[deal.II] Re: Interacting with Python data // external codes

2020-11-24 Thread Bruno Turcksin
Corbin,

deal.II has some limited support for python mainly for mesh manipulation. 
We have some python notebooks here 
.
 
I think what you want to do is similar to the step-62 notebook. Right now, 
the only way to interact with numpy is to print the data to a file and then 
load it (see here 

 
and here 
).
 
If you want to manipulate the mesh directly in python, you need 
boost.python and you need to configure deal.II with 
-DDEAL_II_COMPONENT_PYTHON_BINDING=ON. It's sometimes a little bit tricky 
to enable the python binding so don't hesitate to ask any question on the 
mailing list if you need help.

Best,

Bruno

On Tuesday, November 24, 2020 at 12:16:18 AM UTC-5 corbin@gmail.com 
wrote:

> Hi everyone,
>
> I am new to deal.ii but after reading through the documentation and the 
> tutorials I'm very excited about all the functionality that the software 
> offers! I'm aiming to link a finite element solver with a machine learning 
> code that I have in python. To that end:
>
>- what is the best practice for exporting deal.ii solution data in a 
>way that Python / numpy can interact with it? 
>- Is there a good way for external software to 'hook' into the deal.ii 
>pipeline? Something like:
>   - initialize a triangulation / grid
>   - run the solver
>   - make a call like: new_data = external_software(deal_ii_output, 
>   grid)
>   - reinitialize the grid based on new_data
>   - loop 
>
> Apologies if this is explained elsewhere!
>
> Corbin
>
>
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/2f6de409-374c-43bd-8afa-f86beb3ab205n%40googlegroups.com.


[deal.II] Re: Building on Cluster

2020-11-18 Thread Bruno Turcksin
Zachary,

The Intel compiler does not have its own standard library and instead, it 
uses the one from gcc. Often, you need to load a newer version of gcc and 
then load the Intel compiler to have a compiler *and* a standard library 
that support C++14. Otherwise the compiler supports C++14 but the standard 
library does not.

Best,

Bruno

On Tuesday, November 17, 2020 at 9:22:19 PM UTC-5 zachary...@gmail.com 
wrote:

> Hi everyone,
>
> I am having an issue with building deal.II on my groups cluster. I am 
> trying to build with Intel MPI compilers like mpiicc and mpiicpc. Here is 
> the output where the error is:
>
> - Include 
> /global/home/users/lstreeter/dealii/cmake/checks/check_01_cxx_features.cmake
> -- Performing Test DEAL_II_HAVE_CXX14_FEATURES
> -- Performing Test DEAL_II_HAVE_CXX14_FEATURES - Failed
> -- Performing Test DEAL_II_HAVE_CXX14_CLANGAUTODEBUG_BUG_OK
> -- Performing Test DEAL_II_HAVE_CXX14_CLANGAUTODEBUG_BUG_OK - Failed
> -- Performing Test DEAL_II_HAVE_CXX11_FEATURES
> -- Performing Test DEAL_II_HAVE_CXX11_FEATURES - Failed
> -- Performing Test DEAL_II_HAVE_CXX11_FUNCTIONAL_LLVMBUG20084_OK
> -- Performing Test DEAL_II_HAVE_CXX11_FUNCTIONAL_LLVMBUG20084_OK - Failed
> -- C++14 support is disabled.
> -- C++14 support not available. Try to set -std=c++14 explicitly
> -- Performing Test DEAL_II_HAVE_FLAG_std=c__14
> -- Performing Test DEAL_II_HAVE_FLAG_std=c__14 - Success
> -- Configuration changed. Unsetting cached variable 
> "DEAL_II_HAVE_CXX14_FEATURES" and rerunning checks.
> -- Configuration changed. Unsetting cached variable 
> "DEAL_II_HAVE_CXX14_CLANGAUTODEBUG_BUG_OK" and rerunning checks.
> -- Configuration changed. Unsetting cached variable 
> "DEAL_II_HAVE_CXX11_FEATURES" and rerunning checks.
> -- Configuration changed. Unsetting cached variable 
> "DEAL_II_HAVE_CXX11_FUNCTIONAL_LLVMBUG20084_OK" and rerunning checks.
> -- Performing Test DEAL_II_HAVE_CXX14_FEATURES
> -- Performing Test DEAL_II_HAVE_CXX14_FEATURES - Failed
> -- Performing Test DEAL_II_HAVE_CXX14_CLANGAUTODEBUG_BUG_OK
> -- Performing Test DEAL_II_HAVE_CXX14_CLANGAUTODEBUG_BUG_OK - Success
> -- Performing Test DEAL_II_HAVE_CXX11_FEATURES
> -- Performing Test DEAL_II_HAVE_CXX11_FEATURES - Success
> -- Performing Test DEAL_II_HAVE_CXX11_FUNCTIONAL_LLVMBUG20084_OK
> -- Performing Test DEAL_II_HAVE_CXX11_FUNCTIONAL_LLVMBUG20084_OK - Success
> -- C++14 support is disabled.
> CMake Error at cmake/checks/check_01_cxx_features.cmake:315 (MESSAGE):
>
>
> The current version of deal.II requires a compiler with enabled C++14
> support. Make sure to use a modern enough compiler (GCC version 5 onwards,
> Clang version 4 onwards, or Microsoft MS VS 2015 onwards) and check that
> the compiler flag "-std=" is either unset, or set to at least c++14.
>
>
>
> Call Stack (most recent call first):
> cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
> CMakeLists.txt:118 (VERBOSE_INCLUDE)
>
>
> -- Configuring incomplete, errors occurred!
> See also 
> "/global/home/users/lstreeter/dealii/build/CMakeFiles/CMakeOutput.log".
> See also 
> "/global/home/users/lstreeter/dealii/build/CMakeFiles/CMakeError.log”.
>
> —end of error
>
> It’s not passing the -std=c++14 checks though I know the Intel compilers 
> are up to date (2020). I have tried passing the standard into my cmake 
> command but that didn’t work. ( cmake -DWITH_MPI=ON 
> -DCMAKE_CXX_FLAGS=“-std=c++14” .. ) 
>
> The default gcc is too old for the -std=c++14 standard but I did try a 
> newer version and it passed the -std=c++14 checks. This leads me to think 
> either deal.II isn’t checking for the -std=c++14 correctly or when I load 
> in the intel compilers, the cluster is still using the -std found in the 
> default gcc, which is too old (though, I don’t know how this could be). Or 
> many other things but that’s at least what I think at the moment. I did 
> notice the message says GCC, clang, and Microsoft but not Intel; is that 
> anything?
>
> This absolutely could be the cluster environment setup and I have been 
> emailing them throughout the day but nothing fruitful yet. Any suggestions?
>
> Cheers,
>
> Zachary

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/49bc01b2-2ab4-47e8-a7b4-883f2909c3d1n%40googlegroups.com.


Re: [deal.II] Use Gmsh to import external grid calculation elasticity problem

2020-11-06 Thread Bruno Turcksin
Nick,

You didn't declare print_mesh_info and you need to replace

template 
void print_mesh_info(const Triangulation& triangulation, const
std::string& filename) {...}

by
template 
void ElasticProblem::print_mesh_info(const Triangulation&
triangulation, const std::string& filename) {...}

You have the same two problems with grid_1().  These are C++ problems
not deal.II, so I would advise you to read a few tutorials/books on
C++. I cannot debug your entire code for you.

Best,

Bruno


Le ven. 6 nov. 2020 à 03:04, Nick Wang  a écrit :
>
> Thanks, Bruno
> I try to end the fuction  print_mesh_info() at line 107 and re-run the step 
> again, while it still errors that i can't understand.
>
> 2>step-8.obj: error LNK2019: Unresolved external symbol "private: void 
> __cdecl Step8::ElasticProblem<2>::print_mesh_info(void)" 
> (?print_mesh_info@?$ElasticProblem@$01@Step8@@AEAAXXZ)  , The symbol is 
> referenced in the function "public: void __cdecl 
> Step8::ElasticProblem<2>::run(void)" 
> (?run@?$ElasticProblem@$01@Step8@@QEAAXXZ) 2>D:\dealii-9.2.  
> 0\dealii-9.2.0\examples\step-8d\Debug\step-8.exe: fatal error LNK1120: 1 
> unresolved external command
>
> Nick
> 在2020年11月6日星期五 UTC+8 上午6:14:01 写道:
>>
>> Hi,
>>
>> The function print_mesh_info() ends at line 269. It should end at line 107.
>>
>> Best,
>>
>> Bruno
>>
>> On Wednesday, November 4, 2020 at 9:40:57 PM UTC-5 wjs641...@gmail.com wrote:
>>>
>>> Okay, I re-run the program I wrote
>>> vs told me that ,what that mean?
>>>
>>> 2>step-8.obj: error LNK2019: Unresolved external symbol "public: void 
>>> __cdecl Step8::ElasticProblem<2>::run(void)" 
>>> (?run@?$ElasticProblem@$01@Step8@@QEAAXXZ)  , The symbol is quoted in the 
>>> function main 
>>> 2>D:\dealii-9.2.0\dealii-9.2.0\examples\step-8a\Debug\step-8.exe: fatal 
>>> error LNK1120: 1 unresolved external command
>>> 在2020年11月4日星期三 UTC+8 上午11:09:17 写道:

 On 11/3/20 7:33 PM, Nick Wang wrote:
 >
 > After I studied and understood the tutorials of step-8 and step-49.  I 
 > tried
 > to use  step-49 to import external grids to to calculate the force 
 > condition
 > and stress analysis,
 > So I modified the statement of step8 grid generation,
 > while failed...
 > Did I make a mistake or  are there other ways to finish the force 
 > analysis
 > from external grids?

 Help us understand what the error message is that you get. You already 
 have it
 on your screen, but we would need to download your program, put it 
 somewhere,
 compile it, maybe run it. It would take someone a couple of minutes to do 
 that
 -- time we wouldn't have for answering someone else's problems.

 Best
 WB

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

> --
> 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 a topic in the Google 
> Groups "deal.II User Group" group.
> To unsubscribe from this topic, visit 
> https://groups.google.com/d/topic/dealii/iVyeXuUkCXk/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to 
> dealii+unsubscr...@googlegroups.com.
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/dealii/cb8bba7f-190f-45a5-8522-066638740ab6n%40googlegroups.com.

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eMmxv5wuC4JmOLj-fBmLXv64rK0aO-%2BYWecxru1sc4e5w%40mail.gmail.com.


[deal.II] Re: Post-processing velocities with Trilinos vectors during simulation

2020-11-05 Thread Bruno Turcksin
Hi,

On Wednesday, November 4, 2020 at 2:34:05 PM UTC-5 acdaig...@gmail.com 
wrote:

> Hi everyone!
>
> I'm working on post-processing velocities with Trilinos solution vectors 
> during the simulation on Lethe. 
> Calculating average velocities and pressures (, ,  and ) works 
> well using Trilinos vectors with no ghost cells and .equ(...) function.
> The calculation of average Reynolds stress (,  and  and 
> average shear stress (), where u' = u - , is quite not easy. 
> It seems that I can't do what I want in parallel without working with loop.
> The problem is that loops seem to take way too much time on Trilinos 
> vectors and the local_range() function doesn't work with BlockVector. (Am I 
> wrong?)
>
True local_range() does not work on a BlockVector but you can get  the 
local_range of each block in the block vector. Just do 
my_block_vector.block(i).local_range()

I have tried some ways to do it. 
>   1. Trying working with Deal.ii vectors : did not work in parallel
>
What does that mean? Did you use the dealii::Vector or the 
dealii::LinearAlgebra::distributed::Vector 
(https://dealii.org/developer/doxygen/deal.II/classLinearAlgebra_1_1distributed_1_1Vector.html)
 
Only the second one supports MPI

  2. Doing summations and/or multiplications of the vectors 
> local_evaluation_point to get u'u', v'v' and w'w' and replacing the fourth 
> element of the evaluation point with a loop for u'v' : too much time.
>   3. Doing loops on the Trilinos vectors : too much time
>
What does that mean it takes too much time? Did you profile the code? 
What's the bottleneck? 

Does anyone can give me an advice to find a way to get one or two vectors 
> with my precious time-averaged Reynolds stress and time-averaged shear 
> stress?
> I did not mention the exact way I'm trying to calculate the average of all 
> of that, but I'm posting my code where I'm trying to do a loop on the 
> solution vector.
> The variables average_velocities, total_time and inv_range_time are 
> calculated in an other function is my class AverageVelocities.
>
> template 
> VectorType
> AverageVelocities::calculate_reynolds_stress(
>   const VectorType &local_evaluation_point,
>   const std::shared_ptr _control,
>   const DofsType &  locally_owned_dofs,
>   const MPI_Comm &  mpi_communicator)
> {
>   if (simulation_control->get_step_number() == 0)
>   {
> // Reinitializing vectors with zeros at t = 0
> sum_reynolds_stress_dt.reinit(locally_owned_dofs,
>   mpi_communicator);
> reynolds_stress.reinit(locally_owned_dofs,
>mpi_communicator);
>   }
>   else if (abs(total_time) < 1e-6 || total_time > 1e-6)
>   {
> VectorType reynolds_stress_dt(locally_owned_dofs,
>   mpi_communicator);
>
> // ***Won't work with BlockVectors
> if constexpr (std::is_same_v TrilinosWrappers::MPI::Vector>)
> {
>   for (unsigned int i = local_evaluation_point.local_range().first;
>i < local_evaluation_point.local_range().second; i++)
>   {
> if ((i + 4) % 4 == 0)
> {
>   // Calculating (u'u')*dt, (v'v')*dt (w'w')*dt and (u'v')*dt
>   reynolds_stress_dt[i] =
> (local_evaluation_point[i] - average_velocities[i]) *
> (local_evaluation_point[i] - average_velocities[i]) * dt;
>   reynolds_stress_dt[i + 1] =
> (local_evaluation_point[i + 1] - average_velocities[i + 1]) *
> (local_evaluation_point[i + 1] - average_velocities[i + 1]) * 
> dt;
>   reynolds_stress_dt[i + 2] =
> (local_evaluation_point[i + 2] - average_velocities[i + 2]) *
> (local_evaluation_point[i + 2] - average_velocities[i + 2]) * 
> dt;
>   reynolds_stress_dt[i + 3] =
> (local_evaluation_point[i] - average_velocities[i]) *
> (local_evaluation_point[i + 1] - average_velocities[i + 1]) * 
> dt;
>
>   // Summation of all reynolds stress during simulation
>   sum_reynolds_stress_dt += reynolds_stress_dt;
>
>   // Calculating time-averaged reynolds stress if output needed
>   if (simulation_control->is_output_iteration())
> reynolds_stress.equ(inv_range_time, sum_reynolds_stress_dt);
> }
>   }
> }
>   }
>   return reynolds_stress;
> }
>
Your for loop is a little bit strange. I would think that the compiler can 
optimize this code but it would be easier for the compiler to optimize the 
following code
 
const unsigned int begin_index = local_evaluation_point.local_range().first; 
// You do this because otherwise the compiler will call local_range() at 
each evaluation of the for loop condition
const unsigned int end_index = local_evaluation_point.local_range().second;
  for (unsigned int i = begin_index;  i < end_index; i += 4)
  {
   // Remove this if ((i + 4) % 4 == 0)
  
  

[deal.II] Re: Some changes in arpack.h (Functionality to compute only eigenvalues)

2020-11-05 Thread Bruno Turcksin
Animesh,

On Thursday, November 5, 2020 at 1:11:33 PM UTC-5 
animesh...@alumni.iitgn.ac.in wrote:

> However, I have no way of passing it as a parameter to the solver 
> 
>  
> function. I was planning to edit the header file *arpack.h* 
> 
>  
> accordingly which is inside the */usr/local/include/deal.II/lac* to have 
> that functionality. I was actually thinking of passing the flag "rvec" as 
> an argument to the function solve 
> .
>  
> I was wondering if I change the permission of the file to write mode, edit 
> it and save it, would I be able to run my code inside the examples folder. 
> Or do I need to take care of something else while and after editing that 
> headerfile?
>
You should change the source code and reinstall deal.II. I would do what 
you propose only if you cannot compile deal.II on that machine. It might 
work in this particular case but I really advise you against it.

Best,

Bruno
 

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/b88a5389-c5a0-458b-97aa-24715d95d9dan%40googlegroups.com.


Re: [deal.II] Use Gmsh to import external grid calculation elasticity problem

2020-11-05 Thread Bruno Turcksin
Hi,

The function print_mesh_info() ends at line 269. It should end at line 107.

Best,

Bruno

On Wednesday, November 4, 2020 at 9:40:57 PM UTC-5 wjs641...@gmail.com 
wrote:

> Okay, I re-run the program I wrote
> vs told me that ,what that mean?
>
> *2>step-8.obj: error LNK2019: Unresolved external symbol "public: void 
> __cdecl Step8::ElasticProblem<2>::run(void)" 
> (?run@?$ElasticProblem@$01@Step8@@QEAAXXZ)  , The symbol is quoted in the 
> function main 
> 2>D:\dealii-9.2.0\dealii-9.2.0\examples\step-8a\Debug\step-8.exe: fatal 
> error LNK1120: 1 unresolved external command*
> 在2020年11月4日星期三 UTC+8 上午11:09:17 写道:
>
>> On 11/3/20 7:33 PM, Nick Wang wrote: 
>> > 
>> > After I studied and understood the tutorials of step-8 and step-49.  I 
>> tried 
>> > to use  step-49 to import external grids to to calculate the force 
>> condition 
>> > and stress analysis, 
>> > So I modified the statement of step8 grid generation, 
>> > while failed... 
>> > Did I make a mistake or  are there other ways to finish the force 
>> analysis 
>> > from external grids? 
>>
>> Help us understand what the error message is that you get. You already 
>> have it 
>> on your screen, but we would need to download your program, put it 
>> somewhere, 
>> compile it, maybe run it. It would take someone a couple of minutes to do 
>> that 
>> -- time we wouldn't have for answering someone else's problems. 
>>
>> Best 
>> WB 
>>
>> -- 
>>  
>> Wolfgang Bangerth email: bang...@colostate.edu 
>> www: http://www.math.colostate.edu/~bangerth/ 
>>
>>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/7a2ac5d5-2b40-4b82-a0fe-f7dab8dece32n%40googlegroups.com.


[deal.II] Re: Adaptive Time Increment Algorithm

2020-10-15 Thread Bruno Turcksin
James,

On Tuesday, October 13, 2020 at 8:39:42 PM UTC-4 James Gorman wrote:

>
> I am, however, at a loss for how to efficiently make it so that Step-44 
> (or any other script) will automatically decrease a time-step. The only 
> idea I had at the moment was to use a ``for'' loop and run a certain number 
> of iterations, and each time the solution did not converge would be to 
> multiply the time-step by some fraction. However, I am not sure this 
> solution would work well with my previous solution 
>
That's the right idea. You want to be careful that you don't end up 
reducing your time step too much though. Otherwise you could end up with a 
time step that is effectively zero.


> Has anyone done this before, or have thoughts on how one might modify 
> Step-44 to automatically increase and decrease based on the number of 
> iterations required for Newton-Raphson convergence or divergence? Thank you 
> for your help.
>
What you are trying to do  is similar to what embedded methods do but 
instead of using the error you are using the number of Newton iterations. 
Here is how embedded methods work in deal.II 
https://github.com/dealii/dealii/blob/master/include/deal.II/base/time_stepping.templates.h#L770-L857

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/c7cdb4aa-62d9-4741-b8f1-851b8680289an%40googlegroups.com.


Re: [deal.II] Re: APPLY BOUNDARY CONDTION ON INTERNAL FACE

2020-10-13 Thread Bruno Turcksin
Xiang,

Here is an example on how to do it:
https://github.com/geodynamics/aspect/blob/master/cookbooks/prescribed_velocity/prescribed_velocity.cc#L297-L303
As you can see, you need to know which dof you need to constrain

Best,

Bruno

Le mar. 13 oct. 2020 à 11:02, 孙翔  a écrit :
>
>
> Hi, Bruno,
>
> Thank you very much. Does the AffineConstraint force the value at the 
> specified DOF? I need to how the node numbers map to the DOF, right?
>
> Best,
>
> Xiang
> On Monday, 12 October 2020 at 06:21:03 UTC-7 bruno.t...@gmail.com wrote:
>>
>> Xiang,
>>
>> You cannot apply a boundary condition on an internal face. You need to use 
>> the AffineConstraint class to impose the constraints yourself. This is what 
>> we use internally to apply Dirichlet boundary condition.
>>
>> Best,
>>
>> Bruno
>>
>>
>>
>> On Monday, October 12, 2020 at 2:10:15 AM UTC-4 shya...@gmail.com wrote:
>>>
>>> Hi, I want to model injecting heat fluid into a tiny fracture which is 
>>> inside a block. The fracture is modeled as an interface which is an 
>>> internal face shared by two hex elements. Is it possible for us to apply 
>>> the Dirichlet boundary condition on the interface? If not, how should I do 
>>> it?
>>>
>>> Best,
>>>
>>> Xiang
>
> --
> 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 a topic in the Google 
> Groups "deal.II User Group" group.
> To unsubscribe from this topic, visit 
> https://groups.google.com/d/topic/dealii/hv0QjbGuxls/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to 
> dealii+unsubscr...@googlegroups.com.
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/dealii/dc0e5cab-64c7-4af7-b957-2a51f83ee5f4n%40googlegroups.com.

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eP-obzx1%2B0rBq5c9GkP-taGXvPo8dQCRVOM7As%2BsroANw%40mail.gmail.com.


[deal.II] Re: APPLY BOUNDARY CONDTION ON INTERNAL FACE

2020-10-12 Thread Bruno Turcksin
Xiang,

You cannot apply a boundary condition on an internal face. You need to use 
the AffineConstraint 
 
class to impose the constraints yourself. This is what we use internally to 
apply Dirichlet boundary condition.

Best,

Bruno



On Monday, October 12, 2020 at 2:10:15 AM UTC-4 shya...@gmail.com wrote:

> Hi, I want to model injecting heat fluid into a tiny fracture which is 
> inside a block. The fracture is modeled as an interface which is an 
> internal face shared by two hex elements. Is it possible for us to apply 
> the Dirichlet boundary condition on the interface? If not, how should I do 
> it?  
>
> Best,
>
> Xiang
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/3840f39f-e3ae-4d76-886b-c3658bcade13n%40googlegroups.com.


