[deal.II] Output the solution to .h5 file (hdf5)

2022-09-07 Thread Judy Lee 
Hello everyone! 

For the step-3 hdf5 to output the solution data, I have an error message 
returned, like the following:

[ 66%] Built target step-3

[100%] Run step-3 with Debug configuration

Number of active cells: 1024

Number of degrees of freedom: 1089

DEAL:cg::Starting value 0.121094

DEAL:cg::Convergence step 48 value 5.33692e-13

terminate called after throwing an instance of 
'dealii::StandardExceptions::ExcMessage'

what(): 



An error occurred in line <7799> of file 
 
in function

void dealii::DataOutBase::write_hdf5_parallel(const 
std::vector >&, const 
dealii::DataOutBase::DataOutFilter&, bool, const string&, const string&, 
const MPI_Comm&) [with int dim = 2; int spacedim = 2; std::string = 
std::__cxx11::basic_string; MPI_Comm = int]

The violated condition was: 

false

Additional information: 

HDF5 support is disabled.



make[3]: *** [CMakeFiles/run.dir/build.make:77: CMakeFiles/run] Aborted

make[2]: *** [CMakeFiles/Makefile2:237: CMakeFiles/run.dir/all] Error 2

make[1]: *** [CMakeFiles/Makefile2:244: CMakeFiles/run.dir/rule] Error 2

make: *** [Makefile:202: run] Error 2


My modified step-3.cc is attached. I added in the main function (Line 
685-687), in the class step3 to declare *n_refinement_steps* (Line 100), in 
the function void step3::make_grid() (Line 164-165), and in the function 
void step3::output_results() (Line 606-610). Thank you very much. 

Best regards,

Judy

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/* -
 *
 * Copyright (C) 1999 - 2021 by the deal.II authors
 *
 * This file is part of the deal.II library.
 *
 * The deal.II library is free software; you can use it, redistribute
 * it, and/or modify it under the terms of the GNU Lesser General
 * Public License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 * The full text of the license can be found in the file LICENSE.md at
 * the top level directory of deal.II.
 *
 * -

 *
 * Authors: Wolfgang Bangerth, 1999,
 *  Guido Kanschat, 2011
 */


// @sect3{Many new include files}

// These include files are already known to you. They declare the classes
// which handle triangulations and enumeration of degrees of freedom:
#include 
#include 
// And this is the file in which the functions are declared that create grids:
#include 

// This file contains the description of the Lagrange interpolation finite
// element:
#include 

// And this file is needed for the creation of sparsity patterns of sparse
// matrices, as shown in previous examples:
#include 

// The next two files are needed for assembling the matrix using quadrature on
// each cell. The classes declared in them will be explained below:
#include 
#include 

// The following three include files we need for the treatment of boundary
// values:
#include 
#include 
#include 

// We're now almost to the end. The second to last group of include files is
// for the linear algebra which we employ to solve the system of equations
// arising from the finite element discretization of the Laplace equation. We
// will use vectors and full matrices for assembling the system of equations
// locally on each cell, and transfer the results into a sparse matrix. We
// will then use a Conjugate Gradient solver to solve the problem, for which
// we need a preconditioner (in this program, we use the identity
// preconditioner which does nothing, but we need to include the file anyway):
#include 
#include 
#include 
#include 
#include 
#include 

// Finally, this is for output to a file and to the console:
#include 
#include 
#include 

// ...and this is to import the deal.II namespace into the global scope:
using namespace dealii;

// @sect3{The Step3 class}

// Instead of the procedural programming of previous examples, we encapsulate
// everything into a class for this program. The class consists of functions
// which each perform certain aspects of a finite element program, a `main`
// function which controls what is done first and what is done next, and a
// list of member variables.

// The public part of the class is rather short: it has a constructor and a
// function `run` that is called from the outside and acts as something like
// the `main` function: it coordinates which

Re: [deal.II] compiling deal.ii 9.4 on wsl error

2022-09-07 Thread Daniel Arndt 
Qiong,

What CMake settings did you use to configure deal.II?
Does your system indeed provide an MPI installation?

