020-06-03 Thread Bruno Turcksin
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

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

2020-05-26 Thread Bruno Turcksin
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

Re: [deal.II] Re: Evaluating FE-solution on distributed mesh, semi-Lagrangian method

2020-05-12 Thread Bruno Turcksin
nday, May 11, 2020 at 2:49:21 PM UTC+2, Bruno Turcksin wrote: >> >> Konrad, >> >> Unfortunately, you will need to do the communication yourself. You can only >> evaluate the solution on cells that locally owned or on ghost cells. >> >> Best, >> >

[deal.II] Re: Evaluating FE-solution on distributed mesh, semi-Lagrangian method

2020-05-11 Thread Bruno Turcksin
Konrad, Unfortunately, you will need to do the communication yourself. You can only evaluate the solution on cells that locally owned or on ghost cells. Best, Bruno On Monday, May 11, 2020 at 6:26:47 AM UTC-4, Konrad Simon wrote: > > Dear all, > > I am currently working on a semi-Lagrangian

Re: [deal.II] Re: "libpthreads"?

2020-04-28 Thread Bruno Turcksin
On Tuesday, April 28, 2020 at 3:33:06 PM UTC-4, Wolfgang Bangerth wrote: > > > We don't have one. We announce on a variety of mailing lists like > NA-Digest. > But we've been reasonably regular at releasing around the month of May in > recent years if you want to pencil things into your

Re: [deal.II] Re: deal ii 9.1.1. installation fails

2020-04-28 Thread Bruno Turcksin
Stefan, Le mar. 28 avr. 2020 à 04:02, Stefan Knauf a écrit : > thank you, I installed Trilinos 12.18.1 and now it worked. Since the > TRILINOS_VERSION is detected by cmake I would have rather expected a cmake > error (wrong version, as for example for p4est, where also a specific version > is

[deal.II] Re: deal ii 9.1.1. installation fails

2020-04-27 Thread Bruno Turcksin
Stefan, On Saturday, April 25, 2020 at 4:17:20 PM UTC-4, Stefan Knauf wrote: > Unfortuneately now "make install" stops with an error: > [ 42%] Building CXX object > source/lac/CMakeFiles/obj_lac_release.dir/trilinos_precondition_muelu.cc.o >

[deal.II] Re: LinearOperator MPI Parallel Vector

2020-04-24 Thread Bruno Turcksin
On Thursday, April 23, 2020 at 4:50:40 AM UTC-4, peterrum wrote: > Regarding GPU: currently there is only support for matrix-free and non for > matrix-based algorithms. These GPU implementations use currently > LA::dist::Vector. > We actually support matrix-based algorithms on the GPU and we

Re: [deal.II] Re: Deal.ii insttallation issues

2020-04-09 Thread Bruno Turcksin
ll > prefix line. > > On Thu, Apr 9, 2020, 5:18 PM Bruno Turcksin wrote: >> >> I wonder if there is a problem because of the . in the directory name. >> Can you try to rename the directories? >> >> >> Le jeu. 9 avr. 2020 à 16:27, Malik Tahiyat >>

Re: [deal.II] Re: Deal.ii insttallation issues

2020-04-09 Thread Bruno Turcksin
I wonder if there is a problem because of the . in the directory name. Can you try to rename the directories? Le jeu. 9 avr. 2020 à 16:27, Malik Tahiyat a écrit : > > Yes it does. > > On Thu, Apr 9, 2020, 2:49 PM Bruno Turcksin wrote: >> >> Le jeu. 9 avr. 202

Re: [deal.II] Re: Deal.ii insttallation issues

2020-04-09 Thread Bruno Turcksin
Le jeu. 9 avr. 2020 à 14:34, Malik Tahiyat a écrit : > > I get the error : "Make Error: The source directory > "/home/malik/dealii-9.1.1" does not exist." in step 3 Does "/home/malik/dealii-9.1.1" contain a CMakeLists.txt file? Bruno -- The deal.II project is located at http://www.dealii.org/

