Re: [Libmesh-users] error while configuring libmesh 1.6.2

On Fri, Sep 1, 2023 at 1:25 AM INTURU SRINIVAS 20PHD0548 < inturu.srinivas2...@vitstudent.ac.in> wrote: > Hi John, > > I tried with PETSC_DIR=/home/hpcsmec15767/sfw/petsc/3.17.5. I got the > same error as mentioned below > checking for built-in XDR support... yes > checking > /home/hpcsmec15767/sf

Re: [Libmesh-users] error while configuring libmesh 1.6.2

Unfortunately, there is no additional information in the log file beyond configure:4977: result: <<< Could not find a viable PETSc Makefile to > determine PETSC_CC_INCLUDES, etc. >>> which means that your PETSc installation is not how we expected it to be. Based on the args you passed to configu

Re: [Libmesh-users] error while configuring libmesh 1.6.2

Hi, The config.log that you sent this time does not seem to be related to the previous one, but rather to a MOOSE build? And the version of PETSc is totally different from the previous log, it is now PETSc 3.11.4. In any event, the relevant configure output is: configure:34458: checking for > /o

Re: [Libmesh-users] error while configuring libmesh 1.6.2

Hi, Is there a particular reason that you are trying to use libmesh 1.6.2? It's about two years old at this point, and there have been many updates and improvements (including a stable release) since that time, so you will probably have the most success if you use a more up-to-date version. The l

Re: [Libmesh-users] libMesh::System::point_value returning zero values

Hi, I would first verify that the System's solution vector has the expected values after calling "copy_elemental_solution". You could do this by just printing out the solution vector if it is a small enough problem. Once you are sure that part is working, I would have to assume that there is some

Re: [Libmesh-users] Cannot built libmesh with VTK

Hello Omar, Unfortunately, this mailing list does not allow attachments, so I cannot see your config.log. You could create a discussion on the libmesh GitHub page and attach your config.log there, or find some other way to share it. There has been an issue reported with linking against VTK 9.2 ht

Re: [Libmesh-users] imposing boundary conditions inside the domain

On Thu, Aug 18, 2022 at 5:20 AM Yu Zhong wrote: > Dear all, > > For a 2D problem, I'm trying to impose Dirichlet BC on a physical boundary > connecting two subdomains in a full domain (containing more than 2 > subdomains). With the penalty method, I tried with > > c.has_side_boundary_id(ID) > > t

Re: [Libmesh-users] Question about an overflow error for SCM training in Libmesh

On Tue, Apr 12, 2022 at 8:47 AM 강다영 wrote: > Hello, > Thank you for all your information and suggestions. > > You're right that I was using a LAPACK-based solver. > As you recommended, I first tried to use another solver other than LAPACK, > and I ended up with a convergence error in SCM. > > So

Re: [Libmesh-users] Question about an overflow error for SCM training in Libmesh

On Fri, Apr 8, 2022 at 8:25 AM 강다영 wrote: > Dear all, > > I have a question about the overflow error I met during the SCM training in > Libmesh. > > For the training, I used the mesh model with a degree of freedom of > 318,021. > And I got an error message as below: > > [0]PETSC ERROR: --

Re: [Libmesh-users] Problem with parallel execution of element loop

Hi Dan, I created a GitHub Discussion for this email here: https://github.com/libMesh/libmesh/discussions/3086 GitHub discussions seem to be a more effective and productive way for people to ask/answer questions than the mailing list these days. -- John On Wed, Nov 10, 2021 at 1:35 PM Lior, D

Re: [Libmesh-users] Bug in system_of_equations_ex8

On Tue, Aug 31, 2021 at 11:08 AM edgar wrote: > > Hi edgar, > > > > By "general public" do you just mean people that don't have GitHub > > accounts? The Discussions forum allows anyone with a GitHub account to > > start a discussion (e.g. > > https://github.com/libMesh/libmesh/discussions/2994) >

Re: [Libmesh-users] Bug in system_of_equations_ex8

On Tue, Aug 31, 2021 at 10:28 AM edgar wrote: > Regarding the GitHub discussions, it does not allow the general public > to send messages, and it did not have an option for attachments when I > tried it. Hi edgar, By "general public" do you just mean people that don't have GitHub accounts? The

Re: [Libmesh-users] Bug in system_of_equations_ex8

On Tue, Aug 31, 2021 at 8:11 AM Renato Poli wrote: > Hi, > > Can you confirm the output of the example system_of_equations_ex8 is as > expected? > I see that the constrained face has zero displacement, whereas the > neighboring nodes are ok. > Hi Renato, Yes, I see the same issue as you with th

Re: [Libmesh-users] How to avoid complex numbers?