Re: [deal.II] Eigenvalues and Eigenvectors of BlockSparse Matrix

2020-09-28 Thread Bruno Turcksin
Animesh,

Yes, the name are reversed. Basically what happens is that ARPACK uses a 
method called shift inverse which uses the inverse of the operator you 
care. In practice, this means that ARPACK is not using your matrix A but 
only A^{-1} because the largest eigenvalue of A^{-1} is related to the 
smallest eigenvalue of A. When you ask for the largest the eigenvalue you 
get the eigenvalue related to the largest eigenvalue of A^{-1} which is the 
smallest eigenvalue of A.

Best,

Bruno


On Sunday, September 27, 2020 at 3:47:53 PM UTC-4 
animesh...@alumni.iitgn.ac.in wrote:

> Hi Jean,
>
> I need a few more clarifications. Sorry to bother you again.
>
> In my code, when I am using the argument - "smallest_magnitude" for the 
> type of eigenvalue, I am getting a large eigenvalue than when I am using 
> the argument "largest_eigenvalue". I looked at some of the previous 
> discussions on this issue, and found this threads.
>
> https://github.com/dealii/dealii/issues/7385
>
> https://groups.google.com/forum/#!topic/dealii/TabQD_AhXXg
>
> I can understand it has something to do with the "inverse" argument in the 
> solve() function. I was wondering what exactly is the argument "inverse" is 
> when we give it to the solve() function. The document 
>  
> says the following which is not clear. 
>
> inverse - This is the possibly shifted inverse that is actually used 
> instead of A. Only its function vmult() is used.
>
> Should I consider that the largest_magnitude is indeed the 
> smallest_magnitude eigenvalue in my case? More generally, how should I 
> interpret the results of the ARPACK solver..
>
> I am adding the function that I have written below for your reference - 
>
> template 
>   void 
> Solid::solve_eigenvalue_problem(BlockSparseMatrix 
> _matrix)
>   {
>
>
> std::vector>   eigenvalues;
> std::vector >eigenvectors;
> eigenvalues.resize(1);
> eigenvectors.resize(1);
> for (unsigned int i = 0; i < eigenvectors.size(); ++i)
> eigenvectors[i].reinit(tangent_matrix.block(u_dof,u_dof).m());
>
> const unsigned int num_arnoldi_vectors = 20;
> FullMatrix identity 
> (IdentityMatrix(tangent_matrix.block(u_dof,u_dof).m()));
>
> SparseDirectUMFPACK inverse;
> inverse.initialize (tangent_matrix.block(u_dof,u_dof));
> SolverControl solver_control(1000, 1e-9);
> const bool symmetric=true;
>
> ArpackSolver eigensolver(solver_control, 
> ArpackSolver::AdditionalData(num_arnoldi_vectors, 
> ArpackSolver::WhichEigenvalues::smallest_magnitude, symmetric));
>
> std::cout<<"Calculating the smallest eigenvalue and corresponding 
> eigenvector at  "< eigensolver.solve(tangent_matrix.block(u_dof,u_dof), identity, 
> inverse, eigenvalues,   eigenvectors,eigenvalues.size());
>
>  for (unsigned int i = 0; i < eigenvalues.size(); ++i)
>  std::cout<<"Eigenvalue "< eigenvalues[i]<
>   }
>
> Thanks a lot!
>
> AR
> On Sunday, September 27, 2020 at 8:36:20 PM UTC+5:30 Animesh Rastogi IIT 
> Gandhinagar wrote:
>
>> Hi Jean,
>>
>> Thanks a lot for your detailed answer. Using this idea, I was able to 
>> solve the standard eigenvalue problem.
>>
>> Thanks again!
>>
>> Animesh
>>
>> On Saturday, September 26, 2020 at 1:49:10 AM UTC+5:30 Jean-Paul Pelteret 
>> wrote:
>>
>>> Hi Animesh,
>>>
>>> I’m glad to hear that you’ve gotten Arpack working, and that you’re 
>>> getting somewhere with your implementation. When you encounter a crash like 
>>> this, its best to run the program in debug mode (better yet, do all of your 
>>> development in debug mode). In debug mode, there are a lot of additional 
>>> checks that can help you find the source of issues. You can read more about 
>>> this here 
>>> 
>>> .
>>>
>>> I see that you invoke the identity matrix inline with the solve() step 
>>> like this: IdentityMatrix() . According to the documentation 
>>> ,
>>>  
>>> this is incorrect because the matrix is zero sized (i.e. holds no entries). 
>>> You probably want to use this constructor 
>>> ,
>>>  
>>> and because the matrix should have the same size as the tangent matrix you 
>>> would call it like this: IdentityMatrix(tangent_matrix
>>> .block(u_dof,u_dof).m()).
>>>
>>> I am a bit confused of where actually to solve the standard eigenvalue 
>>> problem in the code for my purpose.
>>>
>>>
>>> Well, from your original post it sounds to me like you want to 
>>> investigate some properties of the equilibrium state of your problem. That 
>>> makes sense. So really what you probably want to do is let the nonlinear 
>>> 

[deal.II] Re: install problems with clang@12.0.0 and Xcode12.0 from spack

2020-09-25 Thread Bruno Turcksin
Alex,

Try using less processors. Something like:
spack install -j2 dealii~scalapack ^openblas@develop ^arpack-ng@develop 
^trilinos~mumps

Best,

Bruno

On Friday, September 25, 2020 at 11:21:52 AM UTC-4 alexande...@icloud.com 
wrote:

> Update: 
> I managed to came as far as spack at least tries to install deal.II using 
> the following command:
>
> spack install dealii~scalapack ^openblas@develop ^arpack-ng@develop 
> ^trilinos~mumps
>
> I have no idea whether this makes sense or not, but it was the only way to 
> get that far. Installing deal.II I received the following error message 
> again: 
> Error: ProcessError: Command exited with status 2: 'make' '-j12'
>
> I would like to show you the spack build log, but I can't find that file. 
> Actually, spack does not really abort...just 'strange' things happen that I 
> do not understand. I'll attach the terminal output. In the end I have to 
> abort the process manually since (even after hours) nothing more than what 
> you can see in the terminal output happens.
>
> Again I appreciate any help and ideas!
> Alex
> Alexander Greiner schrieb am Mittwoch, 23. September 2020 um 17:29:01 
> UTC+2:
>
>> Hi,
>>
>> I'm new here (and also relatively new to deal.II). I'm trying to install 
>> dea...@9.2.0 from spack, running into errors. These errors are not directly 
>> linked to deal.II and therefore I'm not sure if this is the right place to 
>> post my problem. Unfortunately, cl...@12.0.0 and Xcode12.0 seem to be quite 
>> new and there is not a lot to find in the www... Furthermore, I'm using 
>> g...@10.2.0.
>>
>> spack install dealii
>>
>> 1) Thereby, installing OpenBlas leads to the error:
>> Error: ProcessError: Command exited with status 2: 'make' '-j12'
>> Then, I tried to install the most recent develop version of OpenBlas -- 
>> with success. And continue with:
>>
>> spack install dealii ^openblas@develop
>>
>> 2) Thereby, installing arpack-ng leads again to:
>> Error: ProcessError: Command exited with status 2: 'make' '-j12'
>> Then, I tried to install the most recent develop version of arpack-ng -- 
>> with success. And continue with:
>>
>> spack install dealii ^openblas@develop ^arpack-ng@develop
>>
>> 3) Thereby, installing netlib-scalapack leads again to:
>> Error: ProcessError: Command exited with status 2: 'make' '-j12'
>> Unfortunately, there is no newer version of this package.
>>
>> Now my question, has anyone else tried to install dealii 9.2.0 and macOS 
>> Catalina with cl...@12.0.0 and Xcode12.0? Or has anyone suggestions how to 
>> overcome these issues? I'm looking forward to any help and ideas! Let me 
>> know if you need more detailed information.
>>
>> Kind regards 
>> Alex
>>
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/2e3d7fa8-44d1-48bb-821a-f8b8e666ae1en%40googlegroups.com.


Re: [deal.II] Re: .msh file triangulation failed

2020-09-22 Thread Bruno Turcksin
Honestly I don't know. I wonder if the terms -1e-07 are the problem. I
told you to remove  SetFactory("OpenCASCADE") because it was the only
difference with my .geo files.

Bruno

Le mar. 22 sept. 2020 à 11:20, yuesu jin  a écrit :
>
> Dear Bruno,
>   The problem was solved after I removed the 'SetFactory("OpenCASCADE")'.  
> Here are two mesh files with and without 'SetFactory("OpenCASCADE")'. Could 
> you tell me why this command made the system unable to work? Thank you very 
> much for your help!
> Best regards,
> Yuesu
>
>
>
> On Tue, Sep 22, 2020 at 10:01 AM Bruno Turcksin  
> wrote:
>>
>> Hmmm. Can you try without the SetFactory("OpenCASCADE"); and can you
>> send me your .msh
>>
>> Bruno
>>
>> Le mar. 22 sept. 2020 à 10:45, yuesu jin  a écrit :
>> >
>> > Dear Bruno,
>> >I did some modification according to your suggestion :
>> > 
>> > Physical Volume("4") = {1};
>> > //+
>> > Physical Surface("0") = {4, 3, 2, 5, 1, 6};
>> > 
>> > I add all external surfaces in one physical group and the volume in 
>> > another group. But the error message remains the same.  I tried a few 
>> > types of grouping combinations, the error message did not change.
>> > Best regards,
>> > Yuesu
>> >
>> > On Tue, Sep 22, 2020 at 9:30 AM Bruno Turcksin  
>> > wrote:
>> >>
>> >> You don't want to set the physical groups for the curves and the
>> >> points. This means nothing in deal.II. A vertex does not have a
>> >> boundary ID. You need all the external surfaces and the volume to have
>> >> a physical group. That's it.
>> >>
>> >> Bruno
>> >>
>> >> Le mar. 22 sept. 2020 à 10:24, yuesu jin  a écrit :
>> >> >
>> >> > Dear Bruno,
>> >> >   Thank you for your help! I added physical groups for volume, 
>> >> > surfaces, curves, and points. But the problem remains the same.  The 
>> >> > modified geo file is attached below.
>> >> > Best regards,
>> >> > Yuesu
>> >> >
>> >> > On Tue, Sep 22, 2020 at 7:55 AM Bruno Turcksin 
>> >> >  wrote:
>> >> >>
>> >> >>
>> >> >> Yuesu,
>> >> >>
>> >> >> I had the same problem recently. Our gmsh reader assumes that the user 
>> >> >> has set boundary id and material id to the mesh. It looks like you 
>> >> >> don't have those and so the file is read incorrectly.
>> >> >>
>> >> >> Best,
>> >> >>
>> >> >> Bruno
>> >> >> On Tuesday, September 22, 2020 at 2:04:17 AM UTC-4 jinyu...@gmail.com 
>> >> >> wrote:
>> >> >>>
>> >> >>> Dear all,
>> >> >>>   I have one problem when I try to input the .msh file with grid_in 
>> >> >>> function. The error message is :
>> >> >>>
>> >> >>> *
>> >> >>>
>> >> >>> Exception on processing:
>> >> >>>
>> >> >>> 
>> >> >>> An error occurred in line <3139> of file 
>> >> >>>  in function
>> >> >>> static void 
>> >> >>> dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
>> >> >>>  std::vector >&, const 
>> >> >>> std::vector, std::allocator > 
>> >> >>> >&, const dealii::SubCellData&, dealii::Triangulation<3, spacedim>&) 
>> >> >>> [with int spacedim = 3]
>> >> >>> The violated condition was:
>> >> >>> false
>> >> >>> Additional information:
>> >> >>> While trying to assign a boundary indicator to a line: the line 
>> >> >>> with end vertices -1 and 0 does not exist.
>> >> >>> 
>> >> >>>
>> >> >>> I attached the gmsh .geo file in this email. There is no vertex -1 
>> >> >>

Re: [deal.II] Re: .msh file triangulation failed

2020-09-22 Thread Bruno Turcksin
Hmmm. Can you try without the SetFactory("OpenCASCADE"); and can you
send me your .msh

Bruno

Le mar. 22 sept. 2020 à 10:45, yuesu jin  a écrit :
>
> Dear Bruno,
>I did some modification according to your suggestion :
> 
> Physical Volume("4") = {1};
> //+
> Physical Surface("0") = {4, 3, 2, 5, 1, 6};
> 
> I add all external surfaces in one physical group and the volume in another 
> group. But the error message remains the same.  I tried a few types of 
> grouping combinations, the error message did not change.
> Best regards,
> Yuesu
>
> On Tue, Sep 22, 2020 at 9:30 AM Bruno Turcksin  
> wrote:
>>
>> You don't want to set the physical groups for the curves and the
>> points. This means nothing in deal.II. A vertex does not have a
>> boundary ID. You need all the external surfaces and the volume to have
>> a physical group. That's it.
>>
>> Bruno
>>
>> Le mar. 22 sept. 2020 à 10:24, yuesu jin  a écrit :
>> >
>> > Dear Bruno,
>> >   Thank you for your help! I added physical groups for volume, surfaces, 
>> > curves, and points. But the problem remains the same.  The modified geo 
>> > file is attached below.
>> > Best regards,
>> > Yuesu
>> >
>> > On Tue, Sep 22, 2020 at 7:55 AM Bruno Turcksin  
>> > wrote:
>> >>
>> >>
>> >> Yuesu,
>> >>
>> >> I had the same problem recently. Our gmsh reader assumes that the user 
>> >> has set boundary id and material id to the mesh. It looks like you don't 
>> >> have those and so the file is read incorrectly.
>> >>
>> >> Best,
>> >>
>> >> Bruno
>> >> On Tuesday, September 22, 2020 at 2:04:17 AM UTC-4 jinyu...@gmail.com 
>> >> wrote:
>> >>>
>> >>> Dear all,
>> >>>   I have one problem when I try to input the .msh file with grid_in 
>> >>> function. The error message is :
>> >>>
>> >>> *
>> >>>
>> >>> Exception on processing:
>> >>>
>> >>> 
>> >>> An error occurred in line <3139> of file 
>> >>>  in function
>> >>> static void 
>> >>> dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
>> >>>  std::vector >&, const 
>> >>> std::vector, std::allocator > 
>> >>> >&, const dealii::SubCellData&, dealii::Triangulation<3, spacedim>&) 
>> >>> [with int spacedim = 3]
>> >>> The violated condition was:
>> >>> false
>> >>> Additional information:
>> >>> While trying to assign a boundary indicator to a line: the line with 
>> >>> end vertices -1 and 0 does not exist.
>> >>> 
>> >>>
>> >>> I attached the gmsh .geo file in this email. There is no vertex -1 
>> >>> actually. Could you tell me what's wrong with my mesh generation?
>> >>>
>> >>> Thank you very much!
>> >>> Best regards,
>> >>>
>> >>> --
>> >>> Yuesu Jin,
>> >>> Ph.D student,
>> >>> University of Houston,
>> >>> College of Natural Sciences and Mathematics,
>> >>> Department of Earth and Atmospheric Sciences,
>> >>> Houston, Texas 77204-5008
>> >>> 346-404-2062
>> >>>
>> >> --
>> >> 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+unsubscr...@googlegroups.com.
>> >> To view this discussion on the web visit 
>> >> https://groups.google.com/d/msgid/dealii/5bf5008c-865d-47df-a49f-e4408028ef1dn%40googlegroups.com.
>> >
>> >
>> >
>> > --
>> > Yuesu Jin,
>> > Ph.D student,
>>

Re: [deal.II] Re: .msh file triangulation failed

2020-09-22 Thread Bruno Turcksin
You don't want to set the physical groups for the curves and the
points. This means nothing in deal.II. A vertex does not have a
boundary ID. You need all the external surfaces and the volume to have
a physical group. That's it.

Bruno

Le mar. 22 sept. 2020 à 10:24, yuesu jin  a écrit :
>
> Dear Bruno,
>   Thank you for your help! I added physical groups for volume, surfaces, 
> curves, and points. But the problem remains the same.  The modified geo file 
> is attached below.
> Best regards,
> Yuesu
>
> On Tue, Sep 22, 2020 at 7:55 AM Bruno Turcksin  
> wrote:
>>
>>
>> Yuesu,
>>
>> I had the same problem recently. Our gmsh reader assumes that the user has 
>> set boundary id and material id to the mesh. It looks like you don't have 
>> those and so the file is read incorrectly.
>>
>> Best,
>>
>> Bruno
>> On Tuesday, September 22, 2020 at 2:04:17 AM UTC-4 jinyu...@gmail.com wrote:
>>>
>>> Dear all,
>>>   I have one problem when I try to input the .msh file with grid_in 
>>> function. The error message is :
>>>
>>> *
>>>
>>> Exception on processing:
>>>
>>> 
>>> An error occurred in line <3139> of file 
>>>  in function
>>> static void 
>>> dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
>>>  std::vector >&, const std::vector, 
>>> std::allocator > >&, const dealii::SubCellData&, 
>>> dealii::Triangulation<3, spacedim>&) [with int spacedim = 3]
>>> The violated condition was:
>>> false
>>> Additional information:
>>> While trying to assign a boundary indicator to a line: the line with 
>>> end vertices -1 and 0 does not exist.
>>> 
>>>
>>> I attached the gmsh .geo file in this email. There is no vertex -1 
>>> actually. Could you tell me what's wrong with my mesh generation?
>>>
>>> Thank you very much!
>>> Best regards,
>>>
>>> --
>>> Yuesu Jin,
>>> Ph.D student,
>>> University of Houston,
>>> College of Natural Sciences and Mathematics,
>>> Department of Earth and Atmospheric Sciences,
>>> Houston, Texas 77204-5008
>>> 346-404-2062
>>>
>> --
>> 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+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/dealii/5bf5008c-865d-47df-a49f-e4408028ef1dn%40googlegroups.com.
>
>
>
> --
> Yuesu Jin,
> Ph.D student,
> University of Houston,
> College of Natural Sciences and Mathematics,
> Department of Earth and Atmospheric Sciences,
> Houston, Texas 77204-5008
> 346-404-2062
>
> --
> 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 a topic in the Google 
> Groups "deal.II User Group" group.
> To unsubscribe from this topic, visit 
> https://groups.google.com/d/topic/dealii/HmoTVW7YfAw/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to 
> dealii+unsubscr...@googlegroups.com.
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/dealii/CA%2B25a%3DLt6Dknw5DzkL0SCjozogiVoEVZQp%3DeurYpBWiUrCrLiQ%40mail.gmail.com.

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eOsJoe4r_2t_eKVKMArv-qS5b93cScOxcivC0SP%3DVXz%3DQ%40mail.gmail.com.


[deal.II] Re: .msh file triangulation failed

2020-09-22 Thread Bruno Turcksin

Yuesu,

I had the same problem recently. Our gmsh reader assumes that the user has 
set boundary id and material id to the mesh. It looks like you don't have 
those and so the file is read incorrectly.

Best,

Bruno
On Tuesday, September 22, 2020 at 2:04:17 AM UTC-4 jinyu...@gmail.com wrote:

> Dear all,
>   I have one problem when I try to input the .msh file with grid_in 
> function. The error message is :
>
> *
>
> Exception on processing:
>
> 
> An error occurred in line <3139> of file 
>  in function
> static void 
> dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
>  
> std::vector >&, const std::vector, 
> std::allocator > >&, const dealii::SubCellData&, 
> dealii::Triangulation<3, spacedim>&) [with int spacedim = 3]
> The violated condition was: 
> false
> Additional information: 
>  *   While trying to assign a boundary indicator to a line: the line with 
> end vertices -1 and 0 does not exist.*
> 
>
> I attached the gmsh .geo file in this email. There is no vertex -1 
> actually. Could you tell me what's wrong with my mesh generation?
>
> Thank you very much!
> Best regards,
>
> -- 
> Yuesu Jin,
> Ph.D student,
> University of Houston,
> College of Natural Sciences and Mathematics,
> Department of Earth and Atmospheric Sciences,
> Houston, Texas 77204-5008

> 346-404-2062 <(346)%20404-2062>
>
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/5bf5008c-865d-47df-a49f-e4408028ef1dn%40googlegroups.com.


[deal.II] Re: Thermal Modelling of Additive Manufacturing Process

2020-09-02 Thread Bruno Turcksin
Pushkar,

What do you want to know? There is no question, so it's hard to help you.

Best,

Bruno

On Wednesday, September 2, 2020 at 8:52:59 AM UTC-4 pushkar...@gmail.com 
wrote:

> Greetings Deal.II Community,
>
> I wish to simulate the thermal profile in additive manufacturing process 
> using inactivation element strategy .Moreover, as a prelude to such a 
> simulation I wish to simulate the thermal model for welding first . So any 
> help in this regard will be beneficial 
>
> Thanks in Advance
> Pushkar
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/eb1a21ec-71fd-4e27-8ddc-10f4b9e47486n%40googlegroups.com.


[deal.II] Re: Anistropic refinement DG - saddle point problem

2020-08-11 Thread Bruno Turcksin
Juan,

Basically the problem is that MeshWorker was not design to handle 
anisotropic refinement. That assert checks that if the faces of two cells 
"match" then they have been refined the same number of times. This is 
obviously not true in case of anisotropic refinement. I think that this is 
just a sanity check and you should be able to remove that assert without 
any bad consequences. So commenting the assert in 
/include/deal.II/meshworker/loop.h line 357 and recompiling deal.II should 
be safe and fix your problem.

Best,

Bruno

On Tuesday, August 11, 2020 at 6:57:24 AM UTC-4, Juan Felipe Giraldo wrote:
>
> Dear community, 
>
> I am working on an adaptive stabilized finite element method which consist 
> in a saddle point problem to obtain: 
>
> - A continuous solution 
> - A discontinuous error estimator (which I use as an adaptive refinement). 
>
> I successfully implemented the method using the sample of the step 30 (for 
> the DG formulation) combining with step 20 for the saddle point, and the 
> step 39 for the error marking. 
>
> Now, I would like to implement an anisotropic refinement, so I am taking 
> the same step 30 as a reference but now with the anisotropic flag actived.
> As I mentioned, If I use only isotropic refinement, it works very well; 
> but,  if I activate the anisotropic flag for the adaptive refinement, it 
> can only refine the first iteration, and then I get the following error:
>
>
> An error occurred in line <357> of file 
>  
> in function
> void dealii::MeshWorker::cell_action(ITERATOR, 
> dealii::MeshWorker::DoFInfoBox&, INFOBOX&, const 
> std::function&, const 
> std::function&, const 
> std::function typename INFOBOX::CellInfo&)>&, const dealii::MeshWorker::LoopControl&) 
> [with INFOBOX = dealii::MeshWorker::IntegrationInfoBox<2, 2>; DOFINFO = 
> dealii::MeshWorker::DoFInfo<2, 2, double>; int dim = 2; int spacedim = 2; 
> ITERATOR = 
> dealii::TriaActiveIterator 2>, false> >; typename INFOBOX::CellInfo = 
> dealii::MeshWorker::IntegrationInfo<2, 2>]
> The violated condition was: 
> cell->level() == neighbor->level()
> Additional information: 
> This exception -- which is used in many places in the library -- 
> usually indicates that some condition which the author of the code thought 
> must be satisfied at a certain point in an algorithm, is not fulfilled. An 
> example would be that the first part of an algorithm sorts elements of an 
> array in ascending order, and a second part of the algorithm later 
> encounters an element that is not larger than the previous one.
> There is usually not very much you can do if you encounter such an 
> exception since it indicates an error in deal.II, not in your own program. 
> Try to come up with the smallest possible program that still demonstrates 
> the error and contact the deal.II mailing lists with it to obtain help.
>
>
> I am wondering to know if anyone have any idea of what It is happening and 
> how can I solve that problem. I will be very grateful for your help.
>
> Thank you so much,
>
>
> Juan Giraldo
>
>
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/5e11f47f-30d3-4a0b-9404-4aef9154d375o%40googlegroups.com.


