Re: [deal.II] Re: Adding an independent DoF to a Trilinos system

2018-03-26 Thread Wolfgang Bangerth 

On 03/22/2018 03:22 PM, Ben Shields wrote:
I did some digging into the Trilinos reinit_matrix, and I've found that 
all of my lost time is coming from the operation


   graph->FillComplete(input_col_map, input_row_map)

This step is accounting for as much as 20 seconds per call for a 
1x200,000 matrix on 4 processors. I also found that this bottleneck is 
non-existent running in serial. There is a check earlier in 
reinit_matrix which calls graph.reset differently for 1 processor vs. 
multiple processors. The comments suggest that there's an explicit 
reason for treating the mpi case this way, but that treatment seems to 
be causing the problem for my case.

I think Martin Kronbichler might have to tell you why this is.

But if you're adventurous, take a look how the FillComplete function in 
Trilinos looks like and whether you could possibly find the same kinds 
of savings there that I found in deal.II. I suspect that it is this 
function:


https://github.com/trilinos/Trilinos/blob/master/packages/epetra/src/Epetra_CrsGraph.cpp#L974

Best
 W.

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Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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[deal.II] deal.II Newsletter #25

2018-03-26 Thread Rene Gassmoeller 
Hello everyone!

This is deal.II newsletter #25.
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:

#6103: CMake: Do not require a special name for TRACK="Continuous" (proposed by 
tamiko; merged) https://github.com/dealii/dealii/pull/6103

#6102: la::p::Vector::compress(insert) now correctly zeroes ghosts (proposed by 
davydden; merged) https://github.com/dealii/dealii/pull/6102

#6101: fix LaTeX in Lapack and ScaLapack (proposed by davydden) 
https://github.com/dealii/dealii/pull/6101

#6100: Fix GridTools::minimal/maximal_cell_diameter for p::d::Triangulation 
(proposed by masterleinad; merged) https://github.com/dealii/dealii/pull/6100

#6099: improve MPI::Partitioner for the case of empty owned DoFs with with 
non-empty ghosts (proposed by davydden; merged) 
https://github.com/dealii/dealii/pull/6099

#6098: CMake: Add rpath to example steps (proposed by tamiko; merged) 
https://github.com/dealii/dealii/pull/6098

#6097: Use TimerOutput::Scope in step-32. (proposed by bangerth) 
https://github.com/dealii/dealii/pull/6097

#6095: give example of Utilities::MPI::Partitioner (proposed by davydden; 
merged) https://github.com/dealii/dealii/pull/6095

#6094: Fix cone_04 (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/6094

#6093: Tests: Do not print memory consumptions in fe/fe_move_0? tests (proposed 
by tamiko; merged) https://github.com/dealii/dealii/pull/6093

#6092: Tests: Provide output variants for clang-6 and libc++ (proposed by 
tamiko; merged) https://github.com/dealii/dealii/pull/6092

#6091: CMake: Also propagate compiler and linker flags to the boost check 
(proposed by tamiko; merged) https://github.com/dealii/dealii/pull/6091

#6090: Fix bug in NormalToMeshProjection (proposed by luca-heltai; merged) 
https://github.com/dealii/dealii/pull/6090

#6089: mpi: add helper function to print PID and hostname and wait (proposed by 
davydden) https://github.com/dealii/dealii/pull/6089

#6088: CMake: Preprocess testsuite parameter files (proposed by tamiko; merged) 
https://github.com/dealii/dealii/pull/6088

#6087: Fix iterating over entries of parallel PETSc matrices. (proposed by 
bangerth) https://github.com/dealii/dealii/pull/6087

#6084: add ScaLAPACKMatrix::pseudoinverse() (proposed by BenBrands) 
https://github.com/dealii/dealii/pull/6084

#6083: Do not make a variable in step-35 static. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/6083

#6082: Fix a grammar error. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/6082

#6081: Fix quadratic behavior of SparsityPattern::copy_from(). (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/6081

#6080: ScaLAPACKMatrix::invert for non-symmetric matrices (proposed by 
BenBrands) https://github.com/dealii/dealii/pull/6080

#6079: VectorTools: Increase max iterations in project_matrix_free (proposed by 
tamiko; merged) https://github.com/dealii/dealii/pull/6079

#6078: tests: lac/*vector_add_and_dot* (proposed by tamiko; merged) 
https://github.com/dealii/dealii/pull/6078

#6077: Fix documentation of Utilities::MPI::MinMaxAvg (proposed by 
masterleinad; merged) https://github.com/dealii/dealii/pull/6077

#6075: Mark more basic Tensor operations as always_inline (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/6075

#6073: tests: sharedtria/communicate_active_fe_indices_01b add an output 
variant (proposed by tamiko; merged) https://github.com/dealii/dealii/pull/6073

#6072: tests: lac/*vector_add_and_dot_complex increase output precision 
(proposed by tamiko; merged) https://github.com/dealii/dealii/pull/6072