On Mon, Aug 23, 2021 at 7:53 AM edgar wrote: > Hi Hubert! > > Thanks. It seems that the option which you are sending is for the > overall libMesh compilation (correct me if I'm wrong). I am interested > in having my libMesh with the ability to process complex numbers, and > just compiling a speci

Re: [Libmesh-users] Little help to get results, please

or some reason: > https://github.com/libMesh/libmesh/discussions/2987 > > Anyway, I have the attachment here (will be there for 1 week): > > https://anonpaste.org/?157252de59d151b1#8CHB81NdEuwjrcnG5AwTLyEnGPeg6z2cx5ZcpuSdL5N5 > > Thank you. > > On 2021-08-17 19:28, John Peters

Re: [Libmesh-users] Little help to get results, please

Hi Edgar, This list does not accept attachments unfortunately, so you'll have to upload it elsewhere and provide a link. Note that we also recently enabled the Discussions feature over on GitHub: https://github.com/libMesh/libmesh/discussions If you start a new topic there, (I think) you can atta

Re: [Libmesh-users] invalid use of incomplete type ... SparseMatrix

I didn't read the code in detail, but is the fix as simple as #include "libmesh/sparse_matrix.h" ? -- John On Mon, Aug 16, 2021 at 10:06 AM edgar wrote: > Hello, > > I'm sorry to bother you. I'm getting an error, and I dont' know how to > solve it. I am trying to restructure some examples fr

Re: [Libmesh-users] using GmshIO to write mesh and system data

On Sat, Aug 14, 2021 at 12:29 PM Charles Puelz wrote: > Hello, > > I am trying to write both a mesh and data corresponding to a libMesh system > to a single MSH file. It looks like this can be done with an MSH file > version > 4. > > At this point I can separately write out a mesh in an MSH file

Re: [Libmesh-users] Dirichlet constraints in NonlinearImplicitSystem

On Thu, Aug 12, 2021 at 3:59 PM Renato Poli wrote: > Thanks, > > As I understood, it just works without any major concern in residual and > jacobian calculations, right? > I must add the DirichletBoundary to the system dof_map and LibMesh handles > the matrix and vectors so Petsc will receive the

Re: [Libmesh-users] Initialize DenseSubMatrix with m x n (non-const) size

On Tue, Aug 10, 2021 at 7:34 PM edgar wrote: > Hello! > > I am trying to do something like this (systems of equations, example 6): > > DenseSubMatrix Ke_var[3][3] = >{ > {DenseSubMatrix(Ke), DenseSubMatrix(Ke), > DenseSubMatrix(Ke)}, > {DenseSubMatrix(Ke), DenseSubM

Re: [Libmesh-users] Error in libmesh + petsc (fail to convert SparseMatrix into PetscMatrix)

On Tue, Aug 10, 2021 at 10:42 AM Renato Poli wrote: > Thanks John. > > I had not realized this was the issue, your explanation was quite > instructive. > > There was indeed a bug on my code, fixed now. > OK, great! -- John ___ Libmesh-users mailing l

Re: [Libmesh-users] Error in libmesh + petsc (fail to convert SparseMatrix into PetscMatrix)

According to frame #6, we are trying to cast a nullptr (oldvar): #6 0x7598d1bf in libMesh::cast_ptr*, libMesh::SparseMatrix > (oldvar=0x0) at ./include/libmesh/libmesh_common.h:582 In libMesh::cast_ptr, we throw an error if the result of the cast is a nullptr (which is what happens when

Re: [Libmesh-users] small doc and efficiency update for ex 3 and 4

e others... -- John On Sun, Jun 27, 2021 at 10:03 PM edgar wrote: > On 2021-06-18 21:45, John Peterson wrote: > > Your compiler flags are definitely far more advanced/aggressive than > > mine, > > I cannot take credit for that, really. I only modified the -O2 to -O3, >

Re: [Libmesh-users] small doc and efficiency update for ex 3 and 4

On Thu, Jun 10, 2021 at 5:55 PM edgar wrote: > On 2021-06-10 19:27, John Peterson wrote: > > I recorded the "Active time" for the "Matrix Assembly Performance" > > PerfLog > > in introduction_ex4 running "./example-opt -d 3 -n 40" for both

Re: [Libmesh-users] small doc and efficiency update for ex 3 and 4

On Thu, Jun 10, 2021 at 12:05 PM edgar wrote: > On 2021-06-10 16:00, John Peterson wrote: > > On Wed, Jun 9, 2021 at 9:11 PM edgar wrote: > > > >> Hi, > >> > >> I am humbly sharing something which I think would improve the > >> documentation an