[deal.II] Re: Deal.ii insttallation issues

2020-04-09 Thread Bruno Turcksin
Hi, To install deal.II, you need to first compile it using `make` which probably happens in ~/projects/dealii-9.1.1/build and then it needs to be installed using `make install`. That second step should move the important files to /home/projects/deal.II It looks to me that you forgot this

Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Bruno Turcksin
that a 1D simulation shoud just be a walk in the park for the two vtk-based heavyweights. Regards, Krishna On Mon, 16 Mar 2020 at 15:51, Bruno Turcksin <mailto:bruno.turck...@gmail.com>> wrote: Krishna, VisIt and Paraview are just two of many visualization software that

Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Bruno Turcksin
Krishna, VisIt and Paraview are just two of many visualization software that can read .vtk and .vtu files. Some people also use vtk to transfer data between programs. Why should we restrict the output because two visualization tools don't support 1D? Best, Bruno On Monday, March 16, 2020 at

[deal.II] Re: Matrix-free: Continuous elements and boundary (face) integrals

2020-03-11 Thread Bruno Turcksin
On Wednesday, March 11, 2020 at 7:36:31 AM UTC-4, Michał Wichrowski wrote: > > I tried to fix that by myself, but I could not locate the source code of > MatrixFree::internal_reinit > Here it is:

Re: [deal.II] Re: Shared Memory Parallel Linear Solver

2020-02-26 Thread Bruno Turcksin
Paras, Le mer. 26 févr. 2020 à 12:27, Paras Kumar a écrit : > For the vectors (solution & rhs), the idea was to copy the values from the > dealii::Vector to dealii::LinearAlgebra::EpetraWrappers::Vector. As an > intermediate step I first copy the dealii::Vector to >

[deal.II] Re: Shared Memory Parallel Linear Solver

2020-02-14 Thread Bruno Turcksin
Paras, You could try to use SuperLU_MT (see https://portal.nersc.gov/project/sparse/superlu/) but we don't have wrapper for it. The Krylov solver in deal.II are multithreaded but the preconditioners are not. What you can try is to use deal.II solvers and STRUMPACK

Re: [deal.II] Re: Installation on cray XC50 | linking to petsc, lapack and blas libraries with different names

2020-02-13 Thread Bruno Turcksin
Le jeu. 13 févr. 2020 à 07:27, vachan potluri a écrit : > > It is working! > > The mistake I did was to open an interactive job and run the executables > through bash. When I instead submitted a job, and executed using aprun > (Cray's equivalent to mpirun) to run the executables, they ran

[deal.II] Re: Installation on cray XC50 | linking to petsc, lapack and blas libraries with different names

2020-02-12 Thread Bruno Turcksin
Vachan, On Wednesday, February 12, 2020 at 12:24:38 AM UTC-5, vachan potluri wrote: > > Step-1 aborts with Illegal Instruction (core dumped). The error msg gdb > prints is the following. > Program received signal SIGILL, Illegal instruction. > __static_initialization_and_destruction_0

Re: [deal.II] Re: Problem installing Dealii-9.0.0

2020-02-11 Thread Bruno Turcksin
Le mar. 11 févr. 2020 à 09:03, Felipe Orellana < felipeorellanarovir...@gmail.com> a écrit : > > 2) I am not understanding well here: > > YW: Why didn't you copy/paste the patch? > > What is 'the patch' ..how can access that text?, > > if I click on Tamiko's post, the web

Re: [deal.II] Re: Problem installing Dealii-9.0.0

2020-02-11 Thread Bruno Turcksin
Felipe, Le mar. 11 févr. 2020 à 08:29, Felipe Orellana < felipeorellanarovir...@gmail.com> a écrit : > > Hi Dan and Bruno, > > I have followed the thread 9117 for solving this problem, by adding > the recommended flag: > > IF(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.16.0") >

[deal.II] Re: Using deal.ii 9.1.1 in a Qt5 program

2020-02-10 Thread Bruno Turcksin
Arnoud, Wolfgang already explained how to get CMake working but I wanted to let you know about an issue (and a solution!) when using QT and deal.II together: https://github.com/dealii/dealii/issues/7524 Best, Bruno On Monday, February 10, 2020 at 4:00:16 PM UTC-5, Arnoud de Geus wrote: > >

