[deal.II] Re: profiling and parallel performance of deal.II user codes

[simon...@gmail.com]

Hi,

I've used the scalasca tool suite for profiling:

https://www.scalasca.org/scalasca/about/about.html

which use score-p for measuring and the cube gui for visualizing the 
results:

https://www.vi-hps.org/projects/score-p
https://www.scalasca.org/scalasca/software/cube-4.x/download.html

I think it is really good. However, it is somewhat difficult to get started 
with. If you are interested, this user guide is a good place to start:

https://www.scalasca.org/scalasca/software/scalasca-2.x/documentation.html

Best,
Simon

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[deal.II] Re: profiling and parallel performance of deal.II user codes

[blais...@gmail.com]

Dear Richard,
I have used valgrind's callgrind tool extensively in the past and it works 
quite well.
It seems Intel VTune is free now. I have used it a lot in the last two 
months to optimize our code and I have found it work very, very well. We 
managed to improve some functions tremendously because of it.
It is also significantly faster than callgrind, enabling you to profile on 
larger cases.
Best
Bruno


On Tuesday, August 3, 2021 at 9:58:07 a.m. UTC-4 richard@gmail.com 
wrote:

> Dear all,
> I spent quite some time on our in-house CFD and FSI solvers, which are 
> matrix-based and use deal.II, MPI and AMG packages of Trilinos and PETSc, 
> all of which are so wonderfully accessible even for engineers like me. My 
> computations now focused on problems with relatively small DoF count - say, 
> max. 10 mio. - and the number of mpi ranks  was eye-balled, staying below 
> 20. At this stage, I would like to know 
>
> a) which (free) profiling tools can you recommend? I watched the video 
> lecture of Wolfgang about that topic, but was looking for more opinions! I 
> want to see which parts of the code take time apart from the (already 
> detailed) TimerOutput.
>
> b) If I use simply "mpirun -n 4 mycode" on a machine with 8 physical 
> cores, why do both PETSc and Trilinos use 8 cores during the AMG setup and 
> solve? I observed that using the htop command, even when using an 
> off-the-shelf "step-40.release" as included in the library. Does anyone 
> else see that? It looks something like this during the AMG setup and solve 
> for "mpirun -n 8 step-40":
> [image: screenshot_trilinos_step40_mpirun_n_8.png]
> It might be linked to the installation on the server, where I used candi. 
> On my local machine, however, this does not happen. 
>
> Any hints are very much welcome, thanks for reading and any tips!
>
> Best regards & greetings from Graz
> Richard
>
>

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[deal.II] Re: profiling and parallel performance of deal.II user codes

[Bruno Turcksin]

Richard,

On Tuesday, August 3, 2021 at 9:58:07 AM UTC-4 richard@gmail.com wrote:

> a) which (free) profiling tools can you recommend? I watched the video 
> lecture of Wolfgang about that topic, but was looking for more opinions! I 
> want to see which parts of the code take time apart from the (already 
> detailed) TimerOutput.
>
I use two tools: Caliper (https://software.llnl.gov/Caliper/) and 
HPCToolkit (http://hpctoolkit.org/). These tools have different goals. 
Caliper is basically a much more powerful version of TimerOutput. You add 
Caliper to your code and you have access to different profiling measures 
and connectors to other profiling tools. The advantage of Caliper is that 
you can use it in your code and then monitor the performance over time. It 
is very easy to use and the Caliper annotation in your code can be used by 
VTune and NVidia NSight.  HPCToolkit on the other hand is a more 
traditional profiling tool. You use it to find the bottlenecks in your 
code. I really like that it is non-invasive. Unlike Caliper, you don't need 
to change anything in your code. I've used it to profile code on small 
cluster but it also works on some of the largest supercomputers at the DOE.

Best,

Bruno
 

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Re: [deal.II] Deal.II programming environment

[Wells, David]

Hi Martin,

Sorry for the slow response - I have been on vacation.

If you save a source file with a new name then you will need to update your 
CMakeLists.txt file - it doesn't know what you intend to do with the new file. 
I recommend reading through

https://www.dealii.org/developer/users/cmake_user.html

to better understand how to set up your own project with CMake.

If you have the virtual machine then it is easiest to just install either 
eclipse or QT creator inside the VM itself with the "apt-get install" command.

Best,
David Wells

From: dealii@googlegroups.com  on behalf of Jiang Hu 

Sent: Wednesday, July 21, 2021 9:59 PM
To: deal.II User Group 
Subject: Re: [deal.II] Deal.II programming environment

Hi David,

Thanks for the detailed explanation.

I suppose below procedure should work:
1 Open Deal.II example, the cpp file,  with text editor
2 make changes to it, and save it as another cpp file
3 Use cMake to run this new cpp file at the command line
4 if no mistake, the new cpp file will run

am I correct?

Last, where should I install the IDE? I am using virtual box machine with 
deal.II package in a window system.
can I install Eclipse in Virtual box machine? it has Ubuntu system in the 
virtual box.

Thanks for your time

Martin

On Thursday, 22 July 2021 at 1:15:10 am UTC+10 Wells, David wrote:
Hi Martin,

No, that's a very good question - it's important to set up a good development 
environment. You CAN use plain text editors and run CMake from the command line 
(in fact, with many tools you will end up still running CMake from a window 
inside them) but its usually better to use something more sophisticated (like 
an IDE that can run a debugger).

If you look on the wiki we have instructions for both Eclipse and QT creator:

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

a lot of people use VS code - we don't have instructions for it, and I don't 
use it, but since we use CMake it shouldn't be that hard to point VS code at 
your build directory and have it extract some information. If anyone actually 
uses VS code I would appreciate if they could weigh in here!

Best,
David Wells

From: dea...@googlegroups.com  on behalf of Jiang Hu 

Sent: Wednesday, July 21, 2021 1:22 AM
To: deal.II User Group 
Subject: [deal.II] Deal.II programming environment

Hello everyone,

Quite excited to find Deal.II and its potential.

I installed virtual machine with Deal.II, and run step 7 on terminal without 
any problem.

The question is if I want to compile bigger program with Deal.II , what is the 
typical working environment?

I assume we can not with terminal for such a purpose. I saw people using Nano 
to run Deal.II, but want to ask the standard tool for such process.

Emacs or Vscode?  Do I need to connect them to Deal.II?

I am very new, and this could be a quite silly question.