#6071: tests: sundials/harmonic_oscillator_04 increase precision (proposed by 
tamiko; merged) https://github.com/dealii/dealii/pull/6071

#6070: tests: metis/metis_02 add yet another output variant (proposed by 
tamiko; merged) https://github.com/dealii/dealii/pull/6070

#6069: tests: make distributed_grids/1d_grid robust (proposed by tamiko; 
merged) https://github.com/dealii/dealii/pull/6069

#6068: tests: Increase output precision for fe/rt_bubbles_(14|15) (proposed by 
tamiko; merged) https://github.com/dealii/dealii/pull/6068

#6067: Bugfix: Set a value to zero with a floating point literal (proposed by 
tamiko; merged) https://github.com/dealii/dealii/pull/6067

#6066: Update a couple places where we do markup by hand. (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/6066

#6064: Avoid deriving from std::iterator (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/6064

#6063: ScaLAPACKMatrix: change setting of state variable at various places 
(proposed by BenBrands; merged) https://github.com/dealii/dealii/pull/6063

#6049:  make Utilities::MPI::sum() support SparseMatrix (proposed by davydden; 
merged) https://github.com/dealii/dealii/pull/6049

#5994: Avoid

Re: [deal.II] Re: use of "meshworker" for FESystem

2018-03-26 Thread JAEKWANG KIM 
Thanks for the attetion.
I overcame this problem, though I don’t recognize what was solution now.
It turns out to be possible…

Thank you for your time

Jaekwang



On Sun, Mar 25, 2018 at 3:13 AM, Daniel Arndt <
daniel.ar...@iwr.uni-heidelberg.de> wrote:

> Jaekwang,
>
> do you have a minimal compilign example that shows the problem?
> Did you call dof_handler.distribute_dofs(fe)?
>
> Best,
> Daniel
>
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Re: [deal.II] Are shell elements available in deal.II?

2018-03-26 Thread Andrew McBride 
Hi

I’ve hesitated to add this link as it predates many of the features in deal.II 
that would have made the implementation a lot more elegant and simple. 
Nevertheless have a look at https://open.uct.ac.za/handle/11427/5552 
 It’s a fully nonlinear shell theory 
due to Simo & Fox implemented in deal.II. 

There is no reason why you can’t implement Mindlin-Reissner  plate theory in 
deal.II. I would start with Timoshenko beam theory and then build up to plates. 

A



> On 26 Mar 2018, at 14:40, Wolfgang Bangerth  wrote:
> 
> On 03/25/2018 11:44 AM, Yuxiang Wang wrote:
>> My current need for shell element is for solid mechanics problem 
>> (Mindlin-Reissner plates). A simple example could be that a thick square 
>> plate, with all its edges fixed, under a force loading at the center. The 
>> dimensions of the plate are around 10x of its thickness; so, as one can 
>> note, there is 1) only in-plate stress in this problem, 2) the plate 
>> thickness remains constant during the deformation, and 3) there is an 
>> approximately linear variation of displacement across the thickness 
>> direction.
>> Do you happen to be aware of any examples in deal.ii, that solves shell 
>> problems for solid mechanics application? If not, I can also try to start 
>> from scratch; but I figured it'd be nice that if I know someone who did this 
>> already and wouldn't need to reinvent the wheels.
> 
> I don't know of any that would be publicly available. I know that Baerbel 
> Janssen's diploma thesis was on biharmonic problems (or at least had them as 
> part). You can get it from here but it is in German:
>  http://www.csc.kth.se/~barbel/link/en/publications.shtml
> 
> I am certain that others have done similar work, but I don't know the 
> details. Of course, we are always grateful to anyone willing to share their 
> codes through the code gallery!
> 
> Best
> Wolfgang
> 
> -- 
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
>   www: http://www.math.colostate.edu/~bangerth/
> 
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Re: [deal.II] Are shell elements available in deal.II?

2018-03-26 Thread Wolfgang Bangerth 

On 03/25/2018 11:44 AM, Yuxiang Wang wrote:


My current need for shell element is for solid mechanics problem 
(Mindlin-Reissner plates). A simple example could be that a thick square 
plate, with all its edges fixed, under a force loading at the center. The 
dimensions of the plate are around 10x of its thickness; so, as one can note, 
there is 1) only in-plate stress in this problem, 2) the plate thickness 
remains constant during the deformation, and 3) there is an approximately 
linear variation of displacement across the thickness direction.


Do you happen to be aware of any examples in deal.ii, that solves shell 
problems for solid mechanics application? If not, I can also try to start from 
scratch; but I figured it'd be nice that if I know someone who did this 
already and wouldn't need to reinvent the wheels.


I don't know of any that would be publicly available. I know that Baerbel 
Janssen's diploma thesis was on biharmonic problems (or at least had them as 
part). You can get it from here but it is in German:

  http://www.csc.kth.se/~barbel/link/en/publications.shtml

I am certain that others have done similar work, but I don't know the details. 
Of course, we are always grateful to anyone willing to share their codes 
through the code gallery!


Best
 Wolfgang

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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