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

Hello, I am attempting to install deal.II using candi in the University of Michigan Great Lakes cluster (2x 3.0 GHz Intel Xeon Gold 6154 processors). For my application, only p4est and deal.II are required, so I commented out the rest of the prerequisites in candi.cfg The loaded modules be

[deal.II] Solution vector data transfer between different meshes not working in parallel

Hello, I have two distinct distributed meshes representing the same spatial domain and (for now) with equal refinement (number of cells), but the finite elements, dof handlers and solution vectors on each mesh are defined differently. I want to interpolate values from a solution vector (solut

Re: [deal.II] Solution vector data transfer between different meshes not working in parallel

Hello, Wolfgang Thank you for your reply. Please see my inline replies below. Best, David On Monday, November 18, 2024 at 9:38:45 PM UTC-5 Wolfgang Bangerth wrote: David: > I have two distinct distributed meshes representing the same spatial > domain and (for now) with equal refinement (num

Re: [deal.II] Solution vector data transfer between different meshes not working in parallel

Thank you, Wolfgang See further comments below. Best, David On Tuesday, November 19, 2024 at 12:44:45 PM UTC-5 Wolfgang Bangerth wrote: > Do I understand correctly that these meshes are identical, but that you > store them in separate variables? Why not just one mesh that two > DoFHandlers

[deal.II] cmake flag to skip a specific example?

I am trying to install deal.II in a cluster and somehow the compiler is not recognizing std::filesystem which is used in step-83. However step-83 isn't marked as having unmet dependencies. As a results the "make" I use for building deal.II fails when building step-83 I can probably modify the

Re: [deal.II] cmake flag to skip a specific example?

[examples/CMakeFiles/example_step_83_release.dir/build.make:106: bin/step-83.release] Error 1 make[1]: *** [CMakeFiles/Makefile2:8634: examples/CMakeFiles/example_step_83_release.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs I will try going with -DDEAL_II_COMPILE_EXAMPLES=OFF. That sho

Re: [deal.II] deal.II candi installation with external petsc

e" to "load". i.e., PACKAGES="${PACKAGES} *load*:petsc" Otherwise it kept trying to download and build *petsc 3.19.0*, and failing. Best, David On Friday, March 14, 2025 at 7:40:26 PM UTC-4 Wolfgang Bangerth wrote: > On 3/14/25 14:49, David Montiel wrote: > >

[deal.II] deal.II candi installation with external petsc

Hello, I want to install deal.II using candi, and I need PETSC amongst other dependencies. When I ran the installation script, candi.sh, I got the error message below. However, I managed to successfully install a newer version of petsc externally. Now the issue is: I would like to the scri

Re: [deal.II] compute_eigenvalues_symmetric lapackerror

Thank you, Wolfgang I'll look into it. Best, David On Thursday, February 20, 2025 at 8:27:18 PM UTC-5 Wolfgang Bangerth wrote: > > On 2/20/25 14:18, David Montiel wrote: > > /An error occurred in line <2204> of file <../source/lac/ > > lapack_full_matrix.cc&

[deal.II] compute_eigenvalues_symmetric lapackerror

Hello, I am getting the runtime error below in a simulation within a deal.II-based CPFE framework. *Error message:* ** *Exception on processing: * ** *An error occurred in line <2204

[deal.II] Solving a time-dependent PDE in cylindrical coordinates

Hello, I would like to solve a PDE using cylindrical coordinates (instead of cartesian) but my equations are rotationally symmetric (do not depend on theta). Therefore, I only need to solve the problem in a 2D domain with coordinates r (radius) and z (direction along the axis). Can I just do that

Re: [deal.II] Solving a time-dependent PDE in cylindrical coordinates

Thank you! I will try that. On Thu, May 27, 2021 at 9:17 AM Wolfgang Bangerth wrote: > On 5/26/21 10:53 PM, David Montiel Taboada wrote: > > > > I would like to solve a PDE using cylindrical coordinates (instead of > > cartesian) but my equations are rotationally symmet

Re: [deal.II] Deal.II Make error || Make release

Hello everyone, A few PRISMS-PF users trying to run the deal.II prepacked image file on MacOS Big Sur are reporting similar issues. Any help with this would be greatly appreciated! David On Fri, Jun 11, 2021 at 1:59 PM Sumanth Theeda wrote: > Hello all, > > I have installed Deal.II (v 9.2) usi

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

Hello, I am running a container of PRISMS-PF (which is built upon the dealii:v9.2.0-focal image). Inside the container, the code compiles successfully, but when I run it, I get the following error message: PRISMS-PF: Exception on processing:

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

This is how I am launching the container, by the way: $ docker run -ti -v ~/DockerWorkspace/phaseField/applications:/home/dealii/phaseField/applications prismspf/prismspf:2.2 On Sat, Aug 7, 2021 at 2:55 PM David Montiel Taboada wrote: > Hello, > > I am running a container of PRISMS-

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

, Aug 7, 2021 at 2:57 PM David Montiel Taboada wrote: > This is how I am launching the container, by the way: > > $ docker run -ti -v > ~/DockerWorkspace/phaseField/applications:/home/dealii/phaseField/applications > prismspf/prismspf:2.2 > > > > On Sat, Aug 7, 2021 at 2:55

