Re: [deal.II] METIS partition error

[David Wells]

Hi Yuesu,

Essentially, yes. If you look at the code for partition_triangulation you
will find

// check for an easy return
if (n_partitions == 1)
  {
for (const auto &cell : triangulation.active_cell_iterators())
  cell->set_subdomain_id(0);
return;
  }

Hence step-17 only tries to use metis (and, if metis is not available,
aborts) if there are multiple partitions for the mesh.

Best,
David


On Mon, Jul 27, 2020 at 12:37 AM yuesu jin  wrote:

> Dear all,
>   I am running step-17 by mpirun, it returns the error message below:
> **
> 
> Exception on processing:
>
> 
> An error occurred in line <69> of file
>  in function
> void dealii::SparsityTools::{anonymous}::partition_metis(const
> dealii::SparsityPattern&, const std::vector&, unsigned int,
> std::vector&)
> The violated condition was:
> false
> Additional information:
> The function you called requires METIS, but you did not configure
> deal.II with METIS.
> 
> This message does't appear when I use a single node to run it.  Does the
> sparsity tools  automatically overload to partition_metis under parallel
> case?
> Thank you!
> 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
>
> --
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> 
> .
>

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Re: [deal.II] dealii installation Mac OS 10.15.5 (Catalina)

[David Wells]

Hi Deepak,

I think that we have now fixed our Mac packages, so at the moment I think
the best answer would be to download the new version of the mac bundle for
deal.II from our GitHub release page. I had exactly the same error as you
did with the older version of the mac bundle and the new version fixed it
for me, so I am optimistic that it will work for you too.

> I don't understand the Mac OS or Linux environment too well, so please
excuse me for asking - but when you say "compile yourself"  - what do you
mean? and is there a documented "procedure" for compiling that I can follow?

This is a completely reasonable question :) I meant that you should
download the source code, configure your local copy for your machine,
compile it, and install it. We have detailed instructions on how to do this
on the web site:

https://www.dealii.org/current/readme.html

Do you see what to do? Please post again if you still have questions.

Best,
David

On Wed, Jun 24, 2020 at 1:19 AM Deepak Kukrety 
wrote:

> Hi David,
>
> Thanks for confirming this. On a related note, may I ask which earlier
> version could be a safe bet to install?
>
> I don't understand the Mac OS or Linux environment too well, so please
> excuse me for asking - but when you say "compile yourself"  - what do you
> mean? and is there a documented "procedure" for compiling that I can
> follow?
>
> Regards
> Deepak
>
>
>
>
> On Tuesday, 23 June 2020 23:30:53 UTC+8, David Wells wrote:
>>
>> Hi Deepak,
>>
>> This is a known issue with the current version of the mac bundle - it
>> doesn't work with Catalina. We are in the process of fixing this. For now,
>> unfortunately, you will have to either use an older version of deal.II or
>> compile it yourself.
>>
>> Sorry,
>> David
>>
>> On Mon, Jun 22, 2020 at 7:05 PM Deepak Kukrety 
>> wrote:
>>
>>> Dear All,
>>>
>>> I recently updated deal ii, but I am unable to run the programs. The
>>> main problem appears as a set of warnings when starting to "make":
>>>
>>> ld: warning: directory not found for option
>>> '-L/Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/zlib-1.2.11-rqiqrujgg5aemhk7eqjk3asbaukff'
>>>
>>> ld: warning: directory not found for option
>>> '-L/Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/dealii-develop-rrf4rjxvntgbw2l44kbr6aoa4xnr4gsb/lib'
>>>
>>> I tried to make run, despite these warnings and get the following
>>> errors:
>>>
>>>
>>> bash-3.2$ make run
>>>
>>> [ 66%] Built target step-1
>>>
>>> *Scanning dependencies of target run*
>>>
>>> [100%] *Run step-1 with Debug configuration*
>>>
>>> dyld: malformed mach-o: load commands size (33848) > 32768
>>>
>>> make[3]: *** [CMakeFiles/run] Abort trap: 6
>>>
>>> make[2]: *** [CMakeFiles/run.dir/all] Error 2
>>>
>>> make[1]: *** [CMakeFiles/run.dir/rule] Error 2
>>>
>>> make: *** [run] Error 2
>>>
>>>
>>>
>>> I have tried re-installing, going back to an older version of make, but
>>> I seem stuck with this problem.
>>>
>>>
>>> Any help will be highly appreciated.
>>>
>>>
>>> Regards
>>>
>>> Deepak
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> The deal.II project is located at http://www.dealii.org/
>>> For mailing list/forum options, see
>>> https://groups.google.com/d/forum/dealii?hl=en
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>>> Groups "deal.II User Group" group.
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>>> .
>>>
>> --
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Re: [deal.II] dealii installation Mac OS 10.15.5 (Catalina)

[David Wells]

Hi Deepak,

This is a known issue with the current version of the mac bundle - it
doesn't work with Catalina. We are in the process of fixing this. For now,
unfortunately, you will have to either use an older version of deal.II or
compile it yourself.

Sorry,
David

On Mon, Jun 22, 2020 at 7:05 PM Deepak Kukrety 
wrote:

> Dear All,
>
> I recently updated deal ii, but I am unable to run the programs. The main
> problem appears as a set of warnings when starting to "make":
>
> ld: warning: directory not found for option
> '-L/Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/zlib-1.2.11-rqiqrujgg5aemhk7eqjk3asbaukff'
>
> ld: warning: directory not found for option
> '-L/Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/dealii-develop-rrf4rjxvntgbw2l44kbr6aoa4xnr4gsb/lib'
>
> I tried to make run, despite these warnings and get the following errors:
>
>
> bash-3.2$ make run
>
> [ 66%] Built target step-1
>
> *Scanning dependencies of target run*
>
> [100%] *Run step-1 with Debug configuration*
>
> dyld: malformed mach-o: load commands size (33848) > 32768
>
> make[3]: *** [CMakeFiles/run] Abort trap: 6
>
> make[2]: *** [CMakeFiles/run.dir/all] Error 2
>
> make[1]: *** [CMakeFiles/run.dir/rule] Error 2
>
> make: *** [run] Error 2
>
>
>
> I have tried re-installing, going back to an older version of make, but I
> seem stuck with this problem.
>
>
> Any help will be highly appreciated.
>
>
> Regards
>
> Deepak
>
>
>
>
>
>
> --
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> .
>

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[deal.II] Upcoming release and a call for last-minute patches and reports

[David Wells]

Dear everyone,

We are in the process of preparing the next (9.2) release of deal.II: it
should be done by the end of the month. Please let us know as soon as
possible if you have any unresolved issues with the master branch on GitHub
or if you have unmerged patches which you believe should be added to the
next release.

Best,
David

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Re: [deal.II] Instantiation of make_hanging_node_constraints() with hp::DoFHandler

[David Wells]

Dear Sebastian,

This is a good question: I took a look at the history of the instantiation
file and I think this is just an oversight (we added explicit nonzero
codimension specializations for the non-hp case years ago and propagated
the lack of hp instantiations along the way).

Would you be willing to put your changes into a pull request so we can fix
this before the release?

Best,
David

On Sat, May 2, 2020 at 6:47 AM 'Sebastian Stark' via deal.II User Group <
dealii@googlegroups.com> wrote:

> Dear all,
>
> I am wondering whether there is a reason that the standard instantiations
> for make_hanging_node_constraints() do not include a version with
> hp::DoFHandler<2,3> as an argument other than that it is not used very
> often. I have added the instantiation before compiling the library and so
> far it appears to work just fine (though, in my application I really only
> use the hp::DoFHandler for extending fields by zero to some regions by
> using FENothing there).
>
> Regards,
> Sebastian
>
> --
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> 
> .
>

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Re: [deal.II] Re: Finding vertices on boundaries

[David Wells]

Hi Shahab,

You are right that vertices themselves don't store any information - this
is an implementation detail of deal.II (points do not store any topological
information in a Triangulation, unlike lines, quadrilaterals, or hexahedra).

Just to check: when you write 'vertices', are you looking for information
about the degrees of freedom on the boundary, or are you interested in the
getting a list of the Point objects that are on the boundary?
What Bruno describes will do the former. If you want to do the later then
something like this will work:

Triangulation triangulation;

// do something to set up the triangulation

std::set> boundary_vertices;
for (const auto &face : triangulation.active_face_iterators())
  if (face->at_boundary())
for (unsigned int v = 0; v < GeometryInfo::vertices_per_face; ++v)
  boundary_vertices.insert(face->vertex(v));

You could also store Point *> objects if you want to manipulate
the points once you have all of them.

Does this answer your question? Please post again if you still need help
figuring this out!

Best,
David


On Thu, Apr 30, 2020 at 11:28 PM Bruno Blais  wrote:

> Dear Shahab,
> I think the best solution (I might be wrong) is to loop through the
> boundary faces and acquire the DOF indices that lie on a boundary face. You
> could then store them in an std::map or a similar structure that prevents
> data duplication.
>
>
> You can create a vector and store the dof indices of a face in a following
> fashion that I believe should work.
> Assuming you already have a vector such as:
> std::vector face_dofs;
>
>
>
>
> In the loops within the cell then the faces, assuming you are at a face
> *face* and that you have a FiniteElement fe, you can do:
> face_dofs.resize(fe.dofs_per_face);
> face->get_dof_indices(face_dofs, cell->active_fe_index());
>
> This will gather all the dofs indices of that given face. If that face is
> a boundary face it means you have gathered all of its dofs location.
> I hope that points you in the right direction and helps you!
> Best
> Bruno
>
>
>
>
> On Thursday, 30 April 2020 23:05:31 UTC-4, Shahab Golshan wrote:
>>
>> Dear all,
>> I want to find all the vertices located on boundaries. It seems the
>> function at_boundary() does not work for vertices (points). Do you have any
>> suggestions how to obtain all the vertices located on the boundaries?
>> Best,
>> Shahab
>>
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>

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

[David Wells]

Dear Wilmar,

I suspect you have already tried this, but I think it is worth
mentioning just in case: are you running Debian or Ubuntu? If so, then
you can use apt-get to install the library without needing to compile
it yourself.

Additionally, if you need to decrease the amount of memory used in
compilation, it would help to use as few external dependencies as
possible. If you do not need complex numbers then it would also help
to provide the option -DDEAL_II_WITH_COMPLEX_VALUES=OFF to cmake.

> (From Brazil, in time of Covirus!)

Greetings from North Carolina. One good thing about being stuck at
home is that I have more time for deal.II these days :)

Best,
David

On Tue, Apr 28, 2020 at 4:33 PM Jean-Paul Pelteret  wrote:
>
> Dear Wilmar,
>
> Indeed, Francis has the right suggestion, although I’m a bit worried that its 
> still not going to help you (unless writing into swap is something that you’d 
> consider). A similar question had been asked a couple of years ago, and the 
> answer that they got at the time was that
>
> 1GB is not enough. I think that you will need 3GB. We try to make it so that 
> we don't require more than 2GB to compile deal.II but I don't think that 2GB 
> is enough for the last few versions.
>
>
> So it is, unfortunately, quite possible that your system doesn’t have enough 
> RAM to compile using even just one process. I do hope that we are wrong in 
> our estimations though. If you still don’t have any luck, might it be 
> possible for you to temporarily acquire (i.e. borrow) some just to build the 
> library? I don’t think that you necessary need that much to run any (or many) 
> of the tutorial programs.
>
> Best of luck,
> Jean-Paul
>
> On 28 Apr 2020, at 14:20, Francis Giraldeau  
> wrote:
>
> Compiling and linking C++ requires a lot of memory and it seems your computer 
> has not much of it.
>
> You can try to compile with only one process at a time: make -j1
>
> You might try some swap, but that will be very slow.
>
> Francis
>
> Le mar. 28 avr. 2020 à 08:08, Wilmar Alves Cruvinel Lima 
>  a écrit :
>>
>> 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!)
>>
>> --
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>
>
>
> --
> Francis
>
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Re: [deal.II] Re: "libpthreads"?

[David Wells]

Hi Victor,

> Is there a 9.1+eps coming up?

No, but we are planning on releasing 9.2.0 in May (tentatively
scheduled for May 15) - if you can wait then that might be the best
choice.

Thanks,
David

On Tue, Apr 28, 2020 at 10:25 AM Victor Eijkhout
 wrote:
>
>
>
> On , 2020Apr24, at 18:03, Marc Fehling  wrote:
>
>  Just compile from the master branch and you're good!
>
>
> I’m allergic to the word “just”.
>
> Considering how laborious our installation process is, I try to install only 
> versions that have official numbers on them. Considering that this is a 
> cmake-interaction, and not any change in functionality, I’ll provide this to 
> the users as 9.1.1.
>
> Is there a 9.1+eps coming up?
>
> Next project: getting dealii to build with trillions, which I think I have a 
> user request for.
>
> Victor.
>
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Re: [deal.II] Periodicity with simultaneous displacement controlled BCs

[David Wells]

Hi David,

There are a lot of different ways to solve this problem, but I think the
relevant solution is to consider a more Lagrangian perspective - I
recommend that you do not modify the Triangulation directly (i.e., don't
move vertices) but instead represent the initial deformation as a finite
element field. You can then combine the initial deformation with
MappingFEField to compute quantities in the deformed configuration - this
should enable you to correctly set periodic boundary conditions without
having to worry about wobbly edges.

Does this work for you?

Thanks,
David

On Wed, Apr 22, 2020 at 12:42 PM David F  wrote:

> Hello everyone,
>
> I'm trying to compute the effective elastic properties of a heterogeneous,
> linear and a bi-periodic system (i.e., left-right and top-bottom periodic
> displacement fields). To this system, I would like to apply a global
> shearing by prescribing the displacement field of the surfaces in the form
> of Dirichlet BCs. This seems slightly contradictory since a bi-periodic
> system doesn't have surfaces.
>
> However, we can still think of the global shearing as an average surface
> displacement around which periodic fluctuations occur (the origin of such
> fluctuations is due to heterogeneous elastic properties). This is
> illustrated in the picture below.
>
>
> [image: bitmap.png]
>
> I would like to know which is the best way to do this in deal.II (I have
> tried with make_periodicity_constraints and interpolate_boundary_values,
> but the problem is that, as I explain before, we set apparently
> contradictory constraints).
>
> Thank you in advance.
>
>
> P.S.: suggestions of alternative procedures to achieve the same goal are
> welcome.
>
> --
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> 
> .
>

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Re: [deal.II] How to simplify a 2D complex problem to a '1D-like' problem?

[David Wells]

Hi Lex,

I think that this is more of a PDE question than a deal.II question
but I will try to answer.

At a fundamental level, if you impose nonzero boundary conditions or
have nonzero forcing on a component you force to equal zero you will
not be able to have a solution that makes sense: you will have to
modify those or you will have an inconsistent system of equations. I
don't think its possible to have a component that is zero without
changing the boundary conditions and forcing to match.

I think the best choice is to use the method of manufactured solutions
(with v_x = 0 and v_y = something nonzero) to obtain the correct
forcing terms and boundary conditions for that exact solution.

Does this work for you?

One alternative (that does involve modifying your governing equations,
boundary conditions, and geometry) is, if you have a linear problem,
to do a Fourier transform in the x direction so that you really will
have a 1D problem. Even though this doesn't fit your listed
constraints it can be a useful tool in some circumstances.

Best,
David

On Fri, Apr 24, 2020 at 8:22 PM Lex Lee  wrote:
>
> Hello Deal.II Users,
>
>
> I am using Deal.II to try to simplify/reduce my complex 2D problem to a 
> 1D-like problem, namely, let the component values at x-direction of all 
> vectors be zero. (for example, V=[v_x,  v_y]' = [0, v_y]') .
> Moreover,  given that the governing equations, boundary conditions and 
> geometry stay the same, operators like gradient or divergence applying on the 
> variables will not alter the values at x-direction during the process. I 
> tried, however, I have no idea how to make it in Deal.II.
>
> I hope you can kindly share your coding experience or give me some hints 
> regarding this problem. Thanks.
>
>
> Best,
> Lex
>
>
>
>
> --
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Re: [deal.II] Question on how MatrixTools::MatrixCreator sets the appropriate flags of FeValues?

[David Wells]

Hi Krishna,

I'm not sure that I understand your question - those two functions
create a mass matrix and a laplace corresponding to the given
parameters (dof handler, mapping, quadrature, etc) - in the first case
only shape values are needed and in the second only shape gradients.
Hence the function knows which fields of UpdateFlags to set without
the need for user input.

> how do these interact when we have an FESystem?

They still create the system mass and laplace matrices :)

Thanks,
David

On Tue, Feb 18, 2020 at 8:17 AM Krishnakumar Gopalakrishnan
 wrote:
>
> In the tutorials, Step-23 suddenly gets rid of the assemble_system() function 
> and introduces MatrixTools::MatrixCreator::create_mass_matrix and 
> MatrixTools::MatrixCreator::create_laplace_matrix
>
> However, there is no discussion whatsoever of how the appropriate update 
> flags (bitfields) of the Fevalues object is set? Can someone help to explain 
> the interface of these two aspects of the library? Additionally, how do these 
> interact when we have an FeSystem?
>
> Krishna
>
> --
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Re: [deal.II] Error in make_hanging_node_constraints() while using parallel::distributed::Triangulation with hp::DoFHandler

[David Wells]

Hi Chaitanya,

I apologize that no one has answered your question yet. Using
hp::DoFHandler with distributed triangulations is a new feature that
is not yet in a current release and there may still be some bugs in
the implementation. I suspect no one has responded to this simply
because no one knows the answer.

It's not a great solution but would it be possible to use
parallel::shared::Triangulation for your application as a stopgap
measure while we try to figure this out? That should work correctly
with hp::DoFHandler.

Thanks,
David

On Wed, Feb 5, 2020 at 11:44 AM Chaitanya Dev  wrote:
>
> Dear Deal.II Community,
>
> I am trying to use parallel::distributed::Triangulation with hp::DoFHandler. 
> I run into the below error in DoFTools::make_hanging_node_constraints..
>
> I work on shape optimization using embedding domain discretization 
> techniques. In my problems, I have to repeatedly refine the mesh and 
> approximate the geometry. Then I assign different FESystem for the cells 
> within and outside the geometry.
>
> I have implemented the code in serial with serial triangulation and 
> hp::DoFHandler and the program works.
>
> Now I wish to solve larger problems so I have decided to parallelize the code 
> and hence I use parallel::distributed::Triangulation.
>
> Here I run into a problem in system_setup, specifically in the function 
> DoFTools::make_hanging_node_constraints.
>
> Hear is the error message.
> 
> An error occurred in line <1119> of file 
> 
>  in function
> void dealii::DoFTools::internal::make_hp_hanging_node_constraints(const 
> DoFHandlerType&, dealii::AffineConstraints&) [with DoFHandlerType = 
> dealii::hp::DoFHandler<2, 2>; number = double]
> The violated condition was:
> cell->face(face)->child(c)->n_active_fe_indices() == 1
> 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.
>
> Stacktrace:
> ---
> #0  
> /opt/dealii-9.1.1/opt/spack/linux-ubuntu18.04-haswell/gcc-7.4.0/dealii-9.1.1-holxtax5bwynpjaccyvwkli2ybveslrl/lib/libdeal_II.g.so.9.1.1:
>  void 
> dealii::DoFTools::internal::make_hp_hanging_node_constraints  2>, double>(dealii::hp::DoFHandler<2, 2> const&, 
> dealii::AffineConstraints&)
> #1  
> /opt/dealii-9.1.1/opt/spack/linux-ubuntu18.04-haswell/gcc-7.4.0/dealii-9.1.1-holxtax5bwynpjaccyvwkli2ybveslrl/lib/libdeal_II.g.so.9.1.1:
>  void 
> dealii::DoFTools::make_hanging_node_constraints, 
> double>(dealii::hp::DoFHandler<2, 2> const&, 
> dealii::AffineConstraints&)
> #2  hp-dist-test: TestProblem<2>::setup_system()
> #3  hp-dist-test: TestProblem<2>::run()
> #4  hp-dist-test: main
> 
>
> This is my setup_system function.
>
> template
> void TestProblem::setup_system() {
>
> dof_handler.initialize(triangulation, fe_collection);
>
> for (auto cell : dof_handler.active_cell_iterators()) {
> if (!cell->is_locally_owned())
> continue;
> if (cell->user_flag_set())
> cell->set_active_fe_index(0);
> else
> cell->set_active_fe_index(1);
> }
>
> dof_handler.distribute_dofs(fe_collection);
> locally_owned_dofs = dof_handler.locally_owned_dofs();
> DoFTools::extract_locally_relevant_dofs(dof_handler, locally_relevant_dofs);
>
> hanging_node_constraints.clear();
> hanging_node_constraints.reinit(locally_relevant_dofs);
>
> DoFTools::make_hanging_node_constraints(dof_handler,
> hanging_node_constraints);
> hanging_node_constraints.close();
> }
>
> I did some debugging and found that the Assert fail 
> cell->face(face)->child(c)->n_active_fe_indices() == 1 is failing on the 
> ghost cells. To avoid this error  I tried to set_active_fe_index for the 
> ghost cells, but this is not allowed.
>
> Please let me know where I am going wrong.
>
> I have attached a MWE. You can reproduce the error with mpirun for np >= 2 
> cores (the code will work for np=1, because no ghost cells).
>
> Thank you,
> Chaitanya Dev.
>
> --
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Re: [deal.II] Running multiple programs at the same time

[David Wells]

Hi Toni,

I think that this is due to each individual program creating the same
number of threads as you have physical processors. Try adding

MultithreadInfo::set_thread_limit(1);

at the top of your code to prevent this from happening. Let us know if
this works!

Thanks,
David

On Tue, Feb 11, 2020 at 11:45 AM Toni Vidal  wrote:
>
>
> Dear deal.ii users and developers,
>
> I am currently running a deal.II based code thousands of times with different 
> input parameters. Each  simulation takes about 30 seconds in a single 
> processor. To do this, I have made a python script that runs 4 simulations at 
> a time (using the multiprocessing module). However, each simulation takes 
> about 60 seconds and my have 8 cores (Intel® Core™ i7-9700K CPU @ 3.60GHz × 
> 8).  Is it not supposed to take approximately the same amount of because the 
> processors are independent? Am I
>
> In order to isolate the problem I have executed deal.II's step 6 (with 12 
> cycles and 1e5 maximum solver steps) 1, 2 and 4 times at the same (using 
> different terminals).
>
> 1 running programs ~ 32 s user time
> 2 running programs ~ 44 s user time
> 4 running programs ~ 80 s user time
>
> Why the programs does not take the same time even though my computer have 8 
> cores?
> Any idea? Am I missing something obvious?
>
> Ton Vidal
>
> --
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Re: [deal.II] Question about the definiteness of the system matrix in Step-20

[David Wells]

Wolfgang pointed out to me that the pivot based answer is wrong -
fortunately I have another explanation :)

If we have the block matrix

A B^T

B 0

where A is SPD and B has linearly independent rows, this matrix has
equal eigenvalues to

 I  0A B^T   A B^T
   *   =
   -B A^-1 I B 00-B A^-1 B^T

since the eigenvalues of the leftmost matrix are all 1 (its triangular
with 1s on the main diagonal). The eigenvalues of the rightmost matrix
are the eigenvalues of A and the eigenvalues of -B A^-1 B^T. Since A
is SPD, we can rewrite A^-1 = L L^T (its Cholesky factorization) so -B
A^-1 B^T  = -B L L^T B^T = -(B L) (B L)^T: a second Cholesky
factorization. Hence the bottom right is negative definite and
therefore the matrix as a whole is indefinite.