Bets,
Daniel

On Wed, Sep 7, 2022 at 10:22 AM jim wo  wrote:

> Hello,
> I want to  develop my own project on wsl with deal.ii 9.4.  after make I
> got this message:
>
> In file included from /home/wu/deal_II/include/deal.II/grid/tria.h:20,
>  from /home/wu/cmakeQuickStart/main.cpp:23:
> /home/wu/deal_II/include/deal.II/base/config.h:540:12: fatal error: mpi.h:
> No such file or directory
>   540 | #  include 
>   |^~~
> compilation terminated.
> thanks for  your help
>  Qiong
>
> --
> 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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Re: [deal.II] Output the solution to .h5 file (hdf5)

2022-09-07 Thread Timo Heister 
You will need to configure deal.II with HDF5 support, see
https://www.dealii.org/developer/readme.html#optional-software

On Wed, Sep 7, 2022 at 1:23 PM Judy Lee  wrote:
>
> Hello everyone!
>
> For the step-3 hdf5 to output the solution data, I have an error message 
> returned, like the following:
>
> [ 66%] Built target step-3
>
> [100%] Run step-3 with Debug configuration
>
> Number of active cells: 1024
>
> Number of degrees of freedom: 1089
>
> DEAL:cg::Starting value 0.121094
>
> DEAL:cg::Convergence step 48 value 5.33692e-13
>
> terminate called after throwing an instance of 
> 'dealii::StandardExceptions::ExcMessage'
>
> what():
>
> 
>
> An error occurred in line <7799> of file 
> 
>  in function
>
> void dealii::DataOutBase::write_hdf5_parallel(const 
> std::vector >&, const 
> dealii::DataOutBase::DataOutFilter&, bool, const string&, const string&, 
> const MPI_Comm&) [with int dim = 2; int spacedim = 2; std::string = 
> std::__cxx11::basic_string; MPI_Comm = int]
>
> The violated condition was:
>
> false
>
> Additional information:
>
> HDF5 support is disabled.
>
> 
>
> make[3]: *** [CMakeFiles/run.dir/build.make:77: CMakeFiles/run] Aborted
>
> make[2]: *** [CMakeFiles/Makefile2:237: CMakeFiles/run.dir/all] Error 2
>
> make[1]: *** [CMakeFiles/Makefile2:244: CMakeFiles/run.dir/rule] Error 2
>
> make: *** [Makefile:202: run] Error 2
>
>
> My modified step-3.cc is attached. I added in the main function (Line 
> 685-687), in the class step3 to declare *n_refinement_steps* (Line 100), in 
> the function void step3::make_grid() (Line 164-165), and in the function void 
> step3::output_results() (Line 606-610). Thank you very much.
>
> Best regards,
>
> Judy
>
> --
> 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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-- 
Timo Heister
http://www.math.clemson.edu/~heister/

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[deal.II] compiling deal.ii 9.4 on wsl error

2022-09-07 Thread jim wo 
Hello,
I want to  develop my own project on wsl with deal.ii 9.4.  after make I 
got this message:
 
In file included from /home/wu/deal_II/include/deal.II/grid/tria.h:20,
 from /home/wu/cmakeQuickStart/main.cpp:23:
/home/wu/deal_II/include/deal.II/base/config.h:540:12: fatal error: mpi.h: 
No such file or directory
  540 | #  include 
  |^~~
compilation terminated.
thanks for  your help
 Qiong

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[deal.II] deal.II Newsletter #224

2022-09-07 Thread 'Rene Gassmoeller' via deal.II User Group 
Hello everyone!

This is deal.II newsletter #224.
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:

#14245: PreconditionRelaxation: add specialization (proposed by peterrum) 
https://github.com/dealii/dealii/pull/14245

#14244: DiagonalMatrix: specialize for LA:d:V (proposed by peterrum) 
https://github.com/dealii/dealii/pull/14244

#14243: [WIP] TensorProductMatrixSymmetricSum for matrices with rows/columns 
filled with zero (proposed by peterrum) 
https://github.com/dealii/dealii/pull/14243

#14242: PreconditionChebyshev: reduce number of writes by one (proposed by 
peterrum; merged) https://github.com/dealii/dealii/pull/14242

#14241: Fix a warning (proposed by kronbichler; merged) 
https://github.com/dealii/dealii/pull/14241

#14240: FEEvaluation: Create temporary copy of Jacobian matrix in submit_XXX 
(proposed by kronbichler; merged) https://github.com/dealii/dealii/pull/14240

#14239: MatrixFree: Fix assertion in presence of FE_Nothing (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/14239