[deal.II] Re: A small question about subdomain renumbering

2020-08-06 Thread Bruno Turcksin
Yuesu,

On Thursday, August 6, 2020 at 12:08:58 AM UTC-4, yuesu jin wrote:
>
> Dear all,
>   I have a question about DoFRenumbering::subdomain_wise(dof_handler). In 
> step-17 tutorial for example, this function doesn't use the argument of 
> n_mpi_processes, how does it know how many subdomains it should divide the 
> dofs into? 
>

The DoFHandler has access to the Triangulation which knows this information 
because we call GridTools::partition_triangulation() before we call 
DoFRenumbering::subdomain_wise().

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/a35c718d-3d54-49a9-98de-643ef6e7f4a9o%40googlegroups.com.


[deal.II] Re: PETSc is not compatible with current MPI

2020-07-23 Thread Bruno Turcksin
Yuesu Jin,

You don't need to compile your own PETSc but you need to use the same MPI 
library than the one that PETSc is using. There are very hard to debug 
problems that appear when PETSc and deal.II use different MPI libraries. I 
think that you want to use this MPI library 
project/cacds/apps/intelmpi/2019.0.117/intel64/lib/release/libmpi.so 
So you probably need to load a module to use Intel MPI.

Best,

Bruno

On Thursday, July 23, 2020 at 7:47:23 PM UTC-4, yuesu jin wrote:
>
> Dear all,
>   I installed the Deal.II on a cluster. 
>
> The first thing I found is that, the 
> /dealii-9.2.0/cmake/configure/configure_1_mpi.cmake 
> automatically set the DEAL_II_WITH_MPI argument as "off", therefore the 
> MPI_FOUND module cannot run. I switched it on and cmake can find the MPI 
> library. 
>
> The second thing I found is very strange. Cmake gives the message "Could 
> not find a sufficient PETSC installation: PETSC is compiled against a 
> different MPI library than the one deal.II picked up." The PETSc library 
> is integrated in the cluster's public library, I can add it by the command 
> "module add". Does this message mean that I need to compile a new version 
> of PETSc different from the one in the public library?  
>
> Thanks!
> Best 
>
>
> **
> -- Include 
> /home/yjin6/DEALII/dealii-9.2.0/cmake/configure/configure_3_petsc.cmake
> -- Found PETSC_LIBRARY
> -- Found PETSC_INCLUDE_DIR_ARCH
> -- Found PETSC_INCLUDE_DIR_COMMON
> -- Found PETSC_PETSCVARIABLES
> -- Found PETSC_LIBRARY_mkl_scalapack_lp64
> -- Found PETSC_LIBRARY_mkl_blacs_intelmpi_lp64
> -- Found PETSC_LIBRARY_mkl_intel_lp64
> -- Found PETSC_LIBRARY_mkl_sequential
> -- Found PETSC_LIBRARY_mkl_core
> -- Found PETSC_LIBRARY_umfpack
> -- Found PETSC_LIBRARY_klu
> -- Found PETSC_LIBRARY_cholmod
> -- Found PETSC_LIBRARY_btf
> -- Found PETSC_LIBRARY_ccolamd
> -- Found PETSC_LIBRARY_colamd
> -- Found PETSC_LIBRARY_camd
> -- Found PETSC_LIBRARY_amd
> -- Found PETSC_LIBRARY_suitesparseconfig
> -- Found PETSC_LIBRARY_HYPRE
> -- Found PETSC_LIBRARY_fftw3xc_intel_pic
> -- Found PETSC_LIBRARY_fftw3x_cdft_lp64_pic
> -- Found PETSC_LIBRARY_mkl_cdft_core
> -- Found PETSC_LIBRARY_mkl_blacs_intelmpi_lp64
> -- Found PETSC_LIBRARY_mkl_intel_lp64
> -- Found PETSC_LIBRARY_mkl_sequential
> -- Found PETSC_LIBRARY_mkl_core
> -- Found PETSC_LIBRARY_mkl_intel_lp64
> -- Found PETSC_LIBRARY_mkl_sequential
> -- Found PETSC_LIBRARY_mkl_core
> -- Found PETSC_LIBRARY_parmetis
> -- Found PETSC_LIBRARY_metis
> -- Performing Test PETSC_LIBRARY_dl
> -- Performing Test PETSC_LIBRARY_dl - Success
> -- Found PETSC_LIBRARY_iomp5
> -- Performing Test PETSC_LIBRARY_pthread
> -- Performing Test PETSC_LIBRARY_pthread - Success
> -- Performing Test PETSC_LIBRARY_rt
> -- Performing Test PETSC_LIBRARY_rt - Success
> -- Found PETSC_LIBRARY_mpifort
> -- Found PETSC_LIBRARY_mpi
> -- Found PETSC_LIBRARY_ifport
> -- Found PETSC_LIBRARY_ifcoremt_pic
> -- Found PETSC_LIBRARY_imf
> -- Found PETSC_LIBRARY_svml
> -- Performing Test PETSC_LIBRARY_m
> -- Performing Test PETSC_LIBRARY_m - Success
> -- Found PETSC_LIBRARY_ipgo
> -- Found PETSC_LIBRARY_irc
> -- Found PETSC_LIBRARY_irc_s
> -- Found PETSC_LIBRARY_iomp5
> --   PETSC_VERSION: 3.10.2.0
> --   PETSC_LIBRARIES: 
> 

[deal.II] Re: KDTree implementation error

2020-07-23 Thread Bruno Turcksin
Heena,

You are missing an include. Try adding #include https://dealii.org/current/doxygen/deal.II/kdtree_8h_source.html>>

Best,

Bruno

On Thursday, July 23, 2020 at 2:55:53 PM UTC-4, heena patel wrote:
>
>
> Dear all,
>   I had tried to implement KDTree in step_1 
> tutoria and header file for kdtree is added to the codel. It is as follows:
>
> void first_grid()
> {
>
>   Triangulation<2> triangulation;
>
>   GridGenerator::hyper_cube(triangulation);
>   triangulation.refine_global(4);
>
>
> *  Point<2>  p;   KDTree<2> tree(10,triangulation.get_vertices());   auto 
> w = tree.get_closest_points(p, 3);*
>   std::ofstream out("grid-1.svg");
>   GridOut   grid_out;
>   grid_out.write_svg(triangulation, out);
>   std::cout << "Grid written to grid-1.svg" << std::endl;
> }
>
>
>
> *It gives me error as below *
>
> /home/heena/Project/examples/step-1/step-1.cc:76:4: error: ‘KDTree’ was 
> not declared in this scope
> KDTree<2> tree(10,triangulation.get_vertices());
> ^~
> /home/heena/Project/examples/step-1/step-1.cc:76:4: note: suggested 
> alternative: ‘free’
> KDTree<2> tree(10,triangulation.get_vertices());
> ^~
> free
> /home/heena/Project/examples/step-1/step-1.cc:76:14: error: ‘tree’ was not 
> declared in this scope
> KDTree<2> tree(10,triangulation.get_vertices());
>   ^~~~
> /home/heena/Project/examples/step-1/step-1.cc:76:14: note: suggested 
> alternative: ‘free’
> KDTree<2> tree(10,triangulation.get_vertices());
>   ^~~~
>   free
>
>
>
> Is there something missing?
>
>
>
> Regards,
> Heena
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/d761c989-ef92-4603-8c8e-85ec4eeb3766o%40googlegroups.com.


Re: [deal.II] Installation stopped

2020-07-23 Thread Bruno Turcksin
Yuesu Lin,

Do you have access to a newer compiler? gcc 4.8.5 is very old.

Best,

Bruno

On Wednesday, July 22, 2020 at 11:26:05 PM UTC-4, yuesu jin wrote:
>
> Dear Timo,
>  The configuration in summary.log file is:
>
> deal.II configuration:
> #CMAKE_BUILD_TYPE:   DebugRelease
> #BUILD_SHARED_LIBS:  ON
> #CMAKE_INSTALL_PREFIX:   /home/yjin6/DEALII/main
> #CMAKE_SOURCE_DIR:   /home/yjin6/DEALII/dealii-9.2.0
> #(version 9.2.0)
> #CMAKE_BINARY_DIR:   /home/yjin6/DEALII/dealii-9.2.0/build
> #CMAKE_CXX_COMPILER: GNU 4.8.5 on platform Linux x86_64
> #/usr/bin/c++
>
> And error message is:
>
> /home/yjin6/DEALII/dealii-9.2.0/build/source/dofs/dof_tools_sparsity.inst:12118:27:
>  
>   required from here
> /home/yjin6/DEALII/dealii-9.2.0/source/dofs/dof_tools_sparsity.cc:1352:55: 
> error: 
> no matching function for call to ‘make_flux_sparsity_pattern(const 
> dealii::hp::DoFHandler<3, 3>&, dealii::BlockDynamicSparsityPattern&, 
> dealii::AffineConstraints&, const bool&, const dealii::Table<2, 
> dealii::DoFTools::Coupling>&, const dealii::Table<2, 
> dealii::DoFTools::Coupling>&, const subdomain_id&,  function type>)’
> /home/yjin6/DEALII/dealii-9.2.0/source/dofs/dof_tools_sparsity.cc:1352:55: 
> note: candidates are:
> /home/yjin6/DEALII/dealii-9.2.0/source/dofs/dof_tools_sparsity.cc:689:3: 
> note: template void 
> dealii::DoFTools::make_flux_sparsity_pattern(const DoFHandlerType&, 
> SparsityPatternType&)
>make_flux_sparsity_pattern(const DoFHandlerType ,
>^
>
> On Wed, Jul 22, 2020 at 9:28 PM Timo Heister  wrote:
>
>> Yuesu Jin,
>>
>> the error message should be higher up in the output. To see them more
>> clearly, you can compile again with "make -j 1". What compiler and
>> what version of deal.II is this? (look at your summary.log)
>>
>> On Wed, Jul 22, 2020 at 7:23 PM yuesu jin  wrote:
>> >
>> > Dear Deal.II team,
>> >
>> >   I am installing the deal.ii on a new cluster. The compiling process 
>> stopped at 62%.
>> >
>> > [ 62%] Building CXX object 
>> source/numerics/CMakeFiles/obj_numerics_debug.dir/vector_tools_project_qpmf.cc.o
>> > [ 62%] [ 62%] Building CXX object 
>> source/fe/CMakeFiles/obj_fe_debug.dir/mapping_q1_eulerian.cc.o
>> > Building CXX object 
>> source/fe/CMakeFiles/obj_fe_debug.dir/mapping_q_eulerian.cc.o
>> > [ 62%] Built target obj_fe_debug
>> > [ 62%] Built target obj_numerics_debug
>> >
>> > The last few lines are:
>> >
>> > /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h: In 
>> member function ‘dealii::IndexSet::IntervalIterator 
>> dealii::IndexSet::IntervalIterator::operator++(int)’:
>> > 
>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h:1192:44: 
>> note: synthesized method 
>> ‘dealii::IndexSet::IntervalIterator::IntervalIterator(const 
>> dealii::IndexSet::IntervalIterator&)’ first required here
>> >const IndexSet::IntervalIterator iter = *this;
>> > ^
>> > In file included from 
>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/lac/vector.h:24:0,
>> >  from 
>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/lac/vector_memory.h:26,
>> >  from 
>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/lac/lapack_full_matrix.h:27,
>> >  from 
>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/tensor.h:29,
>> >  from 
>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/point.h:23,
>> >  from 
>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/quadrature.h:22,
>> >  from 
>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/quadrature_lib.h:22,
>> >  from 
>> /home/yjin6/DEALII/dealii-9.2.0/source/fe/mapping_q_eulerian.cc:16:
>> > /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h:640:5: 
>> warning: unused parameter ‘other’ [-Wunused-parameter]
>> >  IntervalIterator(const IntervalIterator ) = default;
>> >  ^
>> > /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h: In 
>> member function ‘dealii::IndexSet::IntervalIterator 
>> dealii::IndexSet::IntervalIterator::operator++(int)’:
>> > 
>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h:1192:44: 
>> note: synthesized method 
>> ‘dealii::IndexSet::IntervalIterator::IntervalIterator(const 
>> dealii::IndexSet::IntervalIterator&)’ first required here
>> >const IndexSet::IntervalIterator iter = *this;
>> > ^
>> > make: *** [all] Error 2
>> >
>> > Could you give me some instructions about that? Thank you!
>> > --
>> > Yuesu Jin,
>> > Ph.D student,
>> > University of Houston,
>> > College of Natural Sciences and Mathematics,
>> > Department of Earth and Atmospheric Sciences,
>> > Houston, Texas 77204-5008
>> > 346-404-2062
>> >
>> > --
>> > The deal.II project is located at 

[deal.II] Re: Mesh-induced elastic anisotropy and distorting the quad. points as a way to palliate it

2020-07-07 Thread Bruno Turcksin
David,

Unfortunately this is really not my domain of expertise but maybe you can 
randomize the cells 
https://dealii.org/current/doxygen/deal.II/namespaceGridTools.html#aec039d544c93a6e810427ad45ba0c84f
 
instead of randomizing the quadrature points (which you cannot easily do). 

Best,

Bruno

On Friday, July 3, 2020 at 12:06:04 AM UTC-4, David F wrote:
>
> Hello everyone,
>
> I'm trying to solve a 2D solid mechanics homogenization problem, in which 
> I have element-wise constant elastic properties, which are inhomogeneous 
> and isotropic from element to element (i.e., I am assembling the system 
> using the same 4-rank stiffness tensor for all the quadrature points of a 
> certain element, but that tensor is different for each element). For this 
> system, I would like to compute its effective elastic properties, which I 
> do by loading the system under several different loading conditions as is 
> done in standard homogenization approaches. The system should behave as an 
> isotropic solid. However, I observe significant anisotropy (and clearly not 
> due to random fluctuations that might arise because the element-to-element 
> inhomogeneous properties are randomly distributed). I attribute this to a 
> mesh dependency of the solution, since I have solved the same problem with 
> a unstructured triangular mesh with another FEM package and I don't observe 
> this issue. I believe the structured quadrilateral mesh induces some 
> artificial elastic anisotropy, which is not there in the case of the 
> unstructured triangular mesh due to its topological disorder.
>
> I've thought of a way that might palliate this issue, which is to set 
> different elastic properties at the quadrature points themselves (i.e., the 
> properties are no longer element-wise constant). This seems to work to some 
> extent since the system becomes less anisotropic, however it is not good 
> enough.
>
>
> *Q1:* is there a preferred way in dealII in which I could randomly 
> distort a bit the location of the quadrature points? I think this extra 
> distortion might help get rid of the mesh artifacts. Is is possible to do 
> it with the in-built Lagrange linear FE or another type of FE is more 
> suitable within dealII for this task? Basically I have no idea where to 
> start from to do something like this, so any suggestion is welcome.
>
> *Q2:* why the system behaves as anisotropic if its local inhomogeneous 
> elastic properties are isotropic? If you have any comment or suggestion 
> about the problem of mesh-induced elastic anistropy in FEM, I would like to 
> know it.
>
>
> Thanks in advance,
> David.
>
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/eba8c7df-b614-4a7b-807b-9f158ced85afo%40googlegroups.com.


[deal.II] Re: Error while installing dealii

2020-07-06 Thread Bruno Turcksin
Prakash,

How did you configure deal.II?

Best,

Bruno

On Friday, July 3, 2020 at 5:54:23 AM UTC-4, ME20S001 Bardawal Prakash 
wrote:
>
> Hello,
>I got error while installing dealii, can someone help me for 
> solving this issue?
> Here I'm attaching snapshots of that error message
>
> Thanks & Regards,
> Prakash.
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/e70d2377-a0dc-4d31-b047-84f838125239o%40googlegroups.com.


[deal.II] Re: An iterator for all nodes (including midside) in the mesh?

2020-06-22 Thread Bruno Turcksin
Jimmy,

Is this 
https://github.com/dealii/dealii/wiki/Frequently-Asked-Questions#how-to-get-the-mapped-position-of-support-points-of-my-element
 
what you are looking for?

Best,

Bruno

On Monday, June 22, 2020 at 1:32:43 AM UTC-4, Jimmy Ho wrote:
>
> Dear All,
>
> I am trying to write a code to give initial condition for a vector of 
> FullMatrix objects. The initial value of each entry of each matrix 
> is uniquely defined by the corresponding nodal location. Hence, I am 
> looking for an easy way to iterate all nodes (including mid-side nodes) in 
> the mesh and access their coordinates. Is there a way to do so?
>
> I am aware of the Interpolate() function in VectorTools. However, the 
> documentation for this function show that the input function to interpolate 
> must have the same number of components as the number of components in the 
> vector-valued finite element. This is not the case for me, since the 
> initial values of the matrix are not directly linked to the DoFs of the 
> finite element. I also considered making the entries of the matrices as 
> extra DoFs of the finite element, then I will be able to use Interpolate() 
> and some component masks to assign initial values. But this idea is 
> sub-optimal, since in subsequent calculations, the values of the entries 
> can be directly computed using other DoFs of the finite element as well as 
> their previous values. So there's really no point posing them as additional 
> DoFs of the finite element. Is there any suggestions on how to achieve this?
>
> Thanks a lot for any discussions and suggestions! Your help is much 
> appreciated!
>
> Best,
> Jimmy
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/8cf9b254-ca35-414b-b23d-a37454ec0beeo%40googlegroups.com.


Re: [deal.II] Re: My machine did't manage to run Deal.II

2020-06-03 Thread Bruno Turcksin
Prasad,

Packaging deal.II and dependencies is a lot of work. When we release a new 
version of deal.II we update the development version of Debian and from 
there the package goes to other distributions including Ubuntu. So the next 
release of Ubuntu will probably have the latest version of deal.II. 
Maintaining multiple versions of deal.II in Debian is not feasible and 
that's why we only package the latest version.

Best,

Bruno

On Wednesday, June 3, 2020 at 6:01:06 AM UTC-4, Prasad Adhav wrote:
>
> Thank you... its *libdeal.ii-8.5.1*
>
> Is there a reason why the latest or different versions are not available?
>
> On Wednesday, June 3, 2020 at 11:48:10 AM UTC+2, chipszd wrote:
>>
>> Hello,
>>
>> You can try
>>
>> apt search deal
>>
>> to check (no sudo).
>>
>> It's a library, so it will probably be prefixed with "lib". The library 
>> is the development version, so it should end with "dev".
>>
>> Probably try searching for 
>>
>> libdeal.ii-dev 
>>
>> next.
>>
>> On Wed, Jun 3, 2020, 05:35 Prasad Adhav  wrote:
>>
>>> Hello,
>>>
>>> I was searching through the issues to see if anybody else had issues 
>>> compiling dealii.
>>> I am using Ubuntu 18.04LTS.
>>> Is it possible to install a specific version of dealii (v9.1.0)  with 
>>> apt-get?
>>>
>>> Is this the correct library?
>>> sudo apt-get install deal
>>>
>>> Thank you.
>>>
>>> Regards,
>>> Prasad ADAHV
>>>
>>> On Tuesday, April 28, 2020 at 2:08:23 PM UTC+2, Wilmar Alves Cruvinel 
>>> Lima wrote:

 HI,

 First of all I want to thanks professor Wolfgang Bangerth and Mathias 
 Maier. 

   Your advices were very good to go ahead. 

 After instalation, I put the command:

 administrador@administrador-desktop:~/dealii-9.1.1$  *make --jobs=4 
 install*

 I attached the console outputs on archive *Make_Error* here. The 
 command gone ok until 37%. 

 one of the replies:   *virtual memory exhausted*

 and the last lines are:

 make[1]: *** [source/numerics/CMakeFiles/obj_numerics_debug.dir/all] 
 Error 2
 Makefile:149: recipe for target 'all' failed
 make: *** [all] Error 2

 *My PC has the basics data:*
   CPU: Intel Dual Core Pentium G630; 
   Clock speeds: 1 x 1596 Mhz  and  1 x 2138 MHz
   Cache memory: 3072 KB;
   RAM memory: 1,6 GB
   Hard Drive: Almost Empty (85 GB)
   
 It's possible to use this machine to run Deal.II? I would 
 appreciate your help!   Sincerily, Wilmar. (From Brazil, in time of 
 Covirus!)

>>> -- 
>>> 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 dea...@googlegroups.com.
>>> To view this discussion on the web visit 
>>> https://groups.google.com/d/msgid/dealii/1dca3b5a-6310-4192-afc7-451310c8189c%40googlegroups.com
>>>  
>>> 
>>> .
>>>
>>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/1f62f905-c84e-4343-9a64-9f2193136f3b%40googlegroups.com.


[deal.II] Re: Can dealii handle different type of element in a grid

2020-05-26 Thread Bruno Turcksin
Hi,

deal.II only supports quads in 2D and hex in 3D.So if you have triangles 
you will need to split them. For the quads, you probably want to load order 
one quads and then, use a manifold to get the higher order. step 49 
(https://dealii.org/current/doxygen/deal.II/step_49.html)  shows how to 
manipulate meshes.

Best,

Bruno

On Tuesday, May 26, 2020 at 10:13:35 AM UTC-4, 徐辉 wrote:
>
> I want using different type of element in a grid in dealii.
>
> I already have a grid,  I want solve problem based on this grid.  The grid 
> contain different type of element. For example in 2D, I have some one order 
> triangle element and some one order quadrilateral element. Or another 
> example in 2D, I have some some one order quadrilateral element and some 
> two order quadrilateral element.
>
> I search dealii's tutorial do not found any topic talk about using 
> different type element in a grid. And I found in dealii FAQ first item that 
> seems dealii not support triangle or tetrahedra.
>
> Does dealii can only support one kind of element to assemble a discrete 
> system? All element in grid must be same? Is there any reference can help 
> me?
>
> Thanks for your time.
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/175d5891-8b6f-4665-b895-b3a32101f8fa%40googlegroups.com.