Thanks,
David

On Sun, Feb 2, 2020 at 9:41 PM Wolfgang Bangerth  wrote:
>
> On 2/1/20 12:44 PM, Krishnakumar Gopalakrishnan wrote:
> >
> >
> > "_Two difficulties_ arise due to the _*zero pivots*_ in the bottom-right 
> > block
> > of the matrix.
> >
> >  1. Firstly, following a classical result from linear algebra, such matrices
> > are indefinite and the conjugate gradient solver cannot be applied. We
> > would have to resort to other iterative solvers instead, such as MinRes,
> > SymmLQ, or GMRES, that can deal with indefinite systems.
> >  2. Secondly, due to the//zero block, there are zeros on the diagonal and 
> > none
> > of the usual, "simple" preconditioners (Jacobi, SSOR) will work as they
> > require division by diagonal elements"
>
> How about this:
> https://github.com/dealii/dealii/pull/9470
>
> Best
>   W.
>
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
> --
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Re: [deal.II] Question about the definiteness of the system matrix in Step-20

[David Wells]

Dear Krishna,

Allow me to clarify my previous statement. From Strang (intro to
linear algebra, 5th edition, page 352):

When a symmetric matrix S has one of these five properties, it has them all:
1. all n pivots of S are positive.
2. all n upper left determinants are positive.
3. all n eigenvalues of S are positive.
4. x^T S x is positive except at x = 0. This is the energy-based definition.
5. S equals A^T A for a matrix A with independent columns.

i.e., the statement on eigenvalue positivity and the statement on
pivots are *equivalent*, i.e., containing a zero block causes the same
difficulties as the issues with the spectra since one implies the
other.

Thanks

On Sat, Feb 1, 2020 at 2:45 PM Krishnakumar Gopalakrishnan
 wrote:
>
> Dear Dr David Wells,
>
> Thank you for the explanation. However, this only satisfies me partially 
> because the very next statement in that tutorial says:
>
> "We would have to resort to other iterative solvers instead, such as MinRes, 
> SymmLQ, or GMRES, that can deal with indefinite systems. However, then the 
> next problem immediately surfaces: due to the zero block, there are zeros on 
> the diagonal and none of the usual, "simple" preconditioners (Jacobi, SSOR) 
> will work as they require division by diagonal elements."
>
>
> If the cause of the indefiniteness is not due to the eigen-value test, but 
> rather due to the simple fact the pivot elements in the lower-right block is 
> zero, then we have only ONE root cause of  all difficulties.  I am rephrasing 
> the issues as follows (please correct me if my understanding is incorrect)
>
>
> "Two difficulties arise due to the zero pivots in the bottom-right block of 
> the matrix.
>
> Firstly, following a classical result from linear algebra, such matrices are 
> indefinite and the conjugate gradient solver cannot be applied. We would have 
> to resort to other iterative solvers instead, such as MinRes, SymmLQ, or 
> GMRES, that can deal with indefinite systems.
> Secondly, due to the zero block, there are zeros on the diagonal and none of 
> the usual, "simple" preconditioners (Jacobi, SSOR) will work as they require 
> division by diagonal elements"
>
>
> Regards,
> Krishna
>
> On Saturday, February 1, 2020 at 7:13:18 PM UTC, David Wells wrote:
>>
>> Hi Krishna,
>>
>> This is a classic linear algebra result - a symmetric matrix is
>> positive definite if and only if it has positive pivots. Since this
>> matrix has a zero block it does not even have a full set of pivots so
>> it cannot be positive definite.
>>
>> Thanks,
>> David Wells
>>
>> On Sat, Feb 1, 2020 at 9:49 AM Krishnakumar Gopalakrishnan
>>  wrote:
>> >
>> > I realize that this question is not exactly about the code/concepts behind 
>> > deal.II library itself, but rather about a mathematical statement from 
>> > step-20.
>> >
>> > "After assembling the linear system we are faced with the task of solving 
>> > it. The problem here is: the matrix has a zero block at the bottom right 
>> > (there is no term in the bilinear form that couples the pressure p with 
>> > the pressure test function q), and it is indefinite".
>> >
>> > My question is about the indefiniteness of the matrix. In my 
>> > understanding, a matrix is indefinite if it has both positive and negative 
>> > eigen values.  However, there has not been any discussion thus far in 
>> > step-20 that comment about the eigen-values. How was the statement about 
>> > the indefiniteness then made?   Can someone here explain why that matrix 
>> > is indefinite?
>> >
>> > 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
>> > ---
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>> > "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/ec88d69a-4b26-43cb-915b-b3ae1fdfa3aa%40googlegroups.com.
>
> --
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Re: [deal.II] Question about the definiteness of the system matrix in Step-20

[David Wells]

Hi Krishna,

This is a classic linear algebra result - a symmetric matrix is
positive definite if and only if it has positive pivots. Since this
matrix has a zero block it does not even have a full set of pivots so
it cannot be positive definite.

Thanks,
David Wells

On Sat, Feb 1, 2020 at 9:49 AM Krishnakumar Gopalakrishnan
 wrote:
>
> I realize that this question is not exactly about the code/concepts behind 
> deal.II library itself, but rather about a mathematical statement from 
> step-20.
>
> "After assembling the linear system we are faced with the task of solving it. 
> The problem here is: the matrix has a zero block at the bottom right (there 
> is no term in the bilinear form that couples the pressure p with the pressure 
> test function q), and it is indefinite".
>
> My question is about the indefiniteness of the matrix. In my understanding, a 
> matrix is indefinite if it has both positive and negative eigen values.  
> However, there has not been any discussion thus far in step-20 that comment 
> about the eigen-values. How was the statement about the indefiniteness then 
> made?   Can someone here explain why that matrix is indefinite?
>
> Regards,
> Krishna
>
> --
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Re: [deal.II] "PETSc installation does not include a copy of the hypre package" while running the step-40 program

[David Wells]

Yup - deal.II did not pick up HYPRE or MUMPS even though you
configured PETSc with both (which can be seen by checking the end of
PETSc's configure log).

I can only think of one more thing to check - try deleting
CMakeCache.txt in deal.II's build directory and rerun CMake to see if
the cache got stuck in a wrong state. Could you try that?



On Thu, Jan 30, 2020 at 11:29 AM Ihar Suvorau  wrote:
>
> I believe this is the correct file. I see the line 
> "SET(DEAL_II_PETSC_WITH_HYPRE FALSE)” in the file.
>
> --
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>
>
> Best,
> Ihar Suvorau
>
>
>
> > On 30. Jan 2020, at 18:22, David Wells  wrote:
> >
> > OK, that also looks right. Could you also send me, from deal.II's
> > build directory,
> >
> > cmake/config/deal.IIConfig.cmake
> >
> > ?
> >
> > On Thu, Jan 30, 2020 at 11:05 AM Ihar Suvorau  
> > wrote:
> >>
> >> Hi, David,
> >>
> >> yes, here it is.
> >>
> >> On Thursday, January 30, 2020 at 6:02:56 PM UTC+2, David Wells wrote:
> >>>
> >>> Hi Ihar,
> >>>
> >>> I'm not sure what went wrong - everything looks right except that
> >>> deal.II did not find hypre.
> >>>
> >>> Could you also send
> >>>
> >>> /Users/ihar/lib/petsc-3.12.3/arch-darwin-c-debug/include/petscconf.h
> >>>
> >>> to check something else?
> >>>
> >>>
> >>> On Tue, Jan 28, 2020 at 10:14 AM Ihar Suvorau  wrote:
> >>>>
> >>>> Hi, David,
> >>>>
> >>>> okay, please, attaching these files also.
> >>>>
> >>>> On Tuesday, January 28, 2020 at 4:18:44 PM UTC+2, David Wells wrote:
> >>>>>
> >>>>> Hi Ihar,
> >>>>>
> >>>>> It looks like nothing went wrong with PETsc. Would you please also
> >>>>> send a copy of deal.II's detailed.log and, if available,
> >>>>> CMakeCache.txt from the build directory?
> >>>>>
> >>>>> Thanks,
> >>>>> David
> >>>>>
> >>>>> On Mon, Jan 27, 2020 at 5:59 PM Ihar Suvorau  wrote:
> >>>>>>
> >>>>>> Sure, attaching a file, please.
> >>>>>>
> >>>>>> On Monday, January 27, 2020 at 5:42:39 PM UTC+2, David Wells wrote:
> >>>>>>>
> >>>>>>> Hi Ihar,
> >>>>>>>
> >>>>>>> This sounds like something has gone wrong inside either PETSc's or
> >>>>>>> deal.II's build process. Would you please show us a copy of PETSc's
> >>>>>>> configure.log?
> >>>>>>>
> >>>>>>> Thanks,
> >>>>>>> David
> >>>>>>>
> >>>>>>> On Sun, Jan 26, 2020 at 6:59 AM Ihar Suvorau  
> >>>>>>> wrote:
> >>>>>>>>
> >>>>>>>> Not yet, I have a running version via docker images though. I'll try 
> >>>>>>>> the bundle also, thank you, before I was thinking that it shouldn't 
> >>>>>>>> support parallel programming, but now I see it is configured with 
> >>>>>>>> "DEAL_II_WITH_MPI set up with external dependencies" and 
> >>>>>>>> "DEAL_II_WITH_PETSC set up with external dependencies" and has all 
> >>>>>>>> packages installed.
> >>>>>>>>
> >>>>>>>> But I'm still interested in solving the issue with "Your PETSc 
> >>>>>>>> installation does not include a copy of the hypre package necessary 
> >>>>>>>> for this preconditioner" when I do have the hypre package installed 
> >>>>>>>> via the option "--download-hypre=1" while configuring PETSc.
> &g

Re: [deal.II] "PETSc installation does not include a copy of the hypre package" while running the step-40 program

[David Wells]

OK, that also looks right. Could you also send me, from deal.II's
build directory,

cmake/config/deal.IIConfig.cmake

?

On Thu, Jan 30, 2020 at 11:05 AM Ihar Suvorau  wrote:
>
> Hi, David,
>
> yes, here it is.
>
> On Thursday, January 30, 2020 at 6:02:56 PM UTC+2, David Wells wrote:
>>
>> Hi Ihar,
>>
>> I'm not sure what went wrong - everything looks right except that
>> deal.II did not find hypre.
>>
>> Could you also send
>>
>> /Users/ihar/lib/petsc-3.12.3/arch-darwin-c-debug/include/petscconf.h
>>
>> to check something else?
>>
>>
>> On Tue, Jan 28, 2020 at 10:14 AM Ihar Suvorau  wrote:
>> >
>> > Hi, David,
>> >
>> > okay, please, attaching these files also.
>> >
>> > On Tuesday, January 28, 2020 at 4:18:44 PM UTC+2, David Wells wrote:
>> >>
>> >> Hi Ihar,
>> >>
>> >> It looks like nothing went wrong with PETsc. Would you please also
>> >> send a copy of deal.II's detailed.log and, if available,
>> >> CMakeCache.txt from the build directory?
>> >>
>> >> Thanks,
>> >> David
>> >>
>> >> On Mon, Jan 27, 2020 at 5:59 PM Ihar Suvorau  wrote:
>> >> >
>> >> > Sure, attaching a file, please.
>> >> >
>> >> > On Monday, January 27, 2020 at 5:42:39 PM UTC+2, David Wells wrote:
>> >> >>
>> >> >> Hi Ihar,
>> >> >>
>> >> >> This sounds like something has gone wrong inside either PETSc's or
>> >> >> deal.II's build process. Would you please show us a copy of PETSc's
>> >> >> configure.log?
>> >> >>
>> >> >> Thanks,
>> >> >> David
>> >> >>
>> >> >> On Sun, Jan 26, 2020 at 6:59 AM Ihar Suvorau  
>> >> >> wrote:
>> >> >> >
>> >> >> > Not yet, I have a running version via docker images though. I'll try 
>> >> >> > the bundle also, thank you, before I was thinking that it shouldn't 
>> >> >> > support parallel programming, but now I see it is configured with 
>> >> >> > "DEAL_II_WITH_MPI set up with external dependencies" and 
>> >> >> > "DEAL_II_WITH_PETSC set up with external dependencies" and has all 
>> >> >> > packages installed.
>> >> >> >
>> >> >> > But I'm still interested in solving the issue with "Your PETSc 
>> >> >> > installation does not include a copy of the hypre package necessary 
>> >> >> > for this preconditioner" when I do have the hypre package installed 
>> >> >> > via the option "--download-hypre=1" while configuring PETSc.
>> >> >> >
>> >> >> > On Sunday, January 26, 2020 at 11:48:21 AM UTC+2, luca.heltai wrote:
>> >> >> >>
>> >> >> >> Did you try the pre-compiled deal.II package?
>> >> >> >>
>> >> >> >> Both
>> >> >> >>
>> >> >> >> dealii-9.1.1-clang-9.0.0.dmg
>> >> >> >>
>> >> >> >> and
>> >> >> >>
>> >> >> >> dealii-9.1.1-catalina-haswell-ro.dmg.zip
>> >> >> >>
>> >> >> >>
>> >> >> >> from https://github.com/dealii/dealii/releases/tag/v9.1.1
>> >> >> >>
>> >> >> >> should work.
>> >> >> >>
>> >> >> >> Luca.
>> >> >> >>
>> >> >> >> > On 25 Jan 2020, at 21:29, Ihar Suvorau  wrote:
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > Software:
>> >> >> >> > • macOS Catalina 10.15.2
>> >> >> >> > • deal.ii 9.1.1
>> >> >> >> > • PETSc 3.12
>> >> >> >> > Question:
>> >> >> >> >
>> >> >> >> > Hey, does somebody know a potential reason for this message while 
>> >> >> >> > running a well-compiled step-40 program:
>> >> >> >> >
>> >> >> >> > ihar@husky build3

Re: [deal.II] "PETSc installation does not include a copy of the hypre package" while running the step-40 program

[David Wells]

Hi Ihar,

I'm not sure what went wrong - everything looks right except that
deal.II did not find hypre.

Could you also send

/Users/ihar/lib/petsc-3.12.3/arch-darwin-c-debug/include/petscconf.h

to check something else?


On Tue, Jan 28, 2020 at 10:14 AM Ihar Suvorau  wrote:
>
> Hi, David,
>
> okay, please, attaching these files also.
>
> On Tuesday, January 28, 2020 at 4:18:44 PM UTC+2, David Wells wrote:
>>
>> Hi Ihar,
>>
>> It looks like nothing went wrong with PETsc. Would you please also
>> send a copy of deal.II's detailed.log and, if available,
>> CMakeCache.txt from the build directory?
>>
>> Thanks,
>> David
>>
>> On Mon, Jan 27, 2020 at 5:59 PM Ihar Suvorau  wrote:
>> >
>> > Sure, attaching a file, please.
>> >
>> > On Monday, January 27, 2020 at 5:42:39 PM UTC+2, David Wells wrote:
>> >>
>> >> Hi Ihar,
>> >>
>> >> This sounds like something has gone wrong inside either PETSc's or
>> >> deal.II's build process. Would you please show us a copy of PETSc's
>> >> configure.log?
>> >>
>> >> Thanks,
>> >> David
>> >>
>> >> On Sun, Jan 26, 2020 at 6:59 AM Ihar Suvorau  wrote:
>> >> >
>> >> > Not yet, I have a running version via docker images though. I'll try 
>> >> > the bundle also, thank you, before I was thinking that it shouldn't 
>> >> > support parallel programming, but now I see it is configured with 
>> >> > "DEAL_II_WITH_MPI set up with external dependencies" and 
>> >> > "DEAL_II_WITH_PETSC set up with external dependencies" and has all 
>> >> > packages installed.
>> >> >
>> >> > But I'm still interested in solving the issue with "Your PETSc 
>> >> > installation does not include a copy of the hypre package necessary for 
>> >> > this preconditioner" when I do have the hypre package installed via the 
>> >> > option "--download-hypre=1" while configuring PETSc.
>> >> >
>> >> > On Sunday, January 26, 2020 at 11:48:21 AM UTC+2, luca.heltai wrote:
>> >> >>
>> >> >> Did you try the pre-compiled deal.II package?
>> >> >>
>> >> >> Both
>> >> >>
>> >> >> dealii-9.1.1-clang-9.0.0.dmg
>> >> >>
>> >> >> and
>> >> >>
>> >> >> dealii-9.1.1-catalina-haswell-ro.dmg.zip
>> >> >>
>> >> >>
>> >> >> from https://github.com/dealii/dealii/releases/tag/v9.1.1
>> >> >>
>> >> >> should work.
>> >> >>
>> >> >> Luca.
>> >> >>
>> >> >> > On 25 Jan 2020, at 21:29, Ihar Suvorau  wrote:
>> >> >> >
>> >> >> >
>> >> >> > Software:
>> >> >> > • macOS Catalina 10.15.2
>> >> >> > • deal.ii 9.1.1
>> >> >> > • PETSc 3.12
>> >> >> > Question:
>> >> >> >
>> >> >> > Hey, does somebody know a potential reason for this message while 
>> >> >> > running a well-compiled step-40 program:
>> >> >> >
>> >> >> > ihar@husky build3 % ./step-40
>> >> >> >
>> >> >> >
>> >> >> > Running with PETSc on 1 MPI rank(s)...
>> >> >> >
>> >> >> > Cycle 0:
>> >> >> >
>> >> >> >   Number of active cells:   1024
>> >> >> >
>> >> >> >   Number of degrees of freedom: 4225
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > ---
>> >> >> >
>> >> >> >
>> >> >> > An error occurred in line <543> of file 
>> >> >> >  in 
>> >> >> > function
>> >> >> >
>> >> >> >void 
>> >> >> > dealii::PETScWrappers::PreconditionBoomerAMG::initialize(const 
>> >> >> > dealii::PETScWrappers::MatrixBase &, const 
>> >> >> > dealii::PETScWrappers::PreconditionBoomerAMG::AdditionalData &)
>>

Re: [deal.II] "PETSc installation does not include a copy of the hypre package" while running the step-40 program

[David Wells]

Hi Ihar,

It looks like nothing went wrong with PETsc. Would you please also
send a copy of deal.II's detailed.log and, if available,
CMakeCache.txt from the build directory?

Thanks,
David

On Mon, Jan 27, 2020 at 5:59 PM Ihar Suvorau  wrote:
>
> Sure, attaching a file, please.
>
> On Monday, January 27, 2020 at 5:42:39 PM UTC+2, David Wells wrote:
>>
>> Hi Ihar,
>>
>> This sounds like something has gone wrong inside either PETSc's or
>> deal.II's build process. Would you please show us a copy of PETSc's
>> configure.log?
>>
>> Thanks,
>> David
>>
>> On Sun, Jan 26, 2020 at 6:59 AM Ihar Suvorau  wrote:
>> >
>> > Not yet, I have a running version via docker images though. I'll try the 
>> > bundle also, thank you, before I was thinking that it shouldn't support 
>> > parallel programming, but now I see it is configured with 
>> > "DEAL_II_WITH_MPI set up with external dependencies" and 
>> > "DEAL_II_WITH_PETSC set up with external dependencies" and has all 
>> > packages installed.
>> >
>> > But I'm still interested in solving the issue with "Your PETSc 
>> > installation does not include a copy of the hypre package necessary for 
>> > this preconditioner" when I do have the hypre package installed via the 
>> > option "--download-hypre=1" while configuring PETSc.
>> >
>> > On Sunday, January 26, 2020 at 11:48:21 AM UTC+2, luca.heltai wrote:
>> >>
>> >> Did you try the pre-compiled deal.II package?
>> >>
>> >> Both
>> >>
>> >> dealii-9.1.1-clang-9.0.0.dmg
>> >>
>> >> and
>> >>
>> >> dealii-9.1.1-catalina-haswell-ro.dmg.zip
>> >>
>> >>
>> >> from https://github.com/dealii/dealii/releases/tag/v9.1.1
>> >>
>> >> should work.
>> >>
>> >> Luca.
>> >>
>> >> > On 25 Jan 2020, at 21:29, Ihar Suvorau  wrote:
>> >> >
>> >> >
>> >> > Software:
>> >> > • macOS Catalina 10.15.2
>> >> > • deal.ii 9.1.1
>> >> > • PETSc 3.12
>> >> > Question:
>> >> >
>> >> > Hey, does somebody know a potential reason for this message while 
>> >> > running a well-compiled step-40 program:
>> >> >
>> >> > ihar@husky build3 % ./step-40
>> >> >
>> >> >
>> >> > Running with PETSc on 1 MPI rank(s)...
>> >> >
>> >> > Cycle 0:
>> >> >
>> >> >   Number of active cells:   1024
>> >> >
>> >> >   Number of degrees of freedom: 4225
>> >> >
>> >> >
>> >> >
>> >> > ---
>> >> >
>> >> >
>> >> > An error occurred in line <543> of file 
>> >> >  in 
>> >> > function
>> >> >
>> >> >void dealii::PETScWrappers::PreconditionBoomerAMG::initialize(const 
>> >> > dealii::PETScWrappers::MatrixBase &, const 
>> >> > dealii::PETScWrappers::PreconditionBoomerAMG::AdditionalData &)
>> >> >
>> >> > The violated condition was:
>> >> >
>> >> >false
>> >> >
>> >> > Additional information:
>> >> >
>> >> >Your PETSc installation does not include a copy of the hypre package 
>> >> > necessary for this preconditioner.
>> >> >
>> >> >
>> >> >
>> >> > Stacktrace:
>> >> >
>> >> > ---
>> >> >
>> >> > #0  2   libdeal_II.g.9.1.1.dylib0x00011188b86f 
>> >> > _ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE
>> >> >  + 95: 2   libdeal_II.g.9.1.1.dylib0x00011188b86f 
>> >> > _ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE
>> >> >
>> >> > #1  3   step-40 0x00010643881a 
>> >> > _ZN6Step4014LaplaceProblemILi2EE5solveEv + 266: 3   step-40 
>> >> > 0x00010643881a 
>> >> > _ZN6Step4014LaplaceProblemILi2EE

Re: [deal.II] ParameterHandler question

[David Wells]

Hi Simon,

It sounds like you want to use Patterns::Map or Patterns::List. As far
as I know both can accept an arbitrary number of input arguments.
Would either of those work for you?