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

e code in serial." >> >> I meant it happens whether I try to run the code in serial or parallel >> (e.g., using "./main" or "mprun -n 4 main"). It makes no difference. >> >> Thank you, >> >> David >> >> On Sat, Aug 7, 20

[deal.II] PETSC error with candi installation

Hello, I am trying to install deal.II (v. 9.2.0) using candi on Fedora v. 35 (a virtual machine). I have edited the candi.cfg file to only install the following packages: hdf5, p4est, petsc and dealii. I installed all the packages suggested for the OS, loaded the openmpi module, and set the compi

Re: [deal.II] PETSC error with candi installation

David, > I think this is a problem for the PETSc folks to give you feedback with. > Can > you extract what the command line was with which the PETSc configuration > script was called? > > Best > W> > > On 1/17/22 10:36 AM, David Montiel Taboada wrote: > > ***

Re: [deal.II] PETSC error with candi installation

:41 PM Wolfgang Bangerth >> wrote: >> >>> >>> David, >>> I think this is a problem for the PETSc folks to give you feedback with. >>> Can >>> you extract what the command line was with which the PETSc configuration >>> script was called? &

Re: [deal.II] PETSC error with candi installation

Actually, I looked for it (see below) and it looks like that file does not exist yet: $ find . -name candi_configure ./dealii-candi/tmp/build/hdf5-1.10.7/candi_configure ./dealii-candi/tmp/build/p4est-2.2/candi_configure On Tue, Jan 18, 2022 at 3:20 PM David Montiel Taboada wrote: > Thank

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

Hello, I am working on PRISMS-PF (which is deal.II based) and trying to find an issue with a corner value not being properly set. The problem happens when the code is finding the solution of a poisson type equation iteratively, e.g. \nabla^2 \phi = f(\phi) I set up a 2D system, and I am using a

[deal.II] Installation error of deal.II in the Stampede2 cluster

Hello, I am trying to install deal.II v 9.2.0 on the TACC Stampede2 cluster. I already a working installation but when I tried to install it again using the same instructions I am getting the following error: /opt/apps/gcc/6.3.0/bin/ld.gold: error: ../lib/libdeal_II.so.9.2.0: bad symbol name

[deal.II] "locked" vtu outputs

Hello everyone, We are using PRISMS-PF, a phase field framework finite element built upon the deal.II library (with the MPI and p4est) dependencies. The code uses the deal.II DataOut class (see code snippet at the end of the email) to output simulation results into vtu files at certain time step

Re: [deal.II] "locked" vtu outputs

Thank you, Timo I will look into it! David On Sat, Oct 10, 2020 at 11:30 AM Timo Heister wrote: > Hi David, > > > For example, for the initial conditions, the code is supposed to output > a file with name: > > > > solution-000.vtu > > > > but then it also creates s file with name > > > > s

[deal.II] Strong scaling issue on a deal.II based framework running on Skylake nodes.

Hello, I am using the PRISMS-PF framework (which is based on deal.II) on the Skylake (skx) nodes (with 48 processors each) of the Stampede2 cluster. I recently ran a series of strong scaling tests and noticed that the intra-node performance (i.e. 1 node, 1-48 processors) scales poorly, speci

Re: [deal.II] Strong scaling issue on a deal.II based framework running on Skylake nodes.

e fully memory bound you should see a factor of > ~10-12 of speedup when going from 1 to 48 cores on a node (or a bit less if > the processor has full turbo frequency turned on and thus clocks higher > with 1 core loaded than with all 24 cores loaded per socket), while you > observe muc

[deal.II] deai.II module on Stampede2

Hello, I compiling PRISMS-PF, a deal.II-based framework on Stampede2 by loading the deal.II module, e.g.: module load dealii/9.2.0 I have no errors when compiling the core library. But when I do "cmake" for any particular application I run into the following errors (which also cause "make" t

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

Thank you, Bruno I figured that was going on, that is why I attempted including the option to ignore one of the paths but it did not seem to have any effect. Here is a list of my loaded modules: 1) intel/18.0.2 3) impi/18.0.2 5) autotools/1.17) cmake/3.16.1 9) TACC11) phdf5

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

a different compiler and hope > that the stack was better compiled 3) send an email to the helpdesk. > It looks like there is a problem in the way they built their modules. > > Best, > > Bruno > > Le mar. 16 févr. 2021 à 10:16, David Montiel Taboada > a écrit : > >

[deal.II] Computational Materials Scientist opening at the PRISMS Center (University of Michigan)

Hello everyone, I would like to share that we have an opening for Computational Materials Scientist position at the PRISMS Center of the University of Michigan. The specific area is in the *development and application of our crystal plasticity and fracture simulations codes* that are housed

Re: [deal.II] Getting cmake errors compiling programs

Hello, everyone I tried the new image in my laptop with M2 processor and the Ventura Mac OS (13.6). It worked (I successfully ran and compiled the step-1 example). Looks like the issue was with clang 15? However, I am not sure Alexander will be able to test the new image because his processor

Re: [deal.II] TBB issue on an arm-based Mac

I am encountering a similar runtime error with one of my applications: Assertion 1L > > > > > I've been stuck on this TBB issue for a while. Would you be able to give > me > > some hints on solving this problem? I would really appreciate it.