Re: [deal.II] dealii Installation

[Timo Heister]

Ubuntu 16.04 is a very outdated (and unsupported) system. What compiler
version of GCC are you using? (gcc -v)


-- https://www.math.clemson.edu/~heister/

On Tue, May 28, 2024, 09:07 王艺康  wrote:

> Hello, everyone.
> I'm having a problem installing dealii with candi.I'm installing
> dealii-9.5.1 on Ubuntu 16.0.4 via candi, only then all the dependencies I
> need can be downloaded and installed correctly but I get an error when
> installing dealii.
>
>
>
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:
> In instantiation of ‘std::tuple std::allocator >, std::vector std::allocator >, std::vector std::allocator > >
> dealii::GridTools::internal::guess_owners_of_entities(MPI_Comm, const
> std::vector > >&, const
> std::vector&, double) [with int spacedim = 1; T =
> dealii::Point<1>; MPI_Comm = int]’:
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:6195:71:
>   required from
> ‘dealii::GridTools::internal::DistributedComputePointLocationsInternal spacedim>
> dealii::GridTools::internal::distributed_compute_point_locations(const
> dealii::GridTools::Cache&, const
> std::vector >&, const
> std::vector > >&, const
> std::vector&, double, bool, bool) [with int dim = 1; int spacedim =
> 1]’
> /home/hj/dealii-candi/home/hj/wyk/candi/build/deal.II-v9.5.1/source/grid/grid_tools.inst:1289:12:
>   required from here
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:5970:67:
> error: converting to ‘std::tuple std::allocator >, std::vector std::allocator >, std::vector std::allocator > >’ from initializer list would use explicit
> constructor ‘constexpr std::tuple< 
> >::tuple(_UElements&& ...) [with _UElements = {std::vector std::allocator >, std::vector std::allocator >, std::vector std::allocator >};  = void; _Elements
> = {std::vector >,
> std::vector >,
> std::vector >}]’
>return {std::move(ranks), std::move(ptr), std::move(indices)};
>^
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:
> In instantiation of ‘std::tuple std::allocator >, std::vector std::allocator >, std::vector std::allocator > >
> dealii::GridTools::internal::guess_owners_of_entities(MPI_Comm, const
> std::vector > >&, const
> std::vector&, double) [with int spacedim = 2; T =
> dealii::Point<2, double>; MPI_Comm = int]’:
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:6195:71:
>   required from
> ‘dealii::GridTools::internal::DistributedComputePointLocationsInternal spacedim>
> dealii::GridTools::internal::distributed_compute_point_locations(const
> dealii::GridTools::Cache&, const
> std::vector >&, const
> std::vector > >&, const
> std::vector&, double, bool, bool) [with int dim = 1; int spacedim =
> 2]’
> /home/hj/dealii-candi/home/hj/wyk/candi/build/deal.II-v9.5.1/source/grid/grid_tools.inst:1388:12:
>   required from here
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:5970:67:
> error: converting to ‘std::tuple std::allocator >, std::vector std::allocator >, std::vector std::allocator > >’ from initializer list would use explicit
> constructor ‘constexpr std::tuple< 
> >::tuple(_UElements&& ...) [with _UElements = {std::vector std::allocator >, std::vector std::allocator >, std::vector std::allocator >};  = void; _Elements
> = {std::vector >,
> std::vector >,
> std::vector >}]’
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:
> In instantiation of ‘std::tuple std::allocator >, std::vector std::allocator >, std::vector std::allocator > >
> dealii::GridTools::internal::guess_owners_of_entities(MPI_Comm, const
> std::vector > >&, const
> std::vector&, double) [with int spacedim = 3; T =
> dealii::Point<3, double>; MPI_Comm = int]’:
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:6195:71:
>   required from
> ‘dealii::GridTools::internal::DistributedComputePointLocationsInternal spacedim>
> dealii::GridTools::internal::distributed_compute_point_locations(const
> dealii::GridTools::Cache&, const
> std::vector >&, const
> std::vector > >&, const
> std::vector&, double, bool, bool) [with int dim = 1; int spacedim =
> 3]’
> /home/hj/dealii-candi/home/hj/wyk/candi/build/deal.II-v9.5.1/source/grid/grid_tools.inst:1487:12:
>   required from here
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:5970:67:
> error: converting to ‘std::tuple std::allocator >, std::vector std::allocator >, std::vector std::allocator > >’ from initializer list would use explicit
> constructor ‘constexpr std::tuple< 
> >::tuple(_UElements&& ...) [with _UElements = {std::vector std::allocator >, std::vector std::allocator >, std::vector std::allocator >};  = void; _Elements
> = {std::vector >,
> std::vector >,
> std::vector >}]’
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid

Re: [deal.II] Assembling gradient jump at faces with FESystem

[Timo Heister]

If you use an FESystem, you typically don't need the evaluation done over
all components. Instead, use an FEValuesExtractor and you should have
everything available:
https://www.dealii.org/current/doxygen/deal.II/classFEInterfaceViews_1_1Vector.html
I'd anything is wrong or missing, please open an issue.

-- https://www.math.clemson.edu/~heister/

On Thu, Apr 25, 2024, 15:33 Praveen C  wrote:

> Hello Wolfgang
>
> FEFaceValues has two types of functions
>
> void  get_function_values (const InputVector &fe_function, std::vector<
> typename InputVector::value_type > &values) const
>
> void  get_function_values (const InputVector &fe_function, std::vector<
> Vector< typename InputVector::value_type > > &values) const
>
> But FEInterfaceValues only has the first one, which is for scalar FE.
>
> void  get_jump_in_function_values (const InputVector &fe_function,
> std::vector< typename InputVector::value_type > &values) const
>
> It looks like vector FE case is not implemented fully.
>
> best
> praveen
>
>
> On 25 Apr 2024, at 5:25 PM, Wolfgang Bangerth 
> wrote:
>
> On 4/25/24 01:21, Nils Schween wrote:
>
> I think FEInterfaceValues is not implemented for FESystem. In my case, it
> actually
> just returned zeros without throwing an assertion. It is however more
> than two years ago I experimented with it.
>
>
> That would be a bug. We'd love to have a small test case that illustrates
> this.
>
>
> --
> 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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[deal.II] PDESoft 2024

[Timo Heister]

I would like to post the following announcement as this is likely of
interest for the deal.II community. I hope to see many of you there!

Subject: PDESoft 2024, UK, Jul 2024

We are pleased to announce the PDESoft 2024 conference. PDESoft 2024
is an opportunity for users and developers of software tools for
solving PDEs and allied areas to come together to present and discuss
current and future directions of research.

Areas of focus include: numerical PDE solvers; new and novel software
tools for solving PDEs, including machine learning techniques;
parallel and high-performance computing, including at exascale;
algorithmic and software techniques for novel hardware; numerical
linear algebra and preconditioning; model order reduction; meshing
tools; data visualisation; user interfaces to scientific software; any
other part of the PDE toolchain.

PDESoft 2024 will be held at the Moller Institute, Churchill College,
Cambridge, UK. The conference will begin at 10:00am BST on Monday 1
July and will end at 3:00pm BST on Wednesday 3 July. PDESoft 2024
follows in the successful footsteps of PDESoft 2012 in Munster,
PDESoft 2014 in Heidelberg, PDESoft 2016 in Warwick and PDESoft 2018
in Bergen.

For further information please visit website:
https://pdesoft.org/

--
Timo Heister
http://www.math.clemson.edu/~heister/

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Re: [deal.II] construct TrilinosWrappers::SparseMatrix from TrilinosWrappers::BlockSparseMatrix to use Amesos direct solver

[Timo Heister]

What I have done in several codes (and what is used in ASPECT), is to always 
create block matrices and vectors but to put all DoFs into a single block when 
a direct solver is used. This decision can be made at rintime. Inside the solve 
routine you can just access block_matrix.block(0,0), which is a SparseMatrix. 
Same for the vector. This way, there are no different code paths, different 
types, or copies involved.

--
Timo Heister
http://www.math.clemson.edu/~heister/

From: dealii@googlegroups.com  on behalf of Wolfgang 
Bangerth 
Sent: Monday, December 18, 2023 4:37:34 PM
To: dealii@googlegroups.com 
Subject: Re: [deal.II] construct TrilinosWrappers::SparseMatrix from 
TrilinosWrappers::BlockSparseMatrix to use Amesos direct solver

This Message Is From An External Sender: Use caution when opening links or 
attachments if you do not recognize the sender.

On 12/18/23 12:44, Simon wrote:
>
> I use a BlockSolver for the solution and right hand side of the
> linear system to compute the various norms (non-linear solver) of the
> the individual blocks. For a direct solver, I would now use a
> SparseMatrix as matrix type and a BlockVector as vector type. At each
> solve, I convert the BlockVector to a standard Vector, which I guess
> is not too expensive. This mix (SparseMatrix and BlockVector) should
> not cause any undue problems, right? Or would you not recommend
> this?
No. This seems like a reasonable approach to me.
Best
  W.

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Re: [deal.II] Installation on Arm

[Timo Heister]

Bundled TBB compiles just fine in CI on my M1: 
https://ci.tjhei.info/job/dealii-osx/job/master/lastSuccessfulBuild/

--
Timo Heister
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From: dealii@googlegroups.com  on behalf of Matthias 
Maier 
Sent: Friday, December 1, 2023 3:15:21 PM
To: dealii@googlegroups.com 
Subject: Re: [deal.II] Installation on Arm

This Message Is From An External Sender: Use caution when opening links or 
attachments if you do not recognize the sender.

Can you install tbb externally and link against that one?

I am not surprised that our bundled tbb doesn't compile - it has never
been tested on non x86/amd64.

Best,
Matthias



On Thu, Nov 30, 2023, at 23:23 CST, Jai  wrote:

> Hello ,
> I am installing dealii-9.5.0 on ARM. while running the make command i am
> getting the following error. I used the following cmake command:
>  cmake  -DCMAKE_INSTALL_PREFIX=/abc/dealii-9.5.0/build1
> -DDEAL_II_WITH_MPI=ON -DPETSC_DIR=/home/abc/petsc
>
> Error:
> dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/tools_api/ittnotify_config.h:329:12:
> error: ‘__TBB_machine_fetchadd4’ was not declared in this scope
>   329 | return __TBB_machine_fetchadd4(ptr, 1) + 1L;
>   |^~~
> dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/tools_api/ittnotify_config.h:329:12:
> error: ‘__TBB_machine_fetchadd4’ was not declared in this scope
>   329 | return __TBB_machine_fetchadd4(ptr, 1) + 1L;
>   |^~~
> collect2: error: ld returned 1 exit status
> make[2]: ***
> [cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/build.make:97:
> bin/expand_instantiations] Error 1
> make[1]: *** [CMakeFiles/Makefile2:1522:
> cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs
> make[1]: *** [CMakeFiles/Makefile2:1782:
> bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/all] Error 2
> make[1]: *** [CMakeFiles/Makefile2:1808:
> bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_release.dir/all] Error 2
> [ 15%] Built target bundled_muparser_debug
> [ 15%] Built target bundled_boost_iostreams_debug
> [ 15%] Built target bundled_boost_iostreams_release
> [ 15%] Built target bundled_muparser_release
> [ 15%] Built target bundled_boost_serialization_debug
> [ 15%] Built target bundled_kokkos_debug
> [ 15%] Built target bundled_boost_serialization_release
> [ 15%] Built target bundled_kokkos_release
> make: *** [Makefile:136: all] Error 2
> Thank You.

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Re: [deal.II] Installation on Arm

[Timo Heister]

What compilers are you using? Are you aware of the guide at 
https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX ?

--
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https://www.math.clemson.edu/~heister/


From: dealii@googlegroups.com  on behalf of Jai 

Sent: Friday, December 1, 2023 12:23 AM
To: deal.II User Group
Subject: [deal.II] Installation on Arm

This Message Is From An External Sender: Use caution when opening links or 
attachments if you do not recognize the sender.

Hello ,
I am installing dealii-9.5.0 on ARM. while running the make command i am 
getting the following error. I used the following cmake command:
 cmake  -DCMAKE_INSTALL_PREFIX=/abc/dealii-9.5.0/build1 -DDEAL_II_WITH_MPI=ON 
-DPETSC_DIR=/home/abc/petsc

Error:
dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/tools_api/ittnotify_config.h:329:12: 
error: ‘__TBB_machine_fetchadd4’ was not declared in this scope
  329 | return __TBB_machine_fetchadd4(ptr, 1) + 1L;
  |^~~
dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/tools_api/ittnotify_config.h:329:12: 
error: ‘__TBB_machine_fetchadd4’ was not declared in this scope
  329 | return __TBB_machine_fetchadd4(ptr, 1) + 1L;
  |^~~
collect2: error: ld returned 1 exit status
make[2]: *** 
[cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/build.make:97: 
bin/expand_instantiations] Error 1
make[1]: *** [CMakeFiles/Makefile2:1522: 
cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs
make[1]: *** [CMakeFiles/Makefile2:1782: 
bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:1808: 
bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_release.dir/all] Error 2
[ 15%] Built target bundled_muparser_debug
[ 15%] Built target bundled_boost_iostreams_debug
[ 15%] Built target bundled_boost_iostreams_release
[ 15%] Built target bundled_muparser_release
[ 15%] Built target bundled_boost_serialization_debug
[ 15%] Built target bundled_kokkos_debug
[ 15%] Built target bundled_boost_serialization_release
[ 15%] Built target bundled_kokkos_release
make: *** [Makefile:136: all] Error 2
Thank You.