Thanks,
David

On Sun, Jan 26, 2020 at 2:01 PM Simon Gauvin  wrote:
>
> Greetings!
>
> I currently work on the Lethe project, (https://github.com/lethe-cfd/lethe), 
> and we currently are facing a problem with ParameterHandler.
> We need a way to have a list of variable size in a .prm file (eg; set array = 
> [{set var = bool, set var2 = string, etc}, {...}, ...])
> From reading the official doc, I don't think we can do something like this.
> Or else just having a way to know if a subsection already exists would work, 
> (which we can't do I seem to understand), so we can simply have a variable 
> number of subsections, and know the number of subsections.
> Is there any workaround?
> I was thinking maybe just using JSONs instead of a prm would work.
>
> Thanks for your help! :)
>
> Simon
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see 
> https://groups.google.com/d/forum/dealii?hl=en
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Re: [deal.II] "PETSc installation does not include a copy of the hypre package" while running the step-40 program

[David Wells]

Hi Ihar,

This sounds like something has gone wrong inside either PETSc's or
deal.II's build process. Would you please show us a copy of PETSc's
configure.log?

Thanks,
David

On Sun, Jan 26, 2020 at 6:59 AM Ihar Suvorau  wrote:
>
> Not yet, I have a running version via docker images though. I'll try the 
> bundle also, thank you, before I was thinking that it shouldn't support 
> parallel programming, but now I see it is configured with "DEAL_II_WITH_MPI 
> set up with external dependencies" and "DEAL_II_WITH_PETSC set up with 
> external dependencies" and has all packages installed.
>
> But I'm still interested in solving the issue with "Your PETSc installation 
> does not include a copy of the hypre package necessary for this 
> preconditioner" when I do have the hypre package installed via the option 
> "--download-hypre=1" while configuring PETSc.
>
> On Sunday, January 26, 2020 at 11:48:21 AM UTC+2, luca.heltai wrote:
>>
>> Did you try the pre-compiled deal.II package?
>>
>> Both
>>
>> dealii-9.1.1-clang-9.0.0.dmg
>>
>> and
>>
>> dealii-9.1.1-catalina-haswell-ro.dmg.zip
>>
>>
>> from https://github.com/dealii/dealii/releases/tag/v9.1.1
>>
>> should work.
>>
>> Luca.
>>
>> > On 25 Jan 2020, at 21:29, Ihar Suvorau  wrote:
>> >
>> >
>> > Software:
>> > • macOS Catalina 10.15.2
>> > • deal.ii 9.1.1
>> > • PETSc 3.12
>> > Question:
>> >
>> > Hey, does somebody know a potential reason for this message while running 
>> > a well-compiled step-40 program:
>> >
>> > ihar@husky build3 % ./step-40
>> >
>> >
>> > Running with PETSc on 1 MPI rank(s)...
>> >
>> > Cycle 0:
>> >
>> >   Number of active cells:   1024
>> >
>> >   Number of degrees of freedom: 4225
>> >
>> >
>> >
>> > ---
>> >
>> >
>> > An error occurred in line <543> of file 
>> >  in function
>> >
>> >void dealii::PETScWrappers::PreconditionBoomerAMG::initialize(const 
>> > dealii::PETScWrappers::MatrixBase &, const 
>> > dealii::PETScWrappers::PreconditionBoomerAMG::AdditionalData &)
>> >
>> > The violated condition was:
>> >
>> >false
>> >
>> > Additional information:
>> >
>> >Your PETSc installation does not include a copy of the hypre package 
>> > necessary for this preconditioner.
>> >
>> >
>> >
>> > Stacktrace:
>> >
>> > ---
>> >
>> > #0  2   libdeal_II.g.9.1.1.dylib0x00011188b86f 
>> > _ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE
>> >  + 95: 2   libdeal_II.g.9.1.1.dylib0x00011188b86f 
>> > _ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE
>> >
>> > #1  3   step-40 0x00010643881a 
>> > _ZN6Step4014LaplaceProblemILi2EE5solveEv + 266: 3   step-40
>> >  0x00010643881a _ZN6Step4014LaplaceProblemILi2EE5solveEv
>> >
>> > #2  4   step-40 0x00010642e633 
>> > _ZN6Step4014LaplaceProblemILi2EE3runEv + 451: 4   step-40  
>> >0x00010642e633 _ZN6Step4014LaplaceProblemILi2EE3runEv
>> >
>> > #3  5   step-40 0x00010642e23a main + 106: 
>> > 5   step-40 0x00010642e23a main
>> >
>> > #4  6   libdyld.dylib   0x7fff6350f7fd start + 1: 
>> > 6   libdyld.dylib   0x7fff6350f7fd start
>> >
>> > 
>> >
>> >
>> >
>> > [husky:92536] *** Process received signal ***
>> >
>> > [husky:92536] Signal: Abort trap: 6 (6)
>> >
>> > [husky:92536] Signal code:  (0)
>> >
>> > [husky:92536] [ 0] 0   libsystem_platform.dylib
>> > 0x7fff6370842d _sigtramp + 29
>> >
>> > [husky:92536] [ 1] 0   ??? 
>> > 0x7ffee97d8838 0x0 + 140732815738936
>> >
>> > [husky:92536] [ 2] 0   libsystem_c.dylib   
>> > 0x7fff635dda1c abort + 120
>> >
>> > [husky:92536] [ 3] 0   libdeal_II.g.9.1.1.dylib
>> > 0x0001119ec74d 
>> > _ZN6dealii18deal_II_exceptions9internals5abortERKNS_13ExceptionBaseE + 205
>> >
>> > [husky:92536] [ 4] 0   libdeal_II.g.9.1.1.dylib
>> > 0x00010de0f63f 
>> > _ZN6dealii18deal_II_exceptions9internals20issue_error_noreturnINS_18StandardExceptions10ExcMessageEEEvNS1_17ExceptionHandlingEPKciS7_S7_S7_T_
>> >  + 223
>> >
>> > [husky:92536] [ 5] 0   libdeal_II.g.9.1.1.dylib
>> > 0x00011188b86f 
>> > _ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE
>> >  + 95
>> >
>> > [husky:92536] [ 6] 0   step-40 
>> > 0x00010643881a _ZN6Step4014LaplaceProblemILi2EE5solveEv + 266
>> >
>> > [husky:92536] [ 7] 0   step-40 
>> > 0x00010642e633 _ZN6Step4014LaplaceProblemILi2EE3runEv + 451
>> >
>> > [husky:92536] [ 8] 0   step-40

Re: [deal.II] Re: Math symbols not displayed correctly in debian package documentation for deal.ii

[David Wells]

Hi Gerald,

I am not sure how to fix this, but a good workaround would be to just
download the offline documentation tarball from here

https://github.com/dealii/dealii/releases/tag/v8.4.2

(its under assets at the bottom of the page) and use that directly
instead of the Debian package. Our generic offline documentation does
not use MathJax so it should always work.

Thanks,
David

On Wed, Jan 8, 2020 at 4:50 AM Gerald Marewo  wrote:
>
> PS: I use Firefox.
>
> Regards.
>
> Gerald.
>
> On Wednesday, 8 January 2020 11:40:32 UTC+2, Gerald Marewo wrote:
>>
>> Dear all,
>>
>> I have noticed that unlike the online documentation (deal.ii 8.4.2) which 
>> behaves well, the documentation that comes with the Debian package 
>> (libdeal.ii-doc) on Debian stretch does not display the math symbols 
>> correctly. Instead it displays the LaTeX code as it is. Once in a while I 
>> need to read the documentation offline.
>>
>> Could you please assist me with solving this problem?
>>
>> Regards.
>>
>> Gerald.
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see 
> https://groups.google.com/d/forum/dealii?hl=en
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Re: [deal.II] Re: Fixed Support for 2D Beam Problem

[David Wells]

Happy to help!

On Tue, Jan 7, 2020 at 1:42 PM Mohammed Hassan  wrote:
>
> Hi David,
>
> Yes, I fixed the mesh file and it works fine for the stage of meshing, next I 
> will to try to play with Boundary conditions. Many thanks for your support.
>
> Regards,
>
> On Tuesday, December 10, 2019 at 4:35:20 PM UTC+1, Hasan Tasneem wrote:
>>
>> I am a beginner on Deal.ii. I have installed and run some of the tutorials. 
>> I am now trying to run one specific problem. This problem is 2D and is a 
>> beam problem. My dimension of the beam is 3*100mm. The beam is fixed on one 
>> end and there is 1000N of transverse loading on the other end. I am 
>> following Step-8 which solves an elastic equation. Everything I have 
>> inputted correctly. However, I am stuck on applying the fixed support. I 
>> want the fixed support at x equal to 0. I don't know how to proceed further.
>>
>> VectorTools::interpolate_boundary_values(dof_handler,
>> 0,
>> Functions::ZeroFunction(dim),
>> boundary_values);
>> MatrixTools::apply_boundary_values(boundary_values,
>> system_matrix,
>> solution,
>> system_rhs);
>>
>> How should I alter this to get fixed support at x equal to 0.
>>
>>
> --
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Re: [deal.II] Using deal for induction heating

[David Wells]

Hi Masod,

Welcome to the project!

The project works on Windows with the WSL and also with Microsoft's own
toolchain (visual studio and MSVC): see
https://github.com/dealii/dealii/wiki/Windows
for notes on how to do it. Most of the developers use Linux; I recommend
using Linux for this reason.

Thanks,
David Wells


On Tue, Jan 7, 2020 at 10:21 AM masod sadipour 
wrote:

> Hello dear Dr.  Wells,
> I am a graduate research assistant. I have recieved a project which I
> should solve the advection-diffusion equation using by deal.ii ASAP.
> Could you please let me know about the possibility of using deal.ii by
> windows. Should I do it just in Linux?
> BR.
>
>
> On Tue, Jan 7, 2020 at 6:42 PM David Wells  wrote:
>
>> Dear Andreas,
>>
>> This is a specialized application domain; I am not sure if anyone here
>> has done induction heating but I will do my best to try and point you in a
>> useful direction.
>>
>> 1. I don't think we have any examples in the documentation about how to
>> solve this problem. However, there are other examples of heat transfer in
>> papers citing deal.II: check out the list at
>> https://dealii.org/publications.html
>> 2. For electromagnetism you probably want to use the Nedelec_SZ element.
>> These elements tend to be very complicated so it is probably best to use
>> one that is already in the library.
>> 3. I don't know how to couple the electromagnetic field to the thermal
>> problem.
>>
>> Thanks,
>> David Wells
>> <https://dealii.org/publications.html>
>>
>>
>> On Tue, Jan 7, 2020 at 4:34 AM Andreas Gschwentner <
>> gschwentner.andr...@gmail.com> wrote:
>>
>>> Dear deal.II community,
>>>
>>> i am working on my master thesis (MU Leoben, Austria) with the general
>>> topic "simulation induction heating". I want to try out a new program and
>>> want to use deal.II for the simulation (I have no experience with this
>>> program). Concerning this matter i have some question about deal.II:
>>>
>>>
>>>- First of all, has someone experience with this kind of problem? Is
>>>there a topic in the doc about simulation induction heating?
>>>- The second question is about the elements. What kind of element
>>>formalism is used for the simulation of electromagnet fields, or is it
>>>possible, to implement new elements?
>>>- The third question is about the coupling schemes for coupling the
>>>electromagnetic with the thermal problem. Usable coupling schemes for 
>>> this
>>>problem?
>>>
>>> Many thanks for your help.
>>>
>>> Best regards
>>> Andreas
>>>
>>>
>>>
>>> --
>>> The deal.II project is located at http://www.dealii.org/
>>> For mailing list/forum options, see
>>> https://groups.google.com/d/forum/dealii?hl=en
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>>> Groups "deal.II User Group" group.
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>>> an email to dealii+unsubscr...@googlegroups.com.
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>>> .
>>>
>> --
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>> For mailing list/forum options, see
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>> <https://groups.google.com/d/msgid/dealii/CABrTbYQCAwW84z3ynmrCccBMksETNu4pCWSNt-v4hnaiMg_APg%40mail.gmail.com?utm_medium=email&utm_source=footer>
>> .
>>
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Re: [deal.II] Using deal for induction heating

[David Wells]

Dear Andreas,

This is a specialized application domain; I am not sure if anyone here has
done induction heating but I will do my best to try and point you in a
useful direction.

1. I don't think we have any examples in the documentation about how to
solve this problem. However, there are other examples of heat transfer in
papers citing deal.II: check out the list at
https://dealii.org/publications.html
2. For electromagnetism you probably want to use the Nedelec_SZ element.
These elements tend to be very complicated so it is probably best to use
one that is already in the library.
3. I don't know how to couple the electromagnetic field to the thermal
problem.

Thanks,
David Wells
<https://dealii.org/publications.html>


On Tue, Jan 7, 2020 at 4:34 AM Andreas Gschwentner <
gschwentner.andr...@gmail.com> wrote:

> Dear deal.II community,
>
> i am working on my master thesis (MU Leoben, Austria) with the general
> topic "simulation induction heating". I want to try out a new program and
> want to use deal.II for the simulation (I have no experience with this
> program). Concerning this matter i have some question about deal.II:
>
>
>- First of all, has someone experience with this kind of problem? Is
>there a topic in the doc about simulation induction heating?
>- The second question is about the elements. What kind of element
>formalism is used for the simulation of electromagnet fields, or is it
>possible, to implement new elements?
>- The third question is about the coupling schemes for coupling the
>electromagnetic with the thermal problem. Usable coupling schemes for this
>problem?
>
> Many thanks for your help.
>
> Best regards
> Andreas
>
>
>
> --
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> For mailing list/forum options, see
> https://groups.google.com/d/forum/dealii?hl=en
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> .
>

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Re: [deal.II] Re: Fixed Support for 2D Beam Problem

[David Wells]

Hi Hasan,

I loaded up your mesh in gmsh and it looks like something went wrong
with the extrusion: I only see quadrilaterals on two opposing faces
and no volume mesh at all. I think that if you fix the mesh you will
get past this error.

I attached a picture of what I see in gmsh to this message.

Thanks,
David

On Thu, Jan 2, 2020 at 2:03 PM Mohammed Hassan  wrote:
>
> Hi Dealii Users;
>
> I have a similar problem, I am running a 3D problem for a beam with the 
> following dimensions x=10 mm and y= 1 mm and z =1 mm I am trying to adapt 
> step-8 to my case the I am facing the following challenges :
>
> 1- importing msh file to the dealii, I copied a print_mesh_info function to 
> see the vtu file but the following error pop up.
>
> An error occurred in line <2018> of file 
>  in function
> void dealii::GridIn::read_msh(std::istream&) [with int dim 
> = 3; int spacedim = 3; std::istream = std::basic_istream]
> The violated condition was:
> cells.size() > 0
>
> 2- the purpose of this work is to learn how to implement  the boundary 
> conditions. the .msh file has been meshed as hexahedral where it has 100 
> cells along x axis and 10 cells along y and  10 cells along z axis. I would 
> like to apply 100 N force on the right side of the beam pointing to ( + x 
> axis and the second case + y axis " I mean the direction of the force") and a 
> fixed wall on the left side knowing that I named the cells for the right side 
> of the beam (in  .msh file) force while for the  left side of the beam wall.
>
> Thank you in advance !
>
> Kind Regards.
>
>
>
>
>
> On Tuesday, December 10, 2019 at 4:35:20 PM UTC+1, Hasan Tasneem wrote:
>>
>> I am a beginner on Deal.ii. I have installed and run some of the tutorials. 
>> I am now trying to run one specific problem. This problem is 2D and is a 
>> beam problem. My dimension of the beam is 3*100mm. The beam is fixed on one 
>> end and there is 1000N of transverse loading on the other end. I am 
>> following Step-8 which solves an elastic equation. Everything I have 
>> inputted correctly. However, I am stuck on applying the fixed support. I 
>> want the fixed support at x equal to 0. I don't know how to proceed further.
>>
>> VectorTools::interpolate_boundary_values(dof_handler,
>> 0,
>> Functions::ZeroFunction(dim),
>> boundary_values);
>> MatrixTools::apply_boundary_values(boundary_values,
>> system_matrix,
>> solution,
>> system_rhs);
>>
>> How should I alter this to get fixed support at x equal to 0.
>>
>>
> --
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Re: [deal.II] Constrained linear operator on distributed data structures

[David Wells]

Hi Doug,

If I recall correctly, we added that comment since this is a part of
the library that is not very well tested. The code is probably fine.

Thanks,
David

On Tue, Dec 24, 2019 at 2:33 PM Doug Shi-Dong  wrote:
>
> Hello everyone,
>
> I see that some functions within the constrained_linear_operator.h have a 
> note saying
>
> Currently, this function may not work correctly for distributed data 
> structures.
>
> I am currently using it in parallel and seems to be working fine for a very 
> simple linear elasticity problem with hanging nodes and Dirichlet boundary 
> condition. I was wondering what I should be careful about. In which scenarios 
> would those functions fail?
>
> I couldn't find any issues on GitHub regarding those, or any mention of a 
> specific problem when git blaming.
>
> Happy holidays!
>
> Doug
>
> --
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Re: [deal.II] Symbol dealii not resolved

[David Wells]

Dear Gerald,

This is great to hear! You are most welcome.

Thanks,
David

On Fri, Dec 20, 2019 at 11:50 AM Gerald Marewo  wrote:
>
> Dear David and everyone,
>
> Here is an update and my way of saying that my problem has been completely 
> solved.
>
> Upon watching Wolfgang's Lecturer video 8.01 now I understand that:
>
> I created a new c++ project from scratch inside Eclipse and I told Eclipse 
> where to find the include files. Rebuilding index helped after a bit of 
> tinkering.
> The easier route was to ask CMake to not only create Makefiles for my project 
> but to also create a project for Eclipse.
> Once inside Eclipse I importe project from the workspace then it tried to 
> understand the project by building an index. Worked like a charm.
>
> All is good now.
>
> I rest my case.
>
> Thanks to David and Wolfgang.
>
> Regards.
>
> Gerald.
>
> On Thursday, 19 December 2019 23:13:56 UTC+2, Gerald Marewo wrote:
>>
>> Dear David,
>>
>> Thank you for the reply. I followed your advice and it seems the trick is in 
>> rebuilding the index.
>>
>> All is well now.
>>
>> Cheers.
>>
>> Gerald.
>
> --
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Re: [deal.II] Symbol dealii not resolved

[David Wells]

Hi Gerald,

The best way to do this is to let CMake generate an eclipse project
for you by executing the command

  cmake -G"Eclipse CDT4 - Unix Makefiles" -DDEAL_II_DIR=/path/to/deal.II .

in your project's base directory. See

https://github.com/dealii/dealii/wiki/Eclipse

for more information.

Thanks,
David

On Thu, Dec 19, 2019 at 11:13 AM Gerald Marewo  wrote:
>
> Dear all.
>
> I'm new to dealii. I have libdealii and eclipse 2019-03 installed on both 
> Debian stretch and ubuntu bionic.
>
> I'm working on tutorial step 1. The problem is that eclipse keeps saying 
> symbol dealii not resolved. This results from "using namespace dealii;". 
> Consequently, eclipse doesn't know about for example 
> Triangulation::hyper_cube".
>
> By the way I went to project properties - > c/c++ - > symbols and paths - > 
> added include /usr/include where deal.II is contained but in vain.
>
> Could you please assist me to resolve this problem.
>
> Regards.
>
> Gerald.
>
> --
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Re: [deal.II] Maybe typo on Step-40's webpage

[David Wells]

Dear Zhidong,

Thanks for finding and reporting this :)

When we compile the doxygen documentation we remove all occurrences of

dealii::

since, for a variety of reasons, it's easier to pretend in the manual
that all deal.II classes are in the global namespace. This is done
with, if I recall correctly, a simple text substitution - hence, the
webpage for step-40 has

using namespace ::LinearAlgebraPETSc

instead of what is actually in the source file:

using namespace dealii::LinearAlgebraPETSc

Put another way: this text substitution is wrong for this example and
needs to be fixed. Could you help us by opening a GitHub issue to
track this problem with the documentation?

Thanks,
David

On Wed, Dec 11, 2019 at 1:31 PM Zhidong Brian Zhang
 wrote:
>
> Dear, Colleagues,
>
> I tried to run the code from Step-40's webpage,
> https://www.dealii.org/current/doxygen/deal.II/step_40.html
>
> However, I encountered errors: error: ‘LinearAlgebraPETSc’ is not a 
> namespace-name
>using namespace ::LinearAlgebraPETSc;
>
> So I compared the code from the locally installed file of Step-40 and found 
> there is a slight difference:
>
> Webpage:
> namespace LA
> {
> #if defined(DEAL_II_WITH_PETSC) && !defined(DEAL_II_PETSC_WITH_COMPLEX) && \
> !(defined(DEAL_II_WITH_TRILINOS) && defined(FORCE_USE_OF_TRILINOS))
> using namespace ::LinearAlgebraPETSc;
> # define USE_PETSC_LA
> #elif defined(DEAL_II_WITH_TRILINOS)
> using namespace ::LinearAlgebraTrilinos;
> #else
> # error DEAL_II_WITH_PETSC or DEAL_II_WITH_TRILINOS required
> #endif
> } // namespace LA
>
> Locally installed:
> namespace LA
> {
> #if defined(DEAL_II_WITH_PETSC) && !defined(DEAL_II_PETSC_WITH_COMPLEX) && \
>   !(defined(DEAL_II_WITH_TRILINOS) && defined(FORCE_USE_OF_TRILINOS))
>   using namespace dealii::LinearAlgebraPETSc;
> #  define USE_PETSC_LA
> #elif defined(DEAL_II_WITH_TRILINOS)
>   using namespace dealii::LinearAlgebraTrilinos;
> #else
> #  error DEAL_II_WITH_PETSC or DEAL_II_WITH_TRILINOS required
> #endif
> } // namespace LAEnter code here...
>
> I have highlighted the difference. After adding "dealii", the program can be 
> run successfully.
>
> I guess maybe these are typos. I am new to deal.ii, so I am not sure my guess 
> is correct or not. I am just curious about this (no offence), because I may 
> miss some important point here.
>
> Thank you very much for your attention!
>
> Zhidong Brian Zhang
>
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Re: [deal.II] get_dof_indices() only works on active cells - blocks vector

[David Wells]

Dear Juan,

My best guess is that, at some point in the loop over all active
cells, you are also doing some computations involving the neighbor of
each cell. TriaAccessor::neighbor() returns the neighboring cell which
has, at most, the same level number as the current cell: i.e., if the
neighbor cell has been refined but the current cell has not, then
trying to get the degrees of freedom from the neighbor will throw
exactly this exception since the cell returned by the call to
neighbor() is inactive.

This is only a guess. Could you show us the part of your code that
triggers this exception? That will help us give you a better answer :)

Thanks,
David

On Fri, Dec 6, 2019 at 3:53 AM Juan Felipe Giraldo  wrote:
>
>
> Hi all!
>
> I am currently working on the linear advection problem by using a DG 
> formulation, similar to the problem in step 12 
> https://www.dealii.org/current/doxygen/deal.II/step_12.html, but using a 
> mixed formulation as it is shown in step 20 
> https://www.dealii.org/current/doxygen/deal.II/step_20.html. I can solve the 
> problem without problems using a global refinement, however, when I implement 
> an adaptative refinement I have the following problem after the 1st 
> refinement cycle
>
> An error occurred in line <3792> of file 
> 
>  in function
> void dealii::DoFCellAccessor lda>::get_dof_indices(std::vector&) const [with DoFHandlerType 
> = dealii::DoFHandler<2, 2>; bool level_dof_access = false]
> The violated condition was:
> this->active()
> Additional information:
> get_dof_indices() only works on active cells.
>
>
> I have seen that some people had this problem a couple of years ago, but I 
> have not seen a proper solution to solve it.
>
> Anyone knows how can I solve it?
>
> Thank you so much,
>
> Regards,
>
> Juan Felipe Giraldo
>
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Re: [deal.II] Vector conversion problem: between dealii::PETScWrappers::MPI::Vector and a PETSc Vec

[David Wells]

Hi Zhidong,

I am happy to help!