Re: [deal.II] Re: Problem installing Dealii-9.0.0

2020-02-10 Thread Bruno Turcksin
Le lun. 10 févr. 2020 à 10:41, Daniel Arndt a écrit : > The problem here are the additional quotes in the compiler arguments, see > https://godbolt.org/z/bwDjWy. Strange, I get that problem with gcc 4.8 and 4.9 but it works with the other versions of gcc. Bruno -- The deal.II project is

Re: [deal.II] Re: Problem installing Dealii-9.0.0

2020-02-10 Thread Bruno Turcksin
_II_HAVE_FLAG_Wplacement_new - Failed > > cheers many, > Felipe > > > > On Mon, 10 Feb 2020 at 22:03, Bruno Turcksin wrote: >> >> Felipe, >> >> Le lun. 10 févr. 2020 à 08:49, Felipe Orellana >> a écrit : >> > Here I post the output: >&

Re: [deal.II] Re: Problem installing Dealii-9.0.0

2020-02-10 Thread Bruno Turcksin
Felipe, Le lun. 10 févr. 2020 à 08:49, Felipe Orellana a écrit : > Here I post the output: Can you redo it in a clean directory. The output from CMake is different the first time you run it. Also which compiler are you using? Best, Bruno -- The deal.II project is located at

[deal.II] Re: Problem installing Dealii-9.0.0

2020-02-10 Thread Bruno Turcksin
Felipe, Can you post everything that deal.II prints on the screen. Best, Bruno On Monday, February 10, 2020 at 1:59:16 AM UTC-5, Felipe Orellana wrote: > > > Hello, > > My name is Felipe. I am trying to install dealii-9.0.0 on my local > cluster. > > After commanding > > cmake

[deal.II] Re: deal.II installation on cray XC50 giving MPI_VERSION=0.0

2020-02-10 Thread Bruno Turcksin
Vachan, I saw on the other thread that you were using CMake 3.5. I would advise to download a newer version of CMake. deal.II uses FindMPI from CMake and this was rewritten in CMake 3.10 to fix problems with Cray supercomputers. Best, Bruno On Saturday, February 8, 2020 at 1:43:59 AM UTC-5,

Re: [deal.II] Getting old solution values at quadrature points using MeshWorker::loop

2020-01-30 Thread Bruno Turcksin
On Thursday, January 30, 2020 at 2:28:55 PM UTC-5, Andrew Davis wrote: > > > from the file fe_values.impl.2.inst.in. The Assert(false) seems strange > to me---why doesn't it crash? (I'm in Release mode so that could answer > that). However, should it be calling a different function? > > You

[deal.II] Re: Instantiation problem for Utilities::MPI::sum (const ArrayView< const T > , const MPI_Comm _communicator, const ArrayView< T > )

2020-01-28 Thread Bruno Turcksin
Feimi, You need to have two different ArrayView. It won't work with a single ArrayView. The input one (values) need to be an ArrayView and the output one (sum) an ArrayView. Best, Bruno On Tuesday, January 28, 2020 at 11:40:03 AM UTC-5, Feimi Yu wrote: > > I uploaded a minimal code to

[deal.II] Re: Simple merge_triangulation problem

2020-01-23 Thread Bruno Turcksin
Konrad, What does it mean you cannot merge the cells? Do you get the wrong results? Does the code segfault? Do you get an error message? Best, Bruno On Thursday, January 23, 2020 at 8:56:34 AM UTC-5, Konrad Wiśniewski wrote: > > Hi all! > > I've encountered a problem with very simple

[deal.II] Re: "fatal error: MueLu_CreateEpetraPreconditioner.hpp: No such file or directory" when compiling with Trilinos

2020-01-09 Thread Bruno Turcksin
Hi, This is a known problem with the development version of Trilinos https://github.com/dealii/dealii/pull/9237 Use the latest release of Trilinos instead. Best, Bruno On Thursday, January 9, 2020 at 10:06:13 AM UTC-5, Maxi Miller wrote: > > Hei, > when trying to compile deal.II with one of

[deal.II] Re: Why did the developers of deal.ii choose templates over variadic arguments?