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Re: [deal.II] Re: Helping collaborators write a cluster module for deal.II

[Timo Heister]

David,

spack can be used to build and export modules:
https://spack.readthedocs.io/en/latest/module_file_support.html

candi also generates a module file (but I have to admit I never used it and I 
am not sure how/if it works):
https://github.com/dealii/candi/blob/dc8e8d348533072bc189f5b52e6e9cd63956a22e/deal.II-toolchain/packages/dealii.package#L355

Rene Gassmoeller has built TACC docker/singularity containers of deal.II and 
ASPECT to run on supercomputers, so you can ask him about that option.


--
Timo Heister
https://www.math.clemson.edu/~heister/


From: dealii@googlegroups.com  on behalf of 
blais...@gmail.com 
Sent: Wednesday, November 15, 2023 5:44 PM
To: deal.II User Group
Subject: [deal.II] Re: Helping collaborators write a cluster module for deal.II

This Message Is From An External Sender: Use caution when opening links or 
attachments if you do not recognize the sender.

Dear David,
The Digital Alliance of Canada (Compute Canada) has deal.II on their cluster 
through the use of the module system:
https://docs.alliancecan.ca/wiki/Available_software

You could reach out to them and ask them for their module file. They are 
generallly very chill.
If you need help reaching out, ask me and I can write to them with you in CC.
Best
Bruno


On Wednesday, November 15, 2023 at 8:00:08 a.m. UTC-5 Wells, David wrote:
Hi everyone,

I'm working with a group at another university on a deal.II-powered project 
(yay). I'd like to set things up as a module (i.e., do module load 
dealii/9.5.1) so that everyone there is using the same version of everything.

Are there any published versions of deal.II modules for various Linux 
distributions? Every cluster is different but it would be super helpful to see 
what other people have done to install deal.II and dependencies in this 
situation.

Best,
David Wells

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Re: [deal.II] candi installation issue

[Timo Heister]

Hi Alberto,

Thanks for reporting. I apologize for messing up the server configuration. I 
will fix this today or tomorrow.



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From: dealii@googlegroups.com  on behalf of Alberto 
Salvadori 
Sent: Monday, October 30, 2023 12:43:40 PM
To: deal.II User Group 
Subject: [deal.II] candi installation issue


This Message Is From An External Sender: Use caution when opening links or 
attachments if you do not recognize the sender.

Dear community

while installing deal.ii on a new machine with candi I got this message.

candi tries now to download, configure, build and install:

Project:  deal.II-toolchain
Platform: deal.II-toolchain/platforms/supported/ubuntu.platform

Loading dealii-prepare
Fetching opencascade 0.18.3
Trying to download https://tjhei.info/candi-mirror/OCE-0.18.3.tar.gz
--2023-10-30 17:31:59--  https://tjhei.info/candi-mirror/OCE-0.18.3.tar.gz
Resolving tjhei.info (tjhei.info)... 45.63.8.119
Connecting to tjhei.info (tjhei.info)|45.63.8.119|:443... connected.
WARNING: cannot verify tjhei.info's certificate, issued by 
‘CN=_default,OU=Dev,O=GridPane,L=Bath,ST=Michigan,C=US’:
  Self-signed certificate encountered.
WARNING: certificate common name ‘_default’ doesn't match requested host 
name ‘tjhei.info’.
HTTP request sent, awaiting response... Read error (Connection reset by peer) 
in headers.
Retrying.

Am I missing something? I did try on two different systems with the same 
outcome.
Thank you,

Alberto




Informativa sulla Privacy: https://www.unibs.it/it/node/1452

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Re: [deal.II] Difference between 2 Wasy to Initialize System Matrix in MPI World

[Timo Heister]

Lex,

I would strongly advice against using AffineConstraints::condense() in an MPI 
parallel computation. It is inefficient and also likely incorrect if you run it 
before distribute_sparsity_pattern().
Instead, use distribute_local_to_global during assembly (see step-40 for an 
example).

--
Timo Heister
http://www.math.clemson.edu/~heister/

From: dealii@googlegroups.com  on behalf of Lex Lee 

Sent: Wednesday, September 27, 2023 8:15:14 PM
To: deal.II User Group 
Subject: [deal.II] Difference between 2 Wasy to Initialize System Matrix in MPI 
World


This Message Is From An External Sender: Use caution when opening links or 
attachments if you do not recognize the sender.

Hello all,


Previously, I initialized my system matrix in this way (option A)

DoFTools::make_flux_sparsity_pattern(dof_handler,
dsp,
cell_coupling,
face_coupling);
constraints_newton_update.condense(dsp);
SparsityTools::distribute_sparsity_pattern(dsp,
   hp_index_set,
   mpi_communicator,
   hp_relevant_set);
system_matrix.reinit(hp_index_set,
 hp_index_set,
 dsp,
 mpi_communicator);

However, the generated system matrix is singular. I was stuck by the singular 
matrix problem for about 2 weeks.


Then, I initialized the matrix with option B, which generates a full rank 
matrix. Although, I don't see the difference between these 2 ways.  Can someone 
explain this to me? Thans in advance.

DoFTools::make_flux_sparsity_pattern(dof_handler,
 dsp,
 cell_coupling,
 face_coupling);
constraints_newton_update.condense(dsp);
sparsity_pattern.copy_from(dsp);
system_matrix.reinit(hp_index_set,
 sparsity_pattern,
 mpi_communicator);

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[deal.II] ASPECT 2.5.0 released

[Timo Heister]

Hi all,

We recently released version 2.5.0 of ASPECT, the Advanced Solver for
Problems in Earth's ConvecTion, which is built on deal.II.

If you are curious you can check https://aspect.geodynamics.org/ and
https://github.com/geodynamics/aspect/releases/tag/v2.5.0 for more
information about ASPECT. Also, feel free to get in touch if you have
any questions.

Best,
Timo

-- 
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Re: [deal.II] Deadlock for addition operator

[Timo Heister]

Giang,

Parallel hangs and similar bugs are hard to debug and fix. One thing
that is helpful is to run each rank in a debugger (or attach after
running) and print a stack trace. This will tell you if some ranks are
stuck somewhere earlier. Are you sure all ranks made it to the .add
call?

It could be that you forgot a call to compress() after assembling into
the vector somewhere before this addition.


On Sun, May 28, 2023 at 11:25 PM Giang Huynh  wrote:
>
> Hello everyone, I'm using addition operators on a variable called 
> 'hat_solution' by    hat_solution=0;   hat_solution. add(1. 
> 0, old_solution,timestep, old_vel_solution);   hat_solution. add(0. 
> 5*timestep*timestep*(1. 0-2. 0*beta),old_acc_solution
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> Hello everyone,
>
> I'm using addition operators on a variable called 'hat_solution' by
> 
>   hat_solution=0;
>   hat_solution.add(1.0, old_solution,timestep, old_vel_solution);
>   hat_solution.add(0.5*timestep*timestep*(1.0-2.0*beta),old_acc_solution );
> 
> , the above variables are trillinos block vectors, and initialized by
> 
>   // Actual solution at time step n
>   old_solution.reinit(partition_relevant, mpi_com);
>   old_vel_solution.reinit(partition_relevant, mpi_com);
>   old_acc_solution.reinit(partition_relevant, mpi_com);
>
>   // hat solution at time step n-1
>   hat_solution.reinit(partition_relevant, mpi_com);
> 
> On my personal laptop, the code runs well with multiple cores, but there was 
> a deadlock  when calling  add() function on a supercomputer.
>
> I really appreciate if anyone has some thoughts on this issue.
>
> Thanks,
> Giang
>
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Re: [deal.II] Understanding MeshWorker::mesh_loop order with adaptive refinement

[Timo Heister]

I think this is just a typo in the documentation exactly like you pointed
out. It would be great to see that fixed. Are you willing to do that?

I am not sure I understand your problem you had to work around. If you go
into detail we might be able to figure out the issue (if there is one
inside deal.II)

-- https://www.math.clemson.edu/~heister/

On Wed, May 3, 2023, 20:52 Corbin Foucart  wrote:

> Hi Timo, I replied to this from a different email address, and it doesn't
> seem to have made it to the mailing list; most likely an error on my end.
> Here's what I wrote a few weeks ago: > Do you mean a pull request to the
> documentation? Or
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> Hi Timo, I replied to this from a different email address, and it doesn't
> seem to have made it to the mailing list; most likely an error on my end.
> Here's what I wrote a few weeks ago:
>
> > Do you mean a pull request to the documentation? Or a pull request for
> mesh_loop? I ask because I'm unsure if what I'm seeing with
> AssembleFlags::assemble_own_interior_faces_both is a bug or not.
>
> > I've since re-written my code to assemble all the face data using
> AssembleFlags::assemble_own_interior_faces_once, then computing and
> applying the residuals in a separate mesh_loop call, and I'm once again
> recovering the correct residual in the global refinement and adaptive
> refinement cases; no unexpected behavior there.
>
> Thank you,
> Corbin
>
> On Friday, April 7, 2023 at 2:49:48 PM UTC-4 Timo Heister wrote:
>
>> > to my eye, in both cases, the work on the face is done, followed by the
>> work on the cell. I think, however, the default behavior is to work on the
>> cells first, followed by work on the faces.
>>
>> That is correct. Would you be able to submit a pull request to fix this?
>>
>> On Thu, Apr 6, 2023 at 8:30 AM Corbin Foucart 
>> wrote:
>> >
>> > I also think there may be a small typo in the documentation; "If the
>> flag AssembleFlags: : assemble_own_cells is passed, then the default
>> behavior is to first loop over faces and do the work there, and then
>> compute the actual work on the
>> > ZjQcmQRYFpfptBannerStart
>> > This Message Is From an External Sender
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>> the sender.
>> >
>> > ZjQcmQRYFpfptBannerEnd
>> > I also think there may be a small typo in the documentation;
>> >
>> > "If the flag AssembleFlags::assemble_own_cells is passed, then the
>> default behavior is to first loop over faces and do the work there, and
>> then compute the actual work on the cell. It is possible to perform the
>> integration on the cells after working on faces, by adding the flag
>> AssembleFlags::cells_after_faces."
>> >
>> > to my eye, in both cases, the work on the face is done, followed by the
>> work on the cell. I think, however, the default behavior is to work on the
>> cells first, followed by work on the faces.
>> >
>> > On Mon, Apr 3, 2023 at 6:35 PM Corbin Foucart 
>> wrote:
>> >>
>> >> Hello everyone,
>> >>
>> >> I'm solving a 1D explicit DG-FEM problem and I've encountered behavior
>> that I don't understand using MeshWorker::mesh_loop.
>> >>
>> >> I'm using the MeshWorker::assemble_own_interior_faces_both flag since
>> I want to do work on each face corresponding to the same cell interior
>> >> If the grid is created using typical GridGenerator calls, the order is
>> exactly as I'd expect: first, work is done on the cell, then the faces
>> (boundary or interior), followed by the next cell (further, all mass
>> matrices are the same)
>> >> However, if I manually adapt the mesh by refining some cells, the
>> order seems to change; the face work is done without respect to the cell
>> interior last worked on
>> >>
>> >> I've attached a stripped-down program that illustrates this behavior
>> on a toy mesh in 1D, as well as the output.
>> >>
>> >> Ultimately, my goal is to assemble an inverse mass matrix on each
>> cell, and apply it to a residual vector containing interior and face
>> contributions (which can be done element-wise since the elements are
>> FE_DGQ)
>> >> I was attempting to store the inverse via CopyData and then apply it
>> in the copy worker.
>

Re: [deal.II] Re: How can I visit a face exactly once when running with MPI?

[Timo Heister]

I would suggest that you use MeshWorker::mesh_loop() to do this (or
look at the complicated implementation of it).