Unfortunately, this is a part of deal.II that has some older code that
has accumulated some inconsistencies over time. Both inconsistencies
stem from there, previously, being a third class PETScWrappers::Vector
which was a sequential PETSc vector: both PETScWrappers::Vector and
PETScWrappers::MPI::Vector inherited from PETScWrappers::VectorBase.
Here VectorBase contained most of the functionality that didn't use or
need MPI objects.

1. I don't think that there is a workaround - the problem with that
function is that one could pass in a serial PETSc vector which doesn't
make any sense. Its not quite equivalent, but the closest replacement
is to just create a MPI::Vector and then extract the Vec rather than
creating a Vec and then putting it in an MPI::Vector.
2. This is, mostly, a consequence of the historical design I mentioned
above: the end result is confusing because we have not completely
converted this class. Your understanding is correct except that
MPI::Vector is always a wrapper of VectorBase *where the Vec is a
parallel-distributed vector*.

Does this make sense?

Thanks,
David

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Re: [deal.II] Vector conversion problem: between dealii::PETScWrappers::MPI::Vector and a PETSc Vec

[David Wells]

Hi Zhidong,

In C++ constructors are not inherited, so this function call won't
work: it's not possible to create a PETScWrappers::MPI::Vector from a
Vec object directly.

I think that you can solve your problem by just using VectorBase: you
can create objects of this type directly that wrap around a Vec and
don't destroy it when they go out of scope. Would this work for you?

One alternative would be to always create PETScWrappers::MPI::Vector
objects (instead of ever explicitly creating a Vec) and then using the
conversion operator (part of VectorBase) to get the Vec out when you
need it.

Thanks,
David

On Wed, Dec 4, 2019 at 11:42 AM Zhidong Brian Zhang
 wrote:
>
> Dear, deal.ii colleagues,
>
> A vector conversion problem has been troubled me for a long time.
>
> It is the conversion between between dealii::PETScWrappers::MPI::Vector and a 
> PETSc Vec.
>
> I have some functions written based on PETSc directly. So that I would like 
> to use them directly in deal.ii. However, I need to convert vectors between 
> dealii's MPI vectors to PETSc's generic vectors.
>
> Here is an simplified example:
> Vec a;  // PETSc vector
> VecDuplicate(x, &a);  // x is a dealii::PETScWrappers::MPI Vector generated 
> previously
> VecCopy(x, a);
> dealii::PETScWrappers::MPI::Vector b(a);   // dealii MPI vector
>
> I try to construct a dealii vector named with "b" based on PETSc Vector named 
> "a". This should be OK in my opinion based on the constructor that is 
> VectorBase (const Vec &v) in the deal.ii's document:
> https://www.dealii.org/current/doxygen/deal.II/classPETScWrappers_1_1VectorBase.html#a08f6d7c4850e085271c225c5c19d7502
>
>
> In addition, dealii::PETScWrappers::MPI::Vector is inherited from VectorBase, 
> so the constructor VectorBase (const Vec &v) should be able to be called by 
> dealii::PETScWrappers::MPI::Vector as well.
>
> However, the error reported is:
> no matching function for call to 
> dealii::PETScWrappers::MPI::Vector::Vector(_p_Vec*&)
>
>
> So may I get some information about this vector conversion problem?
> Thank you very much in advance!
>
> Zhidong Brian Zhang
>
>
> BTW, I found some info in the following forum but it is related to Mat 
> conversion between deal.ii and PETSc:
> https://groups.google.com/forum/#!searchin/dealii/petscwrappers$3A$3Avector|sort:date/dealii/1HHsnUeJC28/qgBaE0SVBgAJ
>
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Re: [deal.II] Implementation of boundary condtitions

[David Wells]

Dear Muhammad,

I think Ross implemented vector_value_list() this way so that he could use
one function object to give correct values with multiple material IDs: see

https://github.com/rosskynch/MIT_Forward/blob/master/src/forwardsolver.cc#L724

to see where he uses an object inheriting from EddyCurrentFunction to do
exactly this (though in that case he uses this function to set up the
right-hand side instead of boundary values).

Several are implemented here:

https://github.com/rosskynch/MIT_Forward/blob/master/include/backgroundfield.h#L46

Thanks,
David

On Thu, Sep 12, 2019 at 4:54 AM Muhammad Adil 
wrote:

> Hello,
> I am trying to understand the MIT code written by Ross Kynch.
> I am facing a problem to understand the implementation of boundary
> conditions.
> As we know we impose boundary conditions to calcluate the unknown
> coefficients. I don't understand how is he implementing the code given
> below to determine the coefficients?
>
> I don't know why he defined two functions:
> virtual void vector_value_list (const std::vector > &points,
> std::vector > &values) const;
> virtual void vector_value_list (const std::vector > &points,
> std::vector > &values,
> const types::material_id &mat_id) const;
>
> Header File/
>
>
> template
> class curlFunction : public Function
> {
> public:
> // curlFunction ();//unsigned int n_components = dim+dim);
> virtual void curl_value_list (const std::vector > &points,
> std::vector > &values) const = 0;
> //virtual void perturbed_field_value_list (const std::vector >
> &points,
> // std::vector > &values) const = 0;
> };
>
> template
> class perturbedFunction : public curlFunction
> {
> public:
> // perturbedFunction ();//unsigned int n_components = dim+dim);
> virtual void curl_value_list (const std::vector > &points,
> std::vector > &values) const = 0;
> virtual void perturbed_field_value_list (const std::vector > &
> points,
> std::vector > &values) const = 0;
> };
>
> // Base Function class for all EddyCurrent problems.
> // The idea here is to allow implementation of boundary conditions of the
> type:
> // n x E = f (Dirichlet) and n x curl(E) = g (Neumann)
> //
> // which can be handled through the vector_value_list and curl_value_list
> functions.
> //
> // The RHS of the equation can be handled through the rhs_value_list.
> //
> // The perturbed_field_value_list can be used for comparison with
> analytical/asymptotic formulae.
> //
> // We also include the boolean function zero_xxx() for each to return if
> the function is simply zero.
> // this allows us to avoid wasted computation which are automatically zero
> (e.g. in RHS assembly).
> //
> // We also include the option of passing a material_id to the function.
> Since we are typically
> // dealing with subdomains where we have conducting/non-conducting
> objects, this allows communication
> // from structure in the mesh to the function, if required (default is
> off).
> 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 > &points,
> std::vector > &values) const;
> virtual void vector_value_list (const std::vector > &points,
> std::vector > &values,
> const types::material_id &mat_id) const;
> virtual void curl_value_list (const std::vector > &points,
> std::vector > &values) const;
>
> virtual void curl_value_list (const std::vector > &points,
> std::vector > &values,
> const types::material_id &mat_id) const;
> virtual void perturbed_field_value_list (const std::vector > &
> points,
> std::vector > &values) const;
>
> virtual void perturbed_field_value_list (const std::vector > &
> points,
> std::vector > &values,
> const types::material_id &mat_id) const;
>
> virtual void rhs_value_list (const std::vector > &points,
> std::vector > &values) const;
> virtual void rhs_value_list (const std::vector > &points,
> std::vector > &values,
> const types::material_id &mat_id) const;
> virtual void scattered_field_value_list (const std::vector > &
> points,
> std::vector > &values) const;
> virtual void scattered_field_value_list (const std::vector > &
> points,
> std::vector > &values,
> const types::material_id &mat_id) const;
>
> virtual bool zero_vector() const { return true; }
> virtual bool zero_curl() const { return true; }
> virtual bool zero_perturbed() 

Re: [deal.II] MUMPS with PETScWrappers::MPI::BlockSparseMatrix

[David Wells]

Hi Konrad,

I don't think that it is possible to use MUMPS with a block matrix for
exactly this reason. I think that if you want to use MUMPS you will need to
copy the block matrix into a non-block matrix.

Thanks,
David

On Fri, Sep 6, 2019 at 12:25 PM Konrad  wrote:

> Dear deal.ii community,
>
> is it possible to use MUMPS with a PETScWrappers::MPI::BlockSparseMatrix?
> Don't find anything but I see that PETScWrappers::MPI::BlockSparseMatrix
> does not inherit from PETScWrappers::MatrixBase.
>
> Best,
> Konrad
>
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> 
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>

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Re: [deal.II] On using block-diagonal preconditioner for the mixed Poisson problem from step-20

[David Wells]

Hi Charlie,

The issue is that Trilinos really needs an actual Matrix object (not just a
linear operator) to compute the AMG preconditioner: i.e., it can only
construct the preconditioner if it has access to the actual matrix entries,
which are not available unless you explicitly calculate B (DA)^-1 B^T. To
get this to work you will have to multiply those three matrices together
and then pass that result (stored as a Trilinos matrix) to the initialize
function.

It should be possible to do this with TrilinosWrappers::SparseMatrix::mmult
and TrilinosWrappers::SparseMatrix::Tmmult.

Thanks,
David

On Tue, Aug 27, 2019 at 2:39 PM Charlie Z  wrote:

> Dear all,
>
> I'm trying to use a block-diagonal preconditioner for the mixed Poisson
> problem from step-20, but haven't made it yet.
>
> The diagonal preconditioner of interest is from Powell & Silvester,2003
> . Specifically,
> for the matrix system after discretization with the RT0-DG0 element pair
>   [A  BT
>B  0],
> they suggested a block diagonal preconditioner
>   P =
>   [DA  0
>0 PS],
> where DA is diag(A), and PS is AMG applied to the approximated Schur
> complement SD = B(DA^-1)BT.
>
> As the above idea is quite similar to that in step-55, so I borrowed quite
> a few code blocks from there, e.g. InverseMatrix and
> BlockDiagonalPreconditioner. The resulting solve() with a SolverMinRes solver
> is as follows. (The rest of the code is mainly from step-20)
>
>   template 
>  void MixedLaplaceProblem::solve()
>  {
>TrilinosWrappers::PreconditionJacobi diagA;
>diagA.initialize(system_matrix.block(0, 0));//DA
>
> ApproximateSchurComplement approximate_schur(system_matrix, solution);
> //SD
>
> InverseMatrix approximate_inverse(
> approximate_schur);//PS
>
> const BlockDiagonalPreconditioner ,
>  InverseMatrix >
>  preconditioner(diagA, approximate_inverse);
>
> SolverControl solver_control(system_matrix.m(),
> 1e-6 * system_rhs.l2_norm());
>
> SolverMinRes solver(solver_control
> );
>solver.solve(system_matrix, solution, system_rhs,
>   preconditioner
>  );
>
> std::cout<<"last step = "<  }
>
> However, the code can't compile, and gives the following error message:
>
>   /home/dealii/test.cc:336:5: error: no matching function for call to ‘
> dealii::TrilinosWrappers::PreconditionAMG::initialize(const Step20::
> ApproximateSchurComplement&, dealii::TrilinosWrappers::PreconditionAMG::
> AdditionalData&)’
>   preconditioner.initialize(*matrix, data);
>   ^
>  In file included from /home/dealii/dealii-v9.0.0/include/deal.II/lac/
> generic_linear_algebra.h:141:0,
>   from /home/dealii/test.cc:31:
>  /home/dealii/dealii-v9.0.0/include/deal.II/lac/trilinos_precondition.h:
> 1516:10: note: candidate: void dealii::TrilinosWrappers::PreconditionAMG::
> initialize(const dealii::TrilinosWrappers::SparseMatrix&, const dealii::
> TrilinosWrappers::PreconditionAMG::AdditionalData&)
>   void initialize (const SparseMatrix   &matrix,
>
> The error is related to the use of PreconditionAMG in my implementation of
> InverseMatrix::vmult:
>
>   template 
>  void InverseMatrix::vmult (LinearAlgebraTrilinos::MPI::Vector
>   &dst,
> const LinearAlgebraTrilinos::MPI::
> Vector &src) const
>  {
>SolverControl solver_control(src.size(),
> 1e-6 * src.l2_norm());
>SolverCGcg (solver_control);
>dst = 0;
>
> LinearAlgebraTrilinos::MPI::PreconditionAMG preconditioner;
>LinearAlgebraTrilinos::MPI::PreconditionAMG::AdditionalData data;
>preconditioner.initialize(*matrix, data);
>
> // PreconditionIdentity preconditioner;//A Identity preconditioner
> works fine here
>
> cg.solve (*matrix, dst, src, preconditioner);
>
> std::cout<<"inner last step = "< ;
>  }
>
> It seems that a TrilinosWrappers::PreconditionAMG can't be initialized
> with a user-defined ApproximateSchurComplement object. Instead, a matrix
> form of the approximated Schur complement SD=B(DA^-1)BT is expected.
>
> Could you please give a hint on how to form this matrix?
>
> Attached is a minimal (but not working) code.
>
> Best regards,
> Charlie
>
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Re: [deal.II] Mixed-precision algorithms in deal.II

[David Wells]

Hi Maxi,

The AffineConstraints class does not support using mixed precision and I am
not aware of any alternatives that can solve this problem directly.

There may be a better solution, but one way to solve this problem would be
to set up two different AffineConstraints objects (one for each floating
point type) and then call distribute_local_to_global with a (copied from
the single precision) double precision cell matrix and double precision
cell RHS and (for single precision) do the opposite. This will update both
the global matrix and global RHS correctly.

AffineConstraints objects will do Gaussian elimination with values taken
from the single precision cell matrix to determine the correct values for
the global RHS, so you will lose some accuracy in the RHS due to
truncation. It might be better to either set up both the matrix and RHS in
double precision and then copy the matrix over to single precision to avoid
this problem, or compute the cell matrix in double precision and copy it to
a single precision matrix (instead of the opposite approach given in the
previous paragraph).

Does this make sense?

Thanks,
David


On Mon, Aug 26, 2019 at 8:09 AM 'Maxi Miller' via deal.II User Group <
dealii@googlegroups.com> wrote:

> I tried to implement a simple mixed-precision algorithm in deal.II, which
> creates my matrix using float values, and my vectors using double values.
> Unfortunately, the function distribute_local_to_global(cell_matrix,
> cell_rhs, local_dof_indices, system_matrix, system_rhs) does not support
> mixed types. Is there an alternative function, or do I have to create two
> AffineConstraints-objects, initialize both with different values (double
> and float) and use them separately?
>
> --
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> 
> .
>

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Re: [deal.II] Re: Sparsematrix initialization in P4est program

[David Wells]

Hi Gabriel,

In case you are interested, I have written a patch and a new test for this
issue: its available at

https://github.com/dealii/dealii/pull/7763

Thanks,
David Wells

On Tue, Feb 26, 2019 at 8:45 PM David Wells  wrote:

> Hi Gabriel,
>
> step-32 does use a pressure element of degree 1 lower than the velocity,
> but your main point is still right: step-35 uses multiple dof handlers for
> the velocity and pressure while step-32 uses FESystem to put everything in
> one dof handler. Therefore the step-32 approach won't work unless you
> rewrite step-35 to use FESystem and block vectors.
>
> Regardless, we should support creating sparsity patterns in parallel with
> multiple dof handlers: this is a bug in the make_sparsity_pattern function
> in deal.II.
>
> I am not sure what to suggest you do: the step-35 approach won't work due
> to a bug in the library itself, but rewriting step-35 (or a similar code)
> to use FESystem and blocks is a lot of work. Unfortunately, I think the
> second approach is the most reasonable one since its what the other
> parallel examples do.
>
> Thanks,
> David Wells
>
> On Mon, Feb 25, 2019 at 12:32 PM  wrote:
>
>>
>>
>> Am Montag, 18. Februar 2019 22:21:06 UTC+1 schrieb David Wells:
>>>
>>> Hi Gabriel,
>>>
>>> I believe that you are still using the standard deal.II SparseMatrix
>>> class; is this correct? If so, this class won't work with fully distributed
>>> calculations. You will need to use either the Trilinos or PETSc wrappers
>>> since not all information is available on the local processor with the
>>> default SparseMatrix class.
>>>
>>> Either way: I believe the error message you encountered is a result of a
>>> bug in deal.II. I don't think that the routine
>>> GridTools::get_finest_common_cells(), which is called by that particular
>>> make_sparsity_pattern variant, works with distributed triangulations. If
>>> you want to use distributed triangulations you will need to set up the
>>> coupled sparsity pattern in a different way.
>>>
>>> If you want to parallelize step-35, it may be better to start by looking
>>> at step-32, which shows how to implement the Stokes equations (coupled to a
>>> Boussinesq equation) in a fully distributed setting. I believe they set up
>>> the coupling of the matrix with velocity and pressure blocks in a different
>>> way that should work for you.
>>>
>>> Does this make sense?
>>>
>>> Thanks,
>>> David Wells
>>>
>>>>
>>>>
>> Hey,
>> sorry for the late respons, I had some stuff to work at.
>>
>> Today I had a close look to the  Step-32 and 31 tutorial
>> and I think that this doen't help very much because in the Step-32
>> tutorial the pressure_fe_degree eguals the velocity_fe_degree,
>> which, in my view, makes thi function "make_sparsity_pattern" applicable,
>> because you only have to insert one Dof_Handler object.
>> Thus one can use the same Dof_Handler for velocity and pressure, and
>> everything is created as in the Step-32
>>
>> In my case the velocity_fe_degree is one degree larger then the
>> pressure_fe_degree.
>> If I understood the construction right, I can't perform it in this case.
>>
>> Do you see my problem, or am I wrong?
>>
>> Best Regards
>> Gabriel
>>
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Re: [deal.II] Re: Sparsematrix initialization in P4est program

[David Wells]

Hi Gabriel,

step-32 does use a pressure element of degree 1 lower than the velocity,
but your main point is still right: step-35 uses multiple dof handlers for
the velocity and pressure while step-32 uses FESystem to put everything in
one dof handler. Therefore the step-32 approach won't work unless you
rewrite step-35 to use FESystem and block vectors.

Regardless, we should support creating sparsity patterns in parallel with
multiple dof handlers: this is a bug in the make_sparsity_pattern function
in deal.II.

I am not sure what to suggest you do: the step-35 approach won't work due
to a bug in the library itself, but rewriting step-35 (or a similar code)
to use FESystem and blocks is a lot of work. Unfortunately, I think the
second approach is the most reasonable one since its what the other
parallel examples do.

Thanks,
David Wells

On Mon, Feb 25, 2019 at 12:32 PM  wrote:

>
>
> Am Montag, 18. Februar 2019 22:21:06 UTC+1 schrieb David Wells:
>>
>> Hi Gabriel,
>>
>> I believe that you are still using the standard deal.II SparseMatrix
>> class; is this correct? If so, this class won't work with fully distributed
>> calculations. You will need to use either the Trilinos or PETSc wrappers
>> since not all information is available on the local processor with the
>> default SparseMatrix class.
>>
>> Either way: I believe the error message you encountered is a result of a
>> bug in deal.II. I don't think that the routine
>> GridTools::get_finest_common_cells(), which is called by that particular
>> make_sparsity_pattern variant, works with distributed triangulations. If
>> you want to use distributed triangulations you will need to set up the
>> coupled sparsity pattern in a different way.
>>
>> If you want to parallelize step-35, it may be better to start by looking
>> at step-32, which shows how to implement the Stokes equations (coupled to a
>> Boussinesq equation) in a fully distributed setting. I believe they set up
>> the coupling of the matrix with velocity and pressure blocks in a different
>> way that should work for you.
>>
>> Does this make sense?
>>
>> Thanks,
>> David Wells
>>
>>>
>>>
> Hey,
> sorry for the late respons, I had some stuff to work at.
>
> Today I had a close look to the  Step-32 and 31 tutorial
> and I think that this doen't help very much because in the Step-32
> tutorial the pressure_fe_degree eguals the velocity_fe_degree,
> which, in my view, makes thi function "make_sparsity_pattern" applicable,
> because you only have to insert one Dof_Handler object.
> Thus one can use the same Dof_Handler for velocity and pressure, and
> everything is created as in the Step-32
>
> In my case the velocity_fe_degree is one degree larger then the
> pressure_fe_degree.
> If I understood the construction right, I can't perform it in this case.
>
> Do you see my problem, or am I wrong?
>
> Best Regards
> Gabriel
>
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[deal.II] Re: Sparsematrix initialization in P4est program

[David Wells]

Hi Gabriel,

I believe that you are still using the standard deal.II SparseMatrix class; 
is this correct? If so, this class won't work with fully distributed 
calculations. You will need to use either the Trilinos or PETSc wrappers 
since not all information is available on the local processor with the 
default SparseMatrix class.

Either way: I believe the error message you encountered is a result of a 
bug in deal.II. I don't think that the routine 
GridTools::get_finest_common_cells(), which is called by that particular 
make_sparsity_pattern variant, works with distributed triangulations. If 
you want to use distributed triangulations you will need to set up the 
coupled sparsity pattern in a different way.

If you want to parallelize step-35, it may be better to start by looking at 
step-32, which shows how to implement the Stokes equations (coupled to a 
Boussinesq equation) in a fully distributed setting. I believe they set up 
the coupling of the matrix with velocity and pressure blocks in a different 
way that should work for you.

Does this make sense?

Thanks,
David Wells



On Sunday, February 17, 2019 at 4:29:06 PM UTC-5, gabriel...@koeln.de wrote:
>
> Hey everybody, 
> I have a problem with initializing a Sparsematrix in a parallel program.
>  am using a parallel::distributed::triangulaton (as in the Step40 
> tutorial) on 
> the Navier Stokes Projection solver from the step35 tutorial.
> The problem arises in the function 
>
> NavierStokesProjection::initialize_gradient_operator()
> {
> {
> DynamicSparsityPattern 
> <https://www.dealii.org/current/doxygen/deal.II/classDynamicSparsityPattern.html>
>  
> dsp(dof_handler_velocity.n_dofs(), dof_handler_pressure.n_dofs());
> DoFTools::make_sparsity_pattern 
> <https://www.dealii.org/current/doxygen/deal.II/group__constraints.html#ga38d88a1a559e9fc65d60f3e168921ba5>
>  
> (dof_handler_velocity, dof_handler_pressure, dsp);
> sparsity_pattern_pres_vel.copy_from (dsp);
> }
>
> where I have to use two different FE-spaces, one for the pressure and one 
> for the velocity.
> To perform this in parallel I used the following code (according to the 
> sparsematrices in step40)
>
> {
> DynamicSparsityPattern 
> dsp(locally_relevant_dofs_vel.size(),locally_relevant_dofs_pres.size());
> DoFTools::make_sparsity_pattern (dof_handler_velocity, 
> dof_handler_pressure, dsp); 
> sparsity_pattern_pres_vel.copy_from (dsp);
> }
>
> This code compilates fine, but when Running it with MPI, it stops in the 
> "make_sparsity_pattern" line with the error code
> "this->is_artificial() == false
> Additional information:
> Cant asks for Dofs on articial cells."
>
> Does somebody know how I can fix this? 
>
> My last try was to use the Indexsets instead of their size, when declaring 
> dsp.
> But unfortunately DynamicSparsityPattern can only take on IndexSet.
>
>
> Thanks a lot
>
> Gabriel
>
>
>
>
>

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[deal.II] Re: Trouble Installing: "undefined symbol: cblas_ctrmv"

[David Wells]

Hi Kyle,

deal.II only uses GSL in two places: the Functions::CSpline class (which 
interpolates provided data with splines) and in FESeries::Legendre, (which 
is used in some regularity estimators). Unless you plan on using either of 
these classes directly I suggest just disabling GSL with the cmake flag 
-DDEAL_II_WITH_GSL=OFF.