Re: [deal.II] Re: Evaluating FE-solution on distributed mesh, semi-Lagrangian method

2020-05-12 Thread Bruno Turcksin
Konrad,

There is nothing out of the box. However, deal.II uses p4est which can
use more that one layer of ghost cells. So you should take a look
there to see how hard it is to change the code. If that's the way you
want to go, I am sure that someone will be able to provide you with
some guidance.

Best,

Bruno

Le mar. 12 mai 2020 à 06:04, Konrad Simon  a écrit :
>
> Thank you, Bruno. What is sometimes done for semi-Lagrangian methods is that 
> one defines a halo region around the locally owned cells (like ghost cells) 
> that contains information from previous time steps and then limits the time 
> step so that one never leaves the halo region when asking for information 
> from previous time steps. Is there a way in Deal.ii to control the size of 
> the halo region. In my case I have pretty uniform grids if it helps.
>
> Best,
> Konrad
>
> On Monday, May 11, 2020 at 2:49:21 PM UTC+2, Bruno Turcksin wrote:
>>
>> Konrad,
>>
>> Unfortunately, you will need to do the communication yourself. You can only 
>> evaluate the solution on cells that locally owned or on ghost cells.
>>
>> Best,
>>
>> Bruno
>
> --
> 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 a topic in the Google 
> Groups "deal.II User Group" group.
> To unsubscribe from this topic, visit 
> https://groups.google.com/d/topic/dealii/9li9twVxrGE/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to 
> dealii+unsubscr...@googlegroups.com.
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/dealii/bfc6dd81-abb3-421c-8f6c-539c234b624f%40googlegroups.com.

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eMze2LNFr-aePdLY%3D0ruOO3iqHHnZKnZzeHH9fpofGpvw%40mail.gmail.com.


[deal.II] Re: Evaluating FE-solution on distributed mesh, semi-Lagrangian method

2020-05-11 Thread Bruno Turcksin
Konrad,

Unfortunately, you will need to do the communication yourself. You can only 
evaluate the solution on cells that locally owned or on ghost cells.

Best,

Bruno

On Monday, May 11, 2020 at 6:26:47 AM UTC-4, Konrad Simon wrote:
>
> Dear all,
>
> I am currently working on a semi-Lagrangian method for an 
> advection-diffusion equation. During runtime I must evaluate the (known) 
> FE-solution at a previous time step but the mesh is distributed. 
>
> Problem: It can well be that I must evaluate the solution at a point that 
> is in a cell that is not locally owed by the processor requesting that 
> value or not even a ghost cell. I am aware of the FEFieldFunction class and 
> that it says that an exception will be thrown if the point is found to be 
> in an artificial cell. 
>
> Now, does anyone here have experience with that? Am I doomed and will I 
> have to manually MPI communicate such points to any processor and test if 
> they own the relevant cell?
>
> Any help would be much appreciated.
>
> Best,
> Konrad
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/a8a9ab9f-4855-407f-a519-07c9a81902d3%40googlegroups.com.


Re: [deal.II] Re: "libpthreads"?

2020-04-28 Thread Bruno Turcksin


On Tuesday, April 28, 2020 at 3:33:06 PM UTC-4, Wolfgang Bangerth wrote:
>
>
> We don't have one. We announce on a variety of mailing lists like 
> NA-Digest. 
> But we've been reasonably regular at releasing around the month of May in 
> recent years if you want to pencil things into your calendar :-) (The 
> releases 
> end up on the deal.II github page at 
>https://github.com/dealii/dealii/releases 
> I wonder whether there's a way to get notifications out of that page...) 
>
You can go to Watch and then select Releases Only. You will get a 
notification when the release is tagged.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/8e970662-830e-45c1-a0f8-da9328aad54f%40googlegroups.com.


Re: [deal.II] Re: deal ii 9.1.1. installation fails

2020-04-28 Thread Bruno Turcksin
Stefan,

Le mar. 28 avr. 2020 à 04:02, Stefan Knauf  a écrit :
> thank you, I installed Trilinos 12.18.1 and now it worked. Since the 
> TRILINOS_VERSION is detected by cmake I would have rather expected a cmake 
> error (wrong version, as for example for p4est, where also a specific version 
> is needed and cmake throws an error if the version is too old). Anyway, not 
> it works, thank you once more for the support.

The master branch should throw a warning but Trilinos had been
backward compatible for 10 years so we didn't expect them to break it.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9ePeH%2BrtVAmvbqXF1Egyft4y1MUp82NYrnxSwJ68C960nw%40mail.gmail.com.


[deal.II] Re: deal ii 9.1.1. installation fails

2020-04-27 Thread Bruno Turcksin
Stefan,

On Saturday, April 25, 2020 at 4:17:20 PM UTC-4, Stefan Knauf wrote:

> Unfortuneately now "make install" stops with an error: 
> [ 42%] Building CXX object 
> source/lac/CMakeFiles/obj_lac_release.dir/trilinos_precondition_muelu.cc.o
> /home/stefan/deal/dealii-9.1.1/source/lac/trilinos_precondition_muelu.cc:24:14:
>  
> fatal error: MueLu_CreateEpetraPreconditioner.hpp: No such file or directory
>  #include 
>   ^~
> compilation terminated.
> source/lac/CMakeFiles/obj_lac_release.dir/build.make:1286: recipe for 
> target 
> 'source/lac/CMakeFiles/obj_lac_release.dir/trilinos_precondition_muelu.cc.o' 
> failed
> make[2]: *** 
> [source/lac/CMakeFiles/obj_lac_release.dir/trilinos_precondition_muelu.cc.o] 
> Error 1
> CMakeFiles/Makefile2:1409: recipe for target 
> 'source/lac/CMakeFiles/obj_lac_release.dir/all' failed
> make[1]: *** [source/lac/CMakeFiles/obj_lac_release.dir/all] Error 2
> Makefile:129: recipe for target 'all' failed
> make: *** [all] Error 2
> I have attached detailed.log etc. 
> So I guess I am one step further but still the installation with trilinos 
> support was not successful. Any further idea?
>

This is due to a non-backward compatible change in Trilinos. Unless you 
have a good reason don't use their master. It should work fine with 12.18. 
If you really need Trilinos-master, you need to use the master branch of 
deal.II and disable the wrappers for MueLU.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/db034ea5-7e7d-4e16-95d6-a6855a23a1e4%40googlegroups.com.


[deal.II] Re: LinearOperator MPI Parallel Vector

2020-04-24 Thread Bruno Turcksin

On Thursday, April 23, 2020 at 4:50:40 AM UTC-4, peterrum wrote:

> Regarding GPU: currently there is only support for matrix-free and non for 
> matrix-based algorithms. These GPU implementations use currently 
> LA::dist::Vector. 
>

We actually support matrix-based algorithms on the GPU and we have wrappers 
around cuSOLVER and some cuBLAS fonctions but you have to build a 
SparseMatrix on the CPU first. So it doesn't work with MPI. 

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/35f2b2d9-d389-4d11-aec6-602a2affcc1e%40googlegroups.com.


Re: [deal.II] Re: Deal.ii insttallation issues

2020-04-09 Thread Bruno Turcksin
I have you tried writing the full path instead of using ~ I am not
sure CMake knows how to expand it.

Le jeu. 9 avr. 2020 à 17:27, Malik Tahiyat
 a écrit :
>
> I did try it actually before. Still no results.
>
> I am very confused what the problem is. The issue happens with the install 
> prefix line.
>
> On Thu, Apr 9, 2020, 5:18 PM Bruno Turcksin  wrote:
>>
>> I wonder if there is a problem because of the . in the directory name.
>> Can you try to rename the directories?
>>
>>
>> Le jeu. 9 avr. 2020 à 16:27, Malik Tahiyat
>>  a écrit :
>> >
>> > Yes it does.
>> >
>> > On Thu, Apr 9, 2020, 2:49 PM Bruno Turcksin  
>> > wrote:
>> >>
>> >> Le jeu. 9 avr. 2020 à 14:34, Malik Tahiyat
>> >>  a écrit :
>> >> >
>> >> > I get the error : "Make Error: The source directory 
>> >> > "/home/malik/dealii-9.1.1" does not exist." in step 3
>> >> Does "/home/malik/dealii-9.1.1" contain a CMakeLists.txt file?
>> >>
>> >> Bruno
>> >>
>> >> --
>> >> 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+unsubscr...@googlegroups.com.
>> >> To view this discussion on the web visit 
>> >> https://groups.google.com/d/msgid/dealii/CAGVt9eNQiUPUSaYjozNx7t4KaPLfyvNu8JuypFVu62DsWHyzmw%40mail.gmail.com.
>> >
>> > --
>> > 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 a topic in the 
>> > Google Groups "deal.II User Group" group.
>> > To unsubscribe from this topic, visit 
>> > https://groups.google.com/d/topic/dealii/MPtPbN7yc2k/unsubscribe.
>> > To unsubscribe from this group and all its topics, send an email to 
>> > dealii+unsubscr...@googlegroups.com.
>> > To view this discussion on the web visit 
>> > https://groups.google.com/d/msgid/dealii/CAA_-CQaoi%2BKid%3D%2B2jFQYAxpquSi-eb-zHmiT7aGPhh5uxtCHug%40mail.gmail.com.
>>
>> --
>> 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+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/dealii/CAGVt9eM6GE4tEe9qQUZ8_%2B1Pwxns_dnXdddKoxU%2Bh5praq7izA%40mail.gmail.com.
>
> --
> 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 a topic in the Google 
> Groups "deal.II User Group" group.
> To unsubscribe from this topic, visit 
> https://groups.google.com/d/topic/dealii/MPtPbN7yc2k/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to 
> dealii+unsubscr...@googlegroups.com.
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/dealii/CAA_-CQZ7rb8%3D1pKKgQZLYDjTusSmMm_viERMNBP8z1THihObOg%40mail.gmail.com.

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9ePUMwka5rYfQ8iqs7SJ3ga%3DKcvP4Z2hQHFLaGpse1kdUg%40mail.gmail.com.


Re: [deal.II] Re: Deal.ii insttallation issues

2020-04-09 Thread Bruno Turcksin
I wonder if there is a problem because of the . in the directory name.
Can you try to rename the directories?


Le jeu. 9 avr. 2020 à 16:27, Malik Tahiyat
 a écrit :
>
> Yes it does.
>
> On Thu, Apr 9, 2020, 2:49 PM Bruno Turcksin  wrote:
>>
>> Le jeu. 9 avr. 2020 à 14:34, Malik Tahiyat
>>  a écrit :
>> >
>> > I get the error : "Make Error: The source directory 
>> > "/home/malik/dealii-9.1.1" does not exist." in step 3
>> Does "/home/malik/dealii-9.1.1" contain a CMakeLists.txt file?
>>
>> Bruno
>>
>> --
>> 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+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/dealii/CAGVt9eNQiUPUSaYjozNx7t4KaPLfyvNu8JuypFVu62DsWHyzmw%40mail.gmail.com.
>
> --
> 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 a topic in the Google 
> Groups "deal.II User Group" group.
> To unsubscribe from this topic, visit 
> https://groups.google.com/d/topic/dealii/MPtPbN7yc2k/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to 
> dealii+unsubscr...@googlegroups.com.
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/dealii/CAA_-CQaoi%2BKid%3D%2B2jFQYAxpquSi-eb-zHmiT7aGPhh5uxtCHug%40mail.gmail.com.

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eM6GE4tEe9qQUZ8_%2B1Pwxns_dnXdddKoxU%2Bh5praq7izA%40mail.gmail.com.


Re: [deal.II] Re: Deal.ii insttallation issues

2020-04-09 Thread Bruno Turcksin
Le jeu. 9 avr. 2020 à 14:34, Malik Tahiyat
 a écrit :
>
> I get the error : "Make Error: The source directory 
> "/home/malik/dealii-9.1.1" does not exist." in step 3
Does "/home/malik/dealii-9.1.1" contain a CMakeLists.txt file?

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eNQiUPUSaYjozNx7t4KaPLfyvNu8JuypFVu62DsWHyzmw%40mail.gmail.com.


[deal.II] Re: Deal.ii insttallation issues

2020-04-09 Thread Bruno Turcksin
Hi,

To install deal.II, you need to first compile it using `make` which 
probably happens in ~/projects/dealii-9.1.1/build and then it needs to be 
installed using `make install`. That second step should move the important 
files to /home/projects/deal.II It looks to me that you forgot this second 
step.


Best,

Bruno


On Thursday, April 9, 2020 at 4:38:52 AM UTC-4, Malik Tahiyat wrote:
>
> I was trying to follow this command in READ me section (after downloading 
> and unpacking the dealii-9.1.1.tar.gz to set install directory of deal.II 
>
>   cmake -DCMAKE_INSTALL_PREFIX=/path/to/install/dir ../deal.II   
>
>
> i had changed it to cmake -DCMAKE_INSTALL_PREFIX=/home/projects/deal.II/
>
>
> However, everytime I got the following error
> CMake Error: The source directory "/home/malik/projects/dealii-9.1.1/build" 
> does not appear to contain CMakeLists.txt.
> Specify --help for usage, or press the help button on the CMake GUI.
>
>
> The only way it worked was if i added two dots after the command: 
>
> $ cmake -DCMAKE_INSTALL_PREFIX=/home/projects/deal.II/ ..
>
>
> But then, the installation does not happen in the deal.II directory. THe 
> program is installed in ~/projects/dealii-9.1.1/build
>
> THe deal.II folder stays empty
>
>
> ANd of course i face the error
>
>   *** Could not locate a (sufficiently recent) version of deal.II.  ***
>
>   
>
>   You may want to either pass a flag -DDEAL_II_DIR=/path/to/deal.II to cmake
>
>   or set an environment variable "DEAL_II_DIR" that contains this path.
>
>
> I am fairly new to linux. Can you please say what is happening wrong here?
>
>
> I will be obliged.
>
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/fd647210-bfd5-46d1-acdb-f31c9e36d7e3%40googlegroups.com.


Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Bruno Turcksin

Krishna,

I am not an expert on visualization but I know mayavi 
(https://docs.enthought.com/mayavi/mayavi/) can read vtk and vtu. This 
is more geared towards python users though. If you think that the 
documentation is lacking, feel free to open a pull request ;-)


Best,

Bruno

On 3/16/20 12:14 PM, Krishnakumar Gopalakrishnan wrote:

Hi Bruno,

Thanks for this information.

I am genuinely curious to know about these other programs that are 
capable of reading .vtk and .vtu files.  Everyone says that these 
files are so standard, and claim that there are a lot of tools that 
can read them.   I could not find really find any general purpose 
visualisation software outside of VisIT and Paraview that reads these 
files.  There are also couple of medical simulation 
visualizers/toolkits that again come out of kitware stables.  For an 
open-source framework like the VTK with a business -riendly BSD 
license, it is rather surprising that no other company or university 
has built a competing product.



/Some people also use vtk to transfer data between programs.
/
/
/
What could be examples of such work flow, especially in a 1D context?  
For all practical purposes, 1D .vtu/.vtk files seem useless.  At least 
could we have a warning/note block of text in the write_vtu() and 
write_vtk() pages of the documentation that 1D visualisation using 
.vtk is a non-starter?  I have seen many such notes calling for the 
readers' attention.  I spent nearly two days under the belief that a 
1D simulation shoud just be a walk in the park for the two vtk-based 
heavyweights.



Regards,
Krishna




On Mon, 16 Mar 2020 at 15:51, Bruno Turcksin <mailto:bruno.turck...@gmail.com>> wrote:


Krishna,

VisIt and Paraview are just two of many visualization software
that can read .vtk and .vtu files. Some people also use vtk to
transfer data between programs. Why should we restrict the output
because two visualization tools don't support 1D?

Best,

Bruno

On Monday, March 16, 2020 at 11:37:57 AM UTC-4, Krishnakumar
Gopalakrishnan wrote:

Hi Praveen,

Thank you.  That really helps. I shall definitely check it out
and report back.  I just have standard Q1 linear elements in a
unit (0,1) domain, solving a standard 1D diffusion problem.

Are we all agreeing that sophisticated VisIT and Paraview
cannot produce simple 1D visualizations/animations? If so,
there must be anAssert() pre-condition check for the
DataOut::write_vtk() and DataOut::write_vtu() functions of the
library which return an exception with "dimension not
implemented" error.

Regards,
Krishna



On Mon, 16 Mar 2020 at 15:31, Praveen C
mailto:prav...@tifrbng.res.in>> wrote:

I have a 1d example here


https://bitbucket.org/cpraveen/deal_ii/src/master/dg/1d_scalar_legendre/

The blank lines in the output file denote different
elements. It is not necessary to sort if you use gnuplot
to plot it. gnuplot makes one curve for the solution in
each element. If the FE space is continuous, you will get
a plot which is globally continuous.

Best
praveen


On 16-Mar-2020, at 8:50 PM, Krishnakumar Gopalakrishnan
mailto:krish...@vt.edu>> wrote:

Hi Praveen,

Thanks for your reply. Yes, I had success with gnuplot,
but the following were the difficulties.

 1. Weirdly, the x-axis co-ordinates of the mesh are not
sorted in a particular order (they appear rather
randomly, arranged in  groups of 2 rows with blank
lines between them).
 2. The time-animation is not easy to visualize. 
Paraview has a nice animation player for such sets of
.vtu files.

Is there some trick to visualize time-series of 1D
spatial data?


Regards,
Krishna


-- 
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 a topic in
the Google Groups "deal.II User Group" group.
To unsubscribe from this topic, visit
https://groups.google.com/d/topic/dealii/AFeah4OhYe8/unsubscribe.
To unsubscribe from this group and all its topics, send an email
to dealii+unsubscr...@googlegroups.com
<mailto:dealii+unsubscr...@googlegroups.com>.
To view this discussion on the web visit

https://groups.google.com/d/msgid/dealii/f100beb0-9b91-482e-8e70-16939014ef61%40googlegroups.com

<https://groups.google.com/d/msgid/dealii/f100beb0-9b91-482e-8e70-16939014ef61%40googlegroups.com?utm_medium=email_source=footer>.

--
Th

Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Bruno Turcksin
Krishna,

VisIt and Paraview are just two of many visualization software that can 
read .vtk and .vtu files. Some people also use vtk to transfer data between 
programs. Why should we restrict the output because two visualization tools 
don't support 1D?

Best,

Bruno

On Monday, March 16, 2020 at 11:37:57 AM UTC-4, Krishnakumar Gopalakrishnan 
wrote:
>
> Hi Praveen,
>
> Thank you.  That really helps. I shall definitely check it out and report 
> back.  I just have standard Q1 linear elements in a unit (0,1) domain, 
> solving a standard 1D diffusion problem.
>
> Are we all agreeing that sophisticated VisIT and Paraview cannot produce 
> simple 1D visualizations/animations? If so, there must be an Assert() 
> pre-condition 
> check for the DataOut::write_vtk() and DataOut::write_vtu() functions of 
> the library which return an exception with "dimension not implemented" 
> error.  
>
> Regards,
> Krishna
>
>
>
> On Mon, 16 Mar 2020 at 15:31, Praveen C  wrote:
>
>> I have a 1d example here
>>
>> https://bitbucket.org/cpraveen/deal_ii/src/master/dg/1d_scalar_legendre/
>>
>> The blank lines in the output file denote different elements. It is not 
>> necessary to sort if you use gnuplot to plot it. gnuplot makes one curve 
>> for the solution in each element. If the FE space is continuous, you will 
>> get a plot which is globally continuous.
>>
>> Best
>> praveen
>>
>> On 16-Mar-2020, at 8:50 PM, Krishnakumar Gopalakrishnan  
>> wrote:
>>
>> Hi Praveen,
>>
>> Thanks for your reply. Yes, I had success with gnuplot, but the following 
>> were the difficulties.
>>
>>1. Weirdly, the x-axis co-ordinates of the mesh are not sorted in a 
>>particular order (they appear rather randomly, arranged in  groups of 2 
>>rows with blank lines between them).
>>2. The time-animation is not easy to visualize.  Paraview has a nice 
>>animation player for such sets of .vtu files.
>>
>> Is there some trick to visualize time-series of 1D spatial data?
>>
>>
>> Regards,
>> Krishna
>>
>>
>>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/f100beb0-9b91-482e-8e70-16939014ef61%40googlegroups.com.


[deal.II] Re: Matrix-free: Continuous elements and boundary (face) integrals

2020-03-11 Thread Bruno Turcksin


On Wednesday, March 11, 2020 at 7:36:31 AM UTC-4, Michał Wichrowski wrote:
>
> I tried to fix that by myself, but I could not locate the source code of 
> MatrixFree::internal_reinit
>
Here it is: 
https://github.com/dealii/dealii/blob/master/include/deal.II/matrix_free/matrix_free.templates.h#L352-L681
 
Note that they are two different internal_reinit functions.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/892fa26f-d701-4d6a-852d-26941358c370%40googlegroups.com.


Re: [deal.II] Re: Shared Memory Parallel Linear Solver

2020-02-26 Thread Bruno Turcksin
Paras,

Le mer. 26 févr. 2020 à 12:27, Paras Kumar  a écrit :
> For the vectors (solution & rhs), the idea was to copy the values from the 
> dealii::Vector to dealii::LinearAlgebra::EpetraWrappers::Vector. As an 
> intermediate step I first copy the dealii::Vector to 
> dealii::LinearAlgebra::Vector using the constructor : 
> https://www.dealii.org/current/doxygen/deal.II/classLinearAlgebra_1_1Vector.html#af441b2c23134f8e6e08c833f91a2.
>  This works fine. However, when I try to call 
> dealii::LinearAlgebra::EpetraWrappers::Vector::reinit(dealii::LinearAlgebra::Vector)
>  the following error occurs:
>
> An error occurred in line <85> of file 
> 
>  in function
> virtual void dealii::LinearAlgebra::EpetraWrappers::Vector::reinit(const 
> dealii::LinearAlgebra::VectorSpaceVector&, bool)
> The violated condition was:
> dynamic_cast()!=nullptr
> Additional information:
> (none)
You are not allow to use reinit with a vector of a different type. I
am afraid you will have to copy the elements yourself. I would advise
you to choose this vector
https://www.dealii.org/current/doxygen/deal.II/classTrilinosWrappers_1_1MPI_1_1Vector.html
It is easier to fill in.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eOSbng0MS%3D2ziAASOVtX7PhH-wyZs_2XG9h8Y%3DEMLyVbw%40mail.gmail.com.