On Thu, Apr 27, 2023 at 11:18 AM Bruno Turcksin
 wrote:
>
> Right, it won't clear it everywhere. You would need to use MPI to clear the 
> flag on the other processor. If you would do that you would create a huge 
> amount of messages and your code would be extremely slow. Best, Bruno ‍ ‍ ‍ ‍ 
> ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍
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> Right, it won't clear it everywhere. You would need to use MPI to clear the 
> flag on the other processor. If you would do that you would create a huge 
> amount of messages and your code would be extremely slow.
>
> Best,
>
> Bruno
>
> Le jeu. 27 avr. 2023 à 10:09, Abbas Ballout  a 
> écrit :
>>
>> This works!! Thanks.
>> I am guessing something like:
>>
>> if(cell_neighbour->is_ghost()==true)
>> cell->face(neighbour_face_number)->clear_user_flag();
>>
>> won't clear the user flag everywhere either, because that didn't work.
>> Right?
>>
>> On Thursday, April 27, 2023 at 2:48:23 PM UTC+2 bruno.t...@gmail.com wrote:
>>>
>>> Hello,
>>>
>>> On Thursday, April 27, 2023 at 7:56:50 AM UTC-4 abbas.b...@gmail.com wrote:
>>>
>>> This works with a single MPI but not for more. Is it because the 
>>> cell->face(face)->clear_user_flag()
>>> doesn't clear the user flag in the other distributed meshes?
>>>
>>>
>>> That's correct. The flag is only cleared locally not on the other processor.
>>>
>>> I can't directly loop over faces because there is no 
>>> "face->is_locally_owned()"
>>> I know that meshworker is an option. Is it the only option?
>>>
>>> You can check if the cell that shares the face (use this) is a ghost cell 
>>> (use this). If that's the case, you can ask for the subdomain id of the 
>>> locally owned cell and the ghost cell (use this). Now you can decide that 
>>> only the processor with the lower rank can "touch" the face and the other 
>>> processor should just skip it.
>>>
>>> Best,
>>>
>>> Bruno
>>>
>>
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Re: [deal.II] Problem in installion of deal ii with petsc using candi on WSL

[Timo Heister]

The problem you are seeing is related to network issues in WSL2 and
unrelated to deal.II/candi. It just happens that the "git clone"
command fails. If you google for "WSL git clone failure" you will find
ample documentation and workarounds. For me it helped to adjust the
MTU, but it might be different for you.

> Or is there any easier way?

Yes, you can just install the deal.II Ubuntu/Debian packages as
described at https://github.com/dealii/dealii/wiki/Getting-deal.II

On Tue, Apr 18, 2023 at 3:40 AM sabyasachi chatterjee
 wrote:
>
> Dear All,  I am trying to install deal ii on Windows Subsystem for Linux 
> (WSL). I did the following:   1. Install mpich. (version 4. 1. 1) and added 
> the path of mpich_install to $PATH.   2. Installed blas-lacpack using sudo 
> apt-get install libblas-dev
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> Dear All,
>
> I am trying to install deal ii on Windows Subsystem for Linux (WSL). I did 
> the following:
>
> 1. Install mpich. (version 4.1.1) and added the path of mpich_install to 
> $PATH.
> 2. Installed blas-lacpack using sudo apt-get install libblas-dev 
> liblapack-dev (there was an error saying blas and lapack not found).
> 2. Used candi to install deal ii (9.1.1) with parmetis, hdf5, p4est, petsc 
> (3.16.4).
>
> All the dependencies are installed but candi is not able to clone deal ii 
> through git with the following error:
>
> ===
> Fetching dealii v9.1.1
> Cloning into 'deal.II-v9.1.1'...
> remote: Enumerating objects: 566631, done.
> remote: Counting objects: 100% (509/509), done.
> remote: Compressing objects: 100% (292/292), done.
> error: 1178 bytes of body are still expected3 MiB | 13.00 KiB/s
> fetch-pack: unexpected disconnect while reading sideband packet
> fatal: early EOF
> fatal: fetch-pack: invalid index-pack output
> Failure with exit status: 128
> Exit message: candi: git clone https://github.com/dealii/dealii.git 
> deal.II-v9.1.1 failed
> ==
>
> 1. Please let me know how to get around this issue. Is there a way to 
> download a deal ii tarball and use it instead?
>
> 2. What is the simplest way to compile deal ii with MPI and PETSc (in which 
> order do these need to be installed)? First install mpich manually and pass 
> the path of mpich installation during installation of PETSc; then install 
> PETSc and pass the path of PETSc to the cmake command during deal ii 
> installation?
>
> Or is there any easier way?
>
> These are probably simple questions, however I am having a hard time 
> understanding the installation process.
>
> Thanks and regards,
> Sabyasachi
>
>
>
>
> --
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Re: [deal.II] Understanding MeshWorker::mesh_loop order with adaptive refinement

[Timo Heister]

> to my eye, in both cases, the work on the face is done, followed by the work 
> on the cell. I think, however, the default behavior is to work on the cells 
> first, followed by work on the faces.

That is correct. Would you be able to submit a pull request to fix this?

On Thu, Apr 6, 2023 at 8:30 AM Corbin Foucart  wrote:
>
> I also think there may be a small typo in the documentation; "If the flag 
> AssembleFlags: : assemble_own_cells is passed, then the default behavior is 
> to first loop over faces and do the work there, and then compute the actual 
> work on the
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> I also think there may be a small typo in the documentation;
>
> "If the flag AssembleFlags::assemble_own_cells is passed, then the default 
> behavior is to first loop over faces and do the work there, and then compute 
> the actual work on the cell. It is possible to perform the integration on the 
> cells after working on faces, by adding the flag 
> AssembleFlags::cells_after_faces."
>
> to my eye, in both cases, the work on the face is done, followed by the work 
> on the cell. I think, however, the default behavior is to work on the cells 
> first, followed by work on the faces.
>
> On Mon, Apr 3, 2023 at 6:35 PM Corbin Foucart  
> wrote:
>>
>> Hello everyone,
>>
>> I'm solving a 1D explicit DG-FEM problem and I've encountered behavior that 
>> I don't understand using MeshWorker::mesh_loop.
>>
>> I'm using the MeshWorker::assemble_own_interior_faces_both flag since I want 
>> to do work on each face corresponding to the same cell interior
>> If the grid is created using typical GridGenerator calls, the order is 
>> exactly as I'd expect: first, work is done on the cell, then the faces 
>> (boundary or interior), followed by the next cell (further, all mass 
>> matrices are the same)
>> However, if I manually adapt the mesh by refining some cells, the order 
>> seems to change; the face work is done without respect to the cell interior 
>> last worked on
>>
>> I've attached a stripped-down program that illustrates this behavior on a 
>> toy mesh in 1D, as well as the output.
>>
>> Ultimately, my goal is to assemble an inverse mass matrix on each cell, and 
>> apply it to a residual vector containing interior and face contributions 
>> (which can be done element-wise since the elements are FE_DGQ)
>> I was attempting to store the inverse via CopyData and then apply it in the 
>> copy worker.
>> However, I'm finding that due to the order of execution, I can't rely on the 
>> face work being done immediately after the cell work, and the inverse mass 
>> matrix stored to CopyData is often from another cell than the faces being 
>> worked on.
>> I could do the assembly and application of the inverse mass matrices 
>> separately, or store the inverse mass matrices in a map to the cell 
>> iterators, but I'm curious why this ordering occurs.
>>
>> Am I misunderstanding how mesh_loop is supposed to work? Any guidance would 
>> be appreciated!
>>
>> Corbin
>>
>> --
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>
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Re: [deal.II] Understanding MeshWorker::mesh_loop order with adaptive refinement

[Timo Heister]

Corbin,

Do you know if this problem is only present in 1d?



-- https://www.math.clemson.edu/~heister/

On Mon, Apr 3, 2023, 18:36 Corbin Foucart  wrote:

> Hello everyone,  I'm solving a 1D explicit DG-FEM problem and I've
> encountered behavior that I don't understand using MeshWorker: : mesh_loop.
> I'm using the MeshWorker: : assemble_own_interior_faces_both flag since I
> want to do work on each face
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> Hello everyone,
>
> I'm solving a 1D explicit DG-FEM problem and I've encountered behavior
> that I don't understand using MeshWorker::mesh_loop.
>
>- I'm using the MeshWorker::assemble_own_interior_faces_both flag
>since I want to do work on each face corresponding to the same cell 
> interior
>- If the grid is created using typical GridGenerator calls, the order
>is exactly as I'd expect: first, work is done on the cell, then the faces
>(boundary or interior), followed by the next cell (further, all mass
>matrices are the same)
>- However, if I manually adapt the mesh by refining some cells, the
>order seems to change; the face work is done without respect to the cell
>interior last worked on
>
> I've attached a stripped-down program that illustrates this behavior on a
> toy mesh in 1D, as well as the output.
>
>- Ultimately, my goal is to assemble an inverse mass matrix on each
>cell, and apply it to a residual vector containing interior and face
>contributions (which can be done element-wise since the elements are
>FE_DGQ)
>- I was attempting to store the inverse via CopyData and then apply it
>in the copy worker.
>- However, I'm finding that due to the order of execution, I can't
>rely on the face work being done immediately after the cell work, and the
>inverse mass matrix stored to CopyData is often from another cell than the
>faces being worked on.
>- I could do the assembly and application of the inverse mass matrices
>separately, or store the inverse mass matrices in a map to the cell
>iterators, but I'm curious why this ordering occurs.
>
> Am I misunderstanding how mesh_loop is supposed to work? Any guidance
> would be appreciated!
>
> Corbin
>
> --
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> 
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> 
> .
>

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Re: [deal.II] Using affine constraints object to apply boundary condition at a vertex

[Timo Heister]

It should be as simple as doing

constraints.add_line(y);

Unless you are writing an MPI parallel program. Then you would need to
check if this line can be stored first.

-- https://www.math.clemson.edu/~heister/

On Sun, Mar 12, 2023, 09:17 Wasim Niyaz Munshi ce21d400 <
ce21d...@smail.iitm.ac.in> wrote:

> I am solving an elasticity problem wherein I have a pin support at one
> vertex. Earlier, I was using std: : map object to apply BCs. Now, I am
> trying to solve the same problem using an affine constraint object to apply
> BCs. But, I am facing issues
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> I am solving an elasticity problem wherein I have a pin support at one
> vertex. Earlier, I was using std::map object to apply BCs. Now, I am trying
> to solve the same problem using an affine constraint object to apply BCs.
> But, I am facing issues filling my affine constraint object with the
> information corresponding to the vertex with pin support.
>
> I was doing the following for my std::map boundary_values object:
>
> for (const auto &cell : dof_handler.active_cell_iterators())
> {
> for (const auto &face : cell->face_iterators())
>
> for (const auto vertex_number : cell->vertex_indices())
> {
> const auto vert = cell->vertex(vertex_number);
> if (vertices satisfy the condition)
> {
>
>types::global_dof_index x=
> cell->vertex_dof_index(vertex_number, 0);
> boundary_values[x] = 0;
>
> types::global_dof_index y=
> cell->vertex_dof_index(vertex_number, 1);
> boundary_values[y] = 0;
> }
> }
>
> }
>
> What changes should I do to fill my constraint object with the same
> information?
> Thanks and regards
> Wasim Niyaz
>
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> 
> .
>

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Re: [deal.II] Re: Official conda package

[Timo Heister]

Fascinating. One additional option to install deal.II that I did not know about.

Anyone familiar with conda packaging?

On Fri, Mar 10, 2023 at 11:05 AM Alexander  wrote:
>
> FYI, conda package is used quite extensively. >4k installations of 9. 3. 2: 
> https: //anaconda. org/conda-forge/dealii/files On Friday, March 10, 2023 at 
> 5: 02: 56 PM UTC+1 Alexander wrote: There is one here: https: //github. 
> com/conda-forge/dealii-feedstock
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> FYI, conda package is used quite extensively. >4k installations of 9.3.2: 
> https://anaconda.org/conda-forge/dealii/files
>
> On Friday, March 10, 2023 at 5:02:56 PM UTC+1 Alexander wrote:
>>
>> There is one here: https://github.com/conda-forge/dealii-feedstock
>>
>> But it looks like is not maintained and updated anymore.
>>
>> Did you consider create and maintain an own feedstock?
>>
>> Alexander
>
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-- 
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Re: [deal.II] Reading Boundary Id in deal.ii

[Timo Heister]

Hi Lilanath,

If you check step-50
 
https://www.dealii.org/developer/doxygen/deal.II/step_49.html#Importingfromexternalprograms
you can see an example where it works correctly (including the .geo file
https://github.com/dealii/dealii/blob/master/examples/step-49/example.geo
)
Maybe this is because you assign names instead of just physical ids?

On Sun, Feb 19, 2023 at 11:02 PM Lilanath Ghimire
 wrote:
>
> I have meshed my cad model in gmesh and provided  bounday ids for different 
> surfaces by add physical group option and saved mesh in  .msh file  format. 
> the first few lines of .msh file look like this: $MeshFormat 2. 2 0 8 
> $EndMeshFormat $PhysicalNames
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> I have meshed my cad model in gmesh and provided  bounday ids for different 
> surfaces by add physical group option and saved mesh in  .msh file  format.
> the first few lines of .msh file look like this:
> $MeshFormat
> 2.2 0 8
> $EndMeshFormat
> $PhysicalNames
> 4
> 2 13 "bottom"
> 2 14 "top"
> 2 15 "inner"
> 2 16 "outer"
> $EndPhysicalNames
> $Nodes
> 4556
>
> then i read the mesh file by gridin function as
> Triangulation<3> triangulation;
>
> GridIn<3> gridin;
> gridin.attach_triangulation(triangulation);
> std::ifstream f("input.msh");
> gridin.read_msh(f);
>
> and i tried to access the boundary id by following line of code:
> for (const auto& face : triangulation.active_face_iterators()) {
> if (face->at_boundary()) {
> std::cout << "Face " << face->index()
> << " has boundary ID " << face->boundary_id() << std::endl;
> }
> but  the output of this code shows every face of mesh have boundary id  zero
> as
> ..
> Face 136 has boundary ID 0
> Face 137 has boundary ID 0
> Face 140 has boundary ID 0
> Face 141 has boundary ID 0
> .
>
> it seems like every face/surface is assigned with boundary id zero by default 
> when i read .msh file in deal.ii
> how can i access boundary id (created in gmesh) in deal.ii ?
>
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Re: [deal.II] Installing an older version with candi

[Timo Heister]

The deal.II version can be chosen in candi.cfg. This will only work to
a certain point (dependencies will be too new for deal.II to work
properly), so a safer bet is to go to an older version of candi (by
using git checkout of one of the older dealii-* branches).