Does this work for you? If not we can try to work out a way to get your GSL 
installation working.

Thanks,
David Wells

On Thursday, January 24, 2019 at 4:43:14 PM UTC-5, ky...@math.uh.edu wrote:
>
> Hi all,
>
> I'm having trouble installing deal.II. cmake seems to find gsl just fine, 
> but it looks like there is trouble when linking against it. As you can see 
> in the quicktests.log, the error it gives is that "symbol lookup error: 
> /lib64/libgsl.so.23: undefined symbol: cblas_ctrmv"
>
> I also see that a similar issue had bee reported here 
> https://github.com/dealii/dealii/issues/2757, but this was a couple years 
> ago and a patch was merged. 
>
> The logs you see are for installing the master branch from github, 
> although I got similar errors when trying to install version 8.5 as well.
>
> -Kyle Williams
>

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[deal.II] Re: How to implement GridGenerator::channel_with_cylinder?

[David Wells]

Hi Nick,

I think the following would work:

1. Create a triangulation via GridGenerator::plate_with_a_hole.
2. Create a second Triangulation via GridGenerator::hyper_ball. If you are 
working in 3D then you will have to extrude this. Use GridTools::transform 
to recenter this Triangulation in the center of the hole in the first 
Triangulation. Loop across the cells and set all the material ids.
3. Use GridGenerator::merge_triangulations to combine the two 
Triangulations: this should preserve the material ids.

deal.II 9.0 will not copy manifold ids; however, the current 9.1 prerelease 
will. You will have to verify, however, that the common lines (or quads and 
lines in 3D) of the two Triangulations have the same manifold ids before 
merging. It should be possible to use a PolarManifold or 
CylindricalManifold to place new points on the circle (even though it is in 
the interior).

I think Jean-Paul wrote some code to do this at some point; I am not sure 
what happened to it. Ultimately, since this just involves merging two 
Triangulations, it should not be hard to get something working on your own.

Let me know if this works!

Best,
David Wells

On Tuesday, January 15, 2019 at 10:11:07 PM UTC-5, nboyc...@gmail.com wrote:
>
> Does anybody have an example of how to fill out the hole and assign to it 
> different material ID?
>
> Thank you,
> Nick.
>
> On Wednesday, December 19, 2018 at 12:07:16 PM UTC-5, Daniel Arndt wrote:
>>
>> Chucui,
>>
>> the mesh you are showing degenerates close to the midpoint. This isvery 
>> likely not what you wan't.
>> For the inner part something like shown in 
>> https://www.dealii.org/developer/doxygen/deal.II/classTransfiniteInterpolationManifold.html
>> would be a good idea.
>> Then for the middle part GridGenerator::hyper_cube_with_cylindrical_hole (
>> https://www.dealii.org/9.0.0/doxygen/deal.II/namespaceGridGenerator.html#add14cab546d033c1eaacc9234c64ebcd
>> )
>> should work, you just have to make sure that the vertices align when 
>> merging the two meshes via 
>> GridGenerator::merge_triangulations (
>> https://www.dealii.org/developer/doxygen/deal.II/namespaceGridGenerator.html#a7cd88e7eacd46697dee80ad2b8438d54
>> ).
>> Make sure too choose copy_manifold_ids if you are using a developer 
>> version or set the manifold ids after creating and merging the whole mesh.
>> Finally, for the outer part you would just merge some 
>> GridGenerator::subdivided_hyper_rectangle (
>> https://www.dealii.org/developer/doxygen/deal.II/namespaceGridGenerator.html#ac76417d7404b75cf53c732f456e6e971
>> ).
>> Again make sure that the verices align and make sure the manifold ids are 
>> correct after merging all the meshes.
>>
>> Best,
>> Daniel
>>
>

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Re: [deal.II] Installing the dealii on windows10 problem

[David Wells]

Hey there,

I would be happy to help you, but would you first please start another 
thread (the OP is interested in SIMD configuration on windows, which is not 
the same issue) and post in it your detailed.log file from configuring 
deal.II? Thanks!

Best,
David Wells

On Thursday, December 27, 2018 at 6:39:01 PM UTC-5, 林澤鋐 wrote:
>
> I  have repeated the deallii instruction steps untill the programming has 
> started. 
> Although it did not stick, it still did not found the deallii-lib in the 
> CMake GUI.
> I don't know how to set an environment parameter in dealii.
> Thank you
>

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Re: [deal.II] Re: Install & Configure HDF5 -reg

[David Wells]

Dear Manimaran,

Not a problem. It looks like you installed deal.II correctly but you will
have to compile it again to link it with HDF5.

I recommend using apt to install HDF5; run

sudo apt-get install libhdf5-dev

at the command line to get a copy of HDF5 (that can be used for
development, hence the -dev suffix) installed on your computer. Once its
installed you should delete the deal.II build directory and compile it
again (doing what you did before); it should automatically detect the copy
of HDF5 you just installed (you can double-check this by reading the output
file detailed.log).

Does this make sense? Let me know if you have more questions.

Thanks,
David Wells

On Fri, Dec 21, 2018 at 12:19 AM mani maran  wrote:

> Dear David Wells,
>
>  Thank you for your kind reply. I am a beginner of Ubuntu and deal_II.
> Could you say elaborately.  I am not strong in the command line.
> I installed the deal_ii 9.0.1.  I installed like the following way
>
> cmake -DCMAKE_INSTALL_PREFIX=/home/taylor/bin/dealii-9.0.1 ../
>
> Could you explain HDF5 install, I downloaded the "hdf5-1.10.4.tar.gz".  I
> don't know, where I installed it.
>
> Please suggest me.  Could you say elaborately.
>
>
>
>
>
>
>
>
> On Fri, Dec 21, 2018 at 4:11 AM David Wells  wrote:
>
>> Dear Manimaran,
>>
>> The version of deal.II that can be installed with apt (on ubuntu 16.04;
>> newer versions fix this) does not include HDF5 as a dependency: you will
>> have to compile deal.II by yourself if you want to use it with HDF5.
>>
>> I recommend installing HDF5 (via apt) first and then compiling and
>> installing deal.II in your home directory. CMake should automatically
>> detect your system installation of HDF5: if not, pass
>> -DHDF5_DIR=/path/to/hdf5 to CMake when configuring. Complete directions are
>> available here:
>>
>> https://dealii.org/9.0.0/index.html
>>
>> Let me know if this works for you, or if you have more questions.
>>
>> Thanks,
>> David Wells
>>
>> On Thursday, December 20, 2018 at 2:00:37 PM UTC-5, mani maran wrote:
>>>
>>> Dear all,
>>>
>>> I am new to deal_ii. I have installed deal_ii in my ubuntu 16.04
>>> desktop. I don't know, how to link hdf5 with deal_ii.
>>>
>>> Do suggest a remedy for this issue.
>>>
>>> Thanks and regards
>>> Manimaran J
>>>
>>>
>>> --
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[deal.II] Re: Install & Configure HDF5 -reg

[David Wells]

Dear Manimaran,

The version of deal.II that can be installed with apt (on ubuntu 16.04; 
newer versions fix this) does not include HDF5 as a dependency: you will 
have to compile deal.II by yourself if you want to use it with HDF5.

I recommend installing HDF5 (via apt) first and then compiling and 
installing deal.II in your home directory. CMake should automatically 
detect your system installation of HDF5: if not, pass 
-DHDF5_DIR=/path/to/hdf5 to CMake when configuring. Complete directions are 
available here:

https://dealii.org/9.0.0/index.html

Let me know if this works for you, or if you have more questions.

Thanks,
David Wells

On Thursday, December 20, 2018 at 2:00:37 PM UTC-5, mani maran wrote:
>
> Dear all,
>
> I am new to deal_ii. I have installed deal_ii in my ubuntu 16.04 desktop. 
> I don't know, how to link hdf5 with deal_ii. 
>
> Do suggest a remedy for this issue.
>
> Thanks and regards
> Manimaran J
>
>
>

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[deal.II] Re: How to implement GridGenerator::channel_with_cylinder?

[David Wells]

Dear Chucui,

I would like to extend Daniel's answer slightly.

The source code for channel_with_cylinder is is at about line 2180 of 

https://www.dealii.org/developer/doxygen/deal.II/grid__generator_8cc_source.html

If you want to generate just the grid around the cylinder (i.e., without 
the channel) then look at how cylinder_tria is set up in lines 2250 - 2305: 
you can get the grid you posted by adding more shells (and increasing the 
size of the shell region). The development version of deal.II can copy 
manifold ids, but 9.0 cannot.

Thanks,
David

On Wednesday, December 19, 2018 at 12:07:16 PM UTC-5, Daniel Arndt wrote:
>
> Chucui,
>
> the mesh you are showing degenerates close to the midpoint. This isvery 
> likely not what you wan't.
> For the inner part something like shown in 
> https://www.dealii.org/developer/doxygen/deal.II/classTransfiniteInterpolationManifold.html
> would be a good idea.
> Then for the middle part GridGenerator::hyper_cube_with_cylindrical_hole (
> https://www.dealii.org/9.0.0/doxygen/deal.II/namespaceGridGenerator.html#add14cab546d033c1eaacc9234c64ebcd
> )
> should work, you just have to make sure that the vertices align when 
> merging the two meshes via 
> GridGenerator::merge_triangulations (
> https://www.dealii.org/developer/doxygen/deal.II/namespaceGridGenerator.html#a7cd88e7eacd46697dee80ad2b8438d54
> ).
> Make sure too choose copy_manifold_ids if you are using a developer 
> version or set the manifold ids after creating and merging the whole mesh.
> Finally, for the outer part you would just merge some 
> GridGenerator::subdivided_hyper_rectangle (
> https://www.dealii.org/developer/doxygen/deal.II/namespaceGridGenerator.html#ac76417d7404b75cf53c732f456e6e971
> ).
> Again make sure that the verices align and make sure the manifold ids are 
> correct after merging all the meshes.
>
> Best,
> Daniel
>

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[deal.II] Re: system_matrix.reint(sparsity_pattern)

[David Wells]

Hi Mustafa,

This does sound strange: BlockSparseMatrix::m() should return the number of 
rows of blocks (which is clearly 4 in your code).

Would it be possible for you to post a more complete code fragment that 
shows the problem? I cannot figure out where the problem is with what you 
posted.

Thanks,
David Wells

On Friday, December 14, 2018 at 8:41:10 AM UTC-5, Mustafa Aggul wrote:
>
> Hello,
> I have created my own block sparsity pattern by adding non-zero entries 
> manually, and then compressed it. Upon some testings on this sparsity 
> pattern, I have realized that it is indeed created correctly, in terms of 
> dimension and number of elements it has. However, the system matrix that I 
> initialized with this sparsity pattern looks empty (system_matrix.m() = 0). 
> What would be the possible reason for this?
> Thanks for any response in advance,
>
> sparsity_pattern.reinit(4,4);
>
> if(something happens)
> sparsity_pattern.block(0,0).add(local_dof_indices1[i],local_dof_indices2[j]); 
> //these kind of operations
> sparsity_pattern.compress();
> system_matrix.reinit(sparsity_pattern);
>
> -- 
> *Mustafa Ağgül*
> *Department of Mathematics*
> *Michigan Technological University*
> *1400 Townsend Drive*
> *Houghton, Michigan 49931-1295*
> *Tel: 906-487-3135*
>

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[deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

[David Wells]

Hi Chucui,

StraightBoundary was removed in deal.II 9.0; it should not show up in any 
object files so these errors don't make any sense. Did you use a clean 
build directory?

Thanks,
David Wells

On Thursday, October 18, 2018 at 8:27:40 AM UTC-4, chucu...@gmail.com wrote:
>
> Dear all, 
>
> I want to reinstall my deal.ii because I need to run some codes in 
> parallel just like Step-40, step-55 and Step-32, and I choose deal.ii-9.0.1 
> The command lines I use are: 
>
> $cmake ../dealii-9.0.1/dealii-9.0.1  -DDEAL_II_WITH_MPI=ON  
> -DCMAKE_C_COMPILER=/usr/local/mpi3/bin/mpicc  
> -DCMAKE_CXX_COMPILER=/usr/local/mpi3/bin/mpicxx  
> -DCMAKE_Fortran_COMPILER=/usr/local/mpi3/bin/mpifort 
> -DCMAKE_INSTALL_PREFIX=../dealii-9.0.1/build -DMPI_DIR=/usr/local/mpi3 
> -DP4EST_DIR=../p4est/p4est-2.0 -DPETSC_DIR=../new-petsc-3.7.7/petsc-3.7.7 
> -DHDF5_DIR=/usr/lib64/ -DMETIS_DIR=../metis-5.1.0/metis-5.1.0 
> -DDEAL_II_WITH_METIS=ON -DDEAL_II_WITH_HDF5=OFF -DDEAL_II_WITH_PETSC=ON 
> -DDEAL_II_WITH_P4EST=OFF -DDEAL_II_WITH_MPI=ON 
> -DDEAL_II_FORCE_BUNDLED_BOOST=ON-DDEAL_II_ALLOW_AUTODETECTION=ON
>
> $make
>
> $make install
>
> But after "make install", the installation was interupped, and the errors 
> are showed as:
>
> Scanning dependencies of target obj_rol_debug
> [ 82%] Built target obj_rol_debug
> Scanning dependencies of target step-3.release
> [ 82%] Building CXX object 
> examples/CMakeFiles/step-3.release.dir/step-3/step-3.cc.o
> [ 82%] Linking CXX executable ../bin/step-3.release
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<1, 2>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<1, 1>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<3, 3>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<3, 3>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<2, 2>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<2, 3>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<1, 1>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<1, 3>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<1, 2>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<2, 3>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<2, 2>::StraightBoundary()'
> make[2]: *** [bin/step-3.release] Error 1
> make[1]: *** [examples/CMakeFiles/step-3.release.dir/all] Error 2
> make: *** [all] Error 2
>
> So, I don't what happened and know how to do. Hope some suggestions! 
> Thanks in advance!
>
> Best,
> Chucui
>
>
>
>
>

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[deal.II] Re: Error in example 16

[David Wells]

Dear Maxi,

This is a bug with the current implementation: it looks like one of the 
recent commits broke something.

Thanks for reporting this!

Thanks,
David Wells

On Thursday, October 11, 2018 at 9:46:42 AM UTC-4, Maxi Miller wrote:
>
> When trying to run example 16 on a new installation of deal.II, I get the 
> error
> Cycle 0
>Number of active cells:   80
>Number of degrees of freedom: 89 (by level: 8, 25, 89)
>
> 
> An error occurred in line <1191> of file  /tria_iterator.h> in function
> dealii::TriaActiveIterator::TriaActiveIterator(const dealii
> ::TriaRawIterator&) [with OtherAccessor = dealii::
> DoFCellAccessor, true>; Accessor = dealii::
> DoFCellAccessor, false>]
> The violated condition was: 
> this->accessor.has_children() == false
> Additional information: 
> (none)
>
> Stacktrace:
> ---
> #0  ./step-16: 
> dealii::TriaActiveIterator 2>, false> 
> >::TriaActiveIterator, 
> true> 
> >(dealii::TriaRawIterator, 
> true> > const&)
> #1  ./step-16: std::_Function_handler (dealii::TriaIterator, 
> true> > const&, Step16::ScratchData<2>&, Step16::CopyData&), 
> Step16::LaplaceProblem<2>::assemble_multigrid()::{lambda(dealii::TriaActiveIterator  
> 2>, false> > const&, Step16::ScratchData<2>&, 
> Step16::CopyData&)#1}>::_M_invoke(std::_Any_data const&, 
> dealii::TriaIterator, 
> true> > const&, Step16::ScratchData<2>&, Step16::CopyData&)
> #2  ./step-16: std::function (dealii::TriaIterator, 
> true> > const&, Step16::ScratchData<2>&, 
> Step16::CopyData&)>::operator()(dealii::TriaIterator  
> 2>, true> > const&, Step16::ScratchData<2>&, Step16::CopyData&) const
> #3  ./step-16: 
> dealii::MeshWorker::mesh_loop  
> 2>, true> >, Step16::ScratchData<2>, 
> Step16::CopyData>(dealii::TriaIterator  
> 2>, true> > const&, 
> dealii::identity  
> 2>, true> > >::type const&, dealii::identity (dealii::TriaIterator, 
> true> > const&, Step16::ScratchData<2>&, Step16::CopyData&)> >::type 
> const&, dealii::identity 
> >::type const&, Step16::ScratchData<2> const&, Step16::CopyData const&, 
> dealii::MeshWorker::AssembleFlags, dealii::identity (dealii::TriaIterator, 
> true> > const&, unsigned int, Step16::ScratchData<2>&, Step16::CopyData&)> 
> >::type const&, dealii::identity (dealii::TriaIterator, 
> true> > const&, unsigned int, unsigned int, 
> dealii::TriaIterator, 
> true> > const&, unsigned int, unsigned int, Step16::ScratchData<2>&, 
> Step16::CopyData&)> >::type const&, unsigned int, unsigned 
> int)::{lambda(dealii::TriaIterator  
> 2>, true> > const&, Step16::ScratchData<2>&, 
> Step16::CopyData&)#1}::operator()(dealii::TriaIterator  
> 2>, true> > const&, Step16::ScratchData<2>&, Step16::CopyData&) const
> #4  ./step-16: void 
> dealii::WorkStream::run  
> 2>, true> >, Step16::ScratchData<2>, 
> Step16::CopyData>(dealii::TriaIterator  
> 2>, true> > const&, 
> dealii::identity  
> 2>, true> > >::type const&, dealii::identity (dealii::TriaIterator, 
> true> > const&, Step16::ScratchData<2>&, Step16::CopyData&)> >::type 
> const&, dealii::identity 
> >::type const&, Step16::ScratchData<2> const&, Step16::CopyData const&, 
> dealii::MeshWorker::AssembleFlags, dealii::identity (dealii::TriaIterator, 
> true> > const&, unsigned int, Step16::ScratchData<2>&, Step16::CopyData&)> 
> >::type const&, dealii::identity (dealii::TriaIterator, 
> true> > const&, unsigned int, unsigned int, 
> dealii::TriaIterator, 
> true> > const&, unsigned int, unsigned int, Step16::ScratchData<2>&, 
> Step16::CopyData&)> >::type const&, unsigned int, unsigned 
> int)::{lambda(dealii::TriaIterator  
> 2>, true> > const&, Step16::ScratchData<2>&, Step16::CopyData&)#1}, 
> std::function, 
> dealii::TriaIterator, 
> true> >, Step16::ScratchData<2>, 
> Step16::CopyData>(dealii::TriaIterator  
> 2>, true> > const&, 
> dealii::identity  
> 2>, true> > >::type const&, 
> dealii::MeshWorker::mesh_loop  
> 2>, true> >, Step16::ScratchData<2>, 
> Step16::CopyData>(dealii::TriaIterator  
> 2>, tru

[deal.II] Re: Linking error while compiling examples: "undefined reference to `dealii::VectorizedArray::n_array_elements'"

[David Wells]

Hey there,

I think this may be actually a bug in how we recently fixed a related 
problem:

https://github.com/dealii/dealii/pull/7198

Could you please post the detailed.log file from when you configured the 
library? I think the value for DEAL_II_COMPILER_VECTORIZATION_LEVEL may be 
wrong (or, at least, it is causing problems somewhere else).

Thanks,
David Wells

On Tuesday, October 9, 2018 at 6:29:25 AM UTC-4, Maxi Miller wrote:
>
> I tried to compile deal.II on a new computer, but I got multiple linking 
> errors for some of the examples:
> /usr/lib64/gcc/x86_64-suse-linux/8/../../../../x86_64-suse-linux/bin/ld: 
> ../lib/libdeal_II.g.so.9.1.0-pre: undefined reference to 
> `dealii::VectorizedArray::n_array_elements'
> /usr/lib64/gcc/x86_64-suse-linux/8/../../../../x86_64-suse-linux/bin/ld: 
> ../lib/libdeal_II.g.so.9.1.0-pre: undefined reference to `dealii::
> VectorizedArray::n_array_elements'
>
> The examples in question are all debug versions of the examples, with 
> example number 2, 3, 24, 29, 36, 44, 45, 48, 50, 52, 53, 55, 56, 59, 60. I 
> used the following external libraries/options: 
> ADOL-C, Boost, C++14/17, GSL, HDF5, Lapack, Metis, MPI, nanoflann, P4est, 
> PETSC, ScalaPack, SLEPC, Sundials, Threads, Trilinos, Umfpack and Zlib
> and the internal version of Muparser
> Why do I get that linking error, and how can I fix it? Apparently it is 
> not related to the external libraries, else it would show up. Is that 
> correct?
> Thanks!
>

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Re: [deal.II] Re: Transfinite Interpolation

[David Wells]

ers.push_back(&cell->face(face_n)->vertex(1));
}
}
}
  // de-duplicate
  std::sort(inner_pointers.begin(), inner_pointers.end());
  inner_pointers.erase(std::unique(inner_pointers.begin(),
   inner_pointers.end()),
   inner_pointers.end());

  // find the current center...
  Point<2> center;
  for (const Point<2> *const ptr : inner_pointers)
center += *ptr/double(inner_pointers.size());
  std::cout << "computed center: "
<< center
<< '\n';

  // and recenter at (0.2, 0.2)
  for (Point<2> *const ptr : inner_pointers)
*ptr += Point<2>(0.2, 0.2) - center;

  Point<2> center2;
  for (const Point<2> * const ptr : inner_pointers)
center2 += *ptr/double(inner_pointers.size());
  std::cout << "recomputed center: "
<< center2
<< '\n';

  GridOut go;
  std::ofstream out("grid.eps");
  result_2.refine_global(1);
  go.write_eps(result_2, out);
}

I attached a picture of the output. This script relies on a patch that I 
need to add to deal.II that permits merging triangulations with a tolerance 
(so it won't work yet on 9.0, but hopefully it will soon!).