#14238: Add specializations of PreconditionRelaxation functions (proposed by 
peterrum; merged) https://github.com/dealii/dealii/pull/14238

#14237: Specialize EvaluatorTensorProduct for non-templated 
execution (proposed by peterrum) https://github.com/dealii/dealii/pull/14237

#14236: support XDMF writing with ranks without cells (proposed by tjhei) 
https://github.com/dealii/dealii/pull/14236

#14235: fix: step-50 PETSc (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/14235

#14234: Normal flux constraints: map DoF indices to vector DoF indices 
(proposed by zjiaqi2018) https://github.com/dealii/dealii/pull/14234

#14232: Enable SolverIDR for block vectors (proposed by peterrum; merged) 
https://github.com/dealii/dealii/pull/14232

#14231: Doc update in GridTools. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/14231

#14230: Remove an outdated comment. Link to step-19. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/14230

#14229: Clarify a comment for one of the particle generators. (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/14229

#14228: Precompile TensorProductMatrixSymmetricSum kernels (proposed by 
peterrum; merged) https://github.com/dealii/dealii/pull/14228

#14227: Set another OMP environment variable. (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/14227

#14226: MatrixFree laplace operator: Restructure computation of diagonal 
(proposed by kronbichler; merged) https://github.com/dealii/dealii/pull/14226

#14225: Adjust interface in 'dofs' folder to new datatype 'types::fe_index'. 
(proposed by marcfehling) https://github.com/dealii/dealii/pull/14225

#14224: Fix bug in matrix-free operators regarding diagonal (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/14224

#14223: Update output (proposed by peterrum; merged) 
https://github.com/dealii/dealii/pull/14223

#14222: Fix test case with clang compiler (proposed by kronbichler; merged) 
https://github.com/dealii/dealii/pull/14222

#14221: Fuse some loops in Triangulation::execute_coarsening (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/14221

#14220: Merge two loops in setup of triangulation (proposed by kronbichler; 
merged) https://github.com/dealii/dealii/pull/14220

#14219: MatrixFree: Fix bug in setup of new cell_index for MG (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/14219

#14218: Avoid warning about unused variable (proposed by kronbichler; merged) 
https://github.com/dealii/dealii/pull/14218

#14216: Add specializations of PreconditionChebyshev functions (proposed by 
peterrum; merged) https://github.com/dealii/dealii/pull/14216

#14215: Fix PETSc version detection. (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/14215

#14214: Fix docker build (proposed by bergbauer; merged) 
https://github.com/dealii/dealii/pull/14214

#14213: Clarify comments about get_generalized_support_points(). (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/14213

#14212: Move invalid_fe_index to numbers. (proposed by marcfehling; merged) 
https://github.com/dealii/dealii/pull/14212

#14211: Update checks for AD-types. (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/14211

#14210: Move active_fe_index_type to types. (proposed by marcfehling; merged) 
https://github.com/dealii/dealii/pull/14210

#14209: Optimize PreconditionRelaxation (proposed by peterrum; merged) 
https://github.com/dealii/dealii/pull/14209

#14208: Added get/set functions for future FE indices. (proposed by 
marcfehling; merged) https://github.com/dealii/dealii/pull/14208

#14207: Change get_active_fe_indices() to return the result. (proposed by 
marcfehling; merged)

Re: [deal.II] compiling deal.ii 9.4 on wsl error

2022-09-07 Thread jim wo 
I did install MPI on wsl 
and I congfigure deal.ii with DEAL_II_WITH_PETSC = ON
DEAL_II_WITH_P4EST = ON


在2022年9月7日星期三 UTC+8 23:03:57 写道：

> Qiong,
>
> What CMake settings did you use to configure deal.II?
> Does your system indeed provide an MPI installation?
>
> Bets,
> Daniel
>
> On Wed, Sep 7, 2022 at 10:22 AM jim wo  wrote:
>
>> Hello,
>> I want to  develop my own project on wsl with deal.ii 9.4.  after make I 
>> got this message:
>>  
>> In file included from /home/wu/deal_II/include/deal.II/grid/tria.h:20,
>>  from /home/wu/cmakeQuickStart/main.cpp:23:
>> /home/wu/deal_II/include/deal.II/base/config.h:540:12: fatal error: 
>> mpi.h: No such file or directory
>>   540 | #  include 
>>   |^~~
>> compilation terminated.
>> thanks for  your help
>>  Qiong
>>
>> -- 
>> 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
>> --- 
>> You received this message because you are subscribed to the Google Groups 
>> "deal.II User Group" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to dealii+un...@googlegroups.com.
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>> https://groups.google.com/d/msgid/dealii/c3b2d20c-923f-457f-b938-61ca4e13029fn%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [deal.II] compiling deal.ii 9.4 on wsl error

