[deal.II] An error occurred in line <1467> of file in function dealii::IndexSet dealii::TrilinosWrappers::MPI::Vector::locally_owned_elements() const

2023-10-10 Thread Tiny Y 
Hi al,
I am a freshman in dealii. I have installed Dealii 9.4.2 on 22.04. The 
senior wrote code on the old version of dealii, so I made changes to his 
code to adapt to the new version of dealii, but I encountered some 
problems. The function(locally_owned_elements()) where the error code is 
located has been deleted, but this error still occurs. I want to know where 
this problem comes from and how I can solve it. Thanks in advance!
Regard,
Yi
Error Message

qincai@qincai-OMEN:~/桌面/cracks-master_mod版本更新$ mpirun -n 8 ./cracks 
parameters_ring.prm
Running on 8 cores
Cells: 442

DoFs: 5440 solid + 2720 phase + 2720 pressure = 10880

===
Parameters
==
h (min): 0.0415041
k: 4.15041e-12
eps: 0.166016
G_c: 1.2
gamma penal: 0
Poisson nu: 0.2
E modulus: 1
Lame mu: 4166.67
Lame lambda: 2777.78



An error occurred in line <1467> of file 

 
in function
dealii::IndexSet 
dealii::TrilinosWrappers::MPI::Vector::locally_owned_elements() const
The violated condition was: 
owned_elements.size() == size()
Additional information: 
The locally owned elements have not been properly initialized! This
happens for example if this object has been initialized with exactly
one overlapping IndexSet.

Stacktrace:
---
#0 ./cracks: 
dealii::TrilinosWrappers::MPI::Vector::locally_owned_elements() const
#1 /home/qincai/dealii-candi/deal.II-v9.4.2/lib/libdeal_II.g.so.9.4.2: 
#2  /home/qincai/dealii-candi/deal.II-v9.4.2/lib/libdeal_II.g.so.9.4.2: 
dealii::internal::DataOutImplementation::DataEntry<2, 2, 
double>::DataEntry(dealii::DoFHandler<2,
 
2> const*, dealii::TrilinosWrappers::MPI::BlockVector const*, 
dealii::DataPostprocessor<2> const*)
#3  /home/qincai/dealii-candi/deal.II-v9.4.2/lib/libdeal_II.g.so.9.4.2: 
std::__detail::_MakeUniq >::__single_object 
std::make_unique, dealii::DoFHandler<2, 2> const*, 
dealii::TrilinosWrappers::MPI::BlockVector const*, 
dealii::DataPostprocessor<2> const*>(dealii::DoFHandler<2, 2> const*&&, 
dealii::TrilinosWrappers::MPI::BlockVector const*&&, 
dealii::DataPostprocessor<2> const*&&)
#4  /home/qincai/dealii-candi/deal.II-v9.4.2/lib/libdeal_II.g.so.9.4.2: 
void dealii::DataOut_DoFData<2, 2, 2, 
2>::add_data_vector(dealii::DoFHandler<2,
 
2> const&, dealii::TrilinosWrappers::MPI::BlockVector const&, 
dealii::DataPostprocessor<2> const&)
#5  ./cracks: void dealii::DataOut_DoFData<2, 2, 2, 
2>::add_data_vector(dealii::TrilinosWrappers::MPI::BlockVector
 
const&, dealii::DataPostprocessor<2> const&)
#6  ./cracks: FracturePhaseFieldProblem<2>::output_results() const
#7  ./cracks: FracturePhaseFieldProblem<2>::run()
#8  ./cracks: main


Calling MPI_Abort now.
To break execution in a GDB session, execute 'break MPI_Abort' before 
running. You can also put the following into your ~/.gdbinit:
  set breakpoint pending on
  break MPI_Abort
  set breakpoint pending auto


An error occurred in line <1467> of file 

 
in function
dealii::IndexSet 
dealii::TrilinosWrappers::MPI::Vector::locally_owned_elements() const
The violated condition was: 
owned_elements.size() == size()
Additional information: 
The locally owned elements have not been properly initialized! This
happens for example if this object has been initialized with exactly
one overlapping IndexSet.