Thanks,
David Wells

On Thursday, May 24, 2018 at 8:43:38 AM UTC-4, Martin Kronbichler wrote:
>
> Hi Narenda and David,
>
> Just to add on top of what David Wells said, Luca Heltai and I once had 
> the idea of showing this manifold in a new tutorial program (where we 
> combine it with MappingFEField to show the performance impact). Now step-60 
> does contain some MappingFEField, but on a different topic, so I think we 
> should simply create such a program soon. I will open an issue for that.
>
> Best,
> Martin
>
> On 23.05.2018 23:32, David Wells wrote:
>
> Hi Narendra
>
> We should probably put something like this in step-49. Here is a bit of 
> code that shows how to use the TFI manifold class:
>
> #include 
> #include 
> #include 
> #include 
>
> int main()
> {
>   using namespace dealii;
>
>   Triangulation<2> tria;
>   GridGenerator::hyper_cube_with_cylindrical_hole (tria, 0.05, 0.1);
>   const types::manifold_id tfi_id = 1;
>   for (const auto cell : tria.active_cell_iterators())
> {
>   // set all non-boundary manifold ids to the new TFI manifold id.
>   cell->set_manifold_id(tfi_id);
>   for (unsigned int face_n = 0; face_n < GeometryInfo<2>::
> faces_per_cell;
>++face_n)
> {
>   if (!cell->face(face_n)->at_boundary())
> cell->face(face_n)->set_manifold_id(tfi_id);
> }
> }
>   TransfiniteInterpolationManifold<2> inner_manifold;
>   inner_manifold.initialize(tria);
>   tria.set_manifold(1, inner_manifold);
>
>   tria.refine_global(2);
>
>   GridOut go;
>   std::ofstream out("grid.eps");
>   go.write_eps(tria, out);
> }
>
>
> This creates a nice blend between the inner circle and the outer square. 
> From here you can do something like what is done in step-49 to generate the 
> rest of the grid from Cartesian pieces.
>
> If you are using 8.5 instead of 9.0 you will need to make all Manifold 
> classes (including putting your own PolarManifold on the circle) before the 
> Triangulation.
>
> I hope this helps!
>
> Thanks,
> David Wells
>
>
>
> On Monday, May 21, 2018 at 7:06:19 PM UTC-4, Narendra Nanal wrote: 
>>
>> Hello All, 
>>
>> I am trying to run benchmark case of 2D flow around a cylinder. Here are 
>> the details- 
>>
>> http://www.featflow.de/en/benchmarks/cfdbenchmarking/flow/dfg_benchmark1_re20.html
>> .
>> My question is how to use Transfinite Interpolation class to generate a 
>> mesh with a smooth transition. Thank you. 
>>
>> Regards,
>> Narendra 
>>
> -- 
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> For mailing list/forum options, see 
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>
>
>

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[deal.II] Re: Transfinite Interpolation

[David Wells]

Hi Narendra

We should probably put something like this in step-49. Here is a bit of 
code that shows how to use the TFI manifold class:

#include 
#include 
#include 
#include 

int main()
{
  using namespace dealii;

  Triangulation<2> tria;
  GridGenerator::hyper_cube_with_cylindrical_hole (tria, 0.05, 0.1);
  const types::manifold_id tfi_id = 1;
  for (const auto cell : tria.active_cell_iterators())
{
  // set all non-boundary manifold ids to the new TFI manifold id.
  cell->set_manifold_id(tfi_id);
  for (unsigned int face_n = 0; face_n < GeometryInfo<2>::faces_per_cell
;
   ++face_n)
{
  if (!cell->face(face_n)->at_boundary())
cell->face(face_n)->set_manifold_id(tfi_id);
}
}
  TransfiniteInterpolationManifold<2> inner_manifold;
  inner_manifold.initialize(tria);
  tria.set_manifold(1, inner_manifold);

  tria.refine_global(2);

  GridOut go;
  std::ofstream out("grid.eps");
  go.write_eps(tria, out);
}


This creates a nice blend between the inner circle and the outer square. 
>From here you can do something like what is done in step-49 to generate the 
rest of the grid from Cartesian pieces.

If you are using 8.5 instead of 9.0 you will need to make all Manifold 
classes (including putting your own PolarManifold on the circle) before the 
Triangulation.

I hope this helps!

Thanks,
David Wells



On Monday, May 21, 2018 at 7:06:19 PM UTC-4, Narendra Nanal wrote:
>
> Hello All,
>
> I am trying to run benchmark case of 2D flow around a cylinder. Here are 
> the details- 
>
> http://www.featflow.de/en/benchmarks/cfdbenchmarking/flow/dfg_benchmark1_re20.html
> .
> My question is how to use Transfinite Interpolation class to generate a 
> mesh with a smooth transition. Thank you. 
>
> Regards,
> Narendra 
>

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[deal.II] Re: Problem about modifying CMakeList.txt to add library

[David Wells]

Hi Pai,

I think that there is an easier way to do this. More exactly: armadillo 
should not be a target since we don't have to compile anything: we should 
just be able to specify the library we need to link against and (possibly) 
a path to the headers and be done.

Have you installed armadillo in a standard location? If so then you should 
be able to just append

TARGET_LINK_LIBRARIES(${TARGET} armadillo)

to the end of CMakeLists.txt (after the call to PROJECT and 
DEAL_II_INVOKE_AUTOPILOT)

and things should work correctly.

Thanks,
David Wells

P.S. the CMake module for setting up armadillo looks for a lot of things 
that don't exist on my computer; I recommend avoiding using FIND_PACKAGE.

On Wednesday, May 16, 2018 at 2:54:39 AM UTC-4, Pai Liu wrote:
>
> Hi all,
>
> I am learning Step-8 in the tutorial. I want to use the library 
> "Armadillo" (which is a library for scientific computing and linear 
> algebra) together with dealii in step-8.cc.
> To compile a cpp file that only depends on the Armadillo library, one 
> needs to excute the following commends at the commend line : "g++ 
> example.cpp -o example -O2 -larmadillo"
> So I replace "mylib" in dealii documentation about modifying 
> cmakelist.txt with "armadillo", and modify the CMakeList.txt file as the 
> following
>
> _
> CMAKE_MINIMUM_REQUIRED(VERSION 2.8.12)
>
> FIND_PACKAGE(deal.II 8.5.0 REQUIRED
>   HINTS ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR}
>   )
> DEAL_II_INITIALIZE_CACHED_VARIABLES()
>
> PROJECT(myproject)
>
> ADD_LIBRARY(armadillo)
> DEAL_II_SETUP_TARGET(armadillo)
>
> ADD_EXECUTABLE(mycode step-8.cc)
> DEAL_II_SETUP_TARGET(mycode)
>
> TARGET_LINK_LIBRARIES(mycode armadillo)
> _
>
> And I got the the following error:
>
> -- Using the deal.II-8.5.1 installation found at 
> /home/liu/deal.ii-candi/deal.II-v8.5.1
> -- Include macro 
> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake
> -- Include macro 
> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_setup_target.cmake
> -- Include macro 
> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_query_git_information.cmake
> -- Include macro 
> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake
> -- Include macro 
> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_add_test.cmake
> -- Include macro 
> /home/liu/deal.ii-candi/deal.II-v8.5.1/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake
> You have called ADD_LIBRARY for library armadillo without any source 
> files. This typically indicates a problem with your CMakeLists.txt file
> -- Configuring done
> CMake Error: Cannot determine link language for target "armadillo".
> CMake Error: CMake can not determine linker language for target: armadillo
> -- Generating done
> -- Build files have been written to: /home/liu/P/homogenization
>
>
>
>
>
> Can anyone help me about this issue about add library?
> Many thanks in advance!
>  
>

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[deal.II] Re: How to call project_matrix_free?

[David Wells]

Hi Maxi,

To build on what Daniel said in the other thread:  This function was 
written with the intent that users would just call `project`. 
`project_matrix_free` is not really part of the public interface (though 
perhaps we should change this). You will need to `#include 
` to get the 
`project_matrix_free` template in your program.

A second issue is that (to avoid instantiating a lot more templates) this 
function is only defined for `LinearAlgebra::distributed::Vector` 
and not for the Trilinos wrapper vectors: you will have to copy to and from 
such a vector to get things to work.

Thanks,
David Wells



On Wednesday, March 7, 2018 at 7:51:06 AM UTC-5, Maxi Miller wrote:
>
> Based on my question here: 
> https://groups.google.com/d/msg/dealii/4YoJZ8d2-XM/0k3TjZrqAAAJ I would 
> like to implement the suggested solution using project_matrix_free() and 
> project_matrix_free_vector(). I thus try to call them as
> VectorTools::project_matrix_free(MappingQGeneric(1),
>  dof_handler,
>  hanging_node_constraints,
>  QGauss(fe.degree + 1
> ),
>  InitialValues(),
>  local_solution,
>  false,
>  (dim > 1 ? QGauss >(2):Quadrature(0)),
>  false);
> but the compiler tells me
> error: ‘project_matrix_free’ is not a member of ‘dealii::VectorTools’.
> When including the .h-file where project_matrix_free is defined, I get 
> ~/heat_equation_with_pulse_propagation/heat_equation/source/main.cpp:2390:
> 49: error: no matching function for call to ‘project_matrix_free(dealii::
> MappingQGeneric<2, 2>, dealii::DoFHandler<2, 2>&, dealii::ConstraintMatrix
> &, dealii::QGauss<2>, Step15::InitialValues<2>, dealii::
> LinearAlgebraTrilinos::MPI::Vector&, bool, dealii::Quadrature<1>, bool)’
>  VectorTools::project_matrix_free(MappingQGeneric(1),
>  ^
>   dof_handler,
>   
>   hanging_node_constraints
> ,
>   
> ~
>   QGauss(fe.degree + 
> 1),
>   
> ~~~
>   InitialValues(),
>   ~
>   local_solution,
>   ~~~
>   false,
>   ~~
>   (dim > 1 ? QGauss 1>(2):Quadrature(0)),
>   
> ~~
>   false);
>   ~~
> In file included from ~/heat_equation_with_pulse_propagation/heat_equation
> /source/main.cpp:69:0:
> /opt/dealii/include/deal.II/numerics/vector_tools.templates.h:1026:10: 
> note: candidate: template Number, int spacedim> void dealii::VectorTools::{anonymous}::
> project_matrix_free(const dealii::Mapping&, const dealii::
> DoFHandler&, const dealii::ConstraintMatrix&, const dealii
> ::Quadrature&, const dealii::Function LinearAlgebra::distributed::Vector::value_type>&, dealii::
> LinearAlgebra::distributed::Vector&, bool, const dealii::
> Quadrature<(dim - 1)>&, bool)
>  void project_matrix_free
>   ^~~
> /opt/dealii/include/deal.II/numerics/vector_tools.templates.h:1026:10: 
> note:   template argument deduction/substitution failed:
> ~/heat_equation_with_pulse_propagation/heat_equation/source/main.cpp:2390:
> 49: note:   ‘dealii::LinearAlgebraTrilinos::MPI::Vector {aka dealii::
> TrilinosWrappers::MPI::Vector}’ is not derived from ‘dealii::LinearAlgebra
> ::distributed::Vector’
> roland VectorTools::project_matrix_free(MappingQGeneric
> (1),
>  ^
>   dof_handler,
>   

[deal.II] Re: Error with Transfinite Interpolation

[David Wells]

We merged the fix this morning into the development branch, including a 
test based on your code.

A suggestion: on some versions of GCC, calling 'abs' results in calling the 
C function 'int abs(int)': to be safe, use std::abs.

Let me know if things work :)

Thanks,
David Wells

On Thursday, January 18, 2018 at 8:54:09 PM UTC-5, Juan Carlos Araujo 
Cabarcas wrote:
>
> Thanks a lot for looking at this issue so quickly!
>
> No problem, you can use it. That was the idea of sharing the minimal 
> example! I am always happy to contribute with the library.
>
> So, does this mean that the way I colorize is correct? if there is a 
> better/simpler way plz let me know.
> Is the solution merged with the latest master branch? I would like to have 
> a working library for this particular example.
>
> El jueves, 18 de enero de 2018, 18:39:51 (UTC-5), David Wells escribió:
>>
>> I figured it out: we have an optimization that assumes in one particular 
>> place that, if we have eight points, they must be the vertices of a cube. 
>> However, in 2D, we use eight points to place new points on quadrilaterals: 
>> assuming these are the vertices of a cube is wrong. The original assumption 
>> created a bad initial value for a quasi-newton solver, which then failed to 
>> converge.
>>
>> I got rid of the cube assumption. see 
>> https://github.com/dealii/dealii/pull/5761 for more information.
>>
>> Do you mind if I use a modified version of your code for a new test in 
>> deal.II?
>>
>> Thanks,
>> David Wells
>>
>> On Wednesday, January 17, 2018 at 3:05:48 PM UTC-5, Juan Carlos Araujo 
>> Cabarcas wrote:
>>>
>>> Dear all,
>>>
>>> Since the inclusion of Transfinite interpolation, I have been successful 
>>> on working with this powerful technique in my research. I had coded a mesh 
>>> implementing concentric circles, where the inner most is shifted a small 
>>> distance s. All concentric circles are labeled 100+i, where i is in a loop 
>>> on all circles.
>>>
>>> The mesh was working after 4/Apr/17 when I added the following entry in 
>>> the forum:
>>> https://groups.google.com/forum/#!topic/dealii/hCZqv9g6mKk
>>>
>>> I installed the development version of dealii on the 17/nov/17. The 
>>> details of the installation are also in the forum:
>>> https://groups.google.com/forum/#!topic/dealii/ee2w2X987ig
>>>
>>> and recently I went back and tried to run thhis code, obtaining the 
>>> error at the end of the email.
>>>
>>> I prepared a minimal example that includes the definition of my grid. It 
>>> includes how I colorize each face as explained before, and the rest are 
>>> colorized "1" as the documentation suggests.
>>>
>>> The symptoms are the following:
>>> - If I use refinement=0, everything works and the mesh looks quite nice 
>>> in zeros.vtk and surface with lines mode in Paraview.
>>> - For any higher refinement, it gives the error below.
>>>
>>> Maybe there has been a major change in TransfiniteInterpolation since 
>>> Apr/2017, or maybe the way I colorize is not good anymore for some weird 
>>> reason. Any ideas or comments would be greatly appreciated.
>>>
>>> Juan Carlos Araújo,
>>> Umeå Universitet.
>>>
>>>
>>>
>>> terminate called after throwing an instance of 'dealii::Mapping<2, 
>>> 2>::ExcTransformationFailed'
>>>   what():  
>>> 
>>> An error occurred in line <1554> of file 
>>>  in function
>>> typename dealii::Triangulation::cell_iterator 
>>> dealii::TransfiniteInterpolationManifold>> spacedim>::compute_chart_points(const dealii::ArrayView>> dealii::Point >&, dealii::ArrayView >) const 
>>> [with int dim = 2; int spacedim = 2; typename dealii::Triangulation>> spacedim>::cell_iterator = dealii::TriaIterator 
>>> >]
>>> The violated condition was: 
>>> false
>>> Additional information: 
>>> 
>>> 
>>>
>>> Aborted (core dumped)
>>>
>>>
>>>

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Re: [deal.II] Re: Error with Transfinite Interpolation

[David Wells]

I have to admit that I didn't read your code carefully enough to really
understand how you did the coloring. Regardless, its probably fine: using a
2D approximation for a 2D calculation gets rid of the error in the example
you provided :)

On Thu, Jan 18, 2018 at 8:54 PM, Juan Carlos Araujo Cabarcas <
ju4...@gmail.com> wrote:

> Thanks a lot for looking at this issue so quickly!
>
> No problem, you can use it. That was the idea of sharing the minimal
> example! I am always happy to contribute with the library.
>
> So, does this mean that the way I colorize is correct? if there is a
> better/simpler way plz let me know.
> Is the solution merged with the latest master branch? I would like to have
> a working library for this particular example.
>
>
> El jueves, 18 de enero de 2018, 18:39:51 (UTC-5), David Wells escribió:
>>
>> I figured it out: we have an optimization that assumes in one particular
>> place that, if we have eight points, they must be the vertices of a cube.
>> However, in 2D, we use eight points to place new points on quadrilaterals:
>> assuming these are the vertices of a cube is wrong. The original assumption
>> created a bad initial value for a quasi-newton solver, which then failed to
>> converge.
>>
>> I got rid of the cube assumption. see https://github.com/dealii/deal
>> ii/pull/5761 for more information.
>>
>> Do you mind if I use a modified version of your code for a new test in
>> deal.II?
>>
>> Thanks,
>> David Wells
>>
>> On Wednesday, January 17, 2018 at 3:05:48 PM UTC-5, Juan Carlos Araujo
>> Cabarcas wrote:
>>>
>>> Dear all,
>>>
>>> Since the inclusion of Transfinite interpolation, I have been successful
>>> on working with this powerful technique in my research. I had coded a mesh
>>> implementing concentric circles, where the inner most is shifted a small
>>> distance s. All concentric circles are labeled 100+i, where i is in a loop
>>> on all circles.
>>>
>>> The mesh was working after 4/Apr/17 when I added the following entry in
>>> the forum:
>>> https://groups.google.com/forum/#!topic/dealii/hCZqv9g6mKk
>>>
>>> I installed the development version of dealii on the 17/nov/17. The
>>> details of the installation are also in the forum:
>>> https://groups.google.com/forum/#!topic/dealii/ee2w2X987ig
>>>
>>> and recently I went back and tried to run thhis code, obtaining the
>>> error at the end of the email.
>>>
>>> I prepared a minimal example that includes the definition of my grid. It
>>> includes how I colorize each face as explained before, and the rest are
>>> colorized "1" as the documentation suggests.
>>>
>>> The symptoms are the following:
>>> - If I use refinement=0, everything works and the mesh looks quite nice
>>> in zeros.vtk and surface with lines mode in Paraview.
>>> - For any higher refinement, it gives the error below.
>>>
>>> Maybe there has been a major change in TransfiniteInterpolation since
>>> Apr/2017, or maybe the way I colorize is not good anymore for some weird
>>> reason. Any ideas or comments would be greatly appreciated.
>>>
>>> Juan Carlos Araújo,
>>> Umeå Universitet.
>>>
>>>
>>>
>>> terminate called after throwing an instance of 'dealii::Mapping<2,
>>> 2>::ExcTransformationFailed'
>>>   what():
>>> 
>>> An error occurred in line <1554> of file 
>>> 
>>> in function
>>> typename dealii::Triangulation::cell_iterator
>>> dealii::TransfiniteInterpolationManifold>> spacedim>::compute_chart_points(const dealii::ArrayView>> dealii::Point >&, dealii::ArrayView >)
>>> const [with int dim = 2; int spacedim = 2; typename
>>> dealii::Triangulation::cell_iterator =
>>> dealii::TriaIterator >]
>>> The violated condition was:
>>> false
>>> Additional information:
>>>
>>> 
>>>
>>> Aborted (core dumped)
>>>
>>>
>>> --
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> forum/dealii?hl=en
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[deal.II] Re: Error with Transfinite Interpolation

[David Wells]

I figured it out: we have an optimization that assumes in one particular 
place that, if we have eight points, they must be the vertices of a cube. 
However, in 2D, we use eight points to place new points on quadrilaterals: 
assuming these are the vertices of a cube is wrong. The original assumption 
created a bad initial value for a quasi-newton solver, which then failed to 
converge.

I got rid of the cube assumption. see 
https://github.com/dealii/dealii/pull/5761 for more information.

Do you mind if I use a modified version of your code for a new test in 
deal.II?

Thanks,
David Wells

On Wednesday, January 17, 2018 at 3:05:48 PM UTC-5, Juan Carlos Araujo 
Cabarcas wrote:
>
> Dear all,
>
> Since the inclusion of Transfinite interpolation, I have been successful 
> on working with this powerful technique in my research. I had coded a mesh 
> implementing concentric circles, where the inner most is shifted a small 
> distance s. All concentric circles are labeled 100+i, where i is in a loop 
> on all circles.
>
> The mesh was working after 4/Apr/17 when I added the following entry in 
> the forum:
> https://groups.google.com/forum/#!topic/dealii/hCZqv9g6mKk
>
> I installed the development version of dealii on the 17/nov/17. The 
> details of the installation are also in the forum:
> https://groups.google.com/forum/#!topic/dealii/ee2w2X987ig
>
> and recently I went back and tried to run thhis code, obtaining the error 
> at the end of the email.
>
> I prepared a minimal example that includes the definition of my grid. It 
> includes how I colorize each face as explained before, and the rest are 
> colorized "1" as the documentation suggests.
>
> The symptoms are the following:
> - If I use refinement=0, everything works and the mesh looks quite nice in 
> zeros.vtk and surface with lines mode in Paraview.
> - For any higher refinement, it gives the error below.
>
> Maybe there has been a major change in TransfiniteInterpolation since 
> Apr/2017, or maybe the way I colorize is not good anymore for some weird 
> reason. Any ideas or comments would be greatly appreciated.
>
> Juan Carlos Araújo,
> Umeå Universitet.
>
>
>
> terminate called after throwing an instance of 'dealii::Mapping<2, 
> 2>::ExcTransformationFailed'
>   what():  
> 
> An error occurred in line <1554> of file 
>  in function
> typename dealii::Triangulation::cell_iterator 
> dealii::TransfiniteInterpolationManifold spacedim>::compute_chart_points(const dealii::ArrayView dealii::Point >&, dealii::ArrayView >) const 
> [with int dim = 2; int spacedim = 2; typename dealii::Triangulation spacedim>::cell_iterator = dealii::TriaIterator 
> >]
> The violated condition was: 
> false
> Additional information: 
> 
> 
>
> Aborted (core dumped)
>
>
>

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[deal.II] Re: Error with Transfinite Interpolation

[David Wells]

Hey there,

I have some familiarity with the transfinite interpolation implementation 
and am looking into this now. It looks like, in the transformation, one of 
the 'reference cell points' is calculated as {20, 20}: I don't yet see why. 
I suspect that we now create a twisted cell (or something else that is 
poorly conditioned) or that there is an issue with how we compute chart 
points: either way, its either something we need to catch with a better 
error message or a bug we need to fix.

Over the last few months Martin has added a lot of optimizations to the TFI 
code, in addition to using it in a more general setting during mesh 
refinement: put another way, our implementation has changed substantially, 
so this problem is at least in an area of the library where we have 
recently made huge changes.