2019-12-20 Thread Bruno Turcksin
Krishna, You can find an extensive discussion on the design choices made here . I think section 2.4 answers your question. The short answer is that using template makes the code run faster because the compiler can do a better job at optimizing everything

Re: [deal.II] Re: Optimization of Laplacea Equation Solver

2019-12-06 Thread Bruno Turcksin
Oleg, Le ven. 6 déc. 2019 à 08:21, Oleg Kmechak a écrit : > So I still have to use MPI to make program multihread, even if it is a single > machine, with 40 processors inside? > Maybe it is rough understanding, but I always thought that for multicomputer > processing is used MPI and for

[deal.II] Re: Optimization of Laplacea Equation Solver

2019-12-05 Thread Bruno Turcksin
Oleg, The first thing to do if you want to speed up you code is to profile your code. How do you know which part of the code is slow? Right now, it sounds that you are assuming that it is in the solver which may be true but it may not be. If you want to speed up your solver, you can 1) get a

Re: [deal.II] Re: installation error_CENTOS 7

2019-11-27 Thread Bruno Turcksin
Behrooz, Le mer. 27 nov. 2019 à 10:30, Behrooz Karami a écrit : > Sorry. Is this the correct one? Yes, that's the one but I don't see anything wrong. Can you try to install deal.II with spack using a smaller number of dependencies. I wonder if the problem is a flag from deal.II or the flag from

Re: [deal.II] Re: installation error_CENTOS 7

2019-11-27 Thread Bruno Turcksin
Behrooz, Le mer. 27 nov. 2019 à 09:25, Behrooz Karami a écrit : > Please find it as attached. This is the one for CMake not the one for deal.II Best, Bruno -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see

[deal.II] Re: installation error_CENTOS 7

2019-11-26 Thread Bruno Turcksin
Behrooz, When you install gcc with spack did you install gfortran at the same time? Best, Bruno On Tuesday, November 26, 2019 at 8:56:19 AM UTC-5, Behrooz Karami wrote: > > > Dear All, > > I am facing an error during last steps of installation of dealii with > SPACK on CENTOS 7. > Could

[deal.II] Re: Compatibility of version 8.5.0 and newer versions (9.1)

2019-11-15 Thread Bruno Turcksin
Teresa, On Friday, November 15, 2019 at 11:40:01 AM UTC-5, Teresa Sanchez Rúa wrote: > > Dear all, > I would like to ask you about the compatibility of version 8.5.0 and the > newer versions of deal.II. > We installed the version 8.5.0 in a Linux server and we developed a code > using it. Now,

Re: [deal.II] Re: step-54 not working

2019-11-07 Thread Bruno Turcksin
I have created a PR https://github.com/dealii/dealii/pull/9016 Thanks for reporting the bug! Best, Bruno Le jeu. 7 nov. 2019 à 08:13, Bruno Turcksin a écrit : > > Hi, > > This looks like a bug in the tutorial. All the cout and endl in that part of > the main are missing std:: I

[deal.II] Re: step-54 not working

2019-11-07 Thread Bruno Turcksin
Hi, This looks like a bug in the tutorial. All the cout and endl in that part of the main are missing std:: I don't know how it ever compiled before. Sorry about that. Best, Bruo On Thursday, November 7, 2019 at 7:30:59 AM UTC-5, Mohammed Hassan wrote: > > Hello everyone! > > > I am fairly

[deal.II] Re: Hanging nodes

2019-10-29 Thread Bruno Turcksin
David, It won't work. The vertices need to match. Best, Bruno On Tuesday, October 29, 2019 at 1:36:41 PM UTC-4, David Ryan wrote: > > Hello, > > I'm merging two geometries in dealii. If the cells of both geometries > don't match up, will that give hanging nodes, or will the code not be able