Thanks

Martin

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Re: [deal.II] Finite Element Software deal.II Version 9.3.0 released

[Wolfgang Bangerth]

All,
this is also the time to point out, as we do for every release, how many many 
people have contributed to this release! The release paper at

  https://www.dealii.org/deal93-preprint.pdf
has 17 authors, all of whom have contributed in many different and significant 
ways to this release. Beyond this, many people have contributed smaller 
patches that we really value -- the release paper lists the following 49 people:

  Pasquale Africa,
  Tyler Anderson,
  Mathias Anselmann,
  Arpit Babbar,
  Nicolas Barnafi,
  Maximilian Bergbauer,
  Michele Bucelli,
  Marcus Calhoun-Lopez,
  David F. Castellanos,
  Fabian Castelli,
  Praveen Chandrashekar,
  Conrad Clevenger,
  Andrew Davis,
  Elias Dejene,
  Niklas Fehn,
  Menno Fraters,
  Ivan Fumagalli,
  Daniel Garcia-Sanchez,
  Nicola Giuliani,
  Krishnakumar Gopalakrishnan,
  Alexander Grayver,
  Olivier Guevremont,
  Jake Harmon,
  Graham Harper,
  Katharina Kormann,
  Christoph Kammer,
  Wenyu Lei,
  Zhou Lei,
  Phillip Mobley,
  Nils Much,
  Pratik Nayak,
  Toni El Geitani Nehme,
  Justin O'Connor,
  Daniel Paukner,
  Lei Qiao,
  Ce Qin,
  Reza Rastak,
  Julian Roth,
  Laura Prieto Saavedra,
  Doug Shi-Dong,
  David Schneider,
  Magdalena Schreter,
  Richard Schussnig,
  Dominic Soldner,
  Simon Sticko,
  Malhar Tidke,
  Ignacio Tomas,
  Benjamin Uekermann,
  Peter Westerbaan.

Thank you to everyone who contributes to this project!

Best
 Wolfgang

--

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

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[deal.II] deal.II Newsletter #176

['Rene Gassmoeller' via deal.II User Group]

Hello everyone!

This is deal.II newsletter #176.
It automatically reports recently merged features and discussions about the 
deal.II finite element library.


## Below you find a list of recently proposed or merged features:

#12620: Add FiniteElement::supports_mass_lumping(). (proposed by drwells) 
https://github.com/dealii/dealii/pull/12620

#12619: Fix a parenthesis. (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/12619

#12618: Extend documentation of TriangulationDescription (proposed by peterrum) 
https://github.com/dealii/dealii/pull/12618

#12617: [WIP] Hanging node constraint masks comp (proposed by peterrum) 
https://github.com/dealii/dealii/pull/12617

#12616: Switch from unsigned int to ConstraintTypes (proposed by peterrum) 
https://github.com/dealii/dealii/pull/12616

#12615: Extend test (proposed by peterrum) 
https://github.com/dealii/dealii/pull/12615

#12614: Standardized output for many `mpi/hp_unify_dof_indices_X` tests. 
(proposed by marcfehling) https://github.com/dealii/dealii/pull/12614

#12613: Fix two comments in TriaAccessor. (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/12613

#12612: Make MassOperator's diagonals true diagonals, not lumped ones. 
(proposed by drwells) https://github.com/dealii/dealii/pull/12612

#12611: Convert some (mislabeled) boundary ids to manifold ids. (proposed by 
drwells; merged) https://github.com/dealii/dealii/pull/12611

#12610: Add more Witherden-Vincent rules (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/12610

#12609: Fix AlignedVector memory management after 
replicate_across_communicator() (proposed by bangerth) 
https://github.com/dealii/dealii/pull/12609

#12607: Fix a few type mistakes in AlignedVector. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/12607

#12605: doc: fix typo in rtree.h (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/12605

#12603: FEInterfaceValues for AD (proposed by zjiaqi2018) 
https://github.com/dealii/dealii/pull/12603

#12602: Fix tolerances in 
GridTools::internal::distributed_compute_point_locations() (proposed by 
peterrum; merged) https://github.com/dealii/dealii/pull/12602

#12601: Deprecated autopartition parameter in 
parallel::DistributedTriangulationBase::load() (proposed by marcfehling) 
https://github.com/dealii/dealii/pull/12601

#12600: Fix Convert for map (proposed by peterrum; merged) 
https://github.com/dealii/dealii/pull/12600

#12599: Let find_active_cell_around_point() return mesh.end() if point is not 
found in BBs (proposed by peterrum; merged) 
https://github.com/dealii/dealii/pull/12599

#12598: Fix documentation of VT::project() (proposed by peterrum; merged) 
https://github.com/dealii/dealii/pull/12598

#12597: Un-deprecate DoFHandler::set_fe. (proposed by marcfehling) 
https://github.com/dealii/dealii/pull/12597

#12596: Load: align dealii and p4est meshes before repartitioning. (proposed by 
marcfehling) https://github.com/dealii/dealii/pull/12596

#12595: Update documentation in a couple of places. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/12595

#12593: Evaluate and integrate hessians (proposed by bergbauer) 
https://github.com/dealii/dealii/pull/12593

#12592: Reduce tolerance in test (proposed by peterrum; merged) 
https://github.com/dealii/dealii/pull/12592

#12591: Intel 18 does not like assertions in nested lambdas. (proposed by 
marcfehling; merged) https://github.com/dealii/dealii/pull/12591

#12590: Fix unused-but-set-variable warnings (proposed by Rombur; merged) 
https://github.com/dealii/dealii/pull/12590

#12589: Add a missing include file. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/12589

#12588: Add clear() to the Table class (proposed by zjiaqi2018; merged) 
https://github.com/dealii/dealii/pull/12588

#12587: Be more explicit about types and taking addresses. (proposed by 
bangerth) https://github.com/dealii/dealii/pull/12587

#12578: Rename MappingQGeneric to MappingQ in python interface (proposed by 
agrayver; merged) https://github.com/dealii/dealii/pull/12578

#12560: Optimize hanging-node constraints in MatrixFree (proposed by peterrum; 
merged) https://github.com/dealii/dealii/pull/12560

#12559: Step-69: Use SolutionTransfer instead of low-level boost archive 
(proposed by tamiko; merged) https://github.com/dealii/dealii/pull/12559

#12556: Allow passing physical units into a VTU file. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/12556

#12554: Add Intel oneAPI to github-actions. (proposed by marcfehling; merged) 
https://github.com/dealii/dealii/pull/12554

#11108: Indentation clang-format 11 (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/11108


## And this is a list of recently opened or closed discussions:

#12608: Lower memory requirements in AlignedVector (opened) 
https://github.com/dealii/dealii/issues/12608

#12606: Replicated AlignedVector 

Re: [deal.II] profiling and parallel performance of deal.II user codes

[Wolfgang Bangerth]

Richard,

a) which (free) profiling tools can you recommend? I watched the video lecture 
of Wolfgang about that topic, but was looking for more opinions! I want to see 
which parts of the code take time apart from the (already detailed) TimerOutput.