Thanks,
David Wells

On Wednesday, January 17, 2018 at 3:05:48 PM UTC-5, Juan Carlos Araujo 
Cabarcas wrote:
>
> Dear all,
>
> Since the inclusion of Transfinite interpolation, I have been successful 
> on working with this powerful technique in my research. I had coded a mesh 
> implementing concentric circles, where the inner most is shifted a small 
> distance s. All concentric circles are labeled 100+i, where i is in a loop 
> on all circles.
>
> The mesh was working after 4/Apr/17 when I added the following entry in 
> the forum:
> https://groups.google.com/forum/#!topic/dealii/hCZqv9g6mKk
>
> I installed the development version of dealii on the 17/nov/17. The 
> details of the installation are also in the forum:
> https://groups.google.com/forum/#!topic/dealii/ee2w2X987ig
>
> and recently I went back and tried to run thhis code, obtaining the error 
> at the end of the email.
>
> I prepared a minimal example that includes the definition of my grid. It 
> includes how I colorize each face as explained before, and the rest are 
> colorized "1" as the documentation suggests.
>
> The symptoms are the following:
> - If I use refinement=0, everything works and the mesh looks quite nice in 
> zeros.vtk and surface with lines mode in Paraview.
> - For any higher refinement, it gives the error below.
>
> Maybe there has been a major change in TransfiniteInterpolation since 
> Apr/2017, or maybe the way I colorize is not good anymore for some weird 
> reason. Any ideas or comments would be greatly appreciated.
>
> Juan Carlos Araújo,
> Umeå Universitet.
>
>
>
> terminate called after throwing an instance of 'dealii::Mapping<2, 
> 2>::ExcTransformationFailed'
>   what():  
> 
> An error occurred in line <1554> of file 
>  in function
> typename dealii::Triangulation::cell_iterator 
> dealii::TransfiniteInterpolationManifold spacedim>::compute_chart_points(const dealii::ArrayView dealii::Point >&, dealii::ArrayView >) const 
> [with int dim = 2; int spacedim = 2; typename dealii::Triangulation spacedim>::cell_iterator = dealii::TriaIterator 
> >]
> The violated condition was: 
> false
> Additional information: 
> 
> 
>
> Aborted (core dumped)
>
>
>

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[deal.II] Re: Distribute constraints on PETSc wrapper

[David Wells]

Hi Jaekwang,

The error message generated by PETSc states that you are trying to insert 
an invalid floating point number into the system matrix. This probably 
means that you are using uninitialized values somewhere in the computation: 
usually this mistake is caught by deal.II. Did you compile your deal.II 
application in debug mode? If not, I suspect that running the program again 
in debug mode will show exactly where something was not initialized 
(deal.II checks this in many places).

Thanks,
David Wells





On Thursday, September 21, 2017 at 2:16:26 PM UTC-4, Jaekwang Kim wrote:
>
> Hi, all 
>
> I was practicing using Petsc library through deal.ii wrappers, 
>
> While, step 17 gives me clear explanation, I am having trouble in 
> distributing hanging node constraints on Petsc system matrix, 
>
> I was modifying step-9 hyperbolic equation solvers with PETSc matrix, but 
> when I compile my code  I run into error message like 
>
> *[0]PETSC ERROR: - Error Message 
> *
>
> *[0]PETSC ERROR: Floating point exception!*
>
> *[0]PETSC ERROR: Inserting nan at matrix entry (0,0)!*
>
> *[0]PETSC ERROR: 
> *
>
> *[0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 6, Mon Feb 11 12:26:34 
> CST 2013 *
>
> *[0]PETSC ERROR: See docs/changes/index.html for recent updates.*
>
> *[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.*
>
> *[0]PETSC ERROR: See docs/index.html for manual pages.*
>
> *[0]PETSC ERROR: 
> *
>
> *[0]PETSC ERROR: ./advection on a dbg named golubh2 by jk12 Thu Sep 21 
> 13:05:46 2017*
>
> *[0]PETSC ERROR: Libraries linked from 
> /usr/local/apps/petsc/3.3-p6/intel/mvapich2-1.6-intel/dbg/lib*
>
> *[0]PETSC ERROR: Configure run at Wed Mar 13 14:51:28 2013*
>
> *[0]PETSC ERROR: Configure options 
> --prefix=/usr/local/apps/petsc/3.3-p6/intel/mvapich2-1.6-intel/dbg 
> --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpicxx 
> --with-shared-libraries=0 --with-mpi=1 --known-mpi-shared=1 
> --with-blas-lapack-lib="[/usr/local/intel-11.1/mkl/lib/em64t/libmkl_intel_lp64.a,/usr/local/intel-11.1/mkl/lib/em64t/libmkl_sequential.a,/usr/local/intel-11.1/mkl/lib/em64t/libmkl_core.a]"*
>
> *[0]PETSC ERROR: 
> *
>
> *[0]PETSC ERROR: MatSetValues() line 1013 in 
> /usr/local/apps/petsc/build/petsc-3.3-p6/src/mat/interface/matrix.c*
>
> *ERROR: Uncaught exception in MPI_InitFinalize on proc 0. Skipping 
> MPI_Finalize() to avoid a deadlock.*
>
> I have checked where I got stuck in my code and found that they are 
> generated when I distribute constraints to (yellow highlighted lines). 
>
> I attached how I made constraints matrix at setup system. 
>
> I would appreciate if any one can suggests where I got stuck... 
>
> Thanks
>
> Jaekwang 
>
>
>
>
>
>  template 
>
> void AdvectionProblem::assemble_system_petsc ()
>
> {
>
> pcout << "assemble system A" << std::endl;
>
> 
>
> const MappingQ mapping (degree);
>
> QGauss   quadrature_formula(3);
>
> QGauss face_quadrature_formula(3);
>
> 
>
> FEValues fe_values (mapping, fe, quadrature_formula,
>
>  update_values   | update_gradients |
>
>  update_quadrature_points | 
> update_JxW_values);
>
> 
>
> FEFaceValues fe_face_values (mapping, fe, 
> face_quadrature_formula,
>
>   update_values| 
> update_normal_vectors | update_gradients |
>
>   update_quadrature_points  | 
> update_JxW_values);
>
> 
>
> const AdvectionField advection_field; //Defined by Tensor 
> Function
>
> const RightHandSide  right_hand_side; //Defined by normal 
> Vector Function
>
> const BoundaryValues boundary_values; //Defined by normal 
> Vector Function
>
> 
>
> const unsigned int   dofs_per_cell = fe.dofs_per_cell;
>
> const unsigned int   n_q_points= quadrature_formula.size();
>
> const unsigned int   n_face_q_points = 
> fe_face_values.get_quadrature().size();
>
> 
>
> FullMatrix   cell_matrix (dofs_per_cell, dofs_per_cell);
>
> Vector   cell_rhs (dofs_per_cell);
>
> 
>
> std::vector local_dof_indices 
> (dofs_per_cell);
>
>

[deal.II] Re: How to initialize PETScWrappers::SparseMatrix from a PETSc Mat

[David Wells]

I think that this is a use case that we should support: for example, 
PETScWrappers::VectorBase can act as a wrapper around a user-provided Vec 
so we should definitely consider providing similar functionality for 
PETScWrappers::MatrixBase.

On Wednesday, May 24, 2017 at 5:18:46 AM UTC-4, Juan Carlos Araujo Cabarcas 
wrote:
>
> Dear all,
>
> I have a matrix written by using PETSc in a Binary file, and I am trying 
> work with it in my dealii environment. For this, I read a system matrix 
> from PETSc:
>
> Mat   M_read;
>
> PetscViewerBinaryOpen(PETSC_COMM_WORLD,file.c_str (),FILE_MODE_READ,&fd);
> MatCreate(PETSC_COMM_WORLD, &M_read);
> MatSetOptionsPrefix( M_read,"m_");
> MatSetFromOptions( M_read );
> MatLoad( local_M ,fd);
> PetscViewerDestroy(&fd);
> MatGetSize( M_read ,&mm,&nn);
> MatGetInfo( M_read ,MAT_LOCAL,&matinfo);
> printf("matinfo.nz_used %g\n", matinfo.nz_used);
>
> and I would like to initialize a *dealii PETScWrappers::SparseMatrix *by 
> using *M_read*.
>
> If I try the naĩve way:
>   PETScWrappers::SparseMatrix M = PETScWrappers::SparseMatrix (M_read);
>
> I get the error:
>
> error: ‘dealii::PETScWrappers::SparseMatrix::SparseMatrix(const 
> dealii::PETScWrappers::SparseMatrix&)’ is private
>  SparseMatrix(const SparseMatrix &);
>
> I know the *PETScWrappers::SparseMatrix* contains the protected member *Mat 
> matrix*, but I quite don't know how to copy it to initialize *M*.
>
> Is there a way to achieve this? any help is appreciated!
>
> Thanks in advance,
> Juan Carlos Araújo,
> Umeå Universitet
>

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Re: [deal.II] Call for Codes

[David Wells]

Hi Toby,

That sentence is not well written. I should have written

I ocassionally scan GitHub to learn what features of deal.II people are 
using in their own projects.

For example, we will not break anyone's codes by removing the PETSc serial 
vector classes: no one is using them anymore (though a few people still 
include the headers).

Thanks,
David Wells


On Thursday, April 20, 2017 at 10:32:52 AM UTC-4, Tobi Young wrote:
>
>
> I ocassionally scan GitHub to see if people are using features in deal.II 
> outside of the library
>
>
> Please, clarify that statement for me. :-\
>
> Best, Toby
>
>
>
>

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[deal.II] Call for Codes

[David Wells]

Dear everyone,

Now that version 8.5 has been released we are working on version 9.0 of 
deal.II. We are considering making small breaking changes that will help us 
clean up things in the library immensely (for example, we would like to 
modify the clone functions to return the new unique_ptr class instead of 
simply a pointer to the heap).

I ocassionally scan GitHub to see if people are using features in deal.II 
outside of the library, but it would be nice to have more projects to look 
at when we make these types of deprecation or removal decisions. My request 
is this: If you are willing to do so, I would appreciate it if you would 
email me (drwells at vt.edu) any source files using deal.II that you are 
willing to share. They don't have to compile, or be complete, or be up to 
date with current versions of deal.II: I just need something to search 
through to see what features of deal.II people are using in their own 
projects.

Thanks,
David Wells

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[deal.II] Re: Problem installing 8.4.1

[David Wells]

Hey there,

This looks like a bug in your system copy of boost. I think that the best 
way to fix this is to try recompiling with the copy of boost deal.II 
bundles, i.e., call cmake as

cmake -DDEAL_II_FORCE_BUNDLED_BOOST=ON -DCMAKE_INSTALL_DIR=/path/to/
installation/ ../



This should compile deal.II with our own bundled subset of boost which is 
known to work. Let me know if that does not fix things.

Thanks,
David Wells

On Sunday, February 5, 2017 at 6:31:56 AM UTC-5, H. Vukman wrote:
>
> I have a problem with the installation. This is the error I get:
>
> In file included from /usr/include/boost/unordered/detail/buckets.hpp:16:0,
>  from /usr/include/boost/unordered/detail/table.hpp:10,
>  from 
> /usr/include/boost/unordered/detail/equivalent.hpp:14,
>  from /usr/include/boost/unordered/unordered_map.hpp:17,
>  from /usr/include/boost/unordered_map.hpp:16,
>  from 
> /home/guntah/Downloads/dealii-8.4.1/include/deal.II/base/graph_coloring.h:24,
>  from 
> /home/guntah/Downloads/dealii-8.4.1/include/deal.II/base/work_stream.h:21,
>  from 
> /home/guntah/Downloads/dealii-8.4.1/source/numerics/data_out.cc:16:
> /usr/local/include/boost/type_traits/aligned_storage.hpp:134:8: error: 
> previous definition of ‘struct 
> boost::is_pod alignment_> >’
>  struct is_pod< 
> ::boost::detail::aligned_storage::aligned_storage_imp > 
> : public true_type{};
> ^
> make[2]: *** 
> [source/numerics/CMakeFiles/obj_numerics.release.dir/data_out.cc.o] Error 1
> make[1]: *** [source/numerics/CMakeFiles/obj_numerics.release.dir/all] 
> Error 2
> make: *** [all] Error 2
>
> I am using Linux Mint 17 Qiana. Attached are the config files.
>
>

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[deal.II] Re: bool ParameterHandler::read_input (const std::string &, const bool, const bool, const std::string &) DEAL_II_DEPRECATED

[David Wells]

Dear Vinayak,

Jean-Paul is right: we got rid of this function in the fall in favor of 
parse_input so that we can mark errors by raising exceptions (instead of 
returning a boolean, which is what read_input does).

Thanks,
David Wells


On Sunday, January 29, 2017 at 1:14:58 PM UTC-5, Jean-Paul Pelteret wrote:
>
> Dear Vinayak,
>
> You must be using the developer version, right? This function has been 
> deprecated and, I believe, is superseded by the function 
> ParameterHandler::parse_input 
> <https://www.dealii.org/developer/doxygen/deal.II/classParameterHandler.html#a4f067f0a84ac392fe26d553aea50541b>
>  .
>
> I hope that this helps.
>
> Regards,
> Jean-Paul
>
> On Sunday, January 29, 2017 at 6:33:17 PM UTC+1, Vinayak Gholap wrote:
>>
>> Hello,
>>
>> I have to use this bool ParameterHandler::read_input() function but since 
>> it is marked Deprecated I get compiler warning
>>
>> " warning: ‘virtual bool dealii::ParameterHandler::read_input(const 
>> string&, bool, bool, const string&)’ is deprecated 
>> [-Wdeprecated-declarations]
>>   prm.read_input (input_file); ". 
>>
>> How do I use it without warnings? Or should I use some other equivalent 
>> function from the ParameterHandler Class?
>>
>> Regards,
>> Vinayak
>>
>

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Re: [deal.II] Re: deal.ii and Reduced Basis method

[David Wells]

Hi Giulia,

I used deal.II in my thesis to do model reduction (Wolfgang was kind enough 
to include a link), but I used POD and not RB. Let me know if you have 
questions about the thesis :)

Thanks,
David Wells

On Thursday, December 1, 2016 at 8:18:56 AM UTC-5, Giulia Deolmi wrote:
>
> Dear Jean-Paul and Wolfgang,
> thanks a lot for your replies! We contacted the developers of pyMOR who 
> will help us to solve the RB problem, using deal.ii as an external software.
> Kind regards,
> Giulia
>
> Il giorno giovedì 1 dicembre 2016 13:07:58 UTC+1, Wolfgang Bangerth ha 
> scritto:
>>
>>
>> Giulia, 
>> there are also this thesis 
>>https://vtechworks.lib.vt.edu/handle/10919/52960 
>> and the pyMOR package has deal.II interfaces: 
>>http://pymor.org/ 
>>
>> Best 
>>   W. 
>>
>>
>> On 12/01/2016 01:05 AM, Jean-Paul Pelteret wrote: 
>> > Dear Giulia, 
>> > 
>> > Judging by the lack of reply it seems that no-one knows of (or has 
>> > implemented) an open-source library to specifically do model order 
>> reduction 
>> > with deal.II. However, at least one of my colleagues uses deal.II to 
>> perform 
>> > ROM via proper orthogonal decomposition, so deal.II definitely provides 
>> all of 
>> > the core functionality to implement this yourself. If its of any use to 
>> you, 
>> > here's a link to his paper (sadly during final editing his text citing 
>> deal.II 
>> > got removed without him noticing): 
>> > http://onlinelibrary.wiley.com/doi/10.1002/gamm.201610011/full 
>> > 
>> > Regards, 
>> > J-P 
>> > 
>> > On Monday, November 14, 2016 at 11:03:16 AM UTC+1, Giulia Deolmi wrote: 
>> > 
>> > Dear all, 
>> > I have implemented a parameter dependent problem in deal.ii and now 
>> I 
>> > would like to apply the Reduced Basis (RB) method to it. 
>> > Do you know if there is already some code available that I can use 
>> where 
>> > the RB has already been implemented (in deal.ii or compatible to 
>> it)? 
>> > So far I have only found a software called pyMOR for the RB method 
>> > (http://pymor.org/). In theory it should be possible to use 
>> deal.ii as an 
>> > external software. The example that is given is not so clear to me, 
>> > though. Is anyone familiar with it? 
>> > Thanks a lot in advance, 
>> > Kind regards, 
>> > Giulia Deolmi 
>> > 
>> > -- 
>> > The deal.II project is located at http://www.dealii.org/ 
>> > For mailing list/forum options, see 
>> https://groups.google.com/d/forum/dealii?hl=en 
>> > --- 
>> > You received this message because you are subscribed to the Google 
>> Groups 
>> > "deal.II User Group" group. 
>> > To unsubscribe from this group and stop receiving emails from it, send 
>> an 
>> > email to dealii+un...@googlegroups.com 
>> > <mailto:dealii+un...@googlegroups.com>. 
>> > For more options, visit https://groups.google.com/d/optout. 
>>
>>
>> -- 
>>  
>> Wolfgang Bangerth  email: bang...@colostate.edu 
>> www: http://www.math.colostate.edu/~bangerth/ 
>>
>>

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[deal.II] Re: CXX flags for SIMD and other optimization flags (GCC@6)

[David Wells]

A useful flag that I use in release mode is -funsafe-loop-optimizations, 
which assumes that loop counters cannot overflow and other such things. I 
don't remember the exact numbers but I do remember that using this flag 
made a small, but measurable, performance improvement.

On Thursday, September 15, 2016 at 8:04:58 AM UTC-4, Denis Davydov wrote:
>
> Dear all,
>
> From the matrix-free tutorials 37 and 48, I see that the recommended flags 
> for VectorizedArrays with GCC are
>
> -DCMAKE_CXX_FLAGS="-march=native"
>
> How about using -O3, -ffast-math, -funroll-loops ? Any other recommended 
> flags for GCC?
>
> Regards,
> Denis.
>

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[deal.II] Re: Step-35 Poiseuille flow in a 3D pipe

[David Wells]

Hi Jiaqi,

I have to admit that it has been about a year since I last really looked at 
step-35 and I do not know the answer off the top of my head for this. I saw 
that Daniel responded to this question elsewhere; was that enough to figure 
things out?

Thanks,
David Wells

On Friday, July 29, 2016 at 9:19:29 PM UTC-4, Jiaqi ZHANG wrote:
>
> Hello David Wells,
>
> Sorry to bother you, but I have a problem about Step-35. I have posted the 
> question
>
> a few days ago, and no one answered me, so I have to search in the mailing 
> list and found
>
> that you have been using it a lot. I was wondering if you could help me, 
> and the following is 
>
> my question:
>
> I read the references listed there and some other papers about projection 
> methods, 
>
> and know that after obtaining the intermediate values for velocity, say 
> v_n, we need to 
>
> correct the velocity by u_n = v_n - grad(2dt/3 phi_n), which is mentioned 
> in the introduction of Step-35, 
>
> but it seems that Step-35 only corrects the pressure, and I cannot find 
> anything in the code that implements the above equation.
>
> However, when I correct the velocity at every time step, the algorithm 
> turns out to be divergent (iterating more than 1000 times at some time 
> step). 
>
> I am very confused, did I misunderstand the algorithm or the code?
>
> Thanks in advance.
>
>
> Best,
> Jiaqi 
>
>
>
> 在 2015年3月17日星期二 UTC-4下午8:14:21，David Wells写道：
>>
>> Hi Joaquin,
>>
>> I used step-35 a lot, so I may be able to assist you here.
>>
>> For the velocity inflow, are you sure that what you have will be zero 
>> flow at the edges? The XY slices don't look quite circular to me, so this 
>> may be a problem if you refine the mesh. Since you are using GMSH, it may 
>> be easiest to use GMSH's extrusion abilities to extrude a circle along the 
>> z axis to solve this.
>>
>> I believe you handled the pressure correctly (as long as the domain 
>> starts at z = 0 and ends at z = 10).
>>
>> At least as of a few months ago, step-35 could not run in 3D due to a 
>> lack of a compressed sparsity pattern. I fixed this in my own copy of 
>> step-35 (see http://www.github.com/drwells/step-35a) (yeah, I know I 
>> should submit a patch...). I tweaked the preconditioners to improve 
>> performance, so my version might be useful to look at.
>>
>> Another thing you might want to look at is how Abner implemented labels 
>> for the different boundaries. According to my experiments (see 
>> https://github.com/drwells/dealii-step-35a/blob/master/cylinderextruded.geo
>> ):
>> 1 is the no-slip edges
>> 2 is the inflow
>> 3 is the outflow
>> 4 is the cylinder (may not apply for you)
>>
>> If your mesh file does not label things correctly then things will get 
>> weird. I hope that this is helpful.
>>
>> Thanks,
>> David Wells
>>
>> On Tuesday, March 17, 2015 at 6:08:02 PM UTC-4, Joaquin wrote:
>>>
>>> Hi,
>>>
>>> I am trying to run step-35 for the unsteady incompressible viscous flow 
>>> in a pipe, for 3D case. The mesh file I used is attached. The graph of 
>>> results 
>>> is attached.  The expected results for any time should be paraboloid 
>>> (or parabolic in 2D), but, I can not get that. The changes I did are: 
>>>
>>>
>>>
>>> *1. namespace EquationData: *template 
>>> double Velocity::value (const Point &p,
>>>  const unsigned int) const
>>> {
>>>   if (this->comp == 0)
>>> {
>>>   const double Um = 1.5;
>>>   const double R  = 2.;
>>>   return Um*(1 - (p(0)*p(0)+p(1)*p(1))/(2*R*R));
>>> }
>>>   else
>>>   return 0.;
>>> }
>>>
>>> *Through the pipe pressure drop **is linear (**I do not how to make 
>>> changes here):* 
>>>
>>> template 
>>> double Pressure::value (const Point &p,
>>>  const unsigned int) const
>>> {
>>>   return 10.-p(2);
>>> }
>>>
>>>  
>>> *2. *
>>>   template 
>>>   void
>>>   NavierStokesProjection::
>>>   create_triangulation_and_dofs (const unsigned int n_refines)
>>>   {
>>> GridIn grid_in;
>>> grid_in.attach_triangulation (triangulation);
>>>
>>> {
>>>   std::string filename = "*cilindro.msh

[deal.II] Re: Development activity over the past year

[David Wells]

Dear everyone,


About a year ago I did a bit of analysis on the commit rate: it has gone up 
significantly over the least few years. Just for fun I attached a plot of 
the total number of commits over time (as well as some important points in 
our history) to visualize this. As far as I can tell, Matthias joining the 
project increased the slope of the line remarkably :)


<https://lh3.googleusercontent.com/-aLBCtfcH8hQ/V6ECjWTUorI/Ae8/gXl754TkR48tn2eUztu8oXgO18QE-TkYgCLcB/s1600/deal-commits.png>

I included the code below in case anyone else wants to play with it.