On Tue, Feb 14, 2023 at 7:17 AM Alberto SALVADORI
 wrote:
>
> Sorted out. Sorry to bother. Alberto Alberto Salvadori  Dipartimento di 
> Ingegneria Meccanica e Industriale (DIMI)  Universita` di Brescia, via Branze 
> 43, 25123 Brescia  Italy  tel 030 3715426 e-mail:  alberto. salvadori@ unibs. 
> it ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍
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> Sorted out. Sorry to bother.
> Alberto
>
> 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, Feb 14, 2023 at 1:09 PM Alberto Salvadori 
>  wrote:
>>
>> Dear community
>>
>> I would like to install the dealii version 9.2.0 via candi. I noticed the 
>> file VERSION and assumed that replacing "9.4.2-r2" with "9.2.0" would work. 
>> Apparently it is not effective, candi is still unpacking in the directory 
>> deal.ii-v9.4.2. Can anyone address me to solve the issue?
>>
>> Many thanks!
>>
>> Alberto
>>
>>
>> Informativa sulla Privacy: https://www.unibs.it/it/node/1452
>>
>> --
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>
>
>
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Re: [deal.II] INSTALLING DEALII ON MAC OSX VENTURA

[Timo Heister]

::__1::basic_string, 
> std::__1::allocator > const&, std::__1::basic_string std::__1::char_traits, std::__1::allocator > const&, 
> Teuchos::RCP > 
> > const&, Teuchos::RCP std::__1::char_traits > > const&) in Thyra_BelosLinearOpWithSolve.cpp.o
>
>   Tpetra::MatrixMarket::Writer Kokkos::Compat::KokkosDeviceWrapperNode > 
> >::writeDenseColumn(std::__1::basic_ostream 
> >&, Tpetra::MultiVector Kokkos::Compat::KokkosDeviceWrapperNode > 
> const&, Teuchos::RCP std::__1::char_traits > > const&, 
> Teuchos::RCP > 
> > const&) in Thyra_BelosLinearOpWithSolve.cpp.o
>
>   "Tpetra::MultiVector Kokkos::Compat::KokkosDeviceWrapperNode 
> >::getLocalLength() const", referenced from:
>
>   Tpetra::MatrixMarket::Writer Kokkos::Compat::KokkosDeviceWrapperNode > 
> >::writeDenseColumn(std::__1::basic_ostream 
> >&, Tpetra::MultiVector Kokkos::Compat::KokkosDeviceWrapperNode > 
> const&, Teuchos::RCP std::__1::char_traits > > const&, 
> Teuchos::RCP > 
> > const&) in Thyra_BelosLinearOpWithSolve.cpp.o
>
>   "Tpetra::MultiVector Kokkos::Compat::KokkosDeviceWrapperNode 
> >::getGlobalLength() const", referenced from:
>
>   Tpetra::MatrixMarket::Writer Kokkos::Compat::KokkosDeviceWrapperNode > 
> >::writeDenseHeader(std::__1::basic_ostream 
> >&, Tpetra::MultiVector Kokkos::Compat::KokkosDeviceWrapperNode > 
> const&, std::__1::basic_string, 
> std::__1::allocator > const&, std::__1::basic_string std::__1::char_traits, std::__1::allocator > const&, 
> Teuchos::RCP > 
> > const&, Teuchos::RCP std::__1::char_traits > > const&) in Thyra_BelosLinearOpWithSolve.cpp.o
>
>   "Tpetra::MultiVector Kokkos::Compat::KokkosDeviceWrapperNode 
> >::get1dCopy(Teuchos::ArrayView const&, unsigned long) const", 
> referenced from:
>
>   Tpetra::MatrixMarket::Writer Kokkos::Compat::KokkosDeviceWrapperNode > 
> >::writeDenseColumn(std::__1::basic_ostream 
> >&, Tpetra::MultiVector Kokkos::Compat::KokkosDeviceWrapperNode > 
> const&, Teuchos::RCP std::__1::char_traits > > const&, 
> Teuchos::RCP > 
> > const&) in Thyra_BelosLinearOpWithSolve.cpp.o
>
>   "Tpetra::MultiVector Kokkos::Compat::KokkosDeviceWrapperNode 
> >::getVector(unsigned long) const", referenced from:
>
>   Tpetra::MatrixMarket::Writer Kokkos::Compat::KokkosDeviceWrapperNode > 
> >::writeDense(std::__1::basic_ostream >&, 
> Tpetra::MultiVector Kokkos::Compat::KokkosDeviceWrapperNode > 
> const&, std::__1::basic_string, 
> std::__1::allocator > const&, std::__1::basic_string std::__1::char_traits, std::__1::allocator > const&, 
> Teuchos::RCP > 
> > const&, Teuchos::RCP std::__1::char_traits > > const&) in Thyra_BelosLinearOpWithSolve.cpp.o
>
> ld: symbol(s) not found for architecture arm64
>
> clang: error: linker command failed with exit code 1 (use -v to see 
> invocation)
>
> make[2]: *** 
> [packages/stratimikos/adapters/belos/src/libstratimikosbelos.13.2.dylib] 
> Error 1
>
> make[1]: *** 
> [packages/stratimikos/adapters/belos/src/CMakeFiles/stratimikosbelos.dir/all] 
> Error 2
>
> make: *** [all] Error 2
>
> Failure with exit status: 2
>
> Exit message: There was a problem building trilinos 13-2-0.
>
>
>
>
> Can anyone provide me some way to address the issue? Is it perhaps related to 
> the version of Trilinos? Can I install a former version (and in case, how 
> to?)?
>
> Many thanks
>
> Erkin
>
>
>
>
>
> Informativa sulla Privacy: https://www.unibs.it/it/node/1452
>
> --
> The deal.II project is located at http://www.dealii.org/
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Re: [deal.II] collect2 linking error when executing make

[Timo Heister]

How did you install deal.II on your new machine? Note that the HDF5
configuration is part of deal.II and not your user project.

On Wed, Jan 4, 2023 at 4:48 AM Simon Wiesheier
 wrote:
>
> I called cmake as follows $ cmake -DDEAL_II_WITH_HDF5=OFF . and get the 
> additional lines //No help, variable specified on the command line. 
> DEAL_II_WITH_HDF5: UNINITIALIZED=OFF in my CMakeCache. txt file. However, 
> after $ make ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍
> ZjQcmQRYFpfptBannerStart
> This Message Is From an External Sender
> Use caution when opening links or attachments if you do not recognize the 
> sender.
>
> ZjQcmQRYFpfptBannerEnd
> I called cmake as follows
> $ cmake -DDEAL_II_WITH_HDF5=OFF .
>
> and get the additional lines
>
> //No help, variable specified on the command line.
> DEAL_II_WITH_HDF5:UNINITIALIZED=OFF
>
> in my CMakeCache.txt file.
>
> However, after
> $ make
>
> the error message is unchanged.
> Best
> Simon
>
>
> Am Di., 3. Jan. 2023 um 20:55 Uhr schrieb Simon Wiesheier 
> :
>>
>> I started from an empty source directory with only a CMakeLists.txt file.
>>
>> I do not need hdf5.
>> At least I was not aware that I had it on my old computer.
>>
>> Is there a way to work around the issue?
>>
>> Best
>> Simon
>>
>>
>> Timo Heister  schrieb am Di., 3. Jan. 2023, 20:19:
>>>
>>> Simon,
>>>
>>> Make sure that you do not transfer any temporary files
>>> (CMakeCache.txt, CMakeFiles/ etc.) but that you start from a fresh
>>> source directory. The error message hints at the fact that your new
>>> system does not have hdf5 installed.
>>>
>>> On Mon, Jan 2, 2023 at 4:21 AM Simon  wrote:
>>> >
>>> > Dear all, First of all, I wish you a happy and prosperous new year 2023! 
>>> > I transferred my dealii project to a different computer and encounter an 
>>> > linking error (command make) after setting up the project (command cmake 
>>> > .). ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍
>>> > ZjQcmQRYFpfptBannerStart
>>> > This Message Is From an External Sender
>>> > Use caution when opening links or attachments if you do not recognize the 
>>> > sender.
>>> >
>>> > ZjQcmQRYFpfptBannerEnd
>>> > Dear all,
>>> >
>>> > First of all, I wish you a happy and prosperous new year 2023!
>>> >
>>> > I transferred my dealii project to a different computer and
>>> > encounter an linking error (command make) after setting up
>>> > the project (command cmake .).
>>> > The error message is attached.
>>> >
>>> > What is the problem?
>>> >
>>> > Best
>>> > 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
>>> > ---
>>> > 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.
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>>> > https://groups.google.com/d/msgid/dealii/ca0ce1f2-cba0-42e1-8ee4-2178806540ebn%40googlegroups.com.
>>>
>>>
>>>
>>> --
>>> Timo Heister
>>> http://www.math.clemson.edu/~heister/
>>>
>>> --
>>> 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] Differences between cell_iterators() and mg_cell_iterators()

[Timo Heister]

This is not documented well and the doxygen types shown are not very
helpful. In the end it boils down to the following:
*_mg_* functions return level or multigrid iterators that have an
accessor (that is inside the iterator) with the template argument
level_dof_access = true. The only difference, if I remember correctly,
is that get_active_or_mg_dof_indices() will return the result of
get_mg_dof_indices() instead of get_dof_indices(). So, if you use
level iterators, you can use get_active_or_mg_dof_indices() in your
assembly and it will automatically do the right thing. This means you
can use the same assembler for active and mg levels.

See 
https://www.dealii.org/developer/doxygen/deal.II/classDoFCellAccessor.html#a15ef35e919b1005dc6050f9bca96956d

On Sun, Jan 1, 2023 at 8:45 AM 'yy.wayne' via deal.II User Group
 wrote:
>
> I'm a bit confused on the effect of cell_iterators (similar ones are 
> cell_iterators_on_level and dof_handler. begin()) and mg_cell_iterators. In 
> step16, begin_mg() is used when assembling multigrid, while in step56 we use 
> cell_iterators rather
> ZjQcmQRYFpfptBannerStart
> This Message Is From an External Sender
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>
> ZjQcmQRYFpfptBannerEnd
> I'm a bit confused on the effect of cell_iterators (similar ones are 
> cell_iterators_on_level and dof_handler.begin()) and mg_cell_iterators. In 
> step16, begin_mg() is used when assembling multigrid, while in step56 we use 
> cell_iterators rather than mg_cell_iterators. I think they both loop through 
> all cells, active or not. In documentation the difference is 
> mg_cell_iterators "return an iterator in their level-cell form".  May some 
> expert explain this a little further?
>
> --
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Re: [deal.II] collect2 linking error when executing make

[Timo Heister]

Simon,

Make sure that you do not transfer any temporary files
(CMakeCache.txt, CMakeFiles/ etc.) but that you start from a fresh
source directory. The error message hints at the fact that your new
system does not have hdf5 installed.

On Mon, Jan 2, 2023 at 4:21 AM Simon  wrote:
>
> Dear all, First of all, I wish you a happy and prosperous new year 2023! I 
> transferred my dealii project to a different computer and encounter an 
> linking error (command make) after setting up the project (command cmake .). 
> ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍ ‍
> ZjQcmQRYFpfptBannerStart
> This Message Is From an External Sender
> Use caution when opening links or attachments if you do not recognize the 
> sender.
>
> ZjQcmQRYFpfptBannerEnd
> Dear all,
>
> First of all, I wish you a happy and prosperous new year 2023!
>
> I transferred my dealii project to a different computer and
> encounter an linking error (command make) after setting up
> the project (command cmake .).
> The error message is attached.
>
> What is the problem?
>
> Best
> Simon
>
> --
> 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] How do I set initial solution vector to boundary values in DG?

[Timo Heister]

I would consider the boundary conditions part of the nonlinear
iteration (in contrast to step-15, where they are strongly enforced
and as such are only needed in step 0). Every step you can evaluate
your nonlinear residual which contains a residual in the boundary
condition and that difference needs to be applied in every step
(assuming you solve for an update in each Newton step).