2022-09-07 Thread jim wo 
I created a new cmake project on wsl with vscode ,I write the 
INCLUDE_DIRETORIES with header file of dealii in the CMakeLists and then 
cmake project ,I am not sure if its going to work . But when I make it 
comes error as follow
[image: 1662600815935.png]
 best 
Qiong
在2022年9月8日星期四 UTC+8 09:23:08 写道：

> I did install MPI on wsl 
> and I congfigure deal.ii with DEAL_II_WITH_PETSC = ON
> DEAL_II_WITH_P4EST = ON
>
>
> 在2022年9月7日星期三 UTC+8 23:03:57 写道：
>
>> Qiong,
>>
>> What CMake settings did you use to configure deal.II?
>> Does your system indeed provide an MPI installation?
>>
>> Bets,
>> Daniel
>>
>> On Wed, Sep 7, 2022 at 10:22 AM jim wo  wrote:
>>
>>> Hello,
>>> I want to  develop my own project on wsl with deal.ii 9.4.  after make I 
>>> got this message:
>>>  
>>> In file included from /home/wu/deal_II/include/deal.II/grid/tria.h:20,
>>>  from /home/wu/cmakeQuickStart/main.cpp:23:
>>> /home/wu/deal_II/include/deal.II/base/config.h:540:12: fatal error: 
>>> mpi.h: No such file or directory
>>>   540 | #  include 
>>>   |^~~
>>> compilation terminated.
>>> thanks for  your help
>>>  Qiong
>>>
>>> -- 
>>> 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
>>> --- 
>>> You received this message because you are subscribed to the Google 
>>> Groups "deal.II User Group" group.
>>> To unsubscribe from this group and stop receiving emails from it, send 
>>> an email to dealii+un...@googlegroups.com.
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>>> https://groups.google.com/d/msgid/dealii/c3b2d20c-923f-457f-b938-61ca4e13029fn%40googlegroups.com
>>>  
>>> 
>>> .
>>>
>>

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Re: [deal.II] compiling deal.ii 9.4 on wsl error

2022-09-07 Thread jim wo 
and at the same time, I write the codes and it comes "the 
deal.II/grid/tria.h not found" I dont konw why
best
Qiong


在2022年9月8日星期四 UTC+8 09:34:59 写道：

> I created a new cmake project on wsl with vscode ,I write the 
> INCLUDE_DIRETORIES with header file of dealii in the CMakeLists and then 
> cmake project ,I am not sure if its going to work . But when I make it 
> comes error as follow
> [image: 1662600815935.png]
>  best 
> Qiong
> 在2022年9月8日星期四 UTC+8 09:23:08 写道：
>
>> I did install MPI on wsl 
>> and I congfigure deal.ii with DEAL_II_WITH_PETSC = ON
>> DEAL_II_WITH_P4EST = ON
>>
>>
>> 在2022年9月7日星期三 UTC+8 23:03:57 写道：
>>
>>> Qiong,
>>>
>>> What CMake settings did you use to configure deal.II?
>>> Does your system indeed provide an MPI installation?
>>>
>>> Bets,
>>> Daniel
>>>
>>> On Wed, Sep 7, 2022 at 10:22 AM jim wo  wrote:
>>>
 Hello,
 I want to  develop my own project on wsl with deal.ii 9.4.  after make 
 I got this message:
  
 In file included from /home/wu/deal_II/include/deal.II/grid/tria.h:20,
  from /home/wu/cmakeQuickStart/main.cpp:23:
 /home/wu/deal_II/include/deal.II/base/config.h:540:12: fatal error: 
 mpi.h: No such file or directory
   540 | #  include 
   |^~~
 compilation terminated.
 thanks for  your help
  Qiong

 -- 
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 For mailing list/forum options, see 
 https://groups.google.com/d/forum/dealii?hl=en
 --- 
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 Groups "deal.II User Group" group.
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 .

>>>

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