[deal.II] Re: Shared Memory Parallel Linear Solver

2020-02-14 Thread Bruno Turcksin
Paras,

You could try to use SuperLU_MT (see 
https://portal.nersc.gov/project/sparse/superlu/) but we don't have wrapper 
for it. The Krylov solver in deal.II are multithreaded but the 
preconditioners are not. What you can try is to use deal.II solvers and 
STRUMPACK (https://github.com/pghysels/STRUMPACK) for the preconditioner 
but again we don't have wrapper for it. 

Best,

Bruno

On Friday, February 14, 2020 at 7:22:15 AM UTC-5, Paras Kumar wrote:
>
> Dear deal.ii Community,
>
> I am working  on finite deformation hyperelasticity problem which is 
> essentially a nonlinear-vector-valued problem with displacement as the 
> unknown at each support point(dim=2,3).  *With regards to parallelism, we 
> currently restrict ourselves to shared memory parallel (SMP) only.* The 
> FE assembly process has been paralleized using the workstream function.
>
> This question pertains to (possibly faster) linear solvers. Currently. For 
> the current 2D problem, we use the SparseDirectUMFPACK solver. As can been 
> seen in the time log below (ths example was computed on a 36 core machine 
> with 64 threads), the linear solver consumes the most time. I also tried 
> using the CG solver, but it was much much slower, probably due to the large 
> condition number stemming out of  highly refined mesh in regions of 
> interest.
>
> Triangulation:
>  Number of active cells: 2059646
>  Number of Degrees of Freedom: 4119454
>
> +-+++
> | Total wallclock time elapsed since start|  7.81e+03s ||
> | |||
> | Section | no. calls |  wall time | % of total |
> +-+---+++
> | Assemble Linear System  |50 |   875s |11% |
> | Linear Solver   |40 |  5.55e+03s |71% |
> | Make Constraints|50 |   255s |   3.3% |
> | PBC setup   | 1 |  1.02s | 0% |
> | Set Boundary IDs| 1 | 0.109s | 0% |
> | Stress Output Computation   |11 |   464s |   5.9% |
> | Stress Output Overall   |12 | 1e+03s |13% |
> | Stress Output Writing   |11 |   379s |   4.9% |
> | Stress output initialize| 1 |   158s | 2% |
> | System Setup| 1 |   260s |   3.3% |
> +-+---+++
>
> While going through the documentation, I came across options for DMP 
> linear solvers but couldn't find any with SMP. 
>
> Could somenone please guide me to any such possibilities within the 
> library or through interface to some external library.
>
> Best regards,
> Paras
>
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/2a2ce382-894d-42ff-a9ea-d1c15612a309%40googlegroups.com.


Re: [deal.II] Re: Installation on cray XC50 | linking to petsc, lapack and blas libraries with different names

2020-02-13 Thread Bruno Turcksin
Le jeu. 13 févr. 2020 à 07:27, vachan potluri
 a écrit :
>
> It is working!
>
> The mistake I did was to open an interactive job and run the executables 
> through bash. When I instead submitted a job, and executed using aprun 
> (Cray's equivalent to mpirun) to run the executables, they ran successfully. 
> I tested step-1, step-18 and my own code too. The installation tests will 
> probably not run though, since they are actually makefile targets.

Glad to hear. You should be able to run the installation tests but you
need to let cmake know that it shouldn't use mpiexec but aprun
instead. This can be done when you configure deal.II by using:

-D MPI_EXEC="aprun"

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eO4jdF-C48awXwffjN4wsmCsOJRA4sGXDuyAfyb5%2Bj1tA%40mail.gmail.com.


[deal.II] Re: Installation on cray XC50 | linking to petsc, lapack and blas libraries with different names

2020-02-12 Thread Bruno Turcksin
Vachan,

On Wednesday, February 12, 2020 at 12:24:38 AM UTC-5, vachan potluri wrote:
>
> Step-1 aborts with Illegal Instruction (core dumped). The error msg gdb 
> prints is the following.
> Program received signal SIGILL, Illegal instruction.
> __static_initialization_and_destruction_0 (__initialize_p=1, 
> __priority=65535)
> at 
> /home/ComptGasDynLab/vachanpotluri/source/dealii-9.1.1/source/numerics/time_dependent.cc:1196
> 1196  std::make_pair(0U, 
> 0.)));
> When I backtrace the error, it leads to this.
> template  
> typename 
> TimeStepBase_Tria_Flags::RefinementFlags::CorrectionRelaxations
>   
> TimeStepBase_Tria_Flags::RefinementFlags::default_correction_relaxations(
> 1, // one element, denoting the first and all subsequent sweeps
> std::vector>(1, // one element, 
> denoting the
> // upper bound for the
> // following relaxation
>  std::make_pair(0U, 0.)));
> Not just step-1, but step.debug, affinity.debug and mpi.debug (and 
> possibly other debug tests may) also terminate with the same error and bt. 
> Can someone explain why this is happening?
>

I am not sure why you have this error. Can you show the whole backtrace? 

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/590fe189-1dbd-412a-927b-b0aa7b0b3e5a%40googlegroups.com.


Re: [deal.II] Re: Problem installing Dealii-9.0.0

2020-02-11 Thread Bruno Turcksin
Le mar. 11 févr. 2020 à 09:03, Felipe Orellana <
felipeorellanarovir...@gmail.com> a écrit :

>
>   2)  I am not understanding well here:
>
> YW:  Why didn't you copy/paste the patch?
>
> What is 'the patch'  ..how can access that text?,
>
>   if I click on Tamiko's post, the web cannot find the site,
> cannot find the commit.
>
Here it is
https://github.com/dealii/dealii/commit/336319966b484889bbdd1da58623293b93980628.patch

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eOX1-9yk95exZ3BXj1vG1z8tEDLER1kw81p%3DwXOvpVdbw%40mail.gmail.com.


Re: [deal.II] Re: Problem installing Dealii-9.0.0

2020-02-11 Thread Bruno Turcksin
Felipe,

Le mar. 11 févr. 2020 à 08:29, Felipe Orellana <
felipeorellanarovir...@gmail.com> a écrit :

>
> Hi Dan and Bruno,
>
>  I have followed the thread 9117 for solving this problem, by adding
> the recommended flag:
>
> IF(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.16.0")
>   LIST(TRANSFORM CMAKE_THREAD_LIBS_INIT PREPEND "-l")
> ENDIF()
>
Why didn't you copy/paste the patch? Also you could just use CMake 3.15.
This should fix your problem.

>
> But I have not succeeded in compiling. The errors posted are similar:
>
> -- Performing Test DEAL_II_HAVE_FLAG_Wplacement_new - Failed
>
That's not really a  problem. This test just checks if your compiler
supports -Wplacement-new if it doesn't, we won't use the flag. So that test
can fail safely.

When you reconfigure deal.II, you should do it in a clean directory or at
least remove cmake's cache.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eOC9WsZPR%3Dp5eTYcoCRP9eY0RCrbDQQivqQr%2BZX3MPM9Q%40mail.gmail.com.


[deal.II] Re: Using deal.ii 9.1.1 in a Qt5 program

2020-02-10 Thread Bruno Turcksin
Arnoud,

Wolfgang already explained how to get CMake working but I wanted to let you 
know about an issue (and a solution!) when using QT and deal.II together: 
https://github.com/dealii/dealii/issues/7524

Best,

Bruno

On Monday, February 10, 2020 at 4:00:16 PM UTC-5, Arnoud de Geus wrote:
>
> Hello,
>
> I'm trying to use deal.ii 9.1.1 in a Qt5 program,
> effectively trying to build a functional FEM UI on deal.ii
> The usage of the Cmake system for Qt and Deal.ii
> do seem to be completely incompatible though.
>
> Has anyone experience with this?
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/a5f17b2a-5901-4465-928c-5b489c0b5136%40googlegroups.com.


Re: [deal.II] Re: Problem installing Dealii-9.0.0

2020-02-10 Thread Bruno Turcksin
Le lun. 10 févr. 2020 à 10:41, Daniel Arndt  a écrit :
> The problem here are the additional quotes in the compiler arguments, see 
> https://godbolt.org/z/bwDjWy.
Strange, I get that problem with gcc 4.8 and 4.9 but it works with the
other versions of gcc.

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eNG0in1v3wmvfvRHqnapwvGPeTh6DB%3DSKq%2Bf8DLROmCcA%40mail.gmail.com.


Re: [deal.II] Re: Problem installing Dealii-9.0.0

2020-02-10 Thread Bruno Turcksin
Felipe,

So this is a strange bug. The problem is from the flag
-Woverloaded-virtual With gcc 4.8 and 4.9 As you can see the flag
alone works https://wandbox.org/permlink/GLbCK7qVqfScXrZp but if I add
another flag it won't compile
https://wandbox.org/permlink/4Lw7aNqGlJkik6SL If you have access to
gcc 5 or later, I would advise you to use that instead. You can also
try the latest version of deal.II maybe we don't use that flag
anymore.

Best,

Bruno

Le lun. 10 févr. 2020 à 09:47, Felipe Orellana
 a écrit :
>
>
>  Bruno !
>
>  Thanks for replying so swiftly.
>
>  Yes, I had forgotten to recreate the dir from scratch to avoid carrying 
> trash.. I recreated a new building directory, did it from there, I attach a 
> log file with the corresponding output.
>
>  My compilers (g++, gcc):  gcc version 4.8.5 20150623 (Red Hat 4.8.5-28) 
> (GCC)
>
>  The log also reads '-- Checking whether /usr/bin/gfortran supports 
> Fortran 90 -- yes '
>
>  Also, I am using CMake 3.16.0-rc3.
>
> The log file accuses several failed tests on Deal_II.. the first one 
> online 106:
> -- Performing Test DEAL_II_HAVE_FLAG_Wplacement_new - Failed
>
> cheers many,
> Felipe
>
>
>
> On Mon, 10 Feb 2020 at 22:03, Bruno Turcksin  wrote:
>>
>> Felipe,
>>
>> Le lun. 10 févr. 2020 à 08:49, Felipe Orellana
>>  a écrit :
>> >   Here I post the output:
>>
>> Can you redo it in a clean directory. The output from CMake is
>> different the first time you run it. Also which compiler are you
>> using?
>>
>> Best,
>>
>> Bruno
>>
>> --
>> 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+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/dealii/CAGVt9eORpe%2B3hubWT%2B7eHA2jHSXKaoK9bMuq4JiLfvDah%3D05Ow%40mail.gmail.com.
>
> --
> 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 a topic in the Google 
> Groups "deal.II User Group" group.
> To unsubscribe from this topic, visit 
> https://groups.google.com/d/topic/dealii/SQ6QW-jNzP8/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to 
> dealii+unsubscr...@googlegroups.com.
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/dealii/CABP9zGWJyJTemkG%3DSOQtLQB5yGAVv-ZokkNyzcxEPAq9jE5d7Q%40mail.gmail.com.

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9ePXianVedF5kV6_v6B3mU%3DzkFGfwcG6ZfSeKwDs%3DTn4BQ%40mail.gmail.com.


Re: [deal.II] Re: Problem installing Dealii-9.0.0

2020-02-10 Thread Bruno Turcksin
Felipe,

Le lun. 10 févr. 2020 à 08:49, Felipe Orellana
 a écrit :
>   Here I post the output:

Can you redo it in a clean directory. The output from CMake is
different the first time you run it. Also which compiler are you
using?

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eORpe%2B3hubWT%2B7eHA2jHSXKaoK9bMuq4JiLfvDah%3D05Ow%40mail.gmail.com.


[deal.II] Re: Problem installing Dealii-9.0.0

2020-02-10 Thread Bruno Turcksin
Felipe,

Can you post everything that deal.II prints on the screen.

Best,

Bruno

On Monday, February 10, 2020 at 1:59:16 AM UTC-5, Felipe Orellana wrote:
>
>
> Hello,
>
> My name is Felipe. I am trying to install dealii-9.0.0 on my local 
> cluster.
>
> After commanding   
>
> cmake -DCMAKE_INSTALL_PREFIX=/path2install /path2source
>
>  with my desired directories (which btw, are the same directory, just  
> /home/Felipe/BIGSOFTWARE/dealii-9.0.0/ ), the system progresses well for 
> almost a minute.. but then I get an error and the installation stops. I 
> paste the error message below.
>
> What is there missing in my system? 
>
> Are there any flags that I could add/write to avoid these errors?
>
> I would appreciate your help,
> cheers,
> Felipe
>
> -- Include 
> /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_scalapack.cmake
> -- DEAL_II_WITH_SCALAPACK has unmet configuration requirements: 
> DEAL_II_WITH_MPI has to be set to "ON".
> -- DEAL_II_WITH_SCALAPACK has unmet configuration requirements: 
> DEAL_II_WITH_LAPACK has to be set to "ON".
> -- 
> -- Include 
> /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_slepc.cmake
> -- DEAL_II_WITH_SLEPC has unmet configuration requirements: 
> DEAL_II_WITH_PETSC has to be set to "ON".
> -- 
> -- Include 
> /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_sundials.cmake
> -- SUNDIALS_LIB_IDAS not found! Call:
> -- FIND_LIBRARY(SUNDIALS_LIB_IDAS NAMES sundials_idas HINTS 
> PATH_SUFFIXES lib lib64 lib)
> -- SUNDIALS_LIB_IDA not found! Call:
> -- FIND_LIBRARY(SUNDIALS_LIB_IDA NAMES sundials_ida HINTS 
> PATH_SUFFIXES lib lib64 lib)
> -- SUNDIALS_LIB_ARKODE not found! Call:
> -- FIND_LIBRARY(SUNDIALS_LIB_ARKODE NAMES sundials_arkode HINTS 
> PATH_SUFFIXES lib lib64 lib)
> -- SUNDIALS_LIB_KINSOL not found! Call:
> -- FIND_LIBRARY(SUNDIALS_LIB_KINSOL NAMES sundials_kinsol HINTS 
> PATH_SUFFIXES lib lib64 lib)
> -- SUNDIALS_LIB_SER not found! Call:
> -- FIND_LIBRARY(SUNDIALS_LIB_SER NAMES sundials_nvecserial HINTS 
> PATH_SUFFIXES lib lib64 li
> -- SUNDIALS_INCLUDE_DIR not found! Call:
> -- FIND_PATH(SUNDIALS_INCLUDE_DIR sundials/sundials_nvector.h HINTS 
> PATH_SUFFIXES include)
> --   SUNDIALS_LIBRARIES: *** Required variable "SUNDIALS_LIB_IDA" set to 
> NOTFOUND ***
> --   SUNDIALS_INCLUDE_DIRS: *** Required variable "SUNDIALS_INCLUDE_DIR" 
> set to NOTFOUND ***
> --   SUNDIALS_USER_INCLUDE_DIRS: *** Required variable 
> "SUNDIALS_INCLUDE_DIR" set to NOTFOUND ***
> -- Could NOT find SUNDIALS
> -- DEAL_II_WITH_SUNDIALS has unmet external dependencies.
> -- 
> -- Include /home/Felipe/BIGSOFTWARE/
> dealii-9.0.0/cmake/setup_cpack.cmake
> -- 
> -- Include 
> /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/setup_custom_targets.cmake
> -- 
> -- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/setup_finalize.cmake
> -- Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG
> -- Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG - Failed
> CMake Error at cmake/setup_finalize.cmake:95 (MESSAGE):
>   
>
> Configuration error: Cannot compile a test program with the final set 
> of
> compiler and linker flags:
>   CXX flags (DEBUG): -pedantic -fPIC -Wall -Wextra -Wpointer-arith 
> -Wwrite-strings -Wsynth -Wsign-compare -Wswitch -Woverloaded-virtual 
> -Wno-deprecated-declarations -Wno-literal-suffix -std=c++11 
> -Wno-parentheses -Wno-unused-local-typedefs -Og -ggdb 
> -Wa,--compress-debug-sections
>   LD flags  (DEBUG): -Wl,--as-needed -rdynamic -fuse-ld=gold pthread 
> -ggdb
>   LIBRARIES (DEBUG): m;dl;/usr/lib64/libz.so;rt;
> 
> Call Stack (most recent call first):
>   cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
>   CMakeLists.txt:132 (VERBOSE_INCLUDE)
>
> -- Configuring incomplete, errors occurred!
> See also 
> "/home/Felipe/BIGSOFTWARE/dealii-9.0.0/build/CMakeFiles/CMakeOutput.log".
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/61c0b52e-23b7-4387-bde1-1361d6f89494%40googlegroups.com.


[deal.II] Re: deal.II installation on cray XC50 giving MPI_VERSION=0.0

2020-02-10 Thread Bruno Turcksin
Vachan,

I saw on the other thread that you were using CMake 3.5. I would advise to 
download a newer version of CMake. deal.II uses FindMPI from CMake and this 
was rewritten in CMake 3.10 to fix problems with Cray supercomputers. 

Best,

Bruno

On Saturday, February 8, 2020 at 1:43:59 AM UTC-5, vachan potluri wrote:
>
> Dear Prof. Bangerth,
>
> Can you attach it to a reply? It would be interesting to see why the 
>> version 
>> detection didn't work. (Although I see that cmake complains that it can't 
>> find 
>> the file, so that is probably the issue. I don't know why it can't find 
>> the 
>> file...)
>
> I really appreciate and value your involvement in this thread. I have 
> attached mpi.h with this mail. I want to mention that I added this line 
> in FindMPI.cmake just before DEAL_II_FIND_FILE(MPI_MPI_H ...): 
> MESSAGE(STATUS "Searching for mpi.h in ${MPI_CXX_INCLUDE_PATH}")
> and found the corresponding output by cmake to be as follows.
> -- Include 
> /home/ComptGasDynLab/vachanpotluri/source/dealii-9.1.1/cmake/configure/configure_1_mpi.cmake
> -- Searching for mpi.h in 
> -- Found MPI_MPI_H
> --   MPI_VERSION: 3.1
> --   MPI_LIBRARIES: 
> --   MPI_INCLUDE_DIRS: 
> --   MPI_USER_INCLUDE_DIRS: 
> --   MPI_CXX_FLAGS: 
> --   MPI_LINKER_FLAGS: 
> -- Found MPI
> -- DEAL_II_WITH_MPI successfully set up with external dependencies.
> Notice that the path is not printed, the variable is empty! Probably the 
> problem is not with reading the header but with the variable being changed 
> somewhere else.
>
> It's still possible that everything links correctly. What happens if you 
>> run 
>> cmake and then compile? Does it work? 
>
> I have not tried compiling the source because there are some other things 
> also that I wanted to figure out. I have started a new thread for this 
> purpose here https://groups.google.com/forum/#!topic/dealii/MCYyPrZNyjg. 
> I request you to have a look at this one too.
>
> Thank you
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/255f3d22-67b0-4fb6-875c-778737e885ab%40googlegroups.com.


Re: [deal.II] Getting old solution values at quadrature points using MeshWorker::loop

2020-01-30 Thread Bruno Turcksin
On Thursday, January 30, 2020 at 2:28:55 PM UTC-5, Andrew Davis wrote:
>
>
> from the file fe_values.impl.2.inst.in. The Assert(false) seems strange 
> to me---why doesn't it crash? (I'm in Release mode so that could answer 
> that). However, should it be calling a different function?
>
> You should always debug your code in Debug mode. It's very possible that 
there is an assert that will catch a problem earlier in the code and so the 
code after that assert makes no sense because you are not supposed to get 
there.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/d3cbd9b5-e564-4571-b22f-fdc9fc537e83%40googlegroups.com.


[deal.II] Re: Instantiation problem for Utilities::MPI::sum (const ArrayView< const T > , const MPI_Comm _communicator, const ArrayView< T > )

2020-01-28 Thread Bruno Turcksin
Feimi,

You need to have two different ArrayView. It won't work with a single 
ArrayView. The input one (values) need to be an ArrayView and 
the output one (sum) an ArrayView.

Best,

Bruno

On Tuesday, January 28, 2020 at 11:40:03 AM UTC-5, Feimi Yu wrote:
>
> I uploaded a minimal code to reproduce the problem I encountered.
>
> Thanks!
> Feimi
>
> On Monday, January 27, 2020 at 1:42:18 PM UTC-5, Feimi Yu wrote:
>>
>> Hi,
>>
>> I was trying to use the the function Utilities::MPI::sum 
>> 
>>  
>> (const ArrayView 
>> < 
>> const T > , const MPI_Comm _communicator, const ArrayView 
>> < T 
>> > )
>> for an std::vector. I created an ArrayView to pack the vector 
>> and passed it into this function. However, the compiler keeps telling me:
>>
>> undefined reference to 'void 
>> dealii::Utilities::MPI::sum, dealii::ArrayView 
>> >(dealii::ArrayView const&, ompi_communicator_t* const&, 
>> dealii::ArrayView&)'
>>
>> I checked base/mpi.inst.in and cmake/config/template-arguments.in. Int 
>> type should be included in the instantiation list, but I could not figure 
>> out why this does not work for me.
>>
>> Thanks!
>> Feimi
>>
>>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/98ae6de0-9751-4f12-9f57-1fae9e9f596b%40googlegroups.com.


[deal.II] Re: Simple merge_triangulation problem

2020-01-23 Thread Bruno Turcksin
Konrad,

What does it mean you cannot merge the cells? Do you get the wrong results? 
Does the code segfault? Do you get an error message?