Re: [Libmesh-users] small doc and efficiency update for ex 3 and 4

On Wed, Jun 9, 2021 at 9:11 PM edgar wrote: > Hi, > > I am humbly sharing something which I think would improve the > documentation and the logic of examples 3 and 4 a bit. I think that this > would apply to other examples as well. (I was planning to keep learning > from the examples, and have a

Re: [Libmesh-users] Example 12 →Example 13

On Wed, May 12, 2021 at 12:50 PM edgar wrote: > On 2021-05-12 16:57, edgar wrote: > > On 2021-05-10 15:59, John Peterson wrote: > >> On Thu, May 6, 2021 at 9:48 PM edgar wrote: > >> We renumbered our examples once (many years ago) so it's possible that > &

Re: [Libmesh-users] Example 12 →Example 13

On Wed, May 12, 2021 at 11:58 AM edgar wrote: > On 2021-05-10 15:59, John Peterson wrote: > > On Thu, May 6, 2021 at 9:48 PM edgar wrote: > > We renumbered our examples once (many years ago) so it's possible that > > references to "ex13" that you see have si

Re: [Libmesh-users] augmented finite elements

On Wed, May 12, 2021 at 4:25 PM Tobias Moehle wrote: > Dear all, > > I hope that someone has experience or some good ideas to help me out: I > am using a setup where the finite element basis is augmented by a > function which contains the most rapidly changing features of the > solution to allow

Re: [Libmesh-users] Example 12 →Example 13

On Thu, May 6, 2021 at 9:48 PM edgar wrote: > Hi! > > There is a small typo in > examples/miscellaneous/ex13/miscellaneous_ex13.C. It reads: > > Miscellaneous Example 12 > > Thanks for letting us know, I fixed the documentation in libmesh commit 8c2c45793. I am guessing that it should be 13.

Re: [Libmesh-users] Are there QBC, non-homogeneous BC, essential BC by modifying equations?

Hi Edgar, Sorry for not responding, your email got kind of lost in my inbox. LibMesh does support penalty BCs, some examples which use penalty BCs are: adjoints_ex1,2,4; adaptivity_ex1,2,4. It sounds like you may be interested in DirichletBoundary objects, which impose the BCs as user-defined con

Re: [Libmesh-users] _ss_id_to_name works for Gmsh

On Wed, Apr 28, 2021 at 5:45 PM edgar wrote: > Dear all, > > I know that some times, the documentation is hard to maintain, and you > may already know what I will tell you now. I just wanted to let you know > that `_ss_id_to_name' (from `BoundaryInfo') works on a mesh that I > created with physic

Re: [Libmesh-users] GetPot interface with UTF-8?

On Thu, Apr 29, 2021 at 4:50 PM edgar wrote: > Dear list, > > I noticed that if I have a GetPot file such as: > > ┌ > │ [./ó] > │ val = 1 > │ [../] > └ > > , that my program would crash. As soon as I change `ó' by `o', it works > fine. This makes me think that the crash arises because

Re: [Libmesh-users] Rotation of coordinates in Tet face

On Thu, Apr 22, 2021 at 1:11 PM Renato Poli wrote: > Thanks John, > > What would be the straightforward way to append normals and tangents in a > single tensor? > The idea is to define them as a base so I can operate and iterate. > It just depends on what data structure you want to use for the t

Re: [Libmesh-users] Rotation of coordinates in Tet face

On Wed, Apr 21, 2021 at 10:39 AM Renato Poli wrote: > Hello, > > I am willing to make a coordinate rotation on a Tet face to calculate > normal and tangent displacements between discontinuous elements. > > As I understand, I need a transformation matrix gathering normal and > tangents to define a

Re: [Libmesh-users] (no subject)

Hi, There was a somewhat recent discussion about this issue on #2565 and #2827, but as far as I know, it was never satisfactorily resolved at that time, otherwise the update would presumably have made it into 1.6.1. Jahrul, just to confirm, are you saying that libmesh master works for you with In

Re: [Libmesh-users] Suggestion: turn some macros into functions

Hi Edgar, Yes, clearly something like this will work: libmesh_example_requires_fun(bool (0), > "TESTME", > __FILE__, > __LINE__); but you then force the user to manually pass __FILE__ and __LINE__

Re: [Libmesh-users] Suggestion: turn some macros into functions

On Mon, Mar 22, 2021 at 1:10 PM wrote: > > Hi Edgar, > > > > I don't think this mailing list --8<-- accept{s} attachments. > > I live in a bubble :P . > > > Second best would be to paste a diff into > > the body of an email (assuming it's not too long, in which case the > > first > > option shoul

Re: [Libmesh-users] Suggestion: turn some macros into functions

On Fri, Mar 19, 2021 at 11:40 AM wrote: > I am sorry, but my e-mail provider refuses to send my mesage as plain > text. I am thus attaching a compressed file in the hope that it reaches > you. > Hi Edgar, I don't think this mailing list requires plain text messages (though I could be wrong abou

Re: [Libmesh-users] AMR repartition in parallel?