Re: [deal.II] Re: optimization, SolverBFGS

2019-10-28 Thread Bruno Turcksin
There is a small bug in the lambda: Le lun. 28 oct. 2019 à 09:36, Juan Carlos Araujo Cabarcas a écrit : > auto my_lambda = [](Vector a, Vectorb) { > return polar.objective_fun(a,b); > }; //polar.Callback (a,b);}; You want the vector to be passed by reference not by

Re: [deal.II] Re: optimization, SolverBFGS

2019-10-28 Thread Bruno Turcksin
Here is a simple example: https://wandbox.org/permlink/fbcldo9PIiHl6tfI In your case, try something like auto my_lambda = [](Vector a, Vectorb) {return polar.Callback(a,b);}; opt.solve ( my_lambda, X ); Bruno Le lun. 28 oct. 2019 à 06:30, Juan Carlos Araujo Cabarcas a écrit : > > Thanks Bruno

[deal.II] Re: optimization, SolverBFGS

2019-10-25 Thread Bruno Turcksin
Juan, Take a look at https://stackoverflow.com/questions/17131768/how-to-directly-bind-a-member-function-to-an-stdfunction-in-visual-studio-11 I advise using a lambda like the second reply suggests Best, Bruno On Friday, October 25, 2019 at 10:53:08 AM UTC-4, Juan Carlos Araujo Cabarcas

Re: [deal.II] Re: Docker MPI

2019-10-24 Thread Bruno Turcksin
Doug, Le mer. 23 oct. 2019 à 18:15, Doug Shi-Dong a écrit : > Are you aware of anyone hosting a "development" Docker build for their own > continuous integration. I know this can be very expensive to keep up with the > commits. Otherwise, I guess I should just build my own Docker with my

[deal.II] Re: Docker MPI

2019-10-22 Thread Bruno Turcksin
Doug, You are using an image build using spack so everything is installed using spack instead of the package manager. If you type `spack find` inside a container, you will see that mpich is installed. Best, Bruno On Monday, October 21, 2019 at 9:53:36 PM UTC-4, Doug Shi-Dong wrote: > > Hello

Re: [deal.II] Re: error during installation with spack on CentOS7

2019-10-14 Thread Bruno Turcksin
Alberto, Le lun. 14 oct. 2019 à 14:18, Alberto Salvadori a écrit : > > Thank you, Bruno. > I did notice the very same error. I do not know either why this error > emerges, the installation of hypre, PETSc was part of the spack installation > process. > Since all preliminary packages have now

Re: [deal.II] Re: error during installation with spack on CentOS7

2019-10-14 Thread Bruno Turcksin
Alberto, If you look in the CMakeError.log, you can see what's the real problem: /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s/lib/libpetsc.so: undefined reference to `hypre_ParCSRMatrixCompleteClone' Hypre is in the linking line

Re: [deal.II] Re: error during installation with spack on CentOS7

2019-10-02 Thread Bruno Turcksin
> > spec: gcc@9.2.0 > > target: x86_64 > > > > Alberto > > > Alberto Salvadori > Dipartimento di Ingegneria Meccanica e Industriale (DIMI) > Universita` di Brescia, via Branze 43, 25123 Brescia > Italy > tel 030 3711239 > fax 030 3711312

Re: [deal.II] Re: error during installation with spack on CentOS7

2019-10-02 Thread Bruno Turcksin
Alberto, On Wednesday, October 2, 2019 at 7:24:32 AM UTC-4, Alberto Salvadori wrote: > > > Thank you so much W and D, > As you pointed out there seems to be a mistake in the most recent version > of perl during installation. > I will propagate this to the proper communities. > > As Denis

[deal.II] Re: Issue with boost serialization and spack?