Best,

Bruno

On Thursday, January 23, 2020 at 8:56:34 AM UTC-5, Konrad Wiśniewski wrote:
>
> Hi all!
>
> I've encountered a problem with very simple two-cells merging in 2D 
> (deal.ii v.9.0.0). 
> Lets say that I have two rectangular cells (for two different material) 
> and I want to merge it together and then refine those cells properly. 
> I don't have a problem with this when I want to merge cells when they are 
> side by side 1):
>
>
> but I cannot merge cells with this configuration 2):
>
> Or even in this configuration 3):
>
> I wonder why it is a case? It seems the most simple case for 
> merge_triangulation() function. Can anyone show me how merge second case 
> properly?
>
> This is my code with the simplest coordinates of vertices:
>
> //FIRST CELL
> static const Point<2> vertices_1[]
> = {
> Point<2>(0.0, 0.0),
> Point<2>(1.0, 0.0),
> Point<2>(0.0, 1.0),
> Point<2>(1.0, 1.0)
>   };
>  
> // Creating CellData and vertices list for this material (in 
> this case for only one cell):
> const unsigned int n_vertices = 4;
> const std::vector> vertices_list_2(_2[0], 
> _2[n_vertices]);
> static const int cell_vertices[] = {0,1,2,3};
> CellData cells_1;
>
> for(unsigned int j=0;j {
> cell_1.vertices[j] = cell_vertices[i][j];
> }
> cell_1.material_id = material_one_id;
>
> // Create triangulation: 
> Triangulationtemp_down_triangulation;
> temp_down_triangulation.create_triangulation(vertices_list_1,
> cell_1,SubCellData());
>
>
> //SECOND CELL
> static const Point<2> vertices_2[]
> = {
> Point<2>(0.0, 1.0),
> Point<2>(1.0, 1.0),
> Point<2>(0.0, 2.0),
> Point<2>(1.0, 2.0)
>   };
> // Creating CellData for second cell
> const std::vector> vertices_list_2(_2[0], 
> _2[n_vertices]);
> CellData cell_2;
>
> for(unsigned int j=0;j cell_2.vertices[j] = cell_vertices_2[i][j];
> }
> cell_2.material_id = material_two_id;
>
> Triangulationtemp_up_triangulation;
> temp_up_triangulation.create_triangulation(vertices_list_2, 
> cell_2, SubCellData());
>
> // MERGING...
> GridGenerator::merge_triangulations(temp_down_triangulation,
> temp_up_triangulation,
> final_triangulation);
>
>
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/3ce2d238-1d5a-48e5-a227-e0fba8cef004%40googlegroups.com.


[deal.II] Re: "fatal error: MueLu_CreateEpetraPreconditioner.hpp: No such file or directory" when compiling with Trilinos

2020-01-09 Thread Bruno Turcksin
Hi,

This is a known problem with the development version of Trilinos 
https://github.com/dealii/dealii/pull/9237 Use the latest release of 
Trilinos instead.

Best,

Bruno

On Thursday, January 9, 2020 at 10:06:13 AM UTC-5, Maxi Miller wrote:
>
> Hei,
> when trying to compile deal.II with one of the latest Trilinos-Versions, 
> compilation fails with "fatal error: MueLu_CreateEpetraPreconditioner.hpp: 
> No such file or directory", but the configuration process goes through 
> without rising any problems. Which modules do I have to enable in Trilinos 
> to fix this warning?
> Thanks!
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/e7af71f6-1645-41a5-9028-a528906e0c4e%40googlegroups.com.


[deal.II] Re: Why did the developers of deal.ii choose templates over variadic arguments?

2019-12-20 Thread Bruno Turcksin
Krishna,

You can find an extensive discussion on the design choices made here 
. I think section 2.4 answers your 
question. The short answer is that using template makes the code run faster 
because the compiler can do a better job at optimizing everything and it 
allows us greater flexibility in the choice of data structure.

Best,

Bruno

On Friday, December 20, 2019 at 8:12:56 AM UTC-5, Krishnakumar 
Gopalakrishnan wrote:
>
> With the highest deference to the amazing quality of software development 
> that deal.ii  developers follow, I wish to ask a question about the 
> particular development paradigm chosen (with no disrespect to any of the 
> developers intended). This question is just out of personal curiosity.
>
> deal.ii makes heavy use of templates for spatial-dimension independent 
> programming.  However, as already acknowledged in the FAQ, compiling 
> template-heavy code takes a long time.
>
> Since the number cases are only 3 (possible spatial dimensions), it 
> strikes me that the variadic arguments feature (facilitated by the 
> cstdarg.h header file) might be a slightly bit more natural choice for 
> this use case? Apologies if I am wrong about this, since I am a novice C++ 
> user.
>  
> Can the developers/users of deal.ii provide an objective reasoning of why 
> they went the template-route instead of variadic arguments?
>
> Regards,
> Krishna
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/15f96801-09e4-438b-b159-e7baf8b5a587%40googlegroups.com.


Re: [deal.II] Re: Optimization of Laplacea Equation Solver

2019-12-06 Thread Bruno Turcksin
Oleg,

Le ven. 6 déc. 2019 à 08:21, Oleg Kmechak  a écrit :
> So I still have to use MPI to make program multihread, even if it is a single 
> machine, with 40 processors inside?
> Maybe it is rough understanding, but I always thought that for multicomputer 
> processing is used MPI and for multiprocessor(on single machine) - 
> OpenMP(Which is embedded in deal.ii as far as I know).
MPI and multithreading are different things. I am not sure what you
mean by multicomputer but you need to use MPI if you have more than
one node. You can use multithreading if all the processors are on the
same motherboard (there are exception to this though). deal.II does
not use OpenMP for multithreading instead it uses TBB but it doesn't
really matter. Also while many operations are multithreaded in deal.II
not all of them are, so if you really want to use all the processors,
you will need to use MPI.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9ePyLhSASDZoProvMoe3q2UL8fNgZk7EwucR0bNFvkdsEg%40mail.gmail.com.


[deal.II] Re: Optimization of Laplacea Equation Solver

2019-12-05 Thread Bruno Turcksin
Oleg,

The first thing to do if you want to speed up you code is to profile your 
code. How do you know which part of the code is slow? Right now, it sounds 
that you are assuming that it is in the solver which may be true but it may 
not be. If you want to speed up your solver, you can 1) get a better 
preconditioner (maybe using algebraic multigrid) 2) make you code parallel. 
deal.II is multithreaded by default but not every operation is. On top of 
that multithreading does not work if the processors need to communicate 
through the network (which might be the case on the cluster you are 
testing). In that case, you will need to use MPI. Take a look at step-40 
 
It solves the Laplace equation with 52 millions DoFs in less than 10 
seconds on 4000 processors.

Best

Bruno

On Thursday, December 5, 2019 at 9:10:19 AM UTC-5, Oleg Kmechak wrote:
>
> Dear All, 
>
> I am working on RiverSIM program(https://github.com/okmechak/RiverSim/) 
>
> This program solves laplace equation on river network geometry, 
> then makes some computaion(integration over these dence points on picture 
> and other processing) which result in river network evolution step by step.
>
> [image: test.jpg]
>
>
> Program is quite big, but all Deal.II dependencies are encapsulated into 
> Solver class(
> https://github.com/okmechak/RiverSim/blob/master/source/river/solver.hpp)
>
> which is adaptation of step-6 from tutorials(
> https://www.dealii.org/current/doxygen/deal.II/step_6.html)
>
>
> It works very well, but I need as much perfomance as it is possible :) 
>
>
> Mesh, as you can see, is very irregular and very dence at some points(see 
> picture above).
>
> On my laptop i5 from wsl(windows subsystem for linux) it takes ~8-10 
> seconds on DoF with 250,000 degrees(65,000 active cells)
>
> And on cluster with 40 processors even longer - 10-13 seconds
>
>
> Also is the solver already(by default) multithread or I should somehow 
> configure the Deal.II?
>
> Regards,
> Oleg Kmecahk
>
>
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/d1595f6a-206f-4350-9c65-7b39feeafc25%40googlegroups.com.


Re: [deal.II] Re: installation error_CENTOS 7

2019-11-27 Thread Bruno Turcksin
Behrooz,

Le mer. 27 nov. 2019 à 10:30, Behrooz Karami  a écrit :
> Sorry. Is this the correct one?
Yes, that's the one but I don't see anything wrong. Can you try to
install deal.II with spack using a smaller number of dependencies. I
wonder if the problem is a flag from deal.II or the flag from another
library. You don't need to compile deal.II just make sure that it
configures correctly. It should be pretty fast because spack should
not recompile anything else.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eOZwMRd3Xmu1NryLQUB4SGVJOs7BNfFiSWMr3Cy%3DPRx%2Bg%40mail.gmail.com.


Re: [deal.II] Re: installation error_CENTOS 7

2019-11-27 Thread Bruno Turcksin
Behrooz,

Le mer. 27 nov. 2019 à 09:25, Behrooz Karami  a écrit :
> Please find it as attached.
This is the one for CMake not the one for deal.II

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9ePMoTTq_iQjo2pkACR1vhrqEkcEMy-t5SZwybWSKj2u4w%40mail.gmail.com.


[deal.II] Re: installation error_CENTOS 7

2019-11-26 Thread Bruno Turcksin
Behrooz,

When you install gcc with spack did you install gfortran at the same time?

Best,

Bruno

On Tuesday, November 26, 2019 at 8:56:19 AM UTC-5, Behrooz Karami wrote:
>
>
> Dear All,
>
> I am facing an error during last steps of installation of dealii with 
> SPACK on CENTOS 7.
> Could anyone have a look at the attached file which includes the error I 
> get during installation.
> Thank you very much.
> Behrooz Karami
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/f33f3aa6-544f-477f-869c-0afc8931c3e2%40googlegroups.com.


[deal.II] Re: Compatibility of version 8.5.0 and newer versions (9.1)

2019-11-15 Thread Bruno Turcksin
Teresa,

On Friday, November 15, 2019 at 11:40:01 AM UTC-5, Teresa Sanchez Rúa wrote:
>
> Dear all,
> I would like to ask you about the compatibility of version 8.5.0 and the 
> newer versions of deal.II. 
> We installed the version 8.5.0 in a Linux server and we developed a code 
> using it. Now, we want to update the version of deal.II but we are not sure 
> about the compatibility of the libraries in the 8.5.0 version and the newer 
> ones. Is there any problem between these two versions?
>
We try as much as possible to keep the code backward compatible but it is 
not always possible. However, we keep track of all the incompatible 
changes. The incompatible changes from 8.5 to 9.0 can be found here: 
https://dealii.org/9.0.0/doxygen/deal.II/changes_between_8_5_0_and_9_0_0.html 
and the incompatible changes from 9.0 to 9.1 can be found here 
https://dealii.org/current/doxygen/deal.II/changes_between_9_0_1_and_9_1_0.html
 

> Is it possible to install two different versions of deal.II in the same 
> server? I mean, the version 8.5.0 for our old code, and the version 9.1 for 
> new tests.
> Thank you very much for your help.
>
Yes, there is no problem. I always have several versions of deal.II 
installed on my machine.

Best,

Bruno
 

>
>   Teresa.
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/b218a826-5f76-423a-a701-649e065970b9%40googlegroups.com.


Re: [deal.II] Re: step-54 not working

2019-11-07 Thread Bruno Turcksin
I have created a PR https://github.com/dealii/dealii/pull/9016 Thanks
for reporting the bug!

Best,

Bruno

Le jeu. 7 nov. 2019 à 08:13, Bruno Turcksin  a écrit :
>
> Hi,
>
> This looks like a bug in the tutorial. All the cout and endl in that part of 
> the main are missing std:: I don't know how it ever compiled before. Sorry 
> about that.
>
> Best,
>
> Bruo
>
> On Thursday, November 7, 2019 at 7:30:59 AM UTC-5, Mohammed Hassan wrote:
>>
>> Hello everyone!
>>
>>
>> I am fairly new user of Deal.ii,  I have started to follow the tutorial as 
>> it recommend in the diagram until I reached tutorial "step-54" which did not 
>> work for me, at the beginning the error was related to OpenCascade package 
>> bellow a details of what I did:
>> 1- I created a folder "FEA" inside it I downloaded the source file 
>> (dealii-9.1.1) and I extract it and I created two empty  folders named it 
>> "build" and "Opencascade" , so now I have three folders inside the main 
>> folder "FEA" they are "dealii-9.1.1", "build" and "Opencascad".
>> 2- I followed instructions shown in the following link 
>> https://www.dealii.org/current/external-libs/opencascade.html to compile 
>> opencascade. this steps I did it inside the "Opencascade" folder.
>> 3- Then I did " >> cd ../build/ " folder to start compiling Dealii-9.1.1. I 
>> used the following command:
>>
>> >>cmake -DDEAL_II_WITH_OPENCASCADE=ON -DOPENCASCADE_DIR=~/OpenCascade/build 
>> >>../dealii-9.1.1/
>> then I called
>> >> make --jobs=4 install
>>
>> Hoping this was the right approach I moved to tutorial step-54 to test it 
>> and I got the following error in the terminal "shown in error.png "
>
> --
> 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 a topic in the Google 
> Groups "deal.II User Group" group.
> To unsubscribe from this topic, visit 
> https://groups.google.com/d/topic/dealii/xH_OLmdCnRI/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to 
> dealii+unsubscr...@googlegroups.com.
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/dealii/85d60941-6a79-4308-854a-a03ab2cbb0f6%40googlegroups.com.

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eMBkQ2KF%2B9Kh-OJAZf%2BCmrbmA5BWFUXaAWLsDUfkeQ%2Bmg%40mail.gmail.com.


[deal.II] Re: step-54 not working

2019-11-07 Thread Bruno Turcksin
Hi, 

This looks like a bug in the tutorial. All the cout and endl in that part 
of the main are missing std:: I don't know how it ever compiled before. 
Sorry about that.

Best,

Bruo

On Thursday, November 7, 2019 at 7:30:59 AM UTC-5, Mohammed Hassan wrote:
>
> Hello everyone!
>
>
> I am fairly new user of Deal.ii,  I have started to follow the tutorial as 
> it recommend in the diagram until I reached tutorial "step-54" which did 
> not work for me, at the beginning the error was related to OpenCascade 
> package bellow a details of what I did:
> 1- I created a folder "FEA" inside it I downloaded the source file 
> (dealii-9.1.1) and I extract it and I created two empty  folders named it 
> "build" and "Opencascade" , so now I have three folders inside the main 
> folder "FEA" they are "dealii-9.1.1", "build" and "Opencascad".
> 2- I followed instructions shown in the following link 
> https://www.dealii.org/current/external-libs/opencascade.html to compile 
> opencascade. this steps I did it inside the "Opencascade" folder.
> 3- Then I did " >> cd ../build/ " folder to start compiling Dealii-9.1.1. 
> I used the following command:
>
> >>cmake -DDEAL_II_WITH_OPENCASCADE=ON 
> -DOPENCASCADE_DIR=~/OpenCascade/build ../dealii-9.1.1/
> then I called 
> >> make --jobs=4 install
>
> Hoping this was the right approach I moved to tutorial step-54 to test it 
> and I got the following error in the terminal "shown in error.png "
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/85d60941-6a79-4308-854a-a03ab2cbb0f6%40googlegroups.com.


[deal.II] Re: Hanging nodes

2019-10-29 Thread Bruno Turcksin
David,

It won't work. The vertices need to match.

Best,

Bruno

On Tuesday, October 29, 2019 at 1:36:41 PM UTC-4, David Ryan wrote:
>
> Hello,
>
> I'm merging two geometries in dealii. If the cells of both geometries 
> don't match up, will that give hanging nodes, or will the code not be able 
> to handle this?
>
> Kind regards,
>
> David
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/da4bfbce-68bc-41c4-b2d0-e56dc7d236e6%40googlegroups.com.


Re: [deal.II] Re: optimization, SolverBFGS

2019-10-28 Thread Bruno Turcksin
There is a small bug in the lambda:

Le lun. 28 oct. 2019 à 09:36, Juan Carlos Araujo Cabarcas
 a écrit :
>   auto my_lambda = [](Vector a, Vectorb) {
>   return polar.objective_fun(a,b);
>   };  //polar.Callback (a,b);};

You want the vector to be passed by reference not by value, otherwise
the result cannot be updated. So it should be:
auto my_lambda = [](const Vector , Vector ) {
   return polar.objective_fun(a,b);
};

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eOXbEZGg7OpkKH0jr_1y8HMLOHF168jpBVFbmA1%3D%2BJctw%40mail.gmail.com.


Re: [deal.II] Re: optimization, SolverBFGS

2019-10-28 Thread Bruno Turcksin
Here is a simple example:
https://wandbox.org/permlink/fbcldo9PIiHl6tfI  In your case, try
something like

auto my_lambda = [](Vector a, Vectorb) {return
polar.Callback(a,b);};
opt.solve ( my_lambda, X );

Bruno

Le lun. 28 oct. 2019 à 06:30, Juan Carlos Araujo Cabarcas
 a écrit :
>
> Thanks Bruno for your prompt reply,
>
> I got the important part of the code compiling, however since I am new to 
> this lambda (functional) functions, I do not know how to pass the new 
> definitions to SolverBFGS.
>
> Looking at your suggestion I do the following:
>
> class Shape_compute {
> public:
> Parameters par;
>
> Shape_compute (Parameters epar):par(epar) {
> Register([=]( Vector ex, Vector dx ){ return 
> objective_fun (ex,dx); });
> }
>
> void Register(std::function, Vector)> 
> Callback) {} //fun = objective_fun;
>
> double objective_fun ( Vector ex, Vector dx) {
>
> vector x (par.design_N), grad (par.design_N);
> for (unsigned int i=0; i < x.size (); i++) {
> x [i] = ex(i);
> }
> Adaptive::DtN_Helmholtz<2> fem (par, x, true);
> fem.run ();
> double objective_function = fem.objective_function;
>
> for (unsigned int i=0; i < par.design_N; i++) {
> if (i < par.design_N) {
> vector aux = x; aux [i] += h;
> Adaptive::DtN_Helmholtz<2> fem (par, aux, false);
> fem.run ();
> grad [i] = (fem.objective_function - objective_function 
> )/h;
> }
> dx(i) = grad [i];
> }
> iteration++;
> return objective_function;
> }
> };
>
>
> Then, when calling the optimization routine:
>
>   Vector X (N);
>
>   SolverControlresidual_control (N, 1e-7);
>   //SolverBFGS::AdditionalData   data (10, true);
>
>   SolverBFGS > opt (residual_control);//, data);
>
>   Shape_compute  polar(par);
>   opt.solve ( polar.Callback, X ); // If this line is commented, it 
> compiles fine!
>
>
> I would appreciate guidance on how to achieve this,
>
> Thanks in advance,
>   Juan Carlos Araújo

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eOUZVF-swxCJOHXyqG_zg_Jg4qht1BEonEV_HZJHgRqTg%40mail.gmail.com.


[deal.II] Re: optimization, SolverBFGS

2019-10-25 Thread Bruno Turcksin
Juan,

Take a look at 
https://stackoverflow.com/questions/17131768/how-to-directly-bind-a-member-function-to-an-stdfunction-in-visual-studio-11
 

I advise using a lambda like the second reply suggests

Best,

Bruno

On Friday, October 25, 2019 at 10:53:08 AM UTC-4, Juan Carlos Araujo 
Cabarcas wrote:
>
> Dear all,
>
> I would like to use SolverBFGS from deal.II/optimization/ in my project, 
> and I try to follow the documentation in
> https://www.dealii.org/current/doxygen/deal.II/classSolverBFGS.html
>
> First, I would like to mention that the documentation would really improve 
> by adding a minimal example on how to use SolverBFGS.
>
> In my project, I cannot just define an independent function to be pass to 
> SolverBFGS.
> Instead, I define a class ShapePolar, which needs to be initialized with 
> some mesh parameters par, as in
>
> ShapePolar polar (par);
> 
> then I have implemented the function 
>
> double ShapePolar::fun (const Vector, Vector)
>
> that computes a scalar value of an objective function and its gradient 
> Vector, when we pass X.
>
>
> Then, my attempt, after looking at the documentation, is to do something 
> like this:
>
>   Vector X (N);
>   
>   SolverControlresidual_control (N, 1e-7);
>   //SolverBFGS::AdditionalData   data (10, true);
>
>   SolverBFGS > opt (residual_control);   //, data);
>
>   ShapePolar  polar (par);
>   std::function, Vector)>  fun = 
> polar.fun;
>
>   opt.solve ( fun, X );
>
> After several failed attempts (syntax errors), I realize that I am missing 
> something fundamental here and could use some guidance.
> I would appreciate any hint on how to achieve using SolverBFGS for the 
> setting described above.
>
> Kind regards, 
> Juan C. Araújo Cabarcas
>
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/6bd4e298-5449-43d6-9123-789f9ad9e1de%40googlegroups.com.


Re: [deal.II] Re: Docker MPI

2019-10-24 Thread Bruno Turcksin
Doug,

Le mer. 23 oct. 2019 à 18:15, Doug Shi-Dong  a écrit :
> Are you aware of anyone hosting a "development" Docker build for their own 
> continuous integration. I know this can be very expensive to keep up with the 
> commits. Otherwise, I guess I should just build my own Docker with my current 
> deal.II fork.
No, I don't know of anyone building a Docker image for each commit in
the master but I guess we could do it. If there is a bug fix or a new
feature in master that I need, I usually just create a new image from
master. Since the library is very stable, I don't need to create a new
image very often.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9ePobT%3DDmd4hw0886ez6oEAKs_VZqh8oOi6ZD-E-Mwk6wg%40mail.gmail.com.


[deal.II] Re: Docker MPI

2019-10-22 Thread Bruno Turcksin
Doug,

You are using an image build using spack so everything is installed using 
spack instead of the package manager. If you type `spack find` inside a 
container, you will see that mpich is installed.

Best,

Bruno

On Monday, October 21, 2019 at 9:53:36 PM UTC-4, Doug Shi-Dong wrote:
>
> Hello everyone,
>
> I would like to use Travis CI to test pull requests, and I am currently 
> following the steps described in 
> https://github.com/dealii/dealii/wiki/Docker-Images
>
> Except I am using the following Docker image: 
> dealii/dealii:v9.1.1-gcc-mpi-fulldepsspack-debugrelease
>
> It seems that this Docker imagine does not contain an MPI package in its 
> installation. Here is a log of my Travis CI build
>
> https://travis-ci.org/dougshidong/PHiLiP/builds/600536273
>
> The command apt search mpi shows that no packages such as openmpi or 
> mpich is available. However, oddly enough, DEAL_II_WITH_MPI is ON, when my 
> CMake checks for it.
>
> If no MPI is available, how do I compile the code within this Docker 
> container?
>
> Best regards,
>
> Doug
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/c164a371-e974-4991-a769-a8d62fa07335%40googlegroups.com.


Re: [deal.II] Re: error during installation with spack on CentOS7

2019-10-14 Thread Bruno Turcksin
Alberto,

Le lun. 14 oct. 2019 à 14:18, Alberto Salvadori
 a écrit :
>
> Thank you, Bruno.
> I did notice the very same error. I do not know either why this error 
> emerges, the installation of hypre, PETSc was part of the spack installation 
> process.
> Since all preliminary packages have now been installed with no further 
> errors, I suspect that some settings shall be redefined in the spack system 
> in order to configure
> the installation of deal.ii. Whom should I address this question to?
I would report that to spack maybe someone there has seen the same
error. The fact that there are missing symbols should not be specific
to deal.II. I guess the solution for now, is to either switch to the
Trilinos stack or to install petsc and hypre by hand :(

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eOCBcGtqrRb%3DNBYfc9B%3Db%3Dsz_9OZxd%3Dom%2BCdr0smSGT%3DA%40mail.gmail.com.