Use valgrind's callgrind tool. The introduction to step-22 shows an example of 
how this looks in practice.


valgrind is single-threaded, but you can call it for every process via
  mpirun -n 8 valgrind --tool callgrind ./step-40
for example, and it will simply profile all 8 instances.

There is also Intel's VTune tool, which is useful to profile communication 
issues, but I have not used it in many years and cannot say much about it.



b) If I use simply "mpirun -n 4 mycode" on a machine with 8 physical cores, 
why do both PETSc and Trilinos use 8 cores during the AMG setup and solve? I 
observed that using the htop command, even when using an off-the-shelf 
"step-40.release" as included in the library. Does anyone else see that? It 
looks something like this during the AMG setup and solve for "mpirun -n 8 
step-40":

screenshot_trilinos_step40_mpirun_n_8.png
It might be linked to the installation on the server, where I used candi. On 
my local machine, however, this does not happen.


It may be that the AMG is using OpenMP under the hood. You will want to set 
the number of threads available to OpenMP to one. There is an environment 
variable for that that you need to set either in your .bashrc or, if you just 
want to do it once, on the command line before running the program.


Best
 W.


--

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   www: http://www.math.colostate.edu/~bangerth/

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[deal.II] Finite Element Software deal.II Version 9.3.0 released

[Matthias Maier]

Version 9.3.0 of deal.II, the object-oriented finite element library awarded the
J. H. Wilkinson Prize for Numerical Software, has been released. It is
available for free under an Open Source license from the deal.II homepage at

   https://www.dealii.org/

The major changes of this release are:

  - Ten new tutorial programs: step-19 introduces particle methods,
and step-68 uses these for tracking locations in a flow
field. step-66 is a matrix-free geometric multigrid solver for a
nonlinear problem. step-71 and step-72 illustrate automatic and
symbolic differentiation. step-77 demonstrates deal.II's SUNDIALS
interfaces to solve a nonlinear problem. step-74 shows the SIPG
approach to discontinuous Galerkin methods. step-76 is an explicit
integrator for the Euler equations. step-78 solves the
Black-Scholes equations, and step-79 solves a topology
optimization problem.

  - Experimental support for simplex and mixed meshes.

  - Improved flexibility of the particle infrastructure.

  - Support for global-coarsening multigrid algorithms.

  - Advances in the matrix-free infrastructure.

  - Usage of MPI-3.0 shared-memory features to reduce memory footprint.

  - Improved support for evaluation and integration at arbitrary points.

  - More than 210 other new features, improvements, and bugfixes.

For more information see:
  - The preprint at https://www.dealii.org/deal93-preprint.pdf
  - The list of changes at

https://www.dealii.org/developer/doxygen/deal.II/changes_between_9_2_0_and_9_3_0.html

The main features of deal.II are:
  - Extensive documentation and 76 fully-functional example programs
  - Support for dimension-independent programming
  - Locally refined adaptive meshes
  - Multigrid support
  - A zoo of different finite elements
  - Fast linear algebra
  - Built-in support for shared memory and distributed parallel computing,
scaling from laptops to clusters with 100,000+ processor cores
  - Interfaces to Trilinos, PETSc, METIS, UMFPACK and other external software
  - Output for a wide variety of visualization platforms.

Matthias Maier and Peter Munch,
on behalf of the deal.II developer team and many contributors.

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Re: [deal.II] Use a coarse grid solution as initial condition for a finer grid

[Wolfgang Bangerth]

On 8/3/21 8:38 AM, vachan potluri wrote:


I also have a simple related question. Can I skip all these steps if the 
triangulation, FE and number of processors of the solution being transferred 
are kept constant? This is one special case which is like restarting a 
completed simulation. In this case (triangulation, FE, and processors kept 
constant), is the partition and dof numbering always going out to be the same? 
I am not doing any mesh refinement (either in dealii or outside).


If yes, then I suppose loading the solution transfer and deserializing it will 
do the job without having to worry about "evaluating" the solution?


Yes, you can reload solutions onto the same Triangulation and DoFHandler. In 
fact, the reload machinery even works if the number of processes is different.


Best
 W.

--

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

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Re: [deal.II] Deal.II programming environment

[Ahmad Shahba]

I just wanted to add that I use CLion for C++ programming. I have been
developing codes (and linking to deal.ii among other libraries) in CLion
for 3 years now. Given that the entry point in CLion is a CMakeList file,
it was quite easy for me to load deal.ii examples and
compile/run/debug/profile them in the IDE

Regards,
Ahmad

On Tue, Aug 3, 2021 at 9:53 AM Raghunandan Pratoori  wrote:

>
> Hi,
>
> I recently started using VS code with deal.ii. I found it very easy to
> work with, especially when you have a wsl installation.
> All you need to do is follow the instructions on these pages -
> https://code.visualstudio.com/docs/cpp/config-wsl
> https://code.visualstudio.com/docs/cpp/cmake-linux
>
> VS code actually looks through the files in your directory and suggests
> extensions you would need.
>
> Best,
> Raghunandan.
> On Wednesday, July 21, 2021 at 10:15:10 AM UTC-5 Wells, David wrote:
>
>> Hi Martin,
>>
>> No, that's a very good question - it's important to set up a good
>> development environment. You CAN use plain text editors and run CMake from
>> the command line (in fact, with many tools you will end up still running
>> CMake from a window inside them) but its usually better to use something
>> more sophisticated (like an IDE that can run a debugger).
>>
>> If you look on the wiki we have instructions for both Eclipse and QT
>> creator:
>>
>> https://github.com/dealii/dealii/wiki
>>
>> a lot of people use VS code - we don't have instructions for it, and I
>> don't use it, but since we use CMake it shouldn't be that hard to point VS
>> code at your build directory and have it extract some information. If
>> anyone actually uses VS code I would appreciate if they could weigh in here!
>>
>> Best,
>> David Wells
>> --
>> *From:* dea...@googlegroups.com  on behalf of
>> Jiang Hu 
>> *Sent:* Wednesday, July 21, 2021 1:22 AM
>> *To:* deal.II User Group 
>> *Subject:* [deal.II] Deal.II programming environment
>>
>> Hello everyone,
>>
>> Quite excited to find Deal.II and its potential.
>>
>> I installed virtual machine with Deal.II, and run step 7 on terminal
>> without any problem.
>>
>> The question is if I want to compile bigger program with Deal.II , what
>> is the typical working environment?
>>
>> I assume we can not with terminal for such a purpose. I saw people using
>> Nano to run Deal.II, but want to ask the standard tool for such process.
>>
>> Emacs or Vscode?  Do I need to connect them to Deal.II?
>>
>> I am very new, and this could be a quite silly question.
>>
>> Thanks
>>
>> Martin
>>
>> --
>> 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.
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>> email to dealii+un...@googlegroups.com.
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>> https://groups.google.com/d/msgid/dealii/164003ac-27fe-4b26-83d4-991149902416n%40googlegroups.com
>> 
>> .
>>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see
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> 
> .
>

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Re: [deal.II] Use a coarse grid solution as initial condition for a finer grid

[vachan potluri]

Peter,

Thanks very much for taking time and providing the resources. I will go
through them and get back if I have any more questions.