On Sat, Dec 3, 2022 at 10:56 AM Wolfgang Bangerth
 wrote:
>
> On 12/3/22 07: 11, Abbas wrote: > > Something like this doesn't work with DG. 
> > Loosely speaking, my initial approach would be to solve a system with just 
> the > BC terms but I am not sure. Do I have other options? In DG methods,
> ZjQcmQRYFpfptBannerStart
> This Message Is From an External Sender
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> ZjQcmQRYFpfptBannerEnd
>
> On 12/3/22 07:11, Abbas wrote:
> >
> > Something like this doesn't work with DG.
> > Loosely speaking, my initial approach would be to solve a system with just 
> > the
> > BC terms but I am not sure. Do I have other options?
>
> In DG methods, you impose boundary values weakly, using the same strategy with
> which you impose continuity between cells weakly. You might want to look at
> papers on DG methods: pretty much every single one will show the jump terms
> corresponding to Dirichlet boundary values.
>
> Best
>   W.
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: 
> https://urldefense.com/v3/__http://www.math.colostate.edu/*bangerth/__;fg!!PTd7Sdtyuw!Vf-IQx7HQQ5bIq8xBQu1BzCdpZiz9Q3UC6emGlg1Z50xBT-oA9UeUBtyamyADtrTV0zLEZpa0RBQ_lV6jh5B8Uo$
>
>
> --
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Re: [deal.II] Fast solver for multigrid coarse level

[Timo Heister]

We have a number of tests that do something more sophisticated like an
AMG (which is probably what you want to do if you are running in
parallel with many coarse cells). See for example
https://github.com/dealii/dealii/blob/915ca70fa7c3c2cfa68b632aa162226145b1907f/tests/multigrid/mg_coarse_01.cc#L434

You should be able to get SparseDirectUMFPACK to work in the same way.

On Thu, Sep 29, 2022 at 3:40 AM 'yy.wayne' via deal.II User Group
 wrote:
>
> Hello everyone!
>
> In tutorials the coarest level multigrid is solved either by householder 
> direct sovler for FullMatrix or by a iterative solver based on 
> MGCoarseGridHouseholder and MGCoarseGridIterativeSolver, respectively. 
> However I want to solve the coarest level with a sparse direct solver. Both 2 
> MGCoarseGrid class access MGCoarseGridBase, so SparseDirectUMFPACK cannot be 
> used.
>
> Take step-16 for example. The only way possible I my mind is using PETScMUMPS 
> and put it in MGCoarseGridIterativeSolver, and matrix & vector type need to 
> be changed to PETSc accordingly. Is this gonna work?
>
> --
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Re: [deal.II] Re: copy_triangulation for a refined distributed Triangulation

[Timo Heister]

Is the destination ("triangulation_coarse_" in your case) empty when
you call the function? I think the error message says that it needs to
be empty.

On Thu, Sep 29, 2022 at 5:08 AM Katharina Jerg  wrote:
>
> Dear all,
>
> I am trying to copy an adaptively refined triangulation (not even 
> parallel::distributed::Triangulation) in order to change the refinement at 
> some parts of the mesh, but still keep the original triangulation for futher 
> calculations.
> When I try to copy a simple (not adaptively refined yet) triangulation using 
> " this->triangulation_coarse_.copy_triangulation(this->triangulation_);" I 
> get the following error:
>
> 
> An error occurred in line <11502> of file 
>  in function
> void dealii::Triangulation<,  
> >::copy_triangulation(const dealii::Triangulation<,  
> >&) [with int dim = 3; int spacedim = 3]
> The violated condition was:
> (vertices.size() == 0) && (levels.size() == 0) && (faces == nullptr)
> Additional information:
> You are trying to perform an operation on a triangulation that is only
> allowed if the triangulation is currently empty. However, it currently
> stores 27 vertices and has cells on 2 levels.
>
> Is there a way to copy adaptively refined triangulations by now? I was not 
> able to find an answer to this question in the mailing list or the 
> documentation. I would like to avoid the workaround suggested here, because I 
> need a new copy of the triangulation multiple times during computation.
>
> Thanks,
> Katharina
>
> On Tuesday, September 22, 2015 at 2:00:39 PM UTC+2 Timo Heister wrote:
>>
>> Hey Ben,
>>
>> yes, unfortunately we haven't gotten around implementing this. It
>> actually shouldn't be too difficult, because there is p4est_copy that
>> one can use to clone the p4est (but the connectivity has to be
>> recreated). Sam's suggestions will work as a workaround...
>>
>> On Tue, Sep 22, 2015 at 5:16 AM, Sam Cox  wrote:
>> > Hi Ben,
>> >
>> > it's my understanding that the mesh will be given the same partitioning
>> > after importing, as this is calculated only from the ordering of the cells.
>> > See https://groups.google.com/d/msg/dealii/94G5GU-flag/WEdBGil2WUoJ for
>> > Wolfgang's comment on this. (A caveat: I'd guess things would break if you
>> > have
>> > parallel::distributed:Triangulation::Settings::no_automatic_repartitioning
>> > set).
>> >
>> > As a workaround, if you are happy to have two meshes existing throughout
>> > execution you could do similar to what I once did (in that same thread, for
>> > a different scenario, but it should work in your case) and generate two
>> > unrefined meshes then apply the same refine/coarsen flags to each at each
>> > stage.
>> >
>> > Sam
>> >
>> > --
>> > The deal.II project is located at http://www.dealii.org/
>> > For mailing list/forum options, see
>> > https://groups.google.com/d/forum/dealii?hl=en
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>>
>>
>>
>> --
>> Timo Heister
>> http://www.math.clemson.edu/~heister/
>
> --
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Re: [deal.II] Output the solution to .h5 file (hdf5)

[Timo Heister]

What does the detailed.log say about HDF5? Did you recompile and
install the library afterwards?

I am asking because the error message should only show up if you are
using deal.II without HDF5 support enabled.

On Wed, Sep 7, 2022 at 9:36 PM Judy Lee  wrote:
>
> Thank you, Dr. Heister.
>
> This is what I did to link hdf5 library to dealii-9.3.2 version:
>
> find usr -iname “*hdf5.h” returned /usr/include/hdf5/mpich/hdf5.h
>
> export CPATH="/usr/include/hdf5/mpich/"
>
> export CPATH="/Downloads/dealii-9.3.2/"
>
> cmake -DDEAL_II_WITH_HDF5=ON -DHDF5_DIR=/usr/include/hdf5/mpich 
> -DHDF5_LIBRARY=/usr/lib/x86_64-linux-gnu/libhdf5_mpich.so 
> -DHDF5_HL_LIBRARY=/usr/lib/x86_64-linux-gnu/libhdf5_mpich_hl.so 
> -DDEAL_II_WITH_MPI=ON ../
>
> I have the same error message returned. How to link hdf5 to dealii correctly?
>
> Thank you very much.
>
> Best regards,
>
> Judy
>
> On Wednesday, September 7, 2022 at 1:40:39 PM UTC-4 Timo Heister wrote:
>>
>> You will need to configure deal.II with HDF5 support, see
>> https://www.dealii.org/developer/readme.html#optional-software
>>
>> On Wed, Sep 7, 2022 at 1:23 PM Judy Lee  wrote:
>> >
>> > Hello everyone!
>> >
>> > For the step-3 hdf5 to output the solution data, I have an error message 
>> > returned, like the following:
>> >
>> > [ 66%] Built target step-3
>> >
>> > [100%] Run step-3 with Debug configuration
>> >
>> > Number of active cells: 1024
>> >
>> > Number of degrees of freedom: 1089
>> >
>> > DEAL:cg::Starting value 0.121094
>> >
>> > DEAL:cg::Convergence step 48 value 5.33692e-13
>> >
>> > terminate called after throwing an instance of 
>> > 'dealii::StandardExceptions::ExcMessage'
>> >
>> > what():
>> >
>> > 
>> >
>> > An error occurred in line <7799> of file 
>> > 
>> >  in function
>> >
>> > void dealii::DataOutBase::write_hdf5_parallel(const 
>> > std::vector >&, const 
>> > dealii::DataOutBase::DataOutFilter&, bool, const string&, const string&, 
>> > const MPI_Comm&) [with int dim = 2; int spacedim = 2; std::string = 
>> > std::__cxx11::basic_string; MPI_Comm = int]
>> >
>> > The violated condition was:
>> >
>> > false
>> >
>> > Additional information:
>> >
>> > HDF5 support is disabled.
>> >
>> > 
>> >
>> > make[3]: *** [CMakeFiles/run.dir/build.make:77: CMakeFiles/run] Aborted
>> >
>> > make[2]: *** [CMakeFiles/Makefile2:237: CMakeFiles/run.dir/all] Error 2
>> >
>> > make[1]: *** [CMakeFiles/Makefile2:244: CMakeFiles/run.dir/rule] Error 2
>> >
>> > make: *** [Makefile:202: run] Error 2
>> >
>> >
>> > My modified step-3.cc is attached. I added in the main function (Line 
>> > 685-687), in the class step3 to declare *n_refinement_steps* (Line 100), 
>> > in the function void step3::make_grid() (Line 164-165), and in the 
>> > function void step3::output_results() (Line 606-610). Thank you very much.
>> >
>> > Best regards,
>> >
>> > Judy
>> >
>> > --
>> > The deal.II project is located at http://www.dealii.org/
>> > For mailing list/forum options, see 
>> > https://groups.google.com/d/forum/dealii?hl=en
>> > ---
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>> > "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/595032ef-037b-43fc-a2fa-ab18c8ffb64cn%40googlegroups.com.
>>
>>
>>
>> --
>> Timo Heister
>> http://www.math.clemson.edu/~heister/
>
> --
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Re: [deal.II] Output the solution to .h5 file (hdf5)

[Timo Heister]

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

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

[Timo Heister]

Material IDs should be correct without any extra work.

If your boundary IDs are directly derived from Material IDs, you can assign
them once on the coarse mesh. Otherwise, attaching to the refinement signal
sound like a great approach. (I would have just done the code after mesh
refinement directly, but that doesn't matter).

On Tue, Aug 23, 2022, 03:07 'maurice rohracker' via deal.II User Group <
dealii@googlegroups.com> wrote:

> Thanks, Timo for your response.
>
> I want to clarify a few things:
> - since our material IDs come from the* .inp* mesh file and the material
> IDs will not change due to some physics, they should always be inherited
> during coarsening and refinement and we do not need to take care of them.
> Is it also ensured that locally owned cells will always know their
> neighboring material IDs, or is there some ghost exchange needed using the
> `dealii::GridTools::exchange_cell_data_to_ghosts()` function?
>
> - we are currently making use of the `triangulation_
> .signals.post_distributed_refinement.connect()` functionality which we
> attach a `set_boundary_ids` function looping over all active cells (do not
> check if a cell is locally owned) and call it right after the mesh is read
> in. Is this enough to ensure that the boundary IDs are set properly, or is
> it safer to use `triangulation_.signals.any_change.connect()`?
>
> Best regards,
> Maurice
>
> Timo Heister schrieb am Freitag, 19. August 2022 um 03:48:09 UTC+2:
>
>> Maurice,
>>
>> Reassigning boundary IDs (or manifold IDs, material IDs) is somewhat
>> tricky in parallel as they need to stay consistent.
>>
>> While you would expect the IDs to only matter for locally owned cells,
>> this is not enough because each process needs to know the correct
>> constraints for all "locally active" DoFs. This requires at least the ghost
>> layer to have the correct boundary conditions. Example: a hanging node
>> constraint near a process boundary and the coarse DoFs have boundary values.
>>
>> There following cases are safe:
>> 1. Create coarse mesh, assign IDs the same way for all cells, then do not
>> change IDs. Any refinement/coarsening will keep IDs updated consistently.
>> 2. Go over all ghost and local cells and reassign IDs after any mesh
>> change (refine/coarsen). This can be a bit tricky to get right in all cases.
>>
>> Best,
>> Timo
>>
>>
>> On Thu, Aug 18, 2022, 03:59 'maurice rohracker' via deal.II User Group <
>> dea...@googlegroups.com> wrote:
>>
>>> Dear all,
>>>
>>> We are wondering about the following:
>>> In step-42 the boundary IDs of all active cells of a parallel
>>> distributed triangulation are set manually. Since we faced some issues
>>> while only setting them on locally owned ones, we would like to know the
>>> reason, because most other operations are only done on locally owned cells.
>>> Is this important for the inheritance and the redistribution of cells in
>>> case of spatial adaptivity as well as the interpolate boundary functions?
>>>
>>> Thanks for your help.
>>>
>>> Best, Maurice
>>>
>>> --
>>> The deal.II project is located at http://www.dealii.org/
>>> <https://urldefense.com/v3/__http://www.dealii.org/__;!!PTd7Sdtyuw!SvVyrnekxuaAMdEHjC9FffEHp0J9Hs3p3QOHYXk-pzOd7QgyVIOSAzL8Jx59q3i_Z0zGYMZwpbGFOo_sANw7$>
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>>> .
>>>
>> --
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Re: [deal.II] Setting boundary IDs in a parallel distributed triangulation

[Timo Heister]

Maurice,

Reassigning boundary IDs (or manifold IDs, material IDs) is somewhat tricky
in parallel as they need to stay consistent.

While you would expect the IDs to only matter for locally owned cells, this
is not enough because each process needs to know the correct constraints
for all "locally active" DoFs. This requires at least the ghost layer to
have the correct boundary conditions. Example: a hanging node constraint
near a process boundary and the coarse DoFs have boundary values.

There following cases are safe:
1. Create coarse mesh, assign IDs the same way for all cells, then do not
change IDs. Any refinement/coarsening will keep IDs updated consistently.
2. Go over all ghost and local cells and reassign IDs after any mesh change
(refine/coarsen). This can be a bit tricky to get right in all cases.