On Wed, Mar 17, 2021 at 7:57 AM Li Luo wrote: > > Dear developers, > > I am using libmesh's AMR in parallel. It seems that when the mesh is > changed significantly, for example, when some local region is refined then > coarsened as an object moves, the partition remains the same. > > As in the be

Re: [Libmesh-users] Setting output directories in libmesh

On Wed, Mar 17, 2021 at 11:17 AM wrote: > Hello, > > I would like to know if someone can help me with some things regarding > compilation, please. > > 1. Is there a way to specify the directory for the examples? (as in > =/usr/share/libmesh/examples=) > Not currently. There's a --prefix, and eve

Re: [Libmesh-users] Error while mesh partitioning by subdomain_partitioner

On Wed, Mar 10, 2021 at 8:01 AM Pilhwa Lee wrote: > Dear John, > > I didn’t point out the actual reason of the problem in the previous > correspondence. > > The issue was “distributed mesh”. In TACC, I need to use “allgather” to > fetch all elements of the mesh. That wasn’t the case in my local >

Re: [Libmesh-users] Error while mesh partitioning by subdomain_partitioner

On Tue, Mar 9, 2021 at 12:59 PM Pilhwa Lee wrote: > Dear All, > > In TACC, I’m trying to do mesh partitioning by subdomain_partitioner. > There comes the following error: > > map_find() error: key "22484" not found in file > /admin/build/admin/rpms/stampede2/BUILD/libmesh-1.6.0/src/partitioning/m

Re: [Libmesh-users] problem with installation

On Thu, Feb 4, 2021 at 1:11 AM Michael Povolotskyi wrote: > Hello, > > I have a problem with libmesh installation: > > <<< C++ compiler is unknown but accepted gcc version >>> > checking for a sed that does not truncate output... /usr/bin/sed > checking for C++ compiler vendor... gnu > configure:

Re: [Libmesh-users] Build error

On Tue, Jan 26, 2021 at 10:11 AM Pedro Rodrigues wrote: > Yes I let PETSc to build MPI with default options Just --download MPI. > Maybe that is the problem. I will try to build it as you suggest > OK, well if using static libs wasn't intentional, I'd suggest you start over and reconfigure/rebui

Re: [Libmesh-users] Build error

On Tue, Jan 26, 2021 at 4:50 AM Pedro Rodrigues wrote: > Hello > > I tried to build under Linux but got this error message: > > > /usr/bin/ld: > > /home/ubuntu/Dev/petsc/arch-linux2-c-debug/lib/libmpi.a(lib_libmpi_la-initthread.o): > relocation R_X86_64_TPOFF32 against hidden symbol `MPIR_Per_thr

Re: [Libmesh-users] Neighbors of element

On Wed, Oct 21, 2020 at 12:39 PM Laura Scarabosio < laura.scarabo...@gmail.com> wrote: > Hi, > > I would like to find the neighbors of a mesh element including those that > share a vertex only with that element, not only those that share an edge > with the element (so the method neighbor_ptr does

Re: [Libmesh-users] how to install libmesh with vtk support

On Sat, Sep 26, 2020 at 1:08 PM Jahrul Alam wrote: > Hello > > First, I get the following error/info regarding vtk support, while > configuring libmesh: > > ./configure --with-vtk-include=/usr/include/vtk/ --with-vtk-lib=/usr/lib64 > > <<< Configuring library with Qhull version 2012.1 support >>>

Re: [Libmesh-users] PetscMatrix::print_matlab

On Fri, Aug 28, 2020 at 11:30 AM Roy Stogner wrote: > > On Fri, 28 Aug 2020, John Peterson wrote: > > > On Fri, Aug 21, 2020 at 9:51 AM Nikhil Vaidya > > wrote: > > > >> I need to print the sparse matrices (Petsc) and vectors involved in my > >> calc

Re: [Libmesh-users] PetscMatrix::print_matlab

On Fri, Aug 21, 2020 at 9:51 AM Nikhil Vaidya wrote: > Hello, > > I need to print the sparse matrices (Petsc) and vectors involved in my > calculations to file using print_matlab(). I have observed that the > matrices and vectors that are written to the matlab scripts in serial and > parallel run