Thanks,

David Wells


#!/usr/bin/env python
import collections
import datetime

import matplotlib.pyplot as plt

# data generated with
#
# git log --date=iso | grep '^Date:' | awk '{print $2}' > 
commit-dates.txt
#
dates = list()
with open('commit-dates.txt', 'r') as file_handle:
for line in file_handle:
dates.append(datetime.datetime.strptime(line[:-1], "%Y-%m-%d"))
dates.sort()

commits_per_day = collections.Counter(dates)
commits_at_day = commits_per_day.copy()

matthias_start_date = datetime.datetime.strptime("2012-02-08", "%Y-%m-%d")
cmake_switch_date = datetime.datetime.strptime("2013-03-07", "%Y-%m-%d")
git_switch_date = datetime.datetime.strptime("2014-07-21", "%Y-%m-%d")

total_commits = 0
for key in sorted(commits_at_day.keys()):
n_commits = commits_at_day[key]
commits_at_day[key] += total_commits
total_commits += n_commits

plot_data = commits_at_day.items()
plot_data.sort()
xs = map(lambda u: u[0], plot_data)
ys = map(lambda u: u[1], plot_data)

plt.clf()
plt.plot(xs, ys, label='Total number of commits')
plt.plot([matthias_start_date, matthias_start_date], [0, commits_at_day[
matthias_start_date]],
 label="Matthias' start date")
plt.plot([cmake_switch_date, cmake_switch_date], [0, commits_at_day[
cmake_switch_date]],
 label="CMake switch date")
plt.plot([git_switch_date, git_switch_date], [0, commits_at_day[
git_switch_date]],
 label="Git switch date")
plt.legend(loc='upper left')
plt.savefig("deal-commits.png")






On Sunday, July 31, 2016 at 10:08:59 PM UTC-4, bangerth wrote:
>
>
> All, 
> I'm writing my annual report to the NSF and wanted to share a few 
> statistics I 
> thought were interesting: 
>
> * 40,000 new lines of code in deal.II (excluding testsuite) over the past 
> year 
> * 77 new testcases 
> * 4 new tutorial programs 
> * 1540 emails to dea...@googlegroups.com  between January to 
> July alone 
> * 725 people are subscribed to the mailing list (+190 compared to last 
> year) 
>
> What this shows to me is that this is a vibrant community that is doing 
> awesome things and helping each other! Thanks to you all for participating 
> in 
> the many ways in which you contribute! 
>
> Best 
>   Wolfgang 
>
> PS: If you haven't actively participated so far, we would love to have you 
> be 
> a more active part of this project! Here are a few ideas: 
>https://github.com/dealii/dealii/blob/master/CONTRIBUTING.md 
>https://www.dealii.org/participate.html 
>
> -- 
>  
> Wolfgang Bangerth   email:bang...@math.tamu.edu 
>  
>  www: http://www.math.tamu.edu/~bangerth/ 
>
>

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Re: [deal.II] Re: Deal.II does not pass quick tests after installation

[David Wells]

I do not understand why we were not able to link successfully with
pthreads; I'll try to get a copy of centOS 5.3 at some point and see if I
can reproduce this. Either way I am glad that we could get you set up
correctly :)

On Wed, Jul 13, 2016 at 12:05 AM, Thien Binh Nguyen 
wrote:

> Thank you very much Mr. Pelteret for handling the case!
>
> Mr. Wells,
>
> I have tried compiling the library without using pthreads. The quicktests
> are now passed successfully
>
> [image: Hình ảnh nội tuyến 1]
>
> For the other question, we have CentOS 5.3 installed in our machine. But I
> have installed necessary packages for Deal.II, i.e. CMake 2.8.10.2, GNU
> make 3.81, as well as gcc 4.7.2 and the other ones.
>
> Thank you very much!
>
> Yours sincerely,
> Nguyen Thien Binh
>
> 2016-07-12 9:17 GMT+09:00 David Wells :
>
>> Thank you JP :)
>>
>>
>>
>>
>> Did you try compiling the library without threads?
>>
>> I believe you said earlier that you were using centOS. What is the exact
>> version information of your operating system?
>>
>> Thanks,
>> David Wells
>>
>> On Mon, Jul 11, 2016 at 2:29 PM, Jean-Paul Pelteret > > wrote:
>>
>>> Thanks for pointing that out David, I didn't see the picture in the
>>> reply. Since I can't edit the posts themselves, I've duplicated the post
>>> here and those that required "censoring". Nguyen's message follows:
>>>
>>> ---
>>> Dear Mr. Wells,
>>>
>>> I am sorry but if you would please kindly delete the attached figure in
>>> the previous mail and replace it with the following?
>>>
>>> [image: Hình ảnh nội tuyến 1]
>>> This is because the previous one contains our machine's IP address.
>>> Since all these messages are supposed to be on public in Deal.II community,
>>> I think it would be better such information is not shown in cases of any
>>> unexpected problems.
>>>
>>> Thank you very much!
>>>
>>> Yours sincerely,
>>> Nguyen Thien Binh
>>>
>>> --
>>> The deal.II project is located at http://www.dealii.org/
>>> For mailing list/forum options, see
>>> https://groups.google.com/d/forum/dealii?hl=en
>>> ---
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>>> Google Groups "deal.II User Group" group.
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>>>
>>
>> --
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>> https://groups.google.com/d/forum/dealii?hl=en
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>>
>
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[deal.II] Re: Problem building dealii with PETSc

[David Wells]

Hi there,

That error (MPI_SEEK_SET) *should* mean (I wrote the check) that the 
library cannot compile because you are missing something defined by, if I 
recall correctly, the MPI 2.0 standard: any version of MPI released in the 
last four or five years should have it. I am not sure why that, of all 
things, shows up and complains, but that means that CMake could not find 
your copy of MPI.

It should not be necessary to have those sorts of SET commands anywhere: 
the CMake scripts will set those variables up by inspecting the paths you 
passed in (related note: it should be CACHE not CASHE).

deal.II does not use the C++ MPI interface (I do not know of any project 
that does, for the record), so you can get away without setting anything 
for them.

I looked through the list of packages for 16.04 and it looks like 
libpetsc3.6.2-dev pulls in an MPI package as a dependency so installing 
just that through apt-get should suffice. What exactly was the error 
message when you tried just that?

Regardless, the library should just work with the latest Ubuntu release so 
this is an issue on our end. Thank you for reporting this.

Thanks,
David Wells

On Monday, July 11, 2016 at 11:58:25 AM UTC-4, Pete Griffin wrote:
>
> I have made another attempt at installing dealii 8.4.1 with PETSc and MPI
>
> First I removed all PETSc and all mpi libraries from the system.
>
> checking with:
>   898  dpkg -l | grep petsc
>   899  dpkg -l | grep mpi
> petsc an openmpi and mpich and mpich2 were and are gone.
>
>
> I used downloaded PETSc source and built with:
>
> ./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran 
> --download-mpich 
> make PETSC_DIR=/home/pgriffin/Documents/Zipstore2/petsc-3.6.4 
> PETSC_ARCH=arch-linux2-c-debug all
> make PETSC_DIR=/home/pgriffin/Documents/Zipstore2/petsc-3.6.4 
> PETSC_ARCH=arch-linux2-c-debug test
> make PETSC_DIR=/home/pgriffin/Documents/Zipstore2/petsc-3.6.4 
> PETSC_ARCH=arch-linux2-c-debug streams NPMAX=1
>
> ran:
>
> cmake -DCMAKE_INSTALL_PREFIX=/home/pgriffin/mylibs/dealii-8.4.1-PETSc 
> -DPETSC_DIR=/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug
>  
> -DPETSC_ARCH=x86_64 -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_PETSC=ON  ../
>
> with
>
> SET(MPI_C_LIBRARIES 
> "/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpich.so;/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpi.so"
>  
> CASHE STRING "")
> SET(MPI_C_INCLUDE_PATH 
> "/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/include" 
> CASHE STRING "")
>
> SET(MPI_CXX_LIBRARIES 
> "/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpichcxx.so;/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpicxx.so"
>  
> CASHE STRING "")
> SET(MPI_CXX_INCLUDE_PATH 
> "/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/include" 
> CASHE STRING "")
>
> SET(MPI_Fortran_LIBRARIES 
> "/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpichf90.so"
>  
> CASHE STRING "")
> SET(MPI_Fortran_INCLUDE_PATH 
> "/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/include" 
> CASHE STRING "")
>
> appended to setup_deal_ii.cmake.
>
> I could only guess which were the MPI_C_LIBRARIES, MPI_CXX_LIBRARIES, 
> MPI_Fortran_LIBRARIES which were required from the trail of errors I got. 
> What is MPI_SEEK_SET?? is that on internal cmake variable?
>
> ===
> The final error I got that is relavant was:
>
> -- 
> -- Include 
> /home/pgriffin/Documents/Zipstore2/dealii-8.4.1-PETSc/cmake/configure/configure_1_mpi.cmake
> -- Found MPI_C: 
> /home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpich.so;/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpi.so;CASHE;STRING;
>  
>  
> -- Found MPI_CXX: 
> /home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpichcxx.so;/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpicxx.so;CASHE;STRING;
>  
>  
> -- Found MPI_Fortran: 
> /home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpichf90.so;CASHE;STRING;
>  
>  
> -- Performing Test MPI_HAVE_MPI_SEEK_SET
> -- Performing Test MPI_HAVE_MPI_SEEK_SET - Failed
> -- Found MPI_MPI_H
> --   MPI_VERSION: 3.0
> --   MPI_LIBRARIES: 
> /home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpichcxx.so;/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpicxx.so;CA

Re: [deal.II] Re: Deal.II does not pass quick tests after installation

[David Wells]

Thank you JP :)




Did you try compiling the library without threads?

I believe you said earlier that you were using centOS. What is the exact
version information of your operating system?

Thanks,
David Wells

On Mon, Jul 11, 2016 at 2:29 PM, Jean-Paul Pelteret 
wrote:

> Thanks for pointing that out David, I didn't see the picture in the reply.
> Since I can't edit the posts themselves, I've duplicated the post here and
> those that required "censoring". Nguyen's message follows:
>
> ---
> Dear Mr. Wells,
>
> I am sorry but if you would please kindly delete the attached figure in
> the previous mail and replace it with the following?
>
> [image: Hình ảnh nội tuyến 1]
> This is because the previous one contains our machine's IP address. Since
> all these messages are supposed to be on public in Deal.II community, I
> think it would be better such information is not shown in cases of any
> unexpected problems.
>
> Thank you very much!
>
> Yours sincerely,
> Nguyen Thien Binh
>
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[deal.II] Re: Deal.II does not pass quick tests after installation

[David Wells]

Someone with administrative priviledges: the last message also has a 
picture in it with an IP address. Could you delete that too?

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Re: [deal.II] Re: Deal.II does not pass quick tests after installation

[David Wells]

Mr. Nguyen,

Well, this is awkward. I looked over your files carefully and I see nothing 
unusual in the configuration. CMake definitely, at some point, recognizes 
that it needs to link against libpthread but it never seems to do it. I 
really hope that we can figure this out because it is probably a bug in our 
CMake code.

I think that one way to get around this temporarily would be to compile the 
library without threads, i.e., compile it with the flag 
-DDEAL_II_WITH_THREADS=OFF. That should let you compile the library but you 
won't be able to use threads (bad, but better than nothing).

I am running out of explanations for this error. Would you humor me and 
check that you do have /usr/lib/libpthread.so or /usr/lib64/libpthread.so 
on your system? Perhaps the libraries are in some strange place that CMake 
cannot find.

Thanks,
David Wells

On Tuesday, July 5, 2016 at 12:02:43 AM UTC-4, deal.II newbie wrote:
>
> Dear Mr. Wells,
>
> Thanks for your help again!
>
> I would like to send you the detailed.log as well as summary.log and 
> quicktests.log. Could you please have a check on the attachment?
>
> I hope these will give some information about the error.
>
> Yours sincerely,
> Nguyen Thien Binh
>
> 2016-07-05 6:40 GMT+09:00 David Wells >:
>
>> Mr. Nguyen,
>>
>> Not a problem; I hope that I can help :)
>>
>> That is odd; it doesn't seem to have linked (or tried to link) against 
>> libpthread at all. This implies that (since it compiled successfully) it 
>> never tried to link with libpthread. Would you please post the file 
>> detailed.log (should be in your build directory)? Mine specifies the 
>> variable THREAD_LINKER_FLAGS; I suspect that variable is not correct in 
>> your copy.
>>
>> Thanks,
>> David Wells
>>
>>
>> On Sun, Jul 3, 2016 at 9:30 PM, Thien Binh Nguyen > > wrote:
>>
>>> Dear Mr. Wells, 
>>>
>>> Thank you very much for your prompt response, and I am also sorry for my 
>>> late reply!
>>>
>>> When ldd either to libdeal_II.so or libdeal_II.g.so, I received the 
>>> following messages
>>>
>>> [image: Hình ảnh nội tuyến 1]
>>> As you noticed, I compiled Deal.II with root privilege. I was trying to 
>>> re-installed and complied Deal.II with my own account. But I still got the 
>>> same error messages.
>>>
>>> Thank you very much!
>>>
>>> Yours sincerely,
>>> Nguyen Thien Binh
>>>
>>> 2016-07-01 23:42 GMT+09:00 David Wells >:
>>>
>>>> Hi there,
>>>>
>>>> Well that is something I have not seen before: it looks like it did not 
>>>> link correctly to your copy of libpthread.so. To confirm this, could you 
>>>> run
>>>>
>>>> ldd build-directory/lib/libdeal_II.so
>>>>
>>>> (where build-directory is whereever you compiled the library)
>>>>
>>>> and see if it did not find a particular library.
>>>>
>>>> Since it looks like the library is in '/root/': did you compile this as 
>>>> root? If so weird things can happen; you should build it as an 
>>>> unprivileged 
>>>> user.
>>>>
>>>> Thanks,
>>>> David Wells
>>>>
>>>> On Thursday, June 30, 2016 at 2:00:22 AM UTC-4, deal.II newbie wrote:
>>>>>
>>>>> Hi! I am a newbie to Deal.II. After the installation, I typed the 
>>>>> command make test for running the quick tests. But all four tests failed 
>>>>> out of four. The reason listed below in the quicktests.log is the same 
>>>>> for 
>>>>> all 4 tests. I would like to ask if anyone could please help indicate 
>>>>> what 
>>>>> the error is and how to fix it? Any help or hints would be much 
>>>>> appreciated! Thank you very much in advance!
>>>>>
>>>>> The error is the same for all 4 tests as follows,
>>>>>
>>>>> Scanning dependencies of target tbb.debug
>>>>> [100%] Building CXX object 
>>>>> tests/quick_tests/CMakeFiles/tbb.debug.dir/tbb.cc.o
>>>>> /root/dealii-8.4.1/tests/quick_tests/tbb.cc:49:6: warning: unused 
>>>>> parameter ‘scratch’ [-Wunused-parameter]
>>>>> Linking CXX executable tbb.debug
>>>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to 
>>>>> `pthread_mutexattr_destroy'
>>>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_

Re: [deal.II] Re: Deal.II does not pass quick tests after installation

[David Wells]

Mr. Nguyen,

Not a problem; I hope that I can help :)

That is odd; it doesn't seem to have linked (or tried to link) against
libpthread at all. This implies that (since it compiled successfully) it
never tried to link with libpthread. Would you please post the file
detailed.log (should be in your build directory)? Mine specifies the
variable THREAD_LINKER_FLAGS; I suspect that variable is not correct in
your copy.

Thanks,
David Wells

On Sun, Jul 3, 2016 at 9:30 PM, Thien Binh Nguyen 
wrote:

> Dear Mr. Wells,
>
> Thank you very much for your prompt response, and I am also sorry for my
> late reply!
>
> When ldd either to libdeal_II.so or libdeal_II.g.so, I received the
> following messages
>
> [image: Hình ảnh nội tuyến 1]
> As you noticed, I compiled Deal.II with root privilege. I was trying to
> re-installed and complied Deal.II with my own account. But I still got the
> same error messages.
>
> Thank you very much!
>
> Yours sincerely,
> Nguyen Thien Binh
>
> 2016-07-01 23:42 GMT+09:00 David Wells :
>
>> Hi there,
>>
>> Well that is something I have not seen before: it looks like it did not
>> link correctly to your copy of libpthread.so. To confirm this, could you run
>>
>> ldd build-directory/lib/libdeal_II.so
>>
>> (where build-directory is whereever you compiled the library)
>>
>> and see if it did not find a particular library.
>>
>> Since it looks like the library is in '/root/': did you compile this as
>> root? If so weird things can happen; you should build it as an unprivileged
>> user.
>>
>> Thanks,
>> David Wells
>>
>> On Thursday, June 30, 2016 at 2:00:22 AM UTC-4, deal.II newbie wrote:
>>>
>>> Hi! I am a newbie to Deal.II. After the installation, I typed the
>>> command make test for running the quick tests. But all four tests failed
>>> out of four. The reason listed below in the quicktests.log is the same for
>>> all 4 tests. I would like to ask if anyone could please help indicate what
>>> the error is and how to fix it? Any help or hints would be much
>>> appreciated! Thank you very much in advance!
>>>
>>> The error is the same for all 4 tests as follows,
>>>
>>> Scanning dependencies of target tbb.debug
>>> [100%] Building CXX object
>>> tests/quick_tests/CMakeFiles/tbb.debug.dir/tbb.cc.o
>>> /root/dealii-8.4.1/tests/quick_tests/tbb.cc:49:6: warning: unused
>>> parameter ‘scratch’ [-Wunused-parameter]
>>> Linking CXX executable tbb.debug
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>>> `pthread_mutexattr_destroy'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_join'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_detach'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>>> `pthread_barrier_wait'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>>> `pthread_mutexattr_settype'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>>> `pthread_mutex_trylock'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>>> `pthread_barrier_init'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `sem_wait'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `sem_init'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>>> `pthread_getspecific'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>>> `pthread_setspecific'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `sem_destroy'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_create'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>>> `pthread_key_delete'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>>> `pthread_key_create'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>>> `pthread_mutexattr_init'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>>> `pthread_attr_getstack'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>>> `pthread_barrier_destroy'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `sem_post'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>>> `pthread_getattr_np'
>>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>>> `pthread_attr_setstacksize'
>>> collect2: error: ld returned 1 exit status
>>> gmake[7]: *** [tests/

[deal.II] Re: Deal.II does not pass quick tests after installation

[David Wells]

Hi there,

Well that is something I have not seen before: it looks like it did not 
link correctly to your copy of libpthread.so. To confirm this, could you run

ldd build-directory/lib/libdeal_II.so

(where build-directory is whereever you compiled the library)

and see if it did not find a particular library.

Since it looks like the library is in '/root/': did you compile this as 
root? If so weird things can happen; you should build it as an unprivileged 
user.

Thanks,
David Wells

On Thursday, June 30, 2016 at 2:00:22 AM UTC-4, deal.II newbie wrote:
>
> Hi! I am a newbie to Deal.II. After the installation, I typed the command 
> make test for running the quick tests. But all four tests failed out of 
> four. The reason listed below in the quicktests.log is the same for all 4 
> tests. I would like to ask if anyone could please help indicate what the 
> error is and how to fix it? Any help or hints would be much appreciated! 
> Thank you very much in advance!
>
> The error is the same for all 4 tests as follows,
>
> Scanning dependencies of target tbb.debug
> [100%] Building CXX object 
> tests/quick_tests/CMakeFiles/tbb.debug.dir/tbb.cc.o
> /root/dealii-8.4.1/tests/quick_tests/tbb.cc:49:6: warning: unused 
> parameter ‘scratch’ [-Wunused-parameter]
> Linking CXX executable tbb.debug
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to 
> `pthread_mutexattr_destroy'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_join'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_detach'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to 
> `pthread_barrier_wait'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to 
> `pthread_mutexattr_settype'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to 
> `pthread_mutex_trylock'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to 
> `pthread_barrier_init'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `sem_wait'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `sem_init'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to 
> `pthread_getspecific'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to 
> `pthread_setspecific'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `sem_destroy'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_create'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to 
> `pthread_key_delete'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to 
> `pthread_key_create'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to 
> `pthread_mutexattr_init'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to 
> `pthread_attr_getstack'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to 
> `pthread_barrier_destroy'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `sem_post'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to 
> `pthread_getattr_np'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to 
> `pthread_attr_setstacksize'
> collect2: error: ld returned 1 exit status
> gmake[7]: *** [tests/quick_tests/tbb.debug] Error 1
> gmake[6]: *** [tests/quick_tests/CMakeFiles/tbb.debug.dir/all] Error 2
> gmake[5]: *** [tests/quick_tests/CMakeFiles/tbb.debug.run.dir/rule] Error 2
> gmake[4]: *** [tbb.debug.run] Error 2
>
>

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[deal.II] Re: Mapping and round-off errors

[David Wells]

Hi Andreas,

Unfortunately, I believe that due to roundoff these functions will always 
produce questionable results when points are near the cell's boundary. If I 
recall correctly, at least for 2D the errors tended to be a couple of 
multiples larger than machine precision when doing these sorts of things, 
so the library functions won't help much.

One possibility would be, if you have a very easy geometry, to try 
MappingCartesian instead. That will have fewer roundoff errors than 
MappingQ1/MappingQGeneric.

If you know that the points are close to a cell face then another possible 
work around would be to project that point onto the face and then see if 
the vector from the point to the projected point faces in or out of the 
cell. 

I hope that one of these helps.

Thanks,
David Wells

On Thursday, May 19, 2016 at 9:47:36 AM UTC-4, Andreas Krämer wrote:
>
> Hi, 
>
> I have just encountered an issue with projecting points into a cell. 
>
> Say, I have a point x which is very close to a cell (e.g. distance = 
> 10^-16) and I want this point to be inside the cell. My first attempt was 
> to map the point to the unit cell, round the coordinates to 0 or 1, and map 
> it back to the real cell. However, the mapping introduces an additional 
> round-off error and cell->point_inside(x) is still false. (I use 
> MappingQ(1))
>
> As a first workaround, I moved the mapped point into the unit cell by 
> 1e-12.
>
> Is there a better way to do it?
>
> Best,
> Andreas
>
> A code snippet is below  (the last assertion gives false)
>
>
> // eliminate round-off errors
> dealii::Point h = pi_unit + increment;
> for (size_t i = 0; i < dim; i++) {
> if (fabs(h[i]) < 1e-12) {
> h[i] = 0;
> }
> if (fabs(h[i] - 1) < 1e-12) {
> h[i] = 1;
> }
> }
> // assert that point is at boundary
> if (2 == dim) {
> assert(h[0] * h[1] * (1 - h[0]) * (1 - h[1]) == 0);
> } else { // 3 == dim
> assert(h[0] * h[1] * h[2] * (1 - h[0]) * (1 - h[1]) * (1 - h[2]) 
> == 0);
> }
>
> // map to real cell
> p_boundary = m_mapping.transform_unit_to_real_cell(ci, h);
>
> cout << "boundary point: " << p_boundary << endl;
>
> assert(cell->point_inside(p_boundary));
>
>
>

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[deal.II] Re: precompiling independent classes as a library and link it to the main project

[David Wells]

Hi Juan,

I use this approach (shared object library for pieces, executable for the 
solver) approach frequently and it is a bit tricky to set up.

What I usually do is have three different CMakeLists.txt files: one to 
control everything, one for the library, and one for the solver. I 
implemented an example of this in the cdr code gallery entry:

https://github.com/dealii/code-gallery/tree/master/cdr

Let me know if this helps.

Thanks,
David Wells

On Monday, May 30, 2016 at 10:35:14 AM UTC-4, Juan Carlos Araujo Cabarcas 
wrote:
>
> Dear all, 
>
> I have several independent classes that use deal.II objects, and I would 
> like to pre-compile them as shared libraries to be linked to the main 
> executable.
> The idea is to be able to do something similar than what is described here:
> http://www.cprogramming.com/tutorial/shared-libraries-linux-gcc.html
> but as I am not really used to the cmake environment I have not been able 
> to reproduce a similar example with deal.ii.
>
> As a test example I would like to remove the class BoundaryValues from 
> step-4:
> https://dealii.org/8.4.0/doxygen/deal.II/step_4.html
> and save it as a file bval.cc pre-compile it to generate a .so file to be 
> linked in the main executable.
>
> Any ideas how to achieve this?
>
> Thanks in advance,
>
> Juan Carlos Araújo
> PhD student at Umeå Universitet
>
>

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