I also have a simple related question. Can I skip all these steps if the
triangulation, FE and number of processors of the solution being
transferred are kept constant? This is one special case which is like
restarting a completed simulation. In this case (triangulation, FE, and
processors kept constant), is the partition and dof numbering always going
out to be the same? I am not doing any mesh refinement (either in dealii or
outside).

If yes, then I suppose loading the solution transfer and deserializing it
will do the job without having to worry about "evaluating" the solution?

On Tue, 3 Aug 2021 at 14:09, 'peterrum' via deal.II User Group <
dealii@googlegroups.com> wrote:

> Hi Vachan,
>
> I don't think you need to use RPE plane. My guess is that you can use
> VectorTools::point_values(), which internally uses PRE (see
> https://github.com/dealii/dealii/blob/e413cbf8ac77606cf4a04e1e2fa75232c08533b4/include/deal.II/numerics/vector_tools_evaluate.h#L230-L343).
> Here you could collect the support points from the new DoFHandler, let
> VT::point_values() do the work and finally set the values at the support
> points.
>
> Further resources are:
> - the test folder
> https://github.com/dealii/dealii/tree/master/tests/remote_point_evaluation
> (in particular
> https://github.com/dealii/dealii/blob/master/tests/remote_point_evaluation/vector_tools_evaluate_at_points_01.cc;
> here, the solution is interpolated between non-matching grids)
> - the usage of RPE and VT::point_values() in DataOutResample (
> https://github.com/dealii/dealii/blob/master/source/numerics/data_out_resample.cc
> )
> - the usage in the two-phase solver adaflo (
> https://github.com/kronbichler/adaflo/blob/master/include/adaflo/sharp_interface_util.h
> )
>
> PM
>
> On Tuesday, 3 August 2021 at 09:03:02 UTC+2 vachanpo...@gmail.com wrote:
>
>> Dr. Wolfgang,
>>
>> Thank you for still taking interest in this thread :)
>>
>> This becomes a very difficult data transfer problem because you want to
>>> evaluate the solution at a point that the current process may know
>>> nothing
>>> about. In essence, you will have to ask all of the other processes about
>>> who
>>> owns a part of the mesh on which a given interpolation point is located,
>>> and
>>> then that process has to send you the value of the function at that
>>> point. You
>>> have to do that for all points. This is going to be an expensive
>>> operation.
>>> You might want to check out the Utilities::MPI::RemotePointEvaluation
>>> class in
>>> the latest (9.3) release for help with this.
>>
>> I understand that the approach I had mentioned is inefficient. I only
>> need to do this once, to start a simulation, so I thought it might be okay.
>>
>> I had a look at Utilities::MPI::RemotePointEvaluation. This is how I
>> think it can be used (correct me if wrong)
>>
>>1. Call reinit() with the dof locations, along with the corresponding
>>triangulation and mapping, where I want to evaluate FEFieldFunction (I
>>suppose the triangulation and mapping here are not of the 
>> FEFieldFunction?).
>>2. Call evaluate_and_process() by passing in the FEFieldFunction.
>>
>> I have a few questions.
>>
>>1. What is the "buffer" argument in evaluate_and_process()?
>>2. The documentation for this function says get_point_ptrs() must be
>>used to "process" the output in case the point-cell map is not one-one. I
>>will surely encounter such cases. How can I use the data returned by
>>get_point_ptrs() and how exactly should I "process" the output?
>>
>> I couldn't find this used in any examples. Any clarifications would be
>> greatly helpful.
>>
>> On Tue, 3 Aug 2021 at 04:47, Wolfgang Bangerth 
>> wrote:
>>
>>> On 7/5/21 11:04 PM, vachan potluri wrote:
>>> >
>>> > So is your fine mesh a refinement of the coarse one? If not, you
>>> may want to
>>> > look at FEFieldFunction.
>>> >
>>> > Yes, it is. But the "refinement" is done by the meshing
>>> software, outside
>>> > dealii. Is there any simplification possible in such a case?
>>>
>>> Not really. If deal.II has no knowledge about the relationship between
>>> cells
>>> on the two meshes, then it is in essence the interpolation from one
>>> unstructured grid to another unstructured grid.
>>>
>>>
>>> > Otherwise, I think FEFieldFunction would be a safe choice. Since I
>>> want to use
>>> > it with p::d::Triangulation, will setting all dofs as relevant do the
>>> job?
>>> > This way the partitioning can also be different.
>>>
>>> This becomes a very difficult data transfer problem because you want to
>>> evaluate the solution at a point that the current process may know
>>> nothing
>>> about. In essence, you will have to ask all of the other processes about
>>> who
>>> owns a part of the mesh on which a given interpolation point is located,
>>> and
>>> then that process has to send 

[deal.II] profiling and parallel performance of deal.II user codes

[richard....@gmail.com]

Dear all,
I spent quite some time on our in-house CFD and FSI solvers, which are 
matrix-based and use deal.II, MPI and AMG packages of Trilinos and PETSc, 
all of which are so wonderfully accessible even for engineers like me. My 
computations now focused on problems with relatively small DoF count - say, 
max. 10 mio. - and the number of mpi ranks  was eye-balled, staying below 
20. At this stage, I would like to know 

a) which (free) profiling tools can you recommend? I watched the video 
lecture of Wolfgang about that topic, but was looking for more opinions! I 
want to see which parts of the code take time apart from the (already 
detailed) TimerOutput.

b) If I use simply "mpirun -n 4 mycode" on a machine with 8 physical cores, 
why do both PETSc and Trilinos use 8 cores during the AMG setup and solve? 
I observed that using the htop command, even when using an off-the-shelf 
"step-40.release" as included in the library. Does anyone else see that? It 
looks something like this during the AMG setup and solve for "mpirun -n 8 
step-40":
[image: screenshot_trilinos_step40_mpirun_n_8.png]
It might be linked to the installation on the server, where I used candi. 
On my local machine, however, this does not happen. 