Re: [Libmesh-users] small problem in example using libmesh

On Wed, Aug 19, 2020 at 11:56 AM Ger ry wrote: > In fact, i hadn't ran "make install". > I must had misinterpreted the instructions. > > now i ran make install. > and it seems successful except for some warnings like the following: > libtool: warning: > '/home/flexwork/Documents/repos/libmesh/co

Re: [Libmesh-users] small problem in example using libmesh

On Wed, Aug 19, 2020 at 7:14 AM Ger ry wrote: > I tried the path > libmesh_config := /usr/local/bin/libmesh-config > and ran > make miscellaneous_ex11.cc > and it gives the following error: > /bin/sh: 1: /usr/local/bin/libmesh-config: not found > /bin/sh: 1: /usr/local/bin/libmesh-config: not fou

Re: [Libmesh-users] small problem in example using libmesh

On Tue, Aug 18, 2020 at 6:40 PM Ger ry wrote: > Thanks once again for your advice. > > I made two variants of the makefile that you provided, as follows: > 1) > changed the following > # installed libmesh location of libmesh-config script > libmesh_config := > /home/flexwork/Documents/repos/libme

Re: [Libmesh-users] small problem in example using libmesh

On Tue, Aug 18, 2020 at 2:48 PM Ger ry wrote: > Thank you very much for your response. > > Indeed i checked that libmesh is installed correctly. After ./configure and > make i ran make check. And now i ran again > > cd build/examples/introduction/introduction_ex1 > make check > > and > cd miscell

Re: [Libmesh-users] small problem in example using libmesh

Hi, Did you test whether the libmesh examples are working, (e.g. assuming you are in the top level of the git repo and you followed the standard build instructions) cd build/examples/introduction/introduction_ex1 make check I would just like to confirm that libmesh was built and installed correc

Re: [Libmesh-users] Poisson w/ Penalty Dirichlet Example

On Thu, Jul 9, 2020 at 11:06 AM Caleb M Phillips wrote: > John, > > I wasn't too sure how to accomplish that, but here is the main file. This > is a module in a larger code, but the function I'm looking at is > "assemble_pressure". > https://github.com/CalebPhillips5/ABM_Ang/blob/master/pressure_

Re: [Libmesh-users] Poisson w/ Penalty Dirichlet Example

On Wed, Jul 8, 2020 at 4:48 PM Caleb M Phillips wrote: > Hey all, > > Quick question that is completely throwing me for a loop. I'm working on a > poisson equation for pressure and wanting to specify dirichlet boundary > conditions. I used the penalty method (per libmesh documentation), and it >

Re: [Libmesh-users] augment sparsity

On Sat, May 16, 2020 at 5:12 PM Gary Hu wrote: > Hello all, > > I am new to libMesh. I am trying to solve a generalized eigen-value problem > for an integral equation. I tried example "Solving a generalized Eigen > Problem" and it works fine. > > Next, I modified the assembly routine to have a sk

Re: [Libmesh-users] make check reduced_basis_ex7 flags

On Tue, May 12, 2020 at 10:10 AM wrote: > On 2020-05-12 14:18, John Peterson wrote: > > The options still exist for people using older versions of PETSc, so > > yes, > > it makes sense to still test for them. > > Of course! Thanks! By the way, I am maintaining an AUR p

Re: [Libmesh-users] make check reduced_basis_ex7 flags

On Mon, May 11, 2020 at 11:50 PM wrote: > > That is very ingenious. Noob question: Is there still a need to test for > options that don't exist? I know there must be a reason behind it :P . > The options still exist for people using older versions of PETSc, so yes, it makes sense to still test f

Re: [Libmesh-users] make check reduced_basis_ex7 flags

On Sun, May 10, 2020 at 10:08 PM wrote: > Hi. > > I want to know if libMesh++ is actually using mumps and superlu, and if > it is not how to fix it. I just recompiled libMesh++, and I am getting > the following message with the reduced_basis_ex7 (this is actually an > improvement, because it used

Re: [Libmesh-users] Best wishes

On Thu, Mar 26, 2020 at 7:45 AM wrote: > Dear libmesh-users, > > I hope that everyone around here is doing well, that we are all fine and > that we can find ways in which to cooperate beyond the adversity. > Please, take care of yourselves and those who surround you :) . > Hi Edgar, Thanks, I h

Re: [Libmesh-users] Mapping from mesh nodes to mesh subdomains

On Thu, Mar 12, 2020 at 5:12 AM Nikhil Vaidya wrote: > Hello, > > Does the libmesh MeshBase class provide a way to find out to which > subdomain(s) a particular node belongs? I looked through the documentation, > but couldn't find a function doing this. > Hi Nikhil, Nodes don't belong to a sing