Best,
Timo


On Thu, Aug 18, 2022, 03:59 'maurice rohracker' via deal.II User Group <
dealii@googlegroups.com> wrote:

> Dear all,
>
> We are wondering about the following:
> In step-42 the boundary IDs of all active cells of a parallel distributed
> triangulation are set manually. Since we faced some issues while only
> setting them on locally owned ones, we would like to know the reason,
> because most other operations are only done on locally owned cells.
> Is this important for the inheritance and the redistribution of cells in
> case of spatial adaptivity as well as the interpolate boundary functions?
>
> Thanks for your help.
>
> Best, Maurice
>
> --
> 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+unsubscr...@googlegroups.com.
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> 
> .
>

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Re: [deal.II] Solving Step-74 by MPI

[Timo Heister]

For error computations using cellwise errors you can use
VectorTools::compute_global_error(), which does the MPI communication
for you:
https://www.dealii.org/developer/doxygen/deal.II/namespaceVectorTools.html#a21eb62d70953182dcc2b15c4e14dd533

See step-55 for example.

On Wed, Aug 17, 2022 at 1:42 PM Wolfgang Bangerth
 wrote:
>
> On 8/17/22 03:10, chong liu wrote:
> >
> > I modified Step-74 based on the error_estimation part of Step-50. I found it
> > can work for the attached step-74-mpi, while it cannot work for the attached
> > step-74-mpi-error. The only difference is the location of the output command
> > as the attached figure 1 shows. This is weird. The error information states
> > that one vector is out of bounds as shown in figure 2.
>
> The location of the print message isn't the problem -- it's just that because
> you don't end the
>std::cout << "...";
> call with std::endl, the text is put into a buffer but never printed to
> screen. You should run the program in a debugger and check where the erroneous
> access comes from. I bet that if the two programs are otherwise the same, they
> should both fail.
>
>
> > In addition, there are three points I would like to ask
> >
> >  1. The direct solver cannot work for the modified MPI program. I changed it
> > to the iterative solver (solver_cg same as Step-40) since I am not
> > familiar with the MPI direct solver. Could you give me some suggestions 
> > on
> > the direct solver for MPI?
>
> There isn't a good option. There are some parallel direct solvers in both the
> PETSc and Trilinos (for which you can probably find information by searching
> the mailing list archives), but at the end of the day, if the problem becomes
> sufficiently large, even parallel direct solvers cannot compete.
>
>
> >  2. Does not ConvergenceTable support the parallel data output? I found that
> > the first parameter for convergencetable.write_text() is std::out. How 
> > can
> > I modify it to pcout for MPI?
>
> I'm not sure the class supports this, but you can always put a
>if (Utilities::MPI::this_mpi_process(...) == 0)
> in front of the place where you generate output.
>
>
> >  3. I guess the l1_norm() calculation for a vector should be modified. For
> > example, the code std::sqrt(energy_norm_square_per_cell.l1_norm()) 
> > should
> > be modified to std::sqrt
> > 
> > <https://urldefense.com/v3/__https://nam10.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.dealii.org*2Fcurrent*2Fdoxygen*2Fdeal.II*2Fnamespacestd.html*23aa2def4dc0bd5b6d07af7aff83feba9b2&data=05*7C01*7CWolfgang.Bangerth*40colostate.edu*7C8676b13756db4734d87408da803061ae*7Cafb58802ff7a4bb1ab21367ff2ecfc8b*7C0*7C0*7C637963243499566483*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C2000*7C*7C*7C&sdata=G7i0Xg9AQIQkzIUAodl745glNO9sRfgnok1piSbkatM*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!PTd7Sdtyuw!QO7eTW5kBhW7q3_5N54yZsv-uBFuFmPb-34csveLecKNqiHWY-Dvroos6-RjWwuJhwHp3T_urOOoL15wN9um0II$
> >   >(Utilities::MPI::sum
> > 
> > <https://urldefense.com/v3/__https://nam10.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.dealii.org*2Fcurrent*2Fdoxygen*2Fdeal.II*2FnamespaceUtilities_1_1MPI.html*23ab544a3bf3301a6dd3e705ee352c5551b&data=05*7C01*7CWolfgang.Bangerth*40colostate.edu*7C8676b13756db4734d87408da803061ae*7Cafb58802ff7a4bb1ab21367ff2ecfc8b*7C0*7C0*7C637963243499566483*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C2000*7C*7C*7C&sdata=dZzc08aCivKuCOOuxnaeEr0ZBSnMB3qRzuVUNDTShvY*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!PTd7Sdtyuw!QO7eTW5kBhW7q3_5N54yZsv-uBFuFmPb-34csveLecKNqiHWY-Dvroos6-RjWwuJhwHp3T_urOOoL15wBuy3vhk$
> >   >(estimated_error_square_per_cell.l1_norm(),
> > mpi_communicator)).
>
> Yes, something like this.
>
> Best
>   W.
>
>
> --
> --------
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: 
> https://urldefense.com/v3/__http://www.math.colostate.edu/*bangerth/__;fg!!PTd7Sdtyuw!QO7eTW5kBhW7q3_5N54yZsv-uBFuFmPb-34csveLecKNqiHWY-Dvroos6-RjWwuJhwHp3T_urOOoL15w0hl1NSs$
>


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Re: [deal.II] Solving Step-74 by MPI

[Timo Heister]

Hi Chong,

MeshWorker does work without much effort in MPI parallel code and is
made to help with exactly this (who assembles what is non-trivial if
you have hanging nodes and processor boundaries). The only thing you
have to watch out for is supplying the right flags that determine the
cells and faces that will be assembled. I don't think we have a
step-12 or -74 with MPI, but there is the error estimator in step-50:
https://www.dealii.org/current/doxygen/deal.II/step_50.html#Theerrorestimator

You probably want the flags
MeshWorker::assemble_own_cells |
MeshWorker::assemble_ghost_faces_once |
MeshWorker::assemble_own_interior_faces_once

(or _both for both of them if you want to assemble each face twice).


On Fri, Aug 12, 2022 at 11:41 PM chong liu  wrote:
>
> Dear community,
>
> I have a problem in the assembly part when solving Step-74 (DG method) by 
> MPI. Generally speaking, we can first determine whether one cell is locally 
> owned or not by cell->is_locally_owned(), and then assemble matrices and 
> residuals by hands (e.g. Step-40 for CG and “Distributed LDG Method” for DG 
> in code gallery). However, Step-74 using Meshworker and FEInterfaceValues 
> classes automatically loops and assembles all cells, faces, and interfaces. 
> My question is how to identify one cell which is locally owned or not in 
> Step-74. Is there any deal.II code combining discontinuous Galerkin method 
> (which uses FEInterfaceValues class, e.g. Step-12 and Step-74) with MPI 
> (either PETSc or Trilinos)? Any help is going to be appreciated.
>
> Thanks and regards,
>
> Chong
>
> --
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Re: [deal.II] Installation problem using spack

[Timo Heister]

Your issue might be related to the 
bug https://github.com/dealii/dealii/issues/14065 (see the discussion and 
the linked PR that should solve the problem for deal.II master, but not 9.4)

On Tuesday, August 9, 2022 at 1:23:55 PM UTC-4 d.arnd...@gmail.com wrote:

> Marco,
>
> It appears that
>
> -- Insufficient hdf5 installation found: hdf5 has to be configured with 
> MPI support.
>
> is the problem. HDF5 has not been compiled with MPI support. Thus, you can 
> either try to make sure that HDF5 is built with MPI support or, in case you 
> are not going to use HDF5 anyway, just disable the dependency.
>
> Best,
> Daniel
>
> On Tue, Aug 9, 2022 at 7:41 AM Marco Nawijn  wrote:
>
>> Dear All,
>>
>> I run into an issue when trying to install dealii using spack. The error 
>> is as follows:
>>
>>   Could not find the hdf5 library!
>>
>>   Insufficient hdf5 installation found!
>>
>>   hdf5 has to be configured with MPI support.
>>
>>   Please ensure that a suitable hdf5 library is installed on your 
>> computer.
>>
>>   If the library is not at a default location, either provide some hints 
>> for
>>   autodetection,
>>
>> A complete log and additional information is provided in the two 
>> attachments.
>> I am a little lost at the moment because as far as I can tell, the 
>> installation process finds the correct HDF5 folder (I checked the tags). In 
>> addition, I installed HDF5 using spack with MPI, C++ and Fortran support (I 
>> added the output of `tree` to the attachment). 
>>
>> I am a little at loss now, because I don't know what dealii is exactly 
>> missing from the HDF5 installation.
>>
>> The system is just a laptop, so nothing cluster like.
>>
>> Just as a side note. I am pretty impressed with the easy and flexibility 
>> of spack. All other dependencies installed without a hitch (petsc, 
>> sundials, trilinios etc.).
>>
>> Does anybody have an idea of what the problem is?
>>
>> Any help is highly appreciated. 
>>
>> Marco
>> P.S. I am a complete novice with dealii, but otherwise comfortable in the 
>> linux eco-system.
>>
>> -- 
>> The deal.II project is located at http://www.dealii.org/
>> For mailing list/forum options, see 
>> https://groups.google.com/d/forum/dealii?hl=en
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>>  
>> 
>> .
>>
>

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[deal.II] ASPECT 2.4.0 released

[Timo Heister]

Hi all,

We recently released version 2.4.0 of ASPECT, the Advanced Solver for
Problems in Earth's ConvecTion, which is built on deal.II.

If you are curious you can check https://aspect.geodynamics.org/ and
https://github.com/geodynamics/aspect/releases/tag/v2.4.0 for more
information about ASPECT.

Best,
Timo

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Re: [deal.II] Unexpected GMRES behavior

[Timo Heister]

Hi Kyle,

> I'm solving a nonlinear, time-dependent problem with a combination of 
> periodic and Dirichlet boundary conditions.

Is your linear system singular (has a nullspace) like constant
pressures or due to periodicity? If yes, that can cause an issue if
your preconditioner does not exactly leave this nullspace alone.
> // Restart after 30 gmres iterations, using left preconditioning.
> SolverGMRES>::AdditionalData 
> additional_data(30,false);

I always recommend using right preconditioning, because the reported
residuals are otherwise preconditioned residuals and depend on the
preconditioner itself.

> Additionally, and most surprisingly, even though convergence is indicated, 
> the solver does not seem to be converging to the desired tolerance.

This is typical with left preconditioning.

> As a side question, can anyone explain why the RHS vector changes when I 
> apply the affine constraints object to it, even though I assembled the matrix 
> with 
> constraints.distribute_local_to_global(local_matrix,local_rhs,local_dof_indices,system_matrix,system_rhs);

distribute() sets constrained values to the correct value (for example
non-homogeneous Dirichlet conditions.


Best,
Timo

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Re: [deal.II] Re: Unable to install using candi - problem building trilinios

[Timo Heister]

Yes, this means you are running out of RAM. Either reduce the number
of cores you compile with (try -j 1) or use a machine with more
memory.

On Sun, Apr 24, 2022 at 6:30 AM Amogh Sanjay  wrote:
>
>
> Hi, my ubuntu version is Ubuntu 20.04.4
> On Sunday, April 24, 2022 at 3:54:40 PM UTC+5:30 Amogh Sanjay wrote:
>>
>> Hello everyone,
>>
>> I tried installing deal.ii today using candi on my Linux. 
>> https://github.com/dealii/candi .I have run into some problems when it was 
>> trying to build trilinios. Is there anything I can do to fix it?
>>
>> Any help would be appreciated. Thanks in advance.
>>
>> Amogh
>>
> --
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[deal.II] Re: Postdoc Position at Clemson University

[Timo Heister]

Hi all,

I am still looking to hire a postdoc and just extended the application
deadline. Please forward this opening to people who might be
interested.

Thanks.

On Tue, Mar 22, 2022 at 10:30 PM Timo Heister  wrote:
>
> Hi all,
>
> I am hiring a postdoc to work on the Finite Element Method and High
> Performance Computing related to deal.II and ASPECT. Expertise in
> solvers (multigrid), CFD, and visualization is a plus.
> The official ad is here: https://apply.interfolio.com/104441
>
> Please feel free to reach out to me!
>
> Best,
> Timo Heister
>
> --
> Timo Heister
> http://www.math.clemson.edu/~heister/



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Re: [deal.II] Error installing dealii by candi on Apple M1

[Timo Heister]

Can you post the output of "grep HDF5 detailed.log" in the directory 
/Users/fr714/dealii-candi-basic/tmp/unpack/deal.II-v9.3.3/ please?