Any hints are very much welcome, thanks for reading and any tips!

Best regards & greetings from Graz
Richard

-- 
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Re: [deal.II] Deal.II programming environment

[Raghunandan Pratoori]

Hi,

I recently started using VS code with deal.ii. I found it very easy to work 
with, especially when you have a wsl installation.
All you need to do is follow the instructions on these pages -
https://code.visualstudio.com/docs/cpp/config-wsl
https://code.visualstudio.com/docs/cpp/cmake-linux

VS code actually looks through the files in your directory and suggests 
extensions you would need.

Best,
Raghunandan.
On Wednesday, July 21, 2021 at 10:15:10 AM UTC-5 Wells, David wrote:

> Hi Martin,
>
> No, that's a very good question - it's important to set up a good 
> development environment. You CAN use plain text editors and run CMake from 
> the command line (in fact, with many tools you will end up still running 
> CMake from a window inside them) but its usually better to use something 
> more sophisticated (like an IDE that can run a debugger).
>
> If you look on the wiki we have instructions for both Eclipse and QT 
> creator:
>
> https://github.com/dealii/dealii/wiki
>
> a lot of people use VS code - we don't have instructions for it, and I 
> don't use it, but since we use CMake it shouldn't be that hard to point VS 
> code at your build directory and have it extract some information. If 
> anyone actually uses VS code I would appreciate if they could weigh in here!
>
> Best,
> David Wells
> --
> *From:* dea...@googlegroups.com  on behalf of 
> Jiang Hu 
> *Sent:* Wednesday, July 21, 2021 1:22 AM
> *To:* deal.II User Group 
> *Subject:* [deal.II] Deal.II programming environment 
>  
> Hello everyone, 
>
> Quite excited to find Deal.II and its potential.
>
> I installed virtual machine with Deal.II, and run step 7 on terminal 
> without any problem.
>
> The question is if I want to compile bigger program with Deal.II , what is 
> the typical working environment? 
>
> I assume we can not with terminal for such a purpose. I saw people using 
> Nano to run Deal.II, but want to ask the standard tool for such process.
>
> Emacs or Vscode?  Do I need to connect them to Deal.II?
>
> I am very new, and this could be a quite silly question.
>
> Thanks 
>
> Martin
>
> -- 
> 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.
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/dealii/164003ac-27fe-4b26-83d4-991149902416n%40googlegroups.com
>  
> 
> .
>

-- 
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For mailing list/forum options, see 
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Re: [deal.II] errors in running step-18 within Xcode

[Alberto Salvadori]

Hi Luca,
thanks for clarifying. Still not succeeded, see below.

1. opened a Rosetta terminal
2. source /Applications/deal.II.app/Contents/MacOS/dealii.conf

  __   _  _ _

|  _  \ | ||_   _|_   _|

| | | |___  __ _| |  | |   | |

| | | / _ \/ _| | |  | |   | |

| |/ /  __/ (_| | |__| |_ _| |_

|___/ \___|\__,_|_(_)___/ \___/


This is a bash shell with CMAKE_PREFIX_PATH and DYLD_LIBRARY_PATH set to
work

with Deal.II. A full spack installation with deal.II is available under


/Applications/deal.II.app/Contents/Resources/spack


If you want to set up your daily Terminal to work with deal.II, add these
lines

to your ~/.profile (or ~/.zshrc, if you prefer zsh):


   export DEAL_II_CONF_SILENT=ON# Turn off this message

   . /Applications/deal.II.app/Contents/MacOS/dealii.conf


deal.II and all its dependencies were installed using spack, and are also

available through spack, e.g.:


spack find # Shows all installed packages


You can find the deal.II examples directory under



  /Applications/deal.II.app/Contents/Resources/Libraries/share/deal.II/examples




3. cmake -G 'Unix Makefiles'
4. make release
5. make

[ 50%] Building CXX object CMakeFiles/step-18.dir/step-18.cc.o

[100%] *Linking CXX executable step-18*

[100%] Built target step-18

albertosalvadori@uu-guest-150-117 step-18 unix % ./step-18

zsh: illegal hardware instruction  ./step-18

albertosalvadori@uu-guest-150-117 step-18 unix % which cmake

/Applications/deal.II.app/Contents/Resources/Libraries/bin/cmake

albertosalvadori@uu-guest-150-117 step-18 unix %




*Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale
(DIMI)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3715426

e-mail:
 alberto.salvad...@unibs.it
web-page:
 http://m4lab.unibs.it/faculty.html



On Tue, Aug 3, 2021 at 1:34 PM Luca Heltai  wrote:

> Actually, not exactly. The instructions are i the screen shot.
>
> Open a Rosetta terminal, and then source the conf file, i.e.
>
> ./Appl/dealii.conf
>
> The command you called opens a normal terminal, and then sources the conf
> file.
>
> Luca
>
> Il giorno 3 ago 2021, alle ore 13:28, Alberto Salvadori <
> alberto.salvad...@unibs.it> ha scritto:
>
> 
> Luca,
> this is what I have done, if I got what you meant:
>
> 1. opened a Rosetta terminal
> 2. /Applications/deal.II.app/Contents/MacOS/dealii-terminal
>
>   __   _  _ _
>
> |  _  \ | ||_   _|_   _|
>
> | | | |___  __ _| |  | |   | |
>
> | | | / _ \/ _| | |  | |   | |
>
> | |/ /  __/ (_| | |__| |_ _| |_
>
> |___/ \___|\__,_|_(_)___/ \___/
>
>
> This is a bash shell with CMAKE_PREFIX_PATH and DYLD_LIBRARY_PATH set to
> work
>
> with Deal.II. A full spack installation with deal.II is available under
>
>
> /Applications/deal.II.app/Contents/Resources/spack
>
>
> If you want to set up your daily Terminal to work with deal.II, add these
> lines
>
> to your ~/.profile (or ~/.zshrc, if you prefer zsh):
>
>
>export DEAL_II_CONF_SILENT=ON# Turn off this message
>
>. /Applications/deal.II.app/Contents/MacOS/dealii.conf
>
>
> deal.II and all its dependencies were installed using spack, and are also
>
> available through spack, e.g.:
>
>
> spack find # Shows all installed packages
>
>
> You can find the deal.II examples directory under
>
>
>
> /Applications/deal.II.app/Contents/Resources/Libraries/share/deal.II/examples
>
>
>
>
> 3. cmake -G 'Unix Makefiles'
> 4. make release
> 5. make
> 6.  ./step-18
>
> Illegal instruction: 4
>
>
>
>
>
>
> *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale
> (DIMI)
>  Universita` di Brescia, via Branze 43, 25123 Brescia
>  Italy
>  tel 030 3715426
>
> e-mail:
>  alberto.salvad...@unibs.it
> web-page:
>  http://m4lab.unibs.it/faculty.html
>
>
>
> On Tue, Aug 3, 2021 at 1:10 PM Luca Heltai  wrote:
>
>> Can you open a Rosetta terminal and follow the instructions to parse
>> deal.ii init files? I think it is just the fact that you are not running
>> under Rosetta, but cannot confirm...
>>
>> Luca
>>
>> Il giorno 3 ago 2021, alle ore 11:28, Alberto Salvadori <
>> alberto.salvad...@unibs.it> ha scritto:
>>
>> Dear community
>>
>> I successfully installed 9.3 on my mac M1 from the dmg . However, I am at
>> present unable to run examples, as for the step-18. For this reason, I
>> share my attempts.
>> I am using Xcode 12.5.1 (12E507) on BigSur 11.2.3 (20D91).
>>
>> After opening a deal.ii terminal from deal.ii.app, the step-18 code
>> compiles well both inside Xcode and from Makefile. When it comes to run the
>> executable, neither of the two apparently work. The output message from
>> terminal is
>>
>> bash-3.2$ ./step-18
>>
>> Illegal instruction: 4
>>
>> whereas the debugger provides some further notifications, as in figure,
>> which I am not able to discern.
>>
>> 
>>
>>
>> I had at my disposal a former installation of 