Re: [Libmesh-users] Unusual memory error due to Eigen solver

On Fri, Feb 14, 2020 at 6:26 AM Bailey Curzadd wrote: > I did a lot of testing with dbg and opt builds. The issue seems to be some > optimization flag activated by -march=native when compiling my own code. > Leaving this out resolves all of the spurious memory errors, which were > probably the re

Re: [Libmesh-users] Unusual memory error due to Eigen solver

On Thu, Feb 13, 2020 at 10:41 AM Roy Stogner wrote: > > On Thu, 13 Feb 2020, Bailey Curzadd wrote: > > > /usr/local/lib/libmesh_opt.so.0 > > Well, this is the first thing you'll want to change. Often times a > bug that exhibits as an incomprehensible segmentation fault in opt > mode will instead

Re: [Libmesh-users] Unusual memory error due to Eigen solver

On Thu, Feb 13, 2020 at 4:59 AM Bailey Curzadd wrote: > I developed a code based on libMesh to optimize components subjected to > extreme thermal loads. I use a gradient-based optimizer, and the > optimization problem has lots of constraint functions, so I have to perform > a direct sensitivity a

Re: [Libmesh-users] MatSetOption error

On Fri, Jan 24, 2020 at 1:33 PM Prashant K. Jha wrote: > Hi All, > > I am building a network of 1-d EDGE2 elements > embedded in 2-d or 3-d. At any given node of the network, it may have more > than 2 elements intersecting. To enforce continuity of flux at such nodes,

Re: [Libmesh-users] building sphere using tetrahedral elements

On Thu, Jan 16, 2020 at 1:21 AM Ramakrishnan Thirumalaisamy < thirumalaisamyr...@gmail.com> wrote: > Dear libmesh users, > > I want to create sphere with tetrahedral elements. I came across this > function MeshTools::Generation::build_square. But this function supports > only HEX8/27 for 3D. Is t

Re: [Libmesh-users] ALE formulation with moving mesh

On Fri, Jan 10, 2020 at 2:34 AM Bin Liu wrote: > Dear libmesh users, > > I am new to this forum and libmesh. I am planning to write a > fluid-structure interaction (FSI) solver under arbitrary > lagrangian-eulerian (ALE) description. I noticed libmesh is a sophisticated > FEM library. There are s

Re: [Libmesh-users] make check Error: Solver is unknown.

On Sat, Dec 21, 2019 at 3:42 PM wrote: > Hello, > > I am getting an error with `make check`. I can live with another > compilation that I already have, but if you want the debugging > information, let me know. > > > ** Compilation set-up of PETSc and libmesh > > My compilation configuration can b

Re: [Libmesh-users] Help with compiling, please

On Fri, Dec 20, 2019 at 6:09 AM wrote: > Hi! > > The compilation with v1.5.1 worked. I attach my PKGBUILD in case that > it's useful (should be self-explanatory even for other flavours of > Linux). > > I'm having trouble with building the documentation, but I'll get to > that. > > By the way, it

Re: [Libmesh-users] problems with pthread_spin_init

On Mon, Dec 9, 2019 at 5:45 PM Povolotskyi, Mykhailo wrote: > Hello John, > > due to some reasons I have to build my code on Windows. > > So, I have cygwin and I managed to locate several pthread.h. They are in > the following directories: > > C:\cygwin64\usr\i686-pc-cygwin\sys-root\usr\include >

Re: [Libmesh-users] problems with pthread_spin_init

On Mon, Dec 9, 2019 at 5:02 PM Povolotskyi, Mykhailo wrote: > Dear Libmesh developers, > > I have problems when I include the header files (see bellow). > > I'll be happy to provide any other files that might help. > > Thank you, > > Michael. > > > In file included from > > /home/michael/libs/lib

Re: [Libmesh-users] failure in libmesh instalation

On Sat, Dec 7, 2019 at 10:29 PM Povolotskyi, Mykhailo wrote: > Hello, > > I'm installing libmesh-1.5.1. > > Here is the error message: > > tecsrc/arrlist.cpp:390:26: error: ‘VALID_REF’ was not declared in this > scope > Boolean_t IsValid = (VALID_REF(ArrayList) && >

Re: [Libmesh-users] Cannot read ABAQUS .inp file with *Surface

On Wed, Oct 30, 2019 at 4:48 PM Yuxiang Wang wrote: > Thank you John for looking at it! I have been reading abaqus_io.C and > think I found out why. > > There are two ways for ABAQUS to define the surface and only #1 is > supported by libMesh now: > 1) By specifying elem_id, side_id. This is the