Stacktrace:
---
#0  ./cracks: 
dealii::TrilinosWrappers::MPI::Vector::locally_owned_elements() const
#1  /home/qincai/dealii-candi/deal.II-v9.4.2/lib/libdeal_II.g.so.9.4.2: 
#2 /home/qincai/dealii-candi/deal.II-v9.4.2/lib/libdeal_II.g.so.9.4.2: 
dealii::internal::DataOutImplementation::DataEntry<2, 2, 
double>::DataEntry(dealii::DoFHandler<2,
 
2> const*, dealii::TrilinosWrappers::MPI::BlockVector const*, 
dealii::DataPostprocessor<2> const*)
#3 /home/qincai/dealii-candi/deal.II-v9.4.2/lib/libdeal_II.g.so.9.4.2: 
std::__detail::_MakeUniq >::__single_object 
std::make_unique, dealii::DoFHandler<2, 2> const*, 
dealii::TrilinosWrappers::MPI::BlockVector const*, 
dealii::DataPostprocessor<2> const*>(dealii::DoFHandler<2, 2> const*&&, 
dealii::TrilinosWrappers::MPI::BlockVector const*&&, 
dealii::DataPostprocessor<2> const*&&)
#4 /home/qincai/dealii-candi/deal.II-v9.4.2/lib/libdeal_II.g.so.9.4.2: void 
dealii::DataOut_DoFData<2, 2, 2, 
2>::add_data_vector(dealii::DoFHandler<2,
 
2> const&, dealii::TrilinosWrappers::MPI::BlockVector const&, 
dealii::DataPostprocessor<2> const&)
#5 ./cracks: void dealii::DataOut_DoFData<2, 2, 2, 
2>::add_data_vector(dealii::TrilinosWrappers::MPI::BlockVector
 
const&, dealii::DataPostprocessor<2> const&)
#6 ./cracks: FracturePhaseFieldProblem<2>::output_results() const
#7 ./cracks: FracturePhaseFieldProblem<2>::run()
#8 ./cracks: main


Calling MPI_Abort now.
To break execution

[deal.II] Re: MUMPS solver with Trilinos

2023-10-10 Thread kendrick zoom 
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On Sunday, October 16, 2022 at 8:42:50 AM UTC-7 grrah...@gmail.com wrote:

> Hello everyone,
>
> I am not able to get Trilinos working with MUMPS direct solver, so I am 
> reaching out for some guidance. 
>
> The Os is MacOs (Apple Silicon) and I am able to install mumps solver 
> using Candi. By default candi installs version 5.4.0.  However, Trilinos 
> with Amesos throws error while compiling. I am suspecting a conflict of 
> scalapack to be the issue here. I am currently using MPICH as my MPI 
> compiler and I think I will need to change it to OpenMPI to solve the issue 
> with scalapack. Also interestingly, Trilinos with Amesos2 do not show any 
> issue. So before I change to OpenMPI and reinstall everything, I thought to 
> clarify a couple of  things.
>
> 1. Does mumps has to be any specific version to compile with  amesos. 
> Trilinos documentation available on net suggest 4.7.3. However, this is 
> fairly old version.
>
> 2. Dealii has no compatibility with Amesos2, right?
>
> Thank you,
> Rahul
>
>
>
>

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[deal.II] Re: deal.II Newsletter #230

2023-10-10 Thread kendrick zoom 
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On Wednesday, October 19, 2022 at 9:00:20 AM UTC-7 rene.gas...@mailbox.org 
wrote:

> Hello everyone!
>
> This is deal.II newsletter #230.
> It automatically reports recently merged features and discussions about 
> the deal.II finite element library.
>
> Below you find a list of recently proposed or merged features:
>
> #14362 : Execute explicit 
> instantiations of compute_intersection_of_cells() (proposed by jh66637 
> )
> #14361 : introduce 
> BoundingBox::is_neighbor() (proposed by jh66637 
> )
> #14360 : Get vertices in 
> CGAL order on face (proposed by jh66637 )
> #14357 : Fix two typos in 
> ConsensusAlgorithm::NBX (proposed by gassmoeller 
> )
> #14356 : [WIP] Remove 
> communication in CollectiveMutex during stack unwinding (proposed by 
> gassmoeller )
> #14355 : Use Ubuntu 20.04 in 
> GitHub actions (proposed by masterleinad 
> )
> #14354 : VectorizedArray: 
> mixed load/store (proposed by peterrum ; 
> merged)
> #14353 : Add tolerance to 
> avoid empty CGAL intersections due to roundoff (proposed by jh66637 
> )
> #14352 : [WIP] Add 
> TrilinosWrappers::SolverBelos (proposed by peterrum 
> )
> #14351 : GitHub CI: update 
> Ubuntu version (proposed by peterrum )
> #14350 : Refactor 
> SolverGMRES::modified_gram_schmidt (proposed by peterrum 
> ; merged)
> #14349 : SolverGMRES: add 
> classical Gram-Schmidt (proposed by peterrum 
> )
> #14348 : Implement 
> ReferenceCell::n_face_orientations(). (proposed by drwells 
> ; merged)
> #14339 : Fix some doxygen 
> problems. (proposed by bangerth ; merged)
>
> And this is a list of recently opened or closed discussions:
>
> #14359  CGAL intersection 
> bug (opened)
> #14358  
> dealii:when i use Gmsh to generate .msh file, Number of coupling 
> nodes: 0 (opened)
>
> A list of all major changes since the last release can be found at this 
> website 
> . 
>
> Thanks for being part of the community!
>
> Let us know about questions, problems, bugs or just share your experience 
> by writing to this mailing list, or by opening issues or pull requests on 
> Github .
> Additional information can be found at our official website 
> . 
>