Re: [deal.II] Re: error during installation with spack on CentOS7

2019-10-14 Thread Bruno Turcksin
Alberto,

If you look in the CMakeError.log, you can see what's the real problem:

/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s/lib/libpetsc.so:
undefined reference to `hypre_ParCSRMatrixCompleteClone'

Hypre is in the linking line so I am not sure what's the problem. I
don't use PETSc and Hypre so I don't know why you have this error.

Best,

Bruno

Le ven. 11 oct. 2019 à 14:04, Alberto Salvadori
 a écrit :
>
> Sorry to invoke your help again,
> since though I am stuck in the very final step, I wonder if anyone can 
> provide some suggestions to the issue below. I really appreciate
> Alberto
>
> Il giorno mercoledì 9 ottobre 2019 09:30:18 UTC+2, Alberto Salvadori ha 
> scritto:
>>
>> Hi Denis
>>
>> thank you very much for pointing out to @balay. His suggestion:
>>
>> spack install slepc~arpack ^hypre@develop
>>
>> indeed works. I will prepare a short report on successful installation on 
>> CentOS7 through spack, summarizing all these issues.
>> I am almost there, but another - hopefully small - problem arises and it is 
>> related to the installation of the deal.ii package, thus this forum should 
>> be appropriate.
>> Here is the error message,
>>
>> ==> Installing dealii
>>
>> ==> Searching for binary cache of dealii
>>
>> ==> Warning: No Spack mirrors are currently configured
>>
>> ==> No binary for dealii found: installing from source
>>
>> ==> Using cached archive: 
>> /home/deal.ii/spack/var/spack/cache/dealii/dealii-9.1.1.tar.gz
>>
>> ==> Staging archive: 
>> /tmp/deal.ii/spack-stage/dealii-9.1.1-3idaq2jucltrqd5z5bdgsdxgfhirhrwx/dealii-9.1.1.tar.gz
>>
>> ==> Created stage in 
>> /tmp/deal.ii/spack-stage/dealii-9.1.1-3idaq2jucltrqd5z5bdgsdxgfhirhrwx
>>
>> ==> No patches needed for dealii
>>
>> ==> Building dealii [CMakePackage]
>>
>> ==> Executing phase: 'cmake'
>>
>> ==> Error: ProcessError: Command exited with status 1:
>>
>> 'cmake' 
>> '/tmp/deal.ii/spack-stage/dealii-9.1.1-3idaq2jucltrqd5z5bdgsdxgfhirhrwx/spack-src'
>>  '-G' 'Unix Makefiles' 
>> '-DCMAKE_INSTALL_PREFIX:PATH=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/dealii-9.1.1-3idaq2jucltrqd5z5bdgsdxgfhirhrwx'
>>  '-DCMAKE_BUILD_TYPE:STRING=DebugRelease' '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' 
>> '-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=FALSE' 
>> 

Re: [deal.II] Re: error during installation with spack on CentOS7

2019-10-02 Thread Bruno Turcksin
Alberto,

So what happens is that spack is using gcc 9.2 like you want but it
usess the libstdc++ from gcc 4.8.5 I usually spack to install a new
compiler and my compilers.yaml looks like your *but* I have the path
to the correct libstdc++ in my LD_LIBRARY_PATH when I load the module.
So I guess you need to add that path somewhere in your compilers.yaml

Best,

Bruno

Le mer. 2 oct. 2019 à 08:51, Alberto Salvadori
 a écrit :
>
> Thank you, Bruno. In fact, my aim was to use my system compiler.
> Here is my  .spack/linux/packages.yaml:
>
> packages:
>
>   all:
>
> compiler: [gcc]
>
> providers:
>
>   mpi: [openmpi]
>
>   openmpi:
>
> version: [3.1.4]
>
> paths:
>
>   openmpi@3.1.4%gcc@9.2.0: /usr/local/
>
> buildable: False
>
>   perl:
>
> paths:
>
>   perl@5.16.3%gcc@9.2.0: /usr
>
>   cmake:
>
> version: [3.15.3]
>
> paths:
>
>   cmake@3.15.3%gcc@9.2.0: /usr/local/
>
>   hdf5:
>
> version: [1.8.12]
>
> paths:
>
>   hdf5@1.8.12%gcc@9.2.0: /usr
>
> variants: +hl+fortran
>
>   netcdf:
>
> version: [7.2.0]
>
> paths:
>
>  netcdf@7.2.0%gcc@9.2.0: /usr
>
>   netcdf-cxx:
>
> version: [4.2.8]
>
> paths:
>
>  netcdf-cxx@4.2.8%gcc@9.2.0: /usr
>
>   dealii:
>
> variants: +optflags~python
>
>
> Shall I perhaps add something to the compiler flag (paths or so)?
> Here is also my  .spack/linux/compilers.yaml
>
> compilers:
>
> - compiler:
>
> environment: {}
>
> extra_rpaths: []
>
> flags: {}
>
> modules: []
>
> operating_system: centos7
>
> paths:
>
>   cc: /usr/bin/gcc
>
>   cxx: /usr/bin/g++
>
>   f77: /usr/bin/gfortran
>
>   fc: /usr/bin/gfortran
>
> spec: gcc@4.8.5
>
> target: x86_64
>
> - compiler:
>
> environment: {}
>
> extra_rpaths: []
>
> flags: {}
>
> modules: []
>
> operating_system: centos7
>
> paths:
>
>   cc: /usr/local/bin/gcc
>
>   cxx: /usr/local/bin/g++
>
>   f77: /usr/local/bin/gfortran
>
>   fc: /usr/local/bin/gfortran
>
> spec: gcc@9.2.0
>
> target: x86_64
>
>
>
> Alberto
>
>
> Alberto Salvadori
>  Dipartimento di Ingegneria Meccanica e Industriale (DIMI)
>  Universita` di Brescia, via Branze 43, 25123 Brescia
>  Italy
>  tel 030 3711239
>  fax 030 3711312
>
> e-mail:
>  alberto.salvad...@unibs.it
> web-page:
>  http://m4lab.unibs.it/faculty.html
>
>
>
> On Wed, Oct 2, 2019 at 2:41 PM Bruno Turcksin  
> wrote:
>>
>> Alberto,
>>
>> On Wednesday, October 2, 2019 at 7:24:32 AM UTC-4, Alberto Salvadori wrote:
>>>
>>>
>>> Thank you so much W and D,
>>> As you pointed out there seems to be a mistake in the most recent version 
>>> of perl during installation.
>>> I will propagate this to the proper communities.
>>>
>>> As Denis proposed, I went on simply tell Spack to use Perl from system:
>>>
>>> perl:
>>> paths:
>>>  perl@5.26.2%gcc@9.2.0: /usr
>>>
>>> but I bumped into another issue:
>>>
>>> [deal.ii@localhost spack]$ spack install dealii^cmake@3.9.4
>>>
>>> ==> libsigsegv is already installed in 
>>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/libsigsegv-2.11-brkulrpubdu66nzym2zt2j6c3h6nw463
>>>
>>> ==> m4 is already installed in 
>>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/m4-1.4.18-23npyrcdfzqehgp4s2mhka4nknjjkbzt
>>>
>>> ==> perl@5.16.3 : externally installed in /usr
>>>
>>> ==> perl@5.16.3 : already registered in DB
>>>
>>> ==> autoconf is already installed in 
>>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/autoconf-2.69-2vk2foufmuyjm2gh47u6nouxezza3p6p
>>>
>>> ==> automake is already installed in 
>>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/automake-1.16.1-z52jybnv7ass3otkgegjazvdbbughw2q
>>>
>>> ==> libtool is already installed in 
>>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/libtool-2.4.6-mr3m4npcnryydzctugoebk2zuoav7zte
>>>
>>> ==> adol-c is already installed in 
>>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/adol-c-develop-xioth2pegguh6rb6mzfzk7zhvb2kgeue
>>>
>>> ==> pkgconf is already installed in 
>>> /home/

Re: [deal.II] Re: error during installation with spack on CentOS7

2019-10-02 Thread Bruno Turcksin
Alberto,

On Wednesday, October 2, 2019 at 7:24:32 AM UTC-4, Alberto Salvadori wrote:
>
>
> Thank you so much W and D,
> As you pointed out there seems to be a mistake in the most recent version 
> of perl during installation.
> I will propagate this to the proper communities. 
>
> As Denis proposed, I went on simply tell Spack to use Perl from system:
>
> perl:
> paths:
>  perl@5.26.2%gcc@9.2.0: /usr
>
> but I bumped into another issue:
>
> [deal.ii@localhost spack]$ spack install dealii^cmake@3.9.4
>
> *==>* libsigsegv is already installed in 
> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/libsigsegv-2.11-brkulrpubdu66nzym2zt2j6c3h6nw463
>
> *==>* m4 is already installed in 
> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/m4-1.4.18-23npyrcdfzqehgp4s2mhka4nknjjkbzt
>
> *==>* perl@5.16.3 : externally installed in /usr
>
> *==>* perl@5.16.3 : already registered in DB
>
> *==>* autoconf is already installed in 
> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/autoconf-2.69-2vk2foufmuyjm2gh47u6nouxezza3p6p
>
> *==>* automake is already installed in 
> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/automake-1.16.1-z52jybnv7ass3otkgegjazvdbbughw2q
>
> *==>* libtool is already installed in 
> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/libtool-2.4.6-mr3m4npcnryydzctugoebk2zuoav7zte
>
> *==>* adol-c is already installed in 
> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/adol-c-develop-xioth2pegguh6rb6mzfzk7zhvb2kgeue
>
> *==>* pkgconf is already installed in 
> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/pkgconf-1.6.1-qtpkfoaa5ae54s4icmqie5hbtz6murqx
>
> *==>* ncurses is already installed in 
> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/ncurses-6.1-awd5putjsuzsddipc35vxiupdjicseao
>
> *==>* zlib is already installed in 
> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/zlib-1.2.11-fa7l75havytsbgz77sh6yyzvqgmmm5dj
>
> *==>* openssl is already installed in 
> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openssl-1.1.1c-ou63dp5nv43t2vudcv44rc753i7yecl2
>
> *==>* *Installing* *cmake*
>
> *==>* Searching for binary cache of cmake
>
> *==>* Warning: No Spack mirrors are currently configured
>
> *==>* No binary for cmake found: installing from source
>
> *==>* Using cached archive: 
> /home/deal.ii/spack/var/spack/cache/cmake/cmake-3.9.4.tar.gz
>
> *==>* Staging archive: 
> /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/cmake-3.9.4.tar.gz
>
> *==>* Created stage in 
> /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4
>
> *==>* Applied patch 
> /home/deal.ii/spack/var/spack/repos/builtin/packages/cmake/nag-response-files.patch
>
> *==>* Building cmake [Package]
>
> *==>* Executing phase: 'bootstrap'
>
> *==>* Error: ProcessError: Command exited with status 11:
>
> './bootstrap' 
> '--prefix=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4'
>  
> '--parallel=12' '--no-system-libs' '--no-qt-gui' '--' 
> '-DCMAKE_USE_OPENSSL=True'
>
>
> 1 error found in build log:
>
>  196/home/deal.ii/spack/lib/spack/env/gcc/g++   -std=gnu++14 
> -I/tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-src/Bootstrap.cmk
>  
>   
> -I/tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-sr
>
> c/Source   
> -I/tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-src/Source/LexerParser
>  
>   
> -I/tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-src/Utilities
>   
> cmAddCustomCommandCommand.o cmAd
>
> dCustomTargetCommand.o cmAddDefinitionsCommand.o 
> cmAddDependenciesCommand.o cmAddExecutableCommand.o cmAddLibraryCommand.o 
> cmAddSubDirectoryCommand.o cmAddTestCommand.o cmBreakCommand.o 
> cmBuildCommand.o cmCMakeMinimumRequired.o cmCMakePoli
>
> cyCommand.o cmCPackPropertiesGenerator.o cmCacheManager.o 
> cmCommand.o cmCommandArgumentParserHelper.o cmCommandArgumentsHelper.o 
> cmCommands.o cmCommonTargetGenerator.o cmComputeComponentGraph.o 
> cmComputeLinkDepends.o cmComputeLinkInformati
>
> on.o cmComputeTargetDepends.o cmConditionEvaluator.o 
> cmConfigureFileCommand.o cmContinueCommand.o cmCoreTryCompile.o 
> cmCreateTestSourceList.o cmCustomCommand.o cmCustomCommandGenerator.o 
> cmDefinePropertyCommand.o cmDefinitions.o cmDepends.
>
> o cmDependsC.o cmDisallowedCommand.o 
> cmDocumentationFormatter.o cmEnableLanguageCommand.o 
> cmEnableTestingCommand.o cmExecProgramCommand.o cmExecuteProcessCommand.o 
> cmExpandedCommandArgument.o cmExportBuildFileGenerator.o cmExportFileGenera
>
> tor.o cmExportInstallFileGenerator.o cmExportSet.o 
> cmExportSetMap.o cmExportTryCompileFileGenerator.o cmExprParserHelper.o 
> cmExternalMakefileProjectGenerator.o 

[deal.II] Re: Issue with boost serialization and spack?

2019-10-02 Thread Bruno Turcksin
Konrad

On Wednesday, October 2, 2019 at 5:50:53 AM UTC-4, Konrad Simon wrote:
>
>  
>
>>
>>> However, now my code runs on the machine I installed it on. But once I 
>>> use slurm to distribute the job across nodes I get "illegal instruction" 
>>> erros. Frustrating.
>>>
>>
>> With HPC I used to have access to they did not use slurm, so I can't 
>> really comment here.
>> If that's during running quick tests or so, it could be related to a 
>> wrong MPIEXEC pickedup by deal.II config.
>> I wanted to fix that in Spack https://github.com/spack/spack/pull/11142 
>> but apparently this solution may not be fully functional for Slurm.
>>
>
> I guess I have a clue why I get the error. My backend nodes run on a 
> different architecture. The openmpi version (i.e. mpirun) is the correct 
> one. This is made sure in the slurm script.
>
That's always a pain to deal with. If you can, I would get an interactive 
session on a compute node and compile everything on the compute node. You 
can also compile everything in batch mode or compute on the login node and 
pass the flag for the architecture of the compute node.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/db27dbf6-135f-4e72-9920-29db9d4bdc3d%40googlegroups.com.


[deal.II] Re: problem about The move mesh func

2019-09-26 Thread Bruno Turcksin
Hi, 

Take a look at 
https://github.com/dealii/dealii/wiki/Frequently-Asked-Questions#in-my-graphical-output-the-solution-appears-discontinuous-at-hanging-nodes

Best,

Bruno

On Thursday, September 26, 2019 at 10:09:16 AM UTC-4, huyanzhuo wrote:
>
> i use The move mesh function, the code is as follows, just like in step-42
> template < int dim >
> void example::move_mesh(const TrilinosWrappers::MPI::Vector 
> _change) const
> {
>   pcout<<"moving the mesh ..." <   std::vector vertex_touched(triangulation.n_vertices(), false);
>
>   for (typename DoFHandler::active_cell_iterator cell 
> =dof_handler.begin_active();cell != dof_handler.end(); ++cell)
> if (cell->is_locally_owned())  
>  
>   for (unsigned int v = 0; v < 
> GeometryInfo::vertices_per_cell; ++v) 
> {
>   if(vertex_touched[cell->vertex_index(v)] == false)
>   {
> vertex_touched[cell->vertex_index(v)] = true;
>
> Point vertex_displacement;
> for (unsigned int d = 0; d < dim; ++d)
>  
>   vertex_displacement[d] = 
> state_change(cell->vertex_dof_index(v, d));
> cell->vertex(v) += vertex_displacement;
>   }
> }
> }
>
> before i use this function ,i use the constraints matrix to distribute the 
> vector like this
> TrilinosWrappers::MPI::BlockVector move_vector(system_state);
> move_vector = system_state;
> all_constraints.distribute(move_vector);
> move_mesh(move_vector.block(0));
>
> but the final result still have a departure on the hanging point as follows
>
> [image: example.png]
>
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/2eed0c77-6382-4890-aa0f-754f9a2e6243%40googlegroups.com.


[deal.II] Re: Specifying internal "boundary" conditions

2019-09-18 Thread Bruno Turcksin
Mélanie,

I am not sure I understand exactly what you want to do but often people who 
want internal boundary conditions, really just want to impose some 
constraints to a few dofs. This can be done using AffineConstraints 
. I 
am sure that you have seen it in the tutorials where it is used to 
constrain hanging nodes and to impose Dirichlet boundary condition. 
Basically, you can create one yourself to impose any constraint you want on 
any dofs.

I hope this help.

Bruno

On Wednesday, September 18, 2019 at 11:34:12 AM UTC-4, Mélanie Gérault 
wrote:
>
> Hi,
>
> I am wondering if anyone has ever implemented/used internal boundary 
> conditions in deal.II. I need to impose displacements inside of a domain. I 
> am assuming that it is feasible with the code, but please let me know if I 
> am wrong.
>
> And in case I need to do it from scratch, I would also appreciate any 
> suggestion you may have.
>
> Thanks a lot!
>
> Mélanie
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/0809d12a-bac9-4f0d-8dc1-430667b90ea3%40googlegroups.com.


[deal.II] Re: On the usage of Utilities::MPI

2019-09-11 Thread Bruno Turcksin
Yang,

Are sure that you compiled deal.II with MPI support? Also can you post  
what you see when you do make VERBOSE=1

Best,

Bruno

On Wednesday, September 11, 2019 at 8:44:29 AM UTC-4, Yang Liu wrote:
>
> Dear Deal.II developers,
>
> Greetings!
>
> I am a new user of Deal.II. Currently I would like to test the hello world 
> program on Utilities::MPI. 
>
> A minimum working example is attached to this email. 
>
> However, when I run the command "mpirun -np 5 ./MPI_TEST", I get the 
> following message,
>
> Hello world from process 0 of 1
> Hello world from process 0 of 1
> Hello world from process 0 of 1
> Hello world from process 0 of 1
> Hello world from process 0 of 1
>
> It seems that 5 cpu cores are used, however, they seemed to have the same 
> rank. 
> Besides, my operating system is Ubuntu 16.04. Looking forward to hearing 
> from you soon. Thank you!
>
> Best Regards,
>
> Yang Liu
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/00946786-1eac-4cd6-9871-8d705e1e913d%40googlegroups.com.


[deal.II] Re: Adaptive TimestepControl

2019-09-05 Thread Bruno Turcksin
Reza,

Take a look at step-52. We have implemented different time stepping methods 
including embedded ones that automatically choose the time step for you. 
These methods will give you an hint on what the time step should be but you 
can always override the value if you have a better criteria. If the error 
is too large, the time step will be automatically reduced.

Best,

Bruno

On Wednesday, September 4, 2019 at 8:13:14 PM UTC-4, Reza Rastak wrote:
>
> Hi,
>
> I recently learned about the class Algorithms::TimestepControl and how it 
> is being used in the Algorithms::ThetaTimestepping class. It has a fairly 
> limited set of strategies (uniform step size and doubling step size). I 
> wonder if we can customize it to allow adaptive time stepping. Let me 
> explain with an example. Suppose we are running a time dependent algorithm 
> and at each time-step we perform a Newton algorithm to solve a nonlinear 
> time-dependent equation. The Newton algorithm reports its convergence 
> quality through a SolverControl object. When we are advancing the time, we 
> need to adjust the time step size based on the results stored in the 
> SolverControl object. If it took too many steps to converge, we should 
> reduce the time step size and if the convergence was easy, we can increase 
> the step size. 
>
> 1. Is there already a class in dealii that can do that?
> 2. If we want to implement this functionality, what are the best designs 
> for the interface?
>
> There is another related functionality that I am also looking for. If the 
> convergence in one of the steps fails, we need to go back in time and redo 
> the calculations with a smaller time step size. Any ideas on how I can make 
> that work?
>
> Thank you
>
> Reza
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/19af2460-7ce5-48ec-a620-c32461b3e743%40googlegroups.com.


[deal.II] Re: Where can I find member function of cell?

2019-08-27 Thread Bruno Turcksin
Yuesu,

For a Triangulation, the list is 
here:https://dealii.org/current/doxygen/deal.II/classCellAccessor-members.html 
(CellAccessor)
For a DofHandler, the list is here: 
https://dealii.org/current/doxygen/deal.II/classDoFCellAccessor-members.html 
(DofCellAccessor)

Best,

Bruno

On Monday, August 26, 2019 at 10:42:00 PM UTC-4, yuesu jin wrote:
>
> Hi all,
>   When we iterate the cell within triangulation/dof_handler, we often use 
> functions such as cell->face(), cell->vertices()  etc. Where can I find all 
> the member function in our documentation webpage? Thanks a lot!
>
> -- 
> Yuesu Jin,
> Ph.D student,
> University of Houston,
> College of Natural Sciences and Mathematics,
> Department of Earth and Atmospheric Sciences,
> Houston, Texas 77204-5008 
> 346-404-2062
>
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/141f7ec4-53af-4336-8bdc-5f4897d5acff%40googlegroups.com.


[deal.II] Re: Real Step-29

2019-08-20 Thread Bruno Turcksin
Adil,

If you look in the output_results 

 
section. You can see the following code:

std::vector solution_names;
solution_names.emplace_back("Re_u");
solution_names.emplace_back("Im_u");
data_out.add_data_vector 
(solution,
 
solution_names);

What happens is that the first component of solution is associated with 
Re_u and the second component with Im_u.

Best,

Bruno

On Tuesday, August 20, 2019 at 12:36:41 AM UTC-4, Muhammad Adil wrote:
>
> Hi Everone,
> In the tutorial step-29 of deal.II 8.3.0, the solution in paraview can be 
> visualized as Real, Imaginary and Intensity.
> Intensity is calculated manually in the tutorial and visualized but how 
> paraview knows that solution ( u[i][0] and u[i][1] ) consits of two parts, 
> one u[i][0] is real and the other u[i][1] is imaginary.
> Because there is nothing in the mentioned in the code. Pleae anyone 
> explain?
>
> Adil
>
> [image: step-29 1.png][image: step-29 3.png][image: step-29 2.png]
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/f641c722-ad99-4784-869c-9292fd50c1e3%40googlegroups.com.


Re: [deal.II] Re: curl_value_list function ?

2019-08-20 Thread Bruno Turcksin
Le lun. 19 août 2019 à 23:53, Muhammad Adil  a écrit :
> I mean Ross kynch used curl_value_list but I couldn't find it in the deal.II 
> 8.3.0 documents. Like I found vector_value_list in the documents.
That's because it is not a function in deal.II Have you tried to grep
curl_value_list in the code?