Re: [deal.II] errors in running step-18 within Xcode

[Luca Heltai]

Actually, not exactly. The instructions are i the screen shot. 

Open a Rosetta terminal, and then source the conf file, i.e.

./Appl/dealii.conf

The command you called opens a normal terminal, and then sources the conf file. 

Luca

> Il giorno 3 ago 2021, alle ore 13:28, Alberto Salvadori 
>  ha scritto:
> 
> 
> Luca,
> this is what I have done, if I got what you meant:
> 
> 1. opened a Rosetta terminal
> 2. /Applications/deal.II.app/Contents/MacOS/dealii-terminal
> 
>   __   _  _ _
> |  _  \ | ||_   _|_   _|
> | | | |___  __ _| |  | |   | |
> | | | / _ \/ _| | |  | |   | |
> | |/ /  __/ (_| | |__| |_ _| |_
> |___/ \___|\__,_|_(_)___/ \___/
> 
> This is a bash shell with CMAKE_PREFIX_PATH and DYLD_LIBRARY_PATH set to work
> with Deal.II. A full spack installation with deal.II is available under 
> 
> /Applications/deal.II.app/Contents/Resources/spack
> 
> If you want to set up your daily Terminal to work with deal.II, add these 
> lines
> to your ~/.profile (or ~/.zshrc, if you prefer zsh):
> 
>export DEAL_II_CONF_SILENT=ON# Turn off this message
>. /Applications/deal.II.app/Contents/MacOS/dealii.conf
> 
> deal.II and all its dependencies were installed using spack, and are also
> available through spack, e.g.:
> 
> spack find # Shows all installed packages
> 
> You can find the deal.II examples directory under 
> 
> 
> /Applications/deal.II.app/Contents/Resources/Libraries/share/deal.II/examples
> 
> 
> 
> 3. cmake -G 'Unix Makefiles'
> 4. make release
> 5. make
> 6.  ./step-18 
> Illegal instruction: 4
> 
> 
> 
> 
> 
> Alberto Salvadori
>  Dipartimento di Ingegneria Meccanica e Industriale (DIMI)
>  Universita` di Brescia, via Branze 43, 25123 Brescia
>  Italy
>  tel 030 3715426
> 
> e-mail: 
>  alberto.salvad...@unibs.it
> web-page:
>  http://m4lab.unibs.it/faculty.html
> 
> 
> 
>> On Tue, Aug 3, 2021 at 1:10 PM Luca Heltai  wrote:
>> Can you open a Rosetta terminal and follow the instructions to parse deal.ii 
>> init files? I think it is just the fact that you are not running under 
>> Rosetta, but cannot confirm...
>> 
>> Luca
>> 
 Il giorno 3 ago 2021, alle ore 11:28, Alberto Salvadori 
  ha scritto:
 
>>> Dear community
>>> 
>>> I successfully installed 9.3 on my mac M1 from the dmg . However, I am at 
>>> present unable to run examples, as for the step-18. For this reason, I 
>>> share my attempts. 
>>> I am using Xcode 12.5.1 (12E507) on BigSur 11.2.3 (20D91).
>>> 
>>> After opening a deal.ii terminal from deal.ii.app, the step-18 code 
>>> compiles well both inside Xcode and from Makefile. When it comes to run the 
>>> executable, neither of the two apparently work. The output message from 
>>> terminal is
>>> 
>>> bash-3.2$ ./step-18 
>>> 
>>> Illegal instruction: 4
>>> 
>>> whereas the debugger provides some further notifications, as in figure, 
>>> which I am not able to discern. 
>>> 
>>> 
>>> 
>>> 
>>> I had at my disposal a former installation of deal.ii.9.2, that I made with 
>>> spack and gcc in a rosetta terminal. In such a case, within a rosetta 
>>> terminal, the step-18 compiles and runs well. Note that deal.ii9.3 does not 
>>> open a rosetta terminal.
>>> 
>>> Hope these evidences can be of help.
>>> 
>>> Best and thanks, as always!
>>> 
>>> Alberto
>>> 
>>> 
>>> 
>>> Informativa sulla Privacy: http://www.unibs.it/node/8155
>>> -- 
>>> The deal.II project is located at http://www.dealii.org/
>>> For mailing list/forum options, see 
>>> https://groups.google.com/d/forum/dealii?hl=en
>>> --- 
>>> You received this message because you are subscribed to the Google Groups 
>>> "deal.II User Group" group.
>>> To unsubscribe from this group and stop receiving emails from it, send an 
>>> email to dealii+unsubscr...@googlegroups.com.
>>> To view this discussion on the web visit 
>>> https://groups.google.com/d/msgid/dealii/9014a8cd-0df9-499d-8aa0-d1b0a3427cfcn%40googlegroups.com.
>>> 
>> 
>> -- 
>> The deal.II project is located at http://www.dealii.org/
>> For mailing list/forum options, see 
>> https://groups.google.com/d/forum/dealii?hl=en
>> --- 
>> You received this message because you are subscribed to the Google Groups 
>> "deal.II User Group" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to dealii+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/dealii/F3E122B8-F84B-406D-BC55-37144F3E6607%40gmail.com.
> 
> 
> Informativa sulla Privacy: http://www.unibs.it/node/8155
> -- 
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see 
> https://groups.google.com/d/forum/dealii?hl=en
> --- 
> You received this message because you are subscribed to the Google Groups 
> "deal.II User Group" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to dealii+unsubscr...@googlegroups.com.
> To 