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[deal.II] Re: Looking for clarification on a few places on Step-44

2023-10-10 Thread kendrick zoom 
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On Friday, September 30, 2022 at 10:16:05 AM UTC-7 mjri...@gmail.com wrote:

> Hi,
>
> Step-44 has a lot going on and really sets you up to tackle a variety of 
> real world problems. There is a significant jump in complexity between this 
> tutorial and steps 8,17 & 18. 
>
> I have been reading the references and I am about there but need few 
> clarifications for why things are the way they are. 
>
> Any assistance would be much appreciated...
>
> My first question deals with the statement "The Euler-Lagrange equations 
> corresponding to the residual"
>
> Directly above this sentence is the residual, whose derivation I 
> understand. Where I am lost is that s tact on to equations. I have only one 
> residual equation. I cannot bridge that disconnect. 
>
> My other question has to deal with the solving procedure for K (see 
> snippet below) 
> [image: Ksolve.png]
>
>
> I am completely lost here. What is the significance of p and J not having 
> derivatives on them that makes it "easy" to solve for those terms in 
> isolation? I am also confused how K_pJ, K_Jp and K_JJ  form a block 
> diagonal matrix. I could get there if I ignore the top row but then the 
> equations below do not make sense I think. Some detail on this part of the 
> process would be great. 
>
> Thanks in advance, 
>
> Matt
>

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

2023-10-10 Thread kendrick zoom 
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On Mon, Oct 9, 2023 at 5:19 PM David Montiel Taboada 
wrote:

> 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 is Intel.
>
> I will test deal.II with the PRISMS-PF applications and report if I see
> any issues.
>
> Thank you for your help, Luca!
>
> David
>
> On Monday, October 9, 2023 at 5:04:25 AM UTC-4 luca@gmail.com wrote:
>
>> Alexander,
>>
>> can you try out our new dmg image?
>>
>>
>> https://github.com/dealii/dealii/releases/download/v9.5.1/dealii-9.5.1-sonoma-arm64-clang15.dmg
>>
>> I’m preparing also a new one, where the compiler is shipped together with
>> the image. This should be robust to the next upgrades in the OS.
>>
>> Best,
>> Luca.
>>
>> > On 6 Oct 2023, at 06:06, Alexander Mensah  wrote:
>> >
>> > If I use the 'step-1' example, I get the same error (mpic++) as with
>> the program I want to run.
>> >
>> > 
>> >
>> > On Thursday, October 5, 2023 at 11:42:27 PM UTC-4 Alexander Mensah
>> wrote:
>> > No luck
>> >
>> >
>> >
>> > On Thursday, October 5, 2023 at 6:47:07 PM UTC-4 Wolfgang Bangerth
>> wrote:
>> >
>> > On 10/5/23 15:14, Alexander Mensah wrote:
>> > >
>> > > Could someone help me fix this?
>> >
>> > I believe that you're trying to call cmake (to configure one of the
>> > example programs) in the directory
>> > /Applications/deal.II.app/Contents/Resources/Libraries/examples/...
>> but
>> > this is a system directory that you can read files in, but not write
>> to.
>> > You might have to copy the tutorial program directory you're trying to
>> > configure into your home directory.
>> >
>> > Best
>> > W.
>> >
>> >
>> > --
>> > The deal.II project is located at http://www.dealii.org/
>> > For mailing list/forum options, see
>> https://groups.google.com/d/forum/dealii?hl=en
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>>
>> > 
>>
>> --
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> 
> .
>

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