On Tuesday, April 5, 2022 at 9:18:01 AM UTC-4 freddri...@gmail.com wrote:

> I also have the same issue, irrespective of whether I try to compile using 
> the v9.3.3 or the master version of deal.ii. I'm on Apple M1 Monterey 12.3.
>
> Here's the compilation error for source/base/hdf5.cc:
>
> In file included from 
> /Users/fr714/dealii-candi-basic/tmp/unpack/deal.II-v9.3.3/source/base/hdf5.cc:20:
>
> /Users/fr714/dealii-candi-basic/tmp/unpack/deal.II-v9.3.3/include/deal.II/base/hdf5.h:1470:30:
>  
> error: use of undeclared identifier 'H5Pset_dxpl_mpio'
>
>   const herr_t ret = H5Pset_dxpl_mpio(plist, H5FD_MPIO_COLLECTIVE);
>
>  ^
>
> /Users/fr714/dealii-candi-basic/tmp/unpack/deal.II-v9.3.3/include/deal.II/base/hdf5.h:1502:21:
>  
> error: use of undeclared identifier 'H5Pget_mpio_actual_io_mode'
>
>   ret = H5Pget_mpio_actual_io_mode(plist, &io_mode);
>
> ^
>
> /Users/fr714/dealii-candi-basic/tmp/unpack/deal.II-v9.3.3/include/deal.II/base/hdf5.h:1505:17:
>  
> error: use of undeclared identifier 'H5Pget_mpio_no_collective_cause'
>
> H5Pget_mpio_no_collective_cause(plist,
>
> ^
>
> 3 errors generated.
>
> Seems odd as the correct version of hdf5 and all associated libraries 
> seems to be found OK in the configuration step.
>
> On Friday, April 1, 2022 at 8:09:31 AM UTC+1 hemi...@stanford.edu wrote:
>
>> Hi! I am also trying to install Dealii on Apple M1 Monterey 12.2.1. I 
>> also got similar "failure with exit status: 2". May I ask what is the 
>> difference between the master version in this conversation and v9.3.3? Many 
>> thanks in advance.
>>
>> On Friday, March 18, 2022 at 7:29:46 AM UTC-7 masou...@gmail.com wrote:
>>
>>> I removed this Master version, and install 9.3.3 version, it worked!
>>> Many thanks Timo.
>>> On Friday, 18 March 2022 at 13:46:01 UTC Masoud Ahmadi wrote:
>>>
>>>> Thanks Timo.
>>>> I removed homebrew entirely, then reinstall it and just run:
>>>> brew install cmake open-mpi gcc
>>>>
>>>> Then I install the master version, this time the setup was completed; 
>>>> however, when I tried to run step-1 example, this happened:
>>>> [image: Screenshot 2022-03-18 at 12.30.12.png]
>>>> On Wednesday, 16 March 2022 at 15:17:09 UTC Timo Heister wrote:
>>>>
>>>>> > # SCALAPACK_LIBRARIES = /opt/homebrew/lib/libscalapack.dylib;-lm;- 
>>>>>
>>>>> It looks like you have a scalapack installation that got picked up and 
>>>>> caused the error. Can you do 
>>>>> cmake -D DEAL_II_WITH_SCALAPACK=OFF . 
>>>>> in the directory where you found the detailed.log? Follow that by 
>>>>> make install 
>>>>> (you can use -j to use more cores of course). 
>>>>>
>>>>>
>>>>> On Wed, Mar 16, 2022 at 9:42 AM Masoud Ahmadi  
>>>>> wrote: 
>>>>> > 
>>>>> > I had removed candi, so I had to reinstall it. 
>>>>> > But again got the same error. 
>>>>> > The requested log file is attached. Please see. 
>>>>> > 
>>>>> > 
>>>>> > 
>>>>> > On Tuesday, 15 March 2022 at 13:00:35 UTC Timo Heister wrote: 
>>>>> >> 
>>>>> >> Can you please post your 
>>>>> /Users/masoud/dealii-candi/tmp/build/deal.II-master/detailed.log ? 
>>>>> >> 
>>>>> >> On Tue, Mar 15, 2022 at 7:18 AM Masoud Ahmadi  
>>>>> wrote: 
>>>>> >>> 
>>>>> >>> Thanks Timo, 
>>>>> >>> 
>>>>> >>> I tried to switch to master, but again the same thing happened. 
>>>>> >>> So, now on the master branch of candi, same error. 
>>>>> >>> I attached the log file, please take a look. 
>>>>> >>> 
>>>>> >>> 
>>>>> >>> On Sunday, 13 March 2022 at 19:55:52 UTC Timo Heister wrote: 
>>>>> >>>> 
>>>>> >>>> What candi git branch are you on? You might need to switch to 
>>>>> master to make things work for now. 
>>>>> >>>> 
>>>>> >

Re: [deal.II] Re: Clemson Computational Math Seminar: Bruno Blais - Feb 4

[Timo Heister]

Hi all,

I can not share a recording at this point, sorry.

On Fri, Apr 1, 2022 at 11:48 PM Praveen C  wrote:
>
> Is the video of this talk archived somewhere ?
> Thanks
> praveen
>
> On Friday, March 25, 2022 at 10:42:11 PM UTC+5:30 Timo Heister wrote:
>>
>> Hi all,
>>
>> I would like to announce the following seminar talk in our Clemson
>> Computational Math seminar that is related to deal.II. If you are
>> interested, feel free to join using the zoom link below.
>>
>> Date and time: Monday, March 28 at 11:15am Eastern time
>> Speaker: Matthias Maier (Texas A&M University)
>> Title: Efficient parallel 3d computation of the compressible
>> Navier-Stokes equations
>>
>> Zoom link: https://clemson.zoom.us/j/96402109287
>>
>> Abstract:
>> A high-performance second-order collocation-type finite-element scheme for
>> solving the compressible Navier-Stokes equations on unstructured meshes is
>> presented. The method uses Strang splitting, is second-order accurate in
>> time and space, and is based on a convex limiting technique introduced by
>> Guermond et al. (SIAM J. Sci. Comput. 40, A3211-A3239, 2018). As such it is
>> invariant-domain preserving, meaning, the solver maintains important
>> physical invariants and is guaranteed to be stable without the use of
>> ad-hoc tuning parameters.
>> In this talk I will introduce the discretization technique, discuss the
>> convex limiting approach and algorithmic design of the method, and comment
>> on a high-performance implementation utilizing SIMD (single instruction
>> multiple data) vectorization.
>>
>> --
>> Timo Heister
>> http://www.math.clemson.edu/~heister/
>
> --
> The deal.II project is located at http://www.dealii.org/
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[deal.II] Re: Clemson Computational Math Seminar: Bruno Blais - Feb 4

[Timo Heister]

Hi all,

I am sorry for messing up the title. The talk is of course given on
Monday by Matthias as written in the body of the email.

Best,
Timo

On Fri, Mar 25, 2022 at 1:11 PM Timo Heister  wrote:
>
> Hi all,
>
> I would like to announce the following seminar talk in our Clemson
> Computational Math seminar that is related to deal.II. If you are
> interested, feel free to join using the zoom link below.
>
> Date and time: Monday, March 28 at 11:15am Eastern time
> Speaker: Matthias Maier (Texas A&M University)
> Title: Efficient parallel 3d computation of the compressible
> Navier-Stokes equations
>
> Zoom link: https://clemson.zoom.us/j/96402109287
>
> Abstract:
> A high-performance second-order collocation-type finite-element scheme for
> solving the compressible Navier-Stokes equations on unstructured meshes is
> presented. The method uses Strang splitting, is second-order accurate in
> time and space, and is based on a convex limiting technique introduced by
> Guermond et al. (SIAM J. Sci. Comput. 40, A3211-A3239, 2018). As such it is
> invariant-domain preserving, meaning, the solver maintains important
> physical invariants and is guaranteed to be stable without the use of
> ad-hoc tuning parameters.
> In this talk I will introduce the discretization technique, discuss the
> convex limiting approach and algorithmic design of the method, and comment
> on a high-performance implementation utilizing SIMD (single instruction
> multiple data) vectorization.
>
> --
> Timo Heister
> http://www.math.clemson.edu/~heister/



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[deal.II] Clemson Computational Math Seminar: Bruno Blais - Feb 4

[Timo Heister]

Hi all,

I would like to announce the following seminar talk in our Clemson
Computational Math seminar that is related to deal.II. If you are
interested, feel free to join using the zoom link below.

Date and time: Monday, March 28 at 11:15am Eastern time
Speaker: Matthias Maier (Texas A&M University)
Title: Efficient parallel 3d computation of the compressible
Navier-Stokes equations

Zoom link: https://clemson.zoom.us/j/96402109287

Abstract:
A high-performance second-order collocation-type finite-element scheme for
solving the compressible Navier-Stokes equations on unstructured meshes is
presented. The method uses Strang splitting, is second-order accurate in
time and space, and is based on a convex limiting technique introduced by
Guermond et al. (SIAM J. Sci. Comput. 40, A3211-A3239, 2018). As such it is
invariant-domain preserving, meaning, the solver maintains important
physical invariants and is guaranteed to be stable without the use of
ad-hoc tuning parameters.
In this talk I will introduce the discretization technique, discuss the
convex limiting approach and algorithmic design of the method, and comment
on a high-performance implementation utilizing SIMD (single instruction
multiple data) vectorization.

-- 
Timo Heister
http://www.math.clemson.edu/~heister/

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[deal.II] Postdoc Position at Clemson University

[Timo Heister]

Hi all,

I am hiring a postdoc to work on the Finite Element Method and High
Performance Computing related to deal.II and ASPECT. Expertise in
solvers (multigrid), CFD, and visualization is a plus.
The official ad is here: https://apply.interfolio.com/104441

Please feel free to reach out to me!

Best,
Timo Heister

-- 
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Re: [deal.II] Error with PETScWrappers::PreconditionILU

[Timo Heister]

PreconditionBlockJacobi is a parallel ILU. I am not sure what you want
to do instead?
(also take a look at the documentation:
https://www.dealii.org/developer/doxygen/deal.II/classPETScWrappers_1_1PreconditionBlockJacobi.html
)

On Fri, Mar 18, 2022 at 11:02 AM Hermes Sampedro
 wrote:
>
> Dear Timo,
>
> thank you for your answer. Is there any other option for ILU with parallel 
> matrices apart of Block Jacobi?
>
> Thank you
> Regards
>
> El martes, 15 de marzo de 2022 a las 18:45:29 UTC+1, Timo Heister escribió:
>>
>> Hi,
>>
>> > [0]PETSC ERROR: See 
>> > https://www.mcs.anl.gov/petsc/documentation/linearsolvertable.html for 
>> > possible LU and Cholesky solvers
>> > [0]PETSC ERROR: Could not locate a solver package for factorization type 
>> > ILU and matrix type mpiaij.
>>
>> This means that ILU is not available for parallel matrices (mpiaij).
>> You need to pick a different preconditioner. You can try
>> PreconditionBlockJacobi which is a blocked ILU and probably what you
>> wanted to do.
>>
>>
>> On Tue, Mar 15, 2022 at 12:39 PM Hermes Sampedro
>>  wrote:
>> >
>> > Dear all,
>> >
>> > I am getting a running error that I can not really understand when calling 
>> > PETScWrappers::PreconditionILU preconditioner(system_matrix). However, it 
>> > seems to work with PETScWrappers::PreconditionBlockJacobi 
>> > preconditioner(system_matrix).
>> >
>> > May I ask for help to understand/solve this issue? The solver function ad 
>> > error that I get is the following:
>> >
>> > void LaplaceProblem::solve()
>> >
>> > {
>> >
>> > PETScWrappers::MPI::Vector 
>> > completely_distributed_solution(locally_owned_dofs,mpi_communicator);
>> >
>> > SolverControl cn(completely_distributed_solution.size(), 1e-8 * 
>> > system_rhs.l2_norm());
>> >
>> > PETScWrappers::SolverGMRES solver(cn, mpi_communicator);
>> >
>> > PETScWrappers::PreconditionILU preconditioner(system_matrix);
>> >
>> > solver.solve(system_matrix, completely_distributed_solution, system_rhs, 
>> > preconditioner);
>> >
>> > constraints.distribute(completely_distributed_solution);
>> >
>> > locally_relevant_solution = completely_distributed_solution;
>> >
>> > }
>> >
>> >
>> > [0]PETSC ERROR: - Error Message 
>> > --
>> >
>> > [0]PETSC ERROR: See 
>> > https://www.mcs.anl.gov/petsc/documentation/linearsolvertable.html for 
>> > possible LU and Cholesky solvers
>> >
>> > [0]PETSC ERROR: Could not locate a solver package for factorization type 
>> > ILU and matrix type mpiaij.
>> >
>> > [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html 
>> > for trouble shooting.
>> >
>> > [0]PETSC ERROR: Petsc Release Version 3.13.1, May 02, 2020
>> >
>> > [0]PETSC ERROR: ./waveLaplaceSolver on a named gbarlogin1 by hsllo Fri Mar 
>> > 11 11:05:23 2022
>> >
>> > [0]PETSC ERROR: Configure options 
>> > --prefix=/zhome/32/9/115503/dealii-candi/petsc-3.13.1 --with-debugging=0 
>> > --with-shared-libraries=1 --with-mpi=1 --with-x=0 --with-64-bit-indices=0 
>> > --download-hypre=1 CC=mpicc CXX=mpicxx FC=mpif90 
>> > --with-blaslapack-dir=/appl/OpenBLAS/0.3.17/XeonE5-2660v3/gcc-11.2.0/lib 
>> > --with-parmetis-dir=/zhome/32/9/115503/dealii-candi/parmetis-4.0.3 
>> > --with-metis-dir=/zhome/32/9/115503/dealii-candi/parmetis-4.0.3 
>> > --download-scalapack=1 --download-mumps=1
>> >
>> > [0]PETSC ERROR: #1 MatGetFactor() line 4492 in 
>> > /zhome/32/9/115503/dealii-candi/tmp/build/petsc-lite-3.13.1/src/mat/interface/matrix.c
>> >
>> > [0]PETSC ERROR: #2 PCSetUp_ILU() line 133 in 
>> > /zhome/32/9/115503/dealii-candi/tmp/build/petsc-lite-3.13.1/src/ksp/pc/impls/factor/ilu/ilu.c
>> >
>> > [0]PETSC ERROR: #3 PCSetUp() line 894 in 
>> > /zhome/32/9/115503/dealii-candi/tmp/build/petsc-lite-3.13.1/src/ksp/pc/interface/precon.c
>> >
>> > 
>> >
>> > Exception on processing:
>> >
>> > 
>> >
>> > An error occurred in line <431> of file 
>> > 
>> >  in function
>> >
>> > void dealii::PETScWrappers::Prec

Re: [deal.II] Error installing dealii by candi on Apple M1

[Timo Heister]

> # SCALAPACK_LIBRARIES = /opt/homebrew/lib/libscalapack.dylib;-lm;-

It looks like you have a scalapack installation that got picked up and
caused the error. Can you do
cmake -D DEAL_II_WITH_SCALAPACK=OFF .
in the directory where you found the detailed.log? Follow that by
make install
(you can use -j to use more cores of course).