2019-10-02 Thread Bruno Turcksin
Konrad On Wednesday, October 2, 2019 at 5:50:53 AM UTC-4, Konrad Simon wrote: > > > >> >>> However, now my code runs on the machine I installed it on. But once I >>> use slurm to distribute the job across nodes I get "illegal instruction" >>> erros. Frustrating. >>> >> >> With HPC I used to

[deal.II] Re: problem about The move mesh func

2019-09-26 Thread Bruno Turcksin
Hi, Take a look at https://github.com/dealii/dealii/wiki/Frequently-Asked-Questions#in-my-graphical-output-the-solution-appears-discontinuous-at-hanging-nodes Best, Bruno On Thursday, September 26, 2019 at 10:09:16 AM UTC-4, huyanzhuo wrote: > > i use The move mesh function, the code is as

[deal.II] Re: Specifying internal "boundary" conditions

2019-09-18 Thread Bruno Turcksin
Mélanie, I am not sure I understand exactly what you want to do but often people who want internal boundary conditions, really just want to impose some constraints to a few dofs. This can be done using AffineConstraints .

[deal.II] Re: On the usage of Utilities::MPI

2019-09-11 Thread Bruno Turcksin
Yang, Are sure that you compiled deal.II with MPI support? Also can you post what you see when you do make VERBOSE=1 Best, Bruno On Wednesday, September 11, 2019 at 8:44:29 AM UTC-4, Yang Liu wrote: > > Dear Deal.II developers, > > Greetings! > > I am a new user of Deal.II. Currently I would

[deal.II] Re: Adaptive TimestepControl

2019-09-05 Thread Bruno Turcksin
Reza, Take a look at step-52. We have implemented different time stepping methods including embedded ones that automatically choose the time step for you. These methods will give you an hint on what the time step should be but you can always override the value if you have a better criteria. If

[deal.II] Re: Where can I find member function of cell?

2019-08-27 Thread Bruno Turcksin
Yuesu, For a Triangulation, the list is here:https://dealii.org/current/doxygen/deal.II/classCellAccessor-members.html (CellAccessor) For a DofHandler, the list is here: https://dealii.org/current/doxygen/deal.II/classDoFCellAccessor-members.html (DofCellAccessor) Best, Bruno On Monday,

[deal.II] Re: Real Step-29

2019-08-20 Thread Bruno Turcksin
Adil, If you look in the output_results section. You can see the following code: std::vector solution_names; solution_names.emplace_back("Re_u"); solution_names.emplace_back("Im_u");

Re: [deal.II] Re: curl_value_list function ?

2019-08-20 Thread Bruno Turcksin
Le lun. 19 août 2019 à 23:53, Muhammad Adil a écrit : > I mean Ross kynch used curl_value_list but I couldn't find it in the deal.II > 8.3.0 documents. Like I found vector_value_list in the documents. That's because it is not a function in deal.II Have you tried to grep curl_value_list in the

Re: [deal.II] Re: curl_value_list function ?

2019-08-19 Thread Bruno Turcksin
Adil Le lun. 19 août 2019 à 09:44, Muhammad Adil a écrit : > Actually the function curl_value_list is look vector_value_list but there is > not any definition in the Ross kynch code, it means that this function is > also from deal.II. What do you mean? > But I search it in the documents there

[deal.II] Re: curl_value_list function ?

2019-08-19 Thread Bruno Turcksin
Adil, This class extends `dealii::Functions`. It implements the function `vector_value_list()` which otherwise does nothing in `dealii::Function` and then adds many new functions. This new class has the functionalities of `dealii::Function` plus new ones. Does it make sense? Best, Bruno On

[deal.II] Re: Problems while solving Implicit Runge Kutta method.

2019-08-09 Thread Bruno Turcksin
Sora, On Thursday, August 8, 2019 at 3:42:54 AM UTC-4, sora wrote: > > I have to solve the continuity equation in 1D using Implicit Runge Kutta > method. > > The formula I made is this: d(U_t+1)/dt = [-grad(\Gamma_e)+R_i]/exp(U_t) > \Gamma_e ,R_i : Load the value calculated by another

Re: [deal.II] Re: Porting tutorials to PETSc from Trilinos

2019-07-19 Thread Bruno Turcksin
Franco Le ven. 19 juil. 2019 à 10:04, Franco Milicchio a écrit : > Is there a small documentation that I can read? For instance, I see there are > several namespaces like LinearAlgebra, PETSc/Epetra/Trilinos/CUDAWrappers, > LinearAlgebraDealii and so on, that might be restructured without >