Re: [Libmesh-users] Cannot read ABAQUS .inp file with *Surface

Hi Yuxiang, I will try and take a look at this when I get a chance... it's likely that there is a bug in our Abaqus reader. There is a certain amount of variation allowed in the formatting of Abaqus files, and we may not support exactly the format you are using. -- John On Tue, Oct 29, 2019 at

Re: [Libmesh-users] QTrap for TRI3SUBDIVISION

On Wed, Aug 28, 2019 at 11:29 AM John Peterson wrote: > > Thanks for your report about the QTrap thing working, I will make a PR for > that shortly. > https://github.com/libMesh/libmesh/pull/2230 -- John ___ Libmesh-users mailing

Re: [Libmesh-users] QTrap for TRI3SUBDIVISION

On Wed, Aug 28, 2019 at 11:20 AM Lee, Jae Ho wrote: > John — > > I just added TRI3SUBDIVISION to quadrature_trap_2D.C as a case, and I > think it’s working now. I am still debugging things one step at a time, and > one place that I got a complaint from is fe_lagrange.C — I may be confusing > myse

Re: [Libmesh-users] QTrap for TRI3SUBDIVISION

Hi Mike, I think this (using QTrap with TRI3SUBDIVISION elements) should work just fine. Did you try it yet? Let us know and we can update the case statements for quadrature. There are many places like this in the library where TRI3 and TRI3SUBDIVISION elements can be used more or less interchange

Re: [Libmesh-users] About moving mesh and redistributing internal mesh

On Fri, Jun 21, 2019 at 9:36 AM 서승진 wrote: > I tried to use the smoother after reading your email, and it seems that > the LaplaceMeshSmoother is quitely similar with smooth function in > MeshTools::Modification namespace. > > After trying this, I found a new problem. > > As you said, boundary

Re: [Libmesh-users] About moving mesh and redistributing internal mesh

On Thu, Jun 20, 2019 at 2:23 AM 서승진 wrote: > Hi. > > I re-send my question (because no enter is recognized in my previous > question) > > I am currently making a code which can treat moving mesh problem. > > I used GmshIO to construct mesh object, andI made a function to move > boundary nodes in

Re: [Libmesh-users] TransientSystem::old_solution vs TransientSystem::old_local_solution

On Mon, Jun 10, 2019 at 12:52 AM Yuxiang Wang wrote: > Dear all, > > Quick question - in using the TransientSystem::old_solution vs > TransientSystem::old_local_solution, I noticed that the former seems to be > exactly the latter plus two size checks. Therefore, can I simply use the > latter (old

Re: [Libmesh-users] FEBase object fails to calculate values

On Wed, Jun 12, 2019 at 4:58 PM John Peterson wrote: > > > On Wed, Jun 12, 2019 at 4:38 PM Nathan Andrew Miller < > nathan.a.mil...@colorado.edu> wrote: > >> I'm trying to compute the xyz, JxW, and other values at arbitrary points >> for a FEBase o

Re: [Libmesh-users] FEBase object fails to calculate values

On Wed, Jun 12, 2019 at 4:38 PM Nathan Andrew Miller < nathan.a.mil...@colorado.edu> wrote: > I'm trying to compute the xyz, JxW, and other values at arbitrary points > for a FEBase object during the evaluation of a MOOSE UserObject. I > implemented the following in code: > > ``` > //Create a vect

Re: [Libmesh-users] Mass lumping and trapezoidal quadrature rule

On Wed, May 22, 2019 at 10:03 AM John Peterson wrote: > > > On Wed, May 22, 2019 at 3:30 AM marco wrote: > >> Mass lumping is defined by using trapezoidal quadrature rule. >> In this way, the weights of a trapezoidal rule should be the integral over >> the element

Re: [Libmesh-users] Generating a triangle shaped object

On Mon, May 27, 2019 at 12:39 PM Amneet Bhalla wrote: > Hi Guys, > > Is there a way to generate a triangle shaped object (and eventually > triangulate it) using libMesh directly? > Yes, this is definitely possible if you configure libmesh with --disable-strict-lgpl so that Triangle support is av

Re: [Libmesh-users] Mass lumping and trapezoidal quadrature rule

On Wed, May 22, 2019 at 3:30 AM marco wrote: > Mass lumping is defined by using trapezoidal quadrature rule. > In this way, the weights of a trapezoidal rule should be the integral over > the element of each basis function. > > I noticed that this is not always true for hexahedral elements. Am I

Re: [Libmesh-users] For diagonal system.matrix, should I create my own NumericVector?