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eMMaUCMg3cwS_QzL%3Dx7XRV4njJNz2KhCe6%3D9B-dYeKCXQ%40mail.gmail.com.


Re: [deal.II] Re: curl_value_list function ?

2019-08-19 Thread Bruno Turcksin
Adil

Le lun. 19 août 2019 à 09:44, Muhammad Adil  a écrit :
> Actually the function curl_value_list is look vector_value_list but there is 
> not any definition in the Ross kynch code, it means that this function is 
> also from deal.II.
What do you mean?

> But I search it in the documents there is not any function in the class 
> function.h like vector_value_list available in this class.
As far as I remember, function never had curl_value_list.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eN6B5VLsZyumSg%3DY3BNLo7pq36CjRStcNvOr_GrQybCSg%40mail.gmail.com.


[deal.II] Re: curl_value_list function ?

2019-08-19 Thread Bruno Turcksin
Adil,

This class extends `dealii::Functions`. It implements the function 
`vector_value_list()` which otherwise does nothing in `dealii::Function` 
and then adds many new functions. This new class has the functionalities of 
`dealii::Function` plus new ones.  Does it make sense?

Best,

Bruno

On Monday, August 19, 2019 at 6:49:27 AM UTC-4, Muhammad Adil wrote:
>
> Hi Everyone,
> I am using Ross Kynch code. Ross Kynch used the deal.II versin 8.3.0.
> I am searching a fucntions which were used by Ross with namee 
> Vector_value_list and Curl_value_list.
> I easily found the function with name vector_value_list in the deal.II 
> version 8.3.0 but I am finding anywhere the later fucntion.
> I will appreciate if anybody can help me to explain because the code is 
> running successfully.
>
> template
> class EddyCurrentFunction : public Function
> {
> public:
> // Leave out constructor for now, we may need to create one which
> // calls the Function constructor with n_components = dim+dim by default).
> //EddyCurrentFunction (unsigned int n_components = dim+dim);
> // We overload each member so that it implements the style found in 
> Function
> // as well as allowing the use of the material_id if required.
> // The obvious way to do this is to implement the Function-style 
> version by
> // calling the material_id version with numbers::invalid_material_id,
> // effectively making it the default value for that argument.
> //
> // Obviously derived classes an bypass this if required.
> virtual void vector_value_list (const std::vector > ,
> std::vector > ) const;
> virtual void vector_value_list (const std::vector > ,
> std::vector > ,
> const types::material_id _id) const;
> virtual void curl_value_list (const std::vector > ,
> std::vector > ) const;
>
> virtual void curl_value_list (const std::vector > ,
> std::vector > ,
> const types::material_id _id) const;
> virtual void perturbed_field_value_list (const std::vector > &
> points,
> std::vector > ) const;
>
> virtual void perturbed_field_value_list (const std::vector > &
> points,
> std::vector > ,
> const types::material_id _id) const;
>
> virtual void rhs_value_list (const std::vector > ,
> std::vector > ) const;
> virtual void rhs_value_list (const std::vector > ,
> std::vector > ,
> const types::material_id _id) const;
> virtual void scattered_field_value_list (const std::vector > &
> points,
> std::vector > ) const;
> virtual void scattered_field_value_list (const std::vector > &
> points,
> std::vector > ,
> const types::material_id _id) const;
>
> virtual bool zero_vector() const { return true; }
> virtual bool zero_curl() const { return true; }
> virtual bool zero_perturbed() const { return true; }
> virtual bool zero_rhs() const { return true; }
> virtual bool zero_scattered() const { return true; }
> };
>
>
> Adil
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/cb812c9e-fed9-4e5e-b4ec-c3eb4357ce84%40googlegroups.com.


[deal.II] Re: Problems while solving Implicit Runge Kutta method.

2019-08-09 Thread Bruno Turcksin
Sora,

On Thursday, August 8, 2019 at 3:42:54 AM UTC-4, sora wrote:
>
> I have to solve the continuity equation in 1D using Implicit Runge Kutta 
> method. 
>
> The formula I made is this: d(U_t+1)/dt = [-grad(\Gamma_e)+R_i]/exp(U_t)
>   \Gamma_e ,R_i : Load the value calculated by another function.
>   U_t : Solution calculated at the previous time.
>
> When implicit_runge_kutta.evolve_one_time_step(..) and 
> evaluate_diffusion_energy(..) is repeated, the value(U_t) I load changes.
> U_t, the value that should be divided, becomes 0 and an error occurs.
>
What becomes zero? U_t or exp(initial_EnergyDensity)? Where is 
initial_EnergyDensity updated?

Best,

Bruno


-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/d507c2d9-9b9e-4df2-822b-d57d166c974d%40googlegroups.com.


Re: [deal.II] Re: Porting tutorials to PETSc from Trilinos

2019-07-19 Thread Bruno Turcksin
Franco

Le ven. 19 juil. 2019 à 10:04, Franco Milicchio
 a écrit :
> Is there a small documentation that I can read? For instance, I see there are 
> several namespaces like LinearAlgebra, PETSc/Epetra/Trilinos/CUDAWrappers, 
> LinearAlgebraDealii and so on, that might be restructured without 
> compromising old codes, adding some uniformity to classes.
No unfortunately we don't have such things. However, most of the new
effort on linear algebra is in the LinearAlgebra namespace.

> 
> An error occurred in line <3781> of file 
> 
>  in function
> void dealii::AffineConstraints::distribute_local_to_global(const 
> FullMatrix &, const Vector &, const std::vector &, 
> MatrixType &, VectorType &, bool, std::integral_constant) const 
> [number = double, MatrixType = dealii::BlockSparseMatrix, VectorType 
> = dealii::BlockVector]
> The violated condition was:
> static_cast std::common_type decltype(global_vector.size())>::type)>::type>(global_matrix.m()) == 
> static_cast std::common_type decltype(global_vector.size())>::type)>::type>(global_vector.size())
> Additional information:
I don't know why this error is so unreadable but if you look at line
3781 in include/deal.II/lac/affine_constraints.templates.h you will
see that the assert checks that the global matrix has as many rows has
the global vector. To me it looks like the problem is that the global
vector as a size of zero.

If you forget about the static_cast in the error message just above
you can actually see what happens:
The violated condition was:
global_matrix.m() == global_vector.size()

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eM%2Bg5HhuJOyQ3%3D-D__EbUyf7tZS5ZqyTu32rxVN1S-vXw%40mail.gmail.com.


Re: [deal.II] Re: Porting tutorials to PETSc from Trilinos

2019-07-18 Thread Bruno Turcksin
Franco,

Le jeu. 18 juil. 2019 à 10:27, Franco Milicchio
 a écrit :
> Thanks for your answer. By the way, would a wrapper for the Eigen library be 
> appealing to anyone?
I am sure it would be useful!

> 
> An error occurred in line <382> of file 
> 
>  in function
> T *dealii::SmartPointer dealii::SparseMatrix >::operator->() const [T = const 
> dealii::SparsityPattern, P = dealii::SparseMatrix]
> The violated condition was:
> pointed_to_object_is_alive
> Additional information:
> The object pointed to is not valid anymore.

It looks like the sparsity pattern does not exist anymore. The matrix
object does not keep a copy of the sparsity pattern, so the sparsity
pattern needs to exist as long as the matrix that uses it is alive.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eNGQNQt9qe389vk8ZWm2e02z_T8_cQ53_d%2B5KQ9%3DdX-jw%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.


Re: [deal.II] Re: Compatibility of Petsc with step 18

2019-07-17 Thread Bruno Turcksin
Ramprasad,

Le mer. 17 juil. 2019 à 11:24, Ramprasad R
 a écrit :
> Yes I did recompile it. The details of the config files are in the attachment.
There is something strange in you installation: detailed.log says that
you are using PETSc but config.h says that you are not. It looks like
you compiled deal.II without PETSc and then in the same directory
recompiled deal.II with PETSc supports. This can cause the strange
behavior that you are seeing. Remove your build directory and
reinstall deal.II from scratch.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eP5bqzDKi5CHFW0%3DeMF1bv%3DALRVJg2z61T2bZZEUronjA%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.


Re: [deal.II] Re: Issue regarding higher order element

2019-07-16 Thread Bruno Turcksin
Krishanu

Le mar. 16 juil. 2019 à 16:00, Krishanu Sen  a écrit :
>
> I am using deal.ii for a nonlinear elasticity problem. And the change in the 
> code that is causing this error message is:
>
>
>  template 
>   ElasticProblem::ElasticProblem ()
> :
> dof_handler (triangulation),
> fe (FE_Q(3), dim)
>   {}
No it's not where the error comes from. It is from somewhere in
Step8::ElasticProblem<1>::assemble_system_matrix() You need to find
which line produces the error.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9eOaE9g2sehRfaT-9B8JVq9pE79jdOV5uqMBF3LFzCQuaw%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.


[deal.II] Re: Issue regarding higher order element

2019-07-16 Thread Bruno Turcksin
Krishanu,

It's impossible to help you with so little information. Somewhere you set 
something to the wrong size. Can you give us a backtrace? We need to see 
the error message and the code that produces it.

Best,

Bruno

On Tuesday, July 16, 2019 at 3:08:42 PM UTC-4, Krishanu Sen wrote:
>
> I am trying to run a code using higher order elements. The code runs fine 
> when I am using linear [FE_Q(1)] or quadratic [FE_Q(2)] elements. 
> But when I tried to use cubic elements [FE_Q(3)], the code stops with 
> an error "ExcIndexRange", which says that the code is trying to access an 
> index of a tensor that exceeds the limit of the tensor indices. I am not 
> sure why would that happen just because of changing the polynomial degree 
> of the element. I would appreciate any help or insight regarding the issue.
>
> Thanks,
> Krishanu
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/4f277d7a-396b-43f7-b887-32c850ae6944%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


Re: [deal.II] Re: Compatibility of Petsc with step 18

2019-07-16 Thread Bruno Turcksin
Ramprasad,

On Tuesday, July 16, 2019 at 11:51:00 AM UTC-4, Ramprasad R wrote:
>
> The version of deal.ii is 9.0.1 and the version of PETSc is 3.10.5. I also 
> changed the config file of deal.ii to have MPI PETSc on.
>
What do you mean by "I changed the config file of deal.II"? You should not 
change any file generated by deal.II. When you compiled deal.II, did you 
use the option -DDEAL_II_WITH_PETSC=ON? If not, deal.II was not compiled 
with PETSc supports.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/0372d95b-ae52-457e-9400-9e8159469a62%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


[deal.II] Re: Porting tutorials to PETSc from Trilinos

2019-07-16 Thread Bruno Turcksin
Franco,

On Tuesday, July 16, 2019 at 3:54:34 AM UTC-4, Franco Milicchio wrote:
>
>
> Can I ask why there are some discrepancies between those two wrappers? 
> Apart from an obvious one, that they're different libraries, but uniformity 
> may help a lot IMO.
>
Because the wrappers have been written over time by different people who 
were not aware of how exactly the other wrapper works (most people use 
either Trilinos or PETSc not both). We are trying to get the interfaces to 
be more similar but it is very difficult because any change in the 
interface will break many codes.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/533ea4e2-44fd-43f0-8bd7-93b77bdbd6ed%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


[deal.II] Re: Can I get the cell numbers of the cells neighbouring a face?

2019-07-10 Thread Bruno Turcksin
Stephen

On Wednesday, July 10, 2019 at 3:56:02 PM UTC-4, Stephen wrote:
>
> I have an error estimator which I need to calculate between edges and I'd 
> like to loop over all edges in the triangulation. I know that I can do this 
> the "traditional" way via looping over all cells and then looping over all 
> faces in the cell but, if I do this, I end up calculating the same thing 
> twice since I then run over non-boundary faces once from one cell and then 
> again from it's neighbour; this is not acceptable since efficiency is 
> really of paramount importance in the code I'm currently writing. Is it 
> possible to instead loop over all active edges in the triangulation and 
> then find the cell IDs of the cells which neighbour this face? This way I 
> should be able to calculate the terms directly on the edge instead of 
> trying to go via the cell first. Thanks!
>
What you can do is to check that the face is not on the boundary and in 
that case only compute your error on the left and the bottom edges (for 
example). I think you could also use this function 

 
to do all the heavy lifting for you.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/a9f98552-5ca3-4bf6-a54e-01fed8f46ade%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


[deal.II] Re: 20 tests failed after make install

2019-07-05 Thread Bruno Turcksin
Zhenbang Wei,

Is it possible that Trilinos was compiled without MPI support? The two 
error you see come from Trilinos functions that uses MPI.

Best,

Bruno

On Thursday, July 4, 2019 at 10:15:51 AM UTC-4, Zb W wrote:
>
> Hello,
> I want to install deal.ii (9.1.1) in the ubuntu 18.04 on Windows 10 WSL.
> I installed the software needed and there are no mistake reports during 
> cmake and make install.
> The install process is shown in the txt file: Install Process.txt
>
> When make test, all tests are failed,(details please see quicktests.log)
> ../../lib/libdeal_II.g.so.9.1.1: error: undefined reference to 
> 'Teuchos::details::safeCommFree(int*)'
> ../../lib/libdeal_II.g.so.9.1.1: error: undefined reference to 
> 'Epetra_MpiComm::Epetra_MpiComm(int)'
> collect2: error: ld returned 1 exit status
>
> Can someone help me to solve this problem?
>
> Thanks.
> Zhenbang Wei
>
>
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/ff2e0d63-3925-431b-8d95-e5782658c3e9%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


[deal.II] Re: Problem installing DEALII 9.0.0 in CentOS cluster

2019-07-05 Thread Bruno Turcksin
Hi, 

Can you post the errors that you see on your screen.

Best,

Bruno

On Thursday, July 4, 2019 at 3:26:18 AM UTC-4, m boron wrote:
>
> Dear all,
> I have installed dealii9.0.0 in my PC and it is working fine. But now, I 
> want to install it in a cluster with CentOS. 
> I have installed 
> gcc 5.2.0
> cmake version 3.13.20181226
> openmpi-1.8.5
> PetSc 3.6.1
> SlePC3.6.3 
> P4est 2.0 in the cluster.
> These external libraries are detected and successfully configured. But at 
> the end of the config, it throws some error. I have attached the CMAKE log 
> files. I am not able to find the error. Kindly help me if anyone can figure 
> out to fix the issue. Thanking you in anticipation.
>
> With Regards,
> Boron
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/4eb22d71-f9da-4a2c-a1c7-6d2f133c9a03%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


[deal.II] Re: configuration with LAPACK/BLAS fails

2019-07-03 Thread Bruno Turcksin
Ahmad,

The first thing is that you should not try to set the flags yourself. You 
should let CMake take care of that. You should just set the paths (BLAS_DIR 
and LAPACK_DIR) and let CMake do the rest. The second thing is that I am 
not sure sure that you are using the right MKL libraries. You can go here 
 to 
check what you need.

Best,

Bruno

On Tuesday, July 2, 2019 at 7:18:40 PM UTC-4, Ahmad Shahba wrote:
>
> I am trying to compile deal.ii (version 9.1.1) on my Ubuntu laptop with 
> gcc compilers. I have tried two methods to configure deal.ii with 
> LAPACK/BLAS and both failed in a similar manner.
>
> *method 1: Using LAPACK/BLAS in my PETSc (version 3.9) installation*
> Motivated by the instructions given here 
> , I use the 
> following CMake command 
>
>
> export PREFIX_PETSC_ARCH=$PETSC_DIR/$PETSC_ARCH
>
> cmake \
>-DDEAL_II_COMPONENT_DOCUMENTATION=OFF \
>-DGSL_DIR=$HOME/workspace/gsl \
>-DHDF5_DIR=$PREFIX_PETSC_ARCH \
>-DMETIS_DIR=$PREFIX_PETSC_ARCH \
>-DP4EST_DIR=$HOME/workspace/p4est-2.2/FAST \
>-DDEAL_II_WITH_P4EST=ON \
>-DPETSC_DIR=$PETSC_DIR \
>-DPETSC_ARCH=$PETSC_ARCH \
>-DSLEPC_DIR=$SLEPC_DIR \
>-DZLIB_DIR=$PREFIX_PETSC_ARCH \
>-DDEAL_II_WITH_LAPACK=ON \
>-DLAPACK_FOUND=true \
>   
>  
> -DLAPACK_LIBRARIES="$PREFIX_PETSC_ARCH/lib/libflapack.a;$PREFIX_PETSC_ARCH/lib/libfblas.a"
>  
> \
>-DLAPACK_LINKER_FLAGS="-lgfortran -lm" \
>-DDEAL_II_WITH_MPI=ON \
>-DCMAKE_INSTALL_PREFIX=path/to/some/installation/directory \
>../
>
> The configuration fails with prints an error message like
>
> BLAS/LAPACK symbol check failed! This usually means that your BLAS/LAPACK
>   installation is incomplete or the link line is broken.
>
> I am attaching some CMake log and error files.
>
> *method 2:Linking to the LAPACK/BLAS whick comes with MKL*
> For another project, I had use gfortran to compile LAPACK/BLAS which comes 
> with Intel MKL. Linking to these libraries also failed in the same manner. 
> Here is the CMake command
>
> export PREFIX_PETSC_ARCH=$PETSC_DIR/$PETSC_ARCH
>
> cmake \
>-DDEAL_II_COMPONENT_DOCUMENTATION=OFF \
>-DGSL_DIR=$HOME/workspace/gsl \
>-DHDF5_DIR=$PREFIX_PETSC_ARCH \
>-DMETIS_DIR=$PREFIX_PETSC_ARCH \
>-DP4EST_DIR=$HOME/workspace/p4est-2.2/FAST \
>-DDEAL_II_WITH_P4EST=ON \
>-DPETSC_DIR=$PETSC_DIR \
>-DPETSC_ARCH=$PETSC_ARCH \
>-DSLEPC_DIR=$SLEPC_DIR \
>-DZLIB_DIR=$PREFIX_PETSC_ARCH \
>-DDEAL_II_WITH_LAPACK=ON \
>-DLAPACK_FOUND=true \
>   
>  
> -DLAPACK_LIBRARIES="${myInstallations}/lib/intel64/libmkl_blas95_lp64.a;${myInstallations}/lib/intel64/libmkl_lapack95_lp64.a;${MKLROOT}/lib/intel64/libmkl_gf_lp64.a;${MKLROOT}/lib/intel64/libmkl_sequential.a;${MKLROOT}/lib/intel64/libmkl_core.a"
>  
> \
>-DLAPACK_LINKER_FLAGS="-lgfortran -lpthread -lm -ldl" \
>-DDEAL_II_WITH_BLAS=ON \
>-DBLAS_FOUND=true \
>   
>  
> -DBLAS_LIBRARIES="${myInstallations}/lib/intel64/libmkl_blas95_lp64.a;${myInstallations}/lib/intel64/libmkl_lapack95_lp64.a;${MKLROOT}/lib/intel64/libmkl_gf_lp64.a;${MKLROOT}/lib/intel64/libmkl_sequential.a;${MKLROOT}/lib/intel64/libmkl_core.a"
>  
> \
>-DBLAS_LINKER_FLAGS="-lgfortran -lpthread -lm -ldl" \
>-DSCALAPACK_DIR==$PREFIX_PETSC_ARCH \
>-DDEAL_II_WITH_MPI=ON \
>-DCMAKE_INSTALL_PREFIX=path/to/some/installation/directory \
>../
>
>
> Any thoughts how I can get this done? 
> Thanks in advance,
> Ahmad
>  
>

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/de32ab59-ef58-4fe9-9a66-3e71ce426493%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


[deal.II] Re: Can the deal.ii support an element only having single degree of freedom at the center of element?

2019-07-01 Thread Bruno Turcksin
Hi,

On Monday, July 1, 2019 at 6:08:45 AM UTC-4, Lee wrote:
>
> Can the deal.ii support an element only having degree of freedom at the 
> center of element?
>
Yes, that's basically what FE_DGQ(0) is.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/15f6acc1-12c4-4c99-83cd-f824ab0812e4%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


[deal.II] Re: How can we get the factorized system matrix when using SparseDirectMUMPS?

2019-06-27 Thread Bruno Turcksin
Kien,

On Wednesday, June 26, 2019 at 10:20:38 PM UTC-4, Phạm Ngọc Kiên wrote:
>
> Hi colleagues,
> I am trying to build codes using  PETScWrappers::SparseDirectMUMPS solver.
> Step-62 shows a very good example for using it.
> However, I really want to know if  we can choose the factorization method 
> in MUMPS by deal.II codes.
>
According to the documentation (see here 
),
 
you can. I don't use PETSc but I think this done using the command line
 

>
> The second question is: do we have a way to get the factorized system 
> matrix when using this direct solver?
> Because I want to reuse the factorized system matrix to solve the problem 
> again with other right hand side.
>
Just call solve() with a different right-hand-side. The factorization 
should only be done the first time the function is called.

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/24c660f9-1450-4c1f-b0f7-d9c0a629fde8%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


Re: [deal.II] Re: NedelecSZ with adaptive mesh refinement

2019-06-25 Thread Bruno Turcksin
Daniel

Le mar. 25 juin 2019 à 13:55, Daniel Garcia-Sanchez
 a écrit :
> Thanks for the reference. Yes, it seems that this is a non-trivial problem. 
> Although from what I understand from the post.
>
> The new FE_NedelecSZ element can be used with complex meshes, but can not be 
> refined
> The old FE_Nedelec element can only be used with a simple grid but it can be 
> refined.
Yes, that's correct. The old Nedelec can be refined but I would trust
it only if you have rectangles/regular hex .

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/CAGVt9ePB8LA-ffUnTKkd4GDPOdMJejnxvufLPoqM4rSAXac4Ng%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.


[deal.II] Re: NedelecSZ with adaptive mesh refinement

2019-06-25 Thread Bruno Turcksin
Dani,

On Tuesday, June 25, 2019 at 12:52:09 PM UTC-4, Daniel Garcia-Sanchez wrote:
>
>
> That means that I can not do adaptive mesh refinement with NedelecSZ?
>
That's correct. 

>
> If that is the case, I would be happy to contribute and make this element 
> compatible with adaptive mesh refinement.
>
> Could you indicate me what is left and which is the direction I should 
> take to add adaptive mesh refinement to NedelecSZ?
>
This post 
 
briefly discuss the problem. Apparently it is non-trivial but I can't 
really comment on it (I've never used Nedelec element)

Best,

Bruno

-- 
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+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/f7dfe94b-e470-4b36-a864-b34efdc3ce6d%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


  1   2   3   4   5   >