Re: [deal.II] Re: Porting tutorials to PETSc from Trilinos

2019-07-18 Thread Bruno Turcksin
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

Re: [deal.II] Re: Compatibility of Petsc with step 18

2019-07-17 Thread Bruno Turcksin
Ramprasad, Le mer. 17 juil. 2019 à 11:24, Ramprasad R a écrit : > Yes I did recompile it. The details of the config files are in the attachment. There is something strange in you installation: detailed.log says that you are using PETSc but config.h says that you are not. It looks like you

Re: [deal.II] Re: Issue regarding higher order element

2019-07-16 Thread Bruno Turcksin
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), >

[deal.II] Re: Issue regarding higher order element

2019-07-16 Thread Bruno Turcksin
Krishanu, It's impossible to help you with so little information. Somewhere you set something to the wrong size. Can you give us a backtrace? We need to see the error message and the code that produces it. Best, Bruno On Tuesday, July 16, 2019 at 3:08:42 PM UTC-4, Krishanu Sen wrote: > > I

Re: [deal.II] Re: Compatibility of Petsc with step 18

2019-07-16 Thread Bruno Turcksin
Ramprasad, On Tuesday, July 16, 2019 at 11:51:00 AM UTC-4, Ramprasad R wrote: > > The version of deal.ii is 9.0.1 and the version of PETSc is 3.10.5. I also > changed the config file of deal.ii to have MPI PETSc on. > What do you mean by "I changed the config file of deal.II"? You should not

[deal.II] Re: Porting tutorials to PETSc from Trilinos

2019-07-16 Thread Bruno Turcksin
Franco, On Tuesday, July 16, 2019 at 3:54:34 AM UTC-4, Franco Milicchio wrote: > > > Can I ask why there are some discrepancies between those two wrappers? > Apart from an obvious one, that they're different libraries, but uniformity > may help a lot IMO. > Because the wrappers have been

[deal.II] Re: Can I get the cell numbers of the cells neighbouring a face?

2019-07-10 Thread Bruno Turcksin
Stephen On Wednesday, July 10, 2019 at 3:56:02 PM UTC-4, Stephen wrote: > > I have an error estimator which I need to calculate between edges and I'd > like to loop over all edges in the triangulation. I know that I can do this > the "traditional" way via looping over all cells and then looping

[deal.II] Re: 20 tests failed after make install

2019-07-05 Thread Bruno Turcksin
Zhenbang Wei, Is it possible that Trilinos was compiled without MPI support? The two error you see come from Trilinos functions that uses MPI. Best, Bruno On Thursday, July 4, 2019 at 10:15:51 AM UTC-4, Zb W wrote: > > Hello, > I want to install deal.ii (9.1.1) in the ubuntu 18.04 on Windows

[deal.II] Re: Problem installing DEALII 9.0.0 in CentOS cluster

2019-07-05 Thread Bruno Turcksin
Hi, Can you post the errors that you see on your screen. Best, Bruno On Thursday, July 4, 2019 at 3:26:18 AM UTC-4, m boron wrote: > > Dear all, > I have installed dealii9.0.0 in my PC and it is working fine. But now, I > want to install it in a cluster with CentOS. > I have installed >

[deal.II] Re: configuration with LAPACK/BLAS fails

2019-07-03 Thread Bruno Turcksin
Ahmad, The first thing is that you should not try to set the flags yourself. You should let CMake take care of that. You should just set the paths (BLAS_DIR and LAPACK_DIR) and let CMake do the rest. The second thing is that I am not sure sure that you are using the right MKL libraries. You

[deal.II] Re: Can the deal.ii support an element only having single degree of freedom at the center of element?

2019-07-01 Thread Bruno Turcksin
Hi, On Monday, July 1, 2019 at 6:08:45 AM UTC-4, Lee wrote: > > Can the deal.ii support an element only having degree of freedom at the > center of element? > Yes, that's basically what FE_DGQ(0) is. Best, Bruno -- The deal.II project is located at http://www.dealii.org/ For mailing

[deal.II] Re: How can we get the factorized system matrix when using SparseDirectMUMPS?