On Sun, May 19, 2019 at 9:15 PM Yuxiang Wang wrote: > Dear all, > > Sorry for the spam and being new to the field. > > I am currently trying to implement an elastodynamics problem with explicit > method (central difference method, to be specific). I am planning to use > lumped mass matrix (and Ra

Re: [Libmesh-users] Projection helgrind error

On Mon, May 13, 2019 at 4:45 PM Alexander Lindsay wrote: > I could maybe think of a libmesh-only case, but if you're willing to run > MOOSE, you can run the > moose/test/tests/geomsearch/nearest_node_locator/nearest_node_locator.i > input file. It appears to reproduce the error every time (with >

Re: [Libmesh-users] Quick question - bandwidth minimization?

On Thu, May 2, 2019 at 12:35 PM Yuxiang Wang wrote: > Dear all, > > A quick question - when using libmesh, should I consciously do bandwidth > minimization when I number my node IDs? Or, are those taken care of at > pre-processing stage of PETSc and other solvers? > I wouldn't try and do anythin

Re: [Libmesh-users] problem with inverse_map()

On Wed, May 1, 2019 at 5:52 PM Manav Bhatia wrote: > Any reason to expect such a sliver element when refining from squares? > No... something else must be wrong, either with the original Mesh, or some bug during the refinement process... -- John ___

Re: [Libmesh-users] problem with inverse_map()

On Wed, May 1, 2019 at 5:40 PM Manav Bhatia wrote: > As a followup, I have attached a screenshot of where the element in the > error message is pointing. It is intriguing that the coordinates of all 4 > nodes have virtually the same y-axis location (hence the hmin of 10^-11). I > have circled the

Re: [Libmesh-users] Face ids in gmesh and libMesh

On Mon, Apr 29, 2019 at 6:02 PM Nikrouz wrote: > Dear all libMesh users, > > I have produced a 3D msh file by Gmesh but I do not define any group > surface in Gmesh. > > In order to identify different faces, is there any class or method in > libMesh or it is neccsary to define id for msh file in

Re: [Libmesh-users] Suitable version for libMesh

On Wed, Apr 24, 2019 at 3:48 PM Nikrouz wrote: > Dear All libMesh users > > For some examples, it is necessary to configure libMesh with slepc. > > Currently, I have PetSC version 3.10.0 which is not compatible with the > new version of slepc. > > How can I find a slepc version suitable for my ca

Re: [Libmesh-users] Boost Libraries

On Tue, Apr 23, 2019 at 5:01 AM Nikhil Vaidya wrote: > Hi all, > > What is the correct way to use the boost libraries in the contrib folder > while configuring libmesh? The version of boost on my system is older than > required and I do not have root access. I would like to use the boost > librar

Re: [Libmesh-users] Error in Configure script

On Wed, Apr 3, 2019 at 3:10 PM Povolotskyi, Mykhailo wrote: > Hello, > > I have got the same error in 1.4.0, but then I used --disable-metaphysicl > I think it wouldn't be exactly the same error, since metaphysicl became a submodule at some point between the 1.3 and 1.4 releases and we don't spe

Re: [Libmesh-users] Error in Configure script

On Mon, Apr 1, 2019 at 2:25 PM Nikhil Vaidya wrote: > I am trying to configure libMesh 1.3. I get the following error in my > configure script: > > configure: WARNING: boost/system/error_code.hpp: present but cannot be > compiled > configure: WARNING: boost/system/error_code.hpp: check for mi

Re: [Libmesh-users] Setting up BC for subdivision FE example

On Thu, Mar 28, 2019 at 11:02 AM Lee, Jae Ho wrote: > I was modifying the subdivision FE example code in miscellaneous/ex11 to > handle large deformations and do a bending and inflation of a circular > plate in Cirak and Ortiz 2001 ( > https://pdfs.semanticscholar.org/6fb5/bf884883eda23383e1502f6

Re: [Libmesh-users] problems with libmesh 1.4.0

On Wed, Mar 27, 2019 at 8:57 AM Povolotskyi, Mykhailo wrote: > Thank you. > > Could you, please, tell when 1.4.1 is going to be released? > There's no set date for this, but if the fix is needed for your code there's a good chance that it will also be needed for others, and this would make us wan

Re: [Libmesh-users] problems with libmesh 1.4.0

On Tue, Mar 26, 2019 at 7:09 PM Povolotskyi, Mykhailo wrote: > Dear Libmesh developers, > > I upgrarded from 1.2.1 to 1.4.0 > > My code stopped working. > > The first error is as follows: > > [0]PETSC ERROR: - Error Message > ---

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