Re: [deal.II] errors in running step-18 within Xcode

[Alberto Salvadori]

Luca,
this is what I have done, if I got what you meant:

1. opened a Rosetta terminal
2. /Applications/deal.II.app/Contents/MacOS/dealii-terminal

  __   _  _ _

|  _  \ | ||_   _|_   _|

| | | |___  __ _| |  | |   | |

| | | / _ \/ _| | |  | |   | |

| |/ /  __/ (_| | |__| |_ _| |_

|___/ \___|\__,_|_(_)___/ \___/


This is a bash shell with CMAKE_PREFIX_PATH and DYLD_LIBRARY_PATH set to
work

with Deal.II. A full spack installation with deal.II is available under


/Applications/deal.II.app/Contents/Resources/spack


If you want to set up your daily Terminal to work with deal.II, add these
lines

to your ~/.profile (or ~/.zshrc, if you prefer zsh):


   export DEAL_II_CONF_SILENT=ON# Turn off this message

   . /Applications/deal.II.app/Contents/MacOS/dealii.conf


deal.II and all its dependencies were installed using spack, and are also

available through spack, e.g.:


spack find # Shows all installed packages


You can find the deal.II examples directory under



/Applications/deal.II.app/Contents/Resources/Libraries/share/deal.II/examples




3. cmake -G 'Unix Makefiles'
4. make release
5. make
6.  ./step-18

Illegal instruction: 4






*Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale
(DIMI)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3715426

e-mail:
 alberto.salvad...@unibs.it
web-page:
 http://m4lab.unibs.it/faculty.html



On Tue, Aug 3, 2021 at 1:10 PM Luca Heltai  wrote:

> Can you open a Rosetta terminal and follow the instructions to parse
> deal.ii init files? I think it is just the fact that you are not running
> under Rosetta, but cannot confirm...
>
> Luca
>
> Il giorno 3 ago 2021, alle ore 11:28, Alberto Salvadori <
> alberto.salvad...@unibs.it> ha scritto:
>
> Dear community
>
> I successfully installed 9.3 on my mac M1 from the dmg . However, I am at
> present unable to run examples, as for the step-18. For this reason, I
> share my attempts.
> I am using Xcode 12.5.1 (12E507) on BigSur 11.2.3 (20D91).
>
> After opening a deal.ii terminal from deal.ii.app, the step-18 code
> compiles well both inside Xcode and from Makefile. When it comes to run the
> executable, neither of the two apparently work. The output message from
> terminal is
>
> bash-3.2$ ./step-18
>
> Illegal instruction: 4
>
> whereas the debugger provides some further notifications, as in figure,
> which I am not able to discern.
>
> 
>
>
> I had at my disposal a former installation of deal.ii.9.2, that I made
> with spack and gcc in a rosetta terminal. In such a case, within a rosetta
> terminal, the step-18 compiles and runs well. Note that deal.ii9.3 does not
> open a rosetta terminal.
>
> Hope these evidences can be of help.
>
> Best and thanks, as always!
>
> Alberto
>
>
> Informativa sulla Privacy: http://www.unibs.it/node/8155
>
> --
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> 
> .
> 
>
> --
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> 
> .
>

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Re: [deal.II] errors in running step-18 within Xcode

[Luca Heltai]

Can you open a Rosetta terminal and follow the instructions to parse deal.ii 
init files? I think it is just the fact that you are not running under Rosetta, 
but cannot confirm...

Luca

> Il giorno 3 ago 2021, alle ore 11:28, Alberto Salvadori 
>  ha scritto:
> 
> Dear community
> 
> I successfully installed 9.3 on my mac M1 from the dmg . However, I am at 
> present unable to run examples, as for the step-18. For this reason, I share 
> my attempts. 
> I am using Xcode 12.5.1 (12E507) on BigSur 11.2.3 (20D91).
> 
> After opening a deal.ii terminal from deal.ii.app, the step-18 code compiles 
> well both inside Xcode and from Makefile. When it comes to run the 
> executable, neither of the two apparently work. The output message from 
> terminal is
> 
> bash-3.2$ ./step-18 
> 
> Illegal instruction: 4
> 
> whereas the debugger provides some further notifications, as in figure, which 
> I am not able to discern. 
> 
> 
> 
> 
> 
> I had at my disposal a former installation of deal.ii.9.2, that I made with 
> spack and gcc in a rosetta terminal. In such a case, within a rosetta 
> terminal, the step-18 compiles and runs well. Note that deal.ii9.3 does not 
> open a rosetta terminal.
> 
> Hope these evidences can be of help.
> 
> Best and thanks, as always!
> 
> Alberto
> 
> 
> 
> Informativa sulla Privacy: http://www.unibs.it/node/8155
> -- 
> 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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> https://groups.google.com/d/msgid/dealii/9014a8cd-0df9-499d-8aa0-d1b0a3427cfcn%40googlegroups.com.
> 

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Re: [deal.II] Use a coarse grid solution as initial condition for a finer grid

['peterrum' via deal.II User Group]

Hi Vachan,

I don't think you need to use RPE plane. My guess is that you can use 
VectorTools::point_values(), which internally uses PRE (see 
https://github.com/dealii/dealii/blob/e413cbf8ac77606cf4a04e1e2fa75232c08533b4/include/deal.II/numerics/vector_tools_evaluate.h#L230-L343).
 
Here you could collect the support points from the new DoFHandler, let 
VT::point_values() do the work and finally set the values at the support 
points.