2019-06-27 Thread Bruno Turcksin
Kien, On Wednesday, June 26, 2019 at 10:20:38 PM UTC-4, Phạm Ngọc Kiên wrote: > > Hi colleagues, > I am trying to build codes using PETScWrappers::SparseDirectMUMPS solver. > Step-62 shows a very good example for using it. > However, I really want to know if we can choose the factorization

Re: [deal.II] Re: NedelecSZ with adaptive mesh refinement

2019-06-25 Thread Bruno Turcksin
Daniel Le mar. 25 juin 2019 à 13:55, Daniel Garcia-Sanchez a écrit : > Thanks for the reference. Yes, it seems that this is a non-trivial problem. > Although from what I understand from the post. > > The new FE_NedelecSZ element can be used with complex meshes, but can not be > refined > The

[deal.II] Re: NedelecSZ with adaptive mesh refinement

2019-06-25 Thread Bruno Turcksin
Dani, On Tuesday, June 25, 2019 at 12:52:09 PM UTC-4, Daniel Garcia-Sanchez wrote: > > > That means that I can not do adaptive mesh refinement with NedelecSZ? > That's correct. > > If that is the case, I would be happy to contribute and make this element > compatible with adaptive mesh

[deal.II] Re: Problems with installing UMFPACK.

2019-06-10 Thread Bruno Turcksin
Sora, On Sunday, June 9, 2019 at 2:40:40 AM UTC-4, solee wrote: > > > So, I read README and installed LAPACK . After installed, I would like to > change -DDEAL_II_WITH_UMFPACK=OFF to ON but it won't. > That won't work. You need to reconfigure deal.II and recompile it. > > What does

Re: [deal.II] Re: Electromagnetic Machine Simulation (Quasi-Poisson Equation in Multiple Domains) Setup

2019-06-05 Thread Bruno Turcksin
Earl, On Wednesday, June 5, 2019 at 1:02:08 AM UTC-4, Earl Fairall wrote: > > Dear Baoyun, > > I too have been looking at this exact application. Building the mesh in > deal.ii is difficult. Deal.ii only has some very fundamental shapes which > require the use of boolean operations for

Re: [deal.II] Re: trouble configuring lapack over a server

2019-06-03 Thread Bruno Turcksin
Swami, Le lun. 3 juin 2019 à 12:11, insaneSwami a écrit : > If I install a local version of scalapack, willl I be able to pass it on to > cmake using -DSCALAPACK_DIR=/path/to/scalapack/installed/locally ? Yes, you will. However, looking at the detailed.log file it looks like you have several

Re: [deal.II] Re: trouble configuring lapack over a server

2019-06-03 Thread Bruno Turcksin
Swami, Le lun. 3 juin 2019 à 11:34, insaneSwami a écrit : > /usr/bin/ld.gold: error: > /usr/local/src/.hashdist/bld/profile/jt2gqapqwvxz/lib/libscalapack.a(slamov.o): > requires dynamic R_X86_64_PC32 reloc against 'slacpy_' which may overflow at > runtime; recompile with -fPIC >

[deal.II] Re: trouble configuring lapack over a server

2019-06-03 Thread Bruno Turcksin
Swami, Can you show exactly the error that you get when you are compiling? You have multiple libraries that were compiled statically so it could come from any of them. Best, Bruno On Sunday, June 2, 2019 at 11:19:45 PM UTC-4, insaneSwami wrote: > > > Hi, > I have recently tried installing

Re: [deal.II] Re: error while using refine_and_coarsen_fixed_number

2019-05-30 Thread Bruno Turcksin
Darius, Le jeu. 30 mai 2019 à 08:48, Darius Barreto a écrit : > Thanks for the reply. By saying spacedim 3, I mean that the rod (being one > dimensional) can deform in the three dimensional space. Sure but does the deformation happens in a plan. If you bend a rod, the deformation is in a plan

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