Further resources are:
- the test 
folder 
https://github.com/dealii/dealii/tree/master/tests/remote_point_evaluation 
(in 
particular 
https://github.com/dealii/dealii/blob/master/tests/remote_point_evaluation/vector_tools_evaluate_at_points_01.cc;
 
here, the solution is interpolated between non-matching grids)
- the usage of RPE and VT::point_values() in 
DataOutResample 
(https://github.com/dealii/dealii/blob/master/source/numerics/data_out_resample.cc)
 
- the usage in the two-phase solver adaflo 
(https://github.com/kronbichler/adaflo/blob/master/include/adaflo/sharp_interface_util.h)

PM

On Tuesday, 3 August 2021 at 09:03:02 UTC+2 vachanpo...@gmail.com wrote:

> Dr. Wolfgang,
>
> Thank you for still taking interest in this thread :)
>
> This becomes a very difficult data transfer problem because you want to
>> evaluate the solution at a point that the current process may know nothing
>> about. In essence, you will have to ask all of the other processes about 
>> who
>> owns a part of the mesh on which a given interpolation point is located, 
>> and
>> then that process has to send you the value of the function at that 
>> point. You
>> have to do that for all points. This is going to be an expensive 
>> operation.
>> You might want to check out the Utilities::MPI::RemotePointEvaluation 
>> class in
>> the latest (9.3) release for help with this.
>
> I understand that the approach I had mentioned is inefficient. I only need 
> to do this once, to start a simulation, so I thought it might be okay.
>
> I had a look at Utilities::MPI::RemotePointEvaluation. This is how I 
> think it can be used (correct me if wrong)
>
>1. Call reinit() with the dof locations, along with the corresponding 
>triangulation and mapping, where I want to evaluate FEFieldFunction (I 
>suppose the triangulation and mapping here are not of the 
> FEFieldFunction?).
>2. Call evaluate_and_process() by passing in the FEFieldFunction.
>
> I have a few questions.
>
>1. What is the "buffer" argument in evaluate_and_process()?
>2. The documentation for this function says get_point_ptrs() must be 
>used to "process" the output in case the point-cell map is not one-one. I 
>will surely encounter such cases. How can I use the data returned by 
>get_point_ptrs() and how exactly should I "process" the output?
>
> I couldn't find this used in any examples. Any clarifications would be 
> greatly helpful.
>
> On Tue, 3 Aug 2021 at 04:47, Wolfgang Bangerth  
> wrote:
>
>> On 7/5/21 11:04 PM, vachan potluri wrote:
>> > 
>> > So is your fine mesh a refinement of the coarse one? If not, you 
>> may want to
>> > look at FEFieldFunction.
>> > 
>> > Yes, it is. But the "refinement" is done by the meshing 
>> software, outside 
>> > dealii. Is there any simplification possible in such a case?
>>
>> Not really. If deal.II has no knowledge about the relationship between 
>> cells 
>> on the two meshes, then it is in essence the interpolation from one 
>> unstructured grid to another unstructured grid.
>>
>>
>> > Otherwise, I think FEFieldFunction would be a safe choice. Since I want 
>> to use 
>> > it with p::d::Triangulation, will setting all dofs as relevant do the 
>> job? 
>> > This way the partitioning can also be different.
>>
>> This becomes a very difficult data transfer problem because you want to 
>> evaluate the solution at a point that the current process may know 
>> nothing 
>> about. In essence, you will have to ask all of the other processes about 
>> who 
>> owns a part of the mesh on which a given interpolation point is located, 
>> and 
>> then that process has to send you the value of the function at that 
>> point. You 
>> have to do that for all points. This is going to be an expensive 
>> operation.
>>
>> You might want to check out the Utilities::MPI::RemotePointEvaluation 
>> class in 
>> the latest (9.3) release for help with this.
>>
>> Best
>>   W.
>>
>>
>> -- 
>> 
>> Wolfgang Bangerth  email: bang...@colostate.edu
>> www: http://www.math.colostate.edu/~bangerth/
>>
>> -- 
>> The deal.II project is located at http://www.dealii.org/
>> For mailing list/forum options, see 
>> https://groups.google.com/d/forum/dealii?hl=en
>> --- 
>> You received this message because you are subscribed to the Google Groups 
>> "deal.II User Group" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to 

Re: [deal.II] Use a coarse grid solution as initial condition for a finer grid

[vachan potluri]

Dr. Wolfgang,

Thank you for still taking interest in this thread :)

This becomes a very difficult data transfer problem because you want to
> evaluate the solution at a point that the current process may know nothing
> about. In essence, you will have to ask all of the other processes about
> who
> owns a part of the mesh on which a given interpolation point is located,
> and
> then that process has to send you the value of the function at that point.
> You
> have to do that for all points. This is going to be an expensive operation.
> You might want to check out the Utilities::MPI::RemotePointEvaluation
> class in
> the latest (9.3) release for help with this.

I understand that the approach I had mentioned is inefficient. I only need
to do this once, to start a simulation, so I thought it might be okay.

I had a look at Utilities::MPI::RemotePointEvaluation. This is how I think
it can be used (correct me if wrong)

   1. Call reinit() with the dof locations, along with the corresponding
   triangulation and mapping, where I want to evaluate FEFieldFunction (I
   suppose the triangulation and mapping here are not of the FEFieldFunction?).
   2. Call evaluate_and_process() by passing in the FEFieldFunction.

I have a few questions.

   1. What is the "buffer" argument in evaluate_and_process()?
   2. The documentation for this function says get_point_ptrs() must be
   used to "process" the output in case the point-cell map is not one-one. I
   will surely encounter such cases. How can I use the data returned by
   get_point_ptrs() and how exactly should I "process" the output?

I couldn't find this used in any examples. Any clarifications would be
greatly helpful.

On Tue, 3 Aug 2021 at 04:47, Wolfgang Bangerth 
wrote:

> On 7/5/21 11:04 PM, vachan potluri wrote:
> >
> > So is your fine mesh a refinement of the coarse one? If not, you may
> want to
> > look at FEFieldFunction.
> >
> > Yes, it is. But the "refinement" is done by the meshing
> software, outside
> > dealii. Is there any simplification possible in such a case?
>
> Not really. If deal.II has no knowledge about the relationship between
> cells
> on the two meshes, then it is in essence the interpolation from one
> unstructured grid to another unstructured grid.
>
>
> > Otherwise, I think FEFieldFunction would be a safe choice. Since I want
> to use
> > it with p::d::Triangulation, will setting all dofs as relevant do the
> job?
> > This way the partitioning can also be different.
>
> This becomes a very difficult data transfer problem because you want to
> evaluate the solution at a point that the current process may know nothing
> about. In essence, you will have to ask all of the other processes about
> who
> owns a part of the mesh on which a given interpolation point is located,
> and
> then that process has to send you the value of the function at that point.
> You
> have to do that for all points. This is going to be an expensive operation.
>
> You might want to check out the Utilities::MPI::RemotePointEvaluation
> class in
> the latest (9.3) release for help with this.
>
> Best
>   W.
>
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see
> https://groups.google.com/d/forum/dealii?hl=en
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> https://groups.google.com/d/msgid/dealii/61601d83-856e-dd27-dc78-3653bd45ec2f%40colostate.edu
> .
>

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