On Wed, Mar 16, 2022 at 9:42 AM Masoud Ahmadi  wrote:
>
> I had removed candi, so I had to reinstall it.
> But again got the same error.
> The requested log file is attached. Please see.
>
>
>
> On Tuesday, 15 March 2022 at 13:00:35 UTC Timo Heister wrote:
>>
>> Can you please post your 
>> /Users/masoud/dealii-candi/tmp/build/deal.II-master/detailed.log ?
>>
>> On Tue, Mar 15, 2022 at 7:18 AM Masoud Ahmadi  wrote:
>>>
>>> Thanks Timo,
>>>
>>> I tried to switch to master, but again the same thing happened.
>>> So, now on the master branch of candi, same error.
>>> I attached the log file, please take a look.
>>>
>>>
>>> On Sunday, 13 March 2022 at 19:55:52 UTC Timo Heister wrote:
>>>>
>>>> What candi git branch are you on? You might need to switch to master to 
>>>> make things work for now.
>>>>
>>>> Can you post how you execute candi.sh including the first few pages of 
>>>> output?
>>>>
>>>> On Sun, Mar 13, 2022, 06:42 Masoud Ahmadi  wrote:
>>>>>
>>>>> Dear Timo,
>>>>>
>>>>> No, I did not change anything; I did exactly what is explained in the 
>>>>> following link, step by step:
>>>>> https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX
>>>>>
>>>>> On Saturday, 12 March 2022 at 16:54:56 UTC Timo Heister wrote:
>>>>>>
>>>>>> Did you make any changes to candi.cfg? Can you also please post how you 
>>>>>> execute candi.sh (what arguments)?
>>>>>>
>>>>>> On Mon, Mar 7, 2022, 12:23 Masoud Ahmadi  wrote:
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I am trying to install dealii on a apple ARM M1 OSX, using the 
>>>>>>> following instructor:
>>>>>>> https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX
>>>>>>>
>>>>>>> However, I get the following error:
>>>>>>>
>>>>>>>
>>>>>>> error: use of undeclared identifier 'H5Pset_dxpl_mpio'
>>>>>>>   status   = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT);
>>>>>>>  ^
>>>>>>> /Users/masoud/dealii-candi/tmp/unpack/deal.II-v9.3.3/source/lac/scalapack.cc:3242:63:
>>>>>>>  warning: unused parameter 'filename' [-Wunused-parameter]
>>>>>>> ScaLAPACKMatrix::load_parallel(const std::string &filename)
>>>>>>>   ^
>>>>>>> /Users/masoud/dealii-candi/tmp/unpack/deal.II-v9.3.3/source/lac/scalapack.cc:2861:20:
>>>>>>>  error: use of undeclared identifier 'H5Pset_fapl_mpio'
>>>>>>>   status = H5Pset_fapl_mpio(plist_id, 
>>>>>>> tmp.grid->mpi_communicator, info);
>>>>>>>^
>>>>>>> /Users/masoud/dealii-candi/tmp/build/deal.II-v9.3.3/source/lac/scalapack.inst:10:16:
>>>>>>>  note: in instantiation of member function 
>>>>>>> 'dealii::ScaLAPACKMatrix::save_parallel' requested here
>>>>>>> template class ScaLAPACKMatrix< double >;
>>>>>>>^
>>>>>>> /Users/masoud/dealii-candi/tmp/unpack/deal.II-v9.3.3/source/lac/scalapack.cc:2861:20:
>>>>>>>  error: use of undeclared identifier 'H5Pset_fapl_mpio'
>>>>>>>   status = H5Pset_fapl_mpio(plist_id, 
>>>>>>> tmp.grid->mpi_communicator, info);
>>>>>>>^
>>>>>>> /Users/masoud/dealii-candi/tmp/build/deal.II-v9.3.3/source/lac/scalapack.inst:20:16:
>>>>>>>  note: in instantiation of member function 
>>>>>>> 'dealii::ScaLAPACKMatrix::save_parallel' requested here
>>>>>>> template class ScaLAPACKMatrix< float >;
>>>>>>>^
>>>>>>> 1 warning and 3 errors generated.
&g

Re: [deal.II] Error with PETScWrappers::PreconditionILU

[Timo Heister]

Hi,

> [0]PETSC ERROR: See 
> https://www.mcs.anl.gov/petsc/documentation/linearsolvertable.html for 
> possible LU and Cholesky solvers
> [0]PETSC ERROR: Could not locate a solver package for factorization type ILU 
> and matrix type mpiaij.

This means that ILU is not available for parallel matrices (mpiaij).
You need to pick a different preconditioner. You can try
PreconditionBlockJacobi which is a blocked ILU and probably what you
wanted to do.


On Tue, Mar 15, 2022 at 12:39 PM Hermes Sampedro
 wrote:
>
> Dear all,
>
> I am getting a running error that I can not really understand when calling 
> PETScWrappers::PreconditionILU preconditioner(system_matrix). However, it 
> seems to work with  PETScWrappers::PreconditionBlockJacobi 
> preconditioner(system_matrix).
>
> May I ask for help to understand/solve this issue? The solver function ad 
> error that I get is the following:
>
> void LaplaceProblem::solve()
>
>{
>
>PETScWrappers::MPI::Vector 
> completely_distributed_solution(locally_owned_dofs,mpi_communicator);
>
>  SolverControl cn(completely_distributed_solution.size(), 1e-8 * 
> system_rhs.l2_norm());
>
>   PETScWrappers::SolverGMRES solver(cn, mpi_communicator);
>
>PETScWrappers::PreconditionILU preconditioner(system_matrix);
>
>  solver.solve(system_matrix, completely_distributed_solution, 
> system_rhs, preconditioner);
>
>constraints.distribute(completely_distributed_solution);
>
>locally_relevant_solution = completely_distributed_solution;
>
>}
>
>
> [0]PETSC ERROR: - Error Message 
> --
>
> [0]PETSC ERROR: See 
> https://www.mcs.anl.gov/petsc/documentation/linearsolvertable.html for 
> possible LU and Cholesky solvers
>
> [0]PETSC ERROR: Could not locate a solver package for factorization type ILU 
> and matrix type mpiaij.
>
> [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for 
> trouble shooting.
>
> [0]PETSC ERROR: Petsc Release Version 3.13.1, May 02, 2020
>
> [0]PETSC ERROR: ./waveLaplaceSolver on a  named gbarlogin1 by hsllo Fri Mar 
> 11 11:05:23 2022
>
> [0]PETSC ERROR: Configure options 
> --prefix=/zhome/32/9/115503/dealii-candi/petsc-3.13.1 --with-debugging=0 
> --with-shared-libraries=1 --with-mpi=1 --with-x=0 --with-64-bit-indices=0 
> --download-hypre=1 CC=mpicc CXX=mpicxx FC=mpif90 
> --with-blaslapack-dir=/appl/OpenBLAS/0.3.17/XeonE5-2660v3/gcc-11.2.0/lib 
> --with-parmetis-dir=/zhome/32/9/115503/dealii-candi/parmetis-4.0.3 
> --with-metis-dir=/zhome/32/9/115503/dealii-candi/parmetis-4.0.3 
> --download-scalapack=1 --download-mumps=1
>
> [0]PETSC ERROR: #1 MatGetFactor() line 4492 in 
> /zhome/32/9/115503/dealii-candi/tmp/build/petsc-lite-3.13.1/src/mat/interface/matrix.c
>
> [0]PETSC ERROR: #2 PCSetUp_ILU() line 133 in 
> /zhome/32/9/115503/dealii-candi/tmp/build/petsc-lite-3.13.1/src/ksp/pc/impls/factor/ilu/ilu.c
>
> [0]PETSC ERROR: #3 PCSetUp() line 894 in 
> /zhome/32/9/115503/dealii-candi/tmp/build/petsc-lite-3.13.1/src/ksp/pc/interface/precon.c
>
> 
>
> Exception on processing:
>
> 
>
> An error occurred in line <431> of file 
> 
>  in function
>
> void dealii::PETScWrappers::PreconditionILU::initialize(const 
> dealii::PETScWrappers::MatrixBase&, const 
> dealii::PETScWrappers::PreconditionILU::AdditionalData&)
>
> The violated condition was:
>
> ierr == 0
>
> Additional information:
>
> deal.II encountered an error while calling a PETSc function.
>
> The description of the error provided by PETSc is "See
>
> https://www.mcs.anl.gov/petsc/documentation/linearsolvertable.html for
>
> possible LU and Cholesky solvers".
>
> The numerical value of the original error code is 92.
>
>
>
>
> Thank you very much
>
> Regards,
>
> H
>
> --
> 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.
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> https://groups.google.com/d/msgid/dealii/c4109bcf-cd4e-453e-9c81-9ed1230a235cn%40googlegroups.com.



-- 
Timo Heister
http://www.math.clemson.edu/~heister/

-- 
The deal.II project is located at http:/

Re: [deal.II] Error when compiling a deal.II app using Trilinos on Apple M1

[Timo Heister]

What program causes the error? Can you post the complete error output?

Updating might help, yes. std::bind1st was removed in c++17 and so
trilinos needs to be updated.

On Tue, Mar 15, 2022 at 10:58 AM blais...@gmail.com
 wrote:
>
> Still can't get it to work. It seems to be related to a specific Tpetra file:
> "Tpetra_Import_def.hpp"
> I'll try with a more recent version of Trilinos to see if this fixes thing. 
> Do you think it might be that step-32 does not include this file ?
>
>
> On Tuesday, March 15, 2022 at 10:55:35 a.m. UTC-4 blais...@gmail.com wrote:
>>
>> Step-32 worked. I think there was an issue with the way I set-up my dylib. 
>> I'll investigate, but it seems that since I was able to run step-32 with 
>> MPI, I should be ok on my side also :)
>> I'll keep you informed if this pops up again.
>>
>>
>> On Monday, March 14, 2022 at 8:57:01 p.m. UTC-4 Timo Heister wrote:
>>>
>>> I worked on that. 😃
>>>
>>> Interestingly, I didn't see this error in my testing of ASPECT. Are
>>> you saying that a deal.II step like step-32 fails? I think we should
>>> try updating Trilinos first.
>>>
>>> Do you want to try 13.2 and see if that works? If not, I will update
>>> the package in candi master when I get to it in a couple of days.
>>>
>>>
>>> On Mon, Mar 14, 2022, 13:25 blais...@gmail.com  wrote:
>>> >
>>> > Dear all,
>>> > Hope you are well
>>> > Using the candi master branch, I succeeded in compiling deal.II using 
>>> > candi. Everything was smooth. I don't know who took care of that, but 
>>> > awesome work.
>>> >
>>> > When trying to compile an example that uses Trilinos (any), I get the 
>>> > following error that arise from an include in Trilinos
>>> >
>>> > Users/blaisb/work/candi/trilinos-release-12-18-1/include/Tpetra_Import_def.hpp:1171:24:
>>> >  error: no member named 'bind1st' in namespace 'std'; did you mean 
>>> > 'boost::container::bind1st'?
>>> >
>>> > std::bind1st (std::equal_to (), -1));
>>> >
>>> > ^
>>> >
>>> > /Users/blaisb/work/candi/deal.II-master/include/deal.II/bundled/boost/container/detail/algorithm.hpp:55:24:
>>> >  note: 'boost::container::bind1st' declared here
>>> >
>>> > inline binder1st bind1st(const Func& func, const T& arg)
>>> >
>>> >
>>> >
>>> > Is there a way around this error? Should I try to manually fix it or 
>>> > switch to another trilinos version?
>>> >
>>> > Thanks!
>>> >
>>> > Bruno
>>> >
>>> >
>>> > --
>>> > The deal.II project is located at http://www.dealii.org/
>>> > For mailing list/forum options, see 
>>> > https://groups.google.com/d/forum/dealii?hl=en
>>> > ---
>>> > You received this message because you are subscribed to the Google Groups 
>>> > "deal.II User Group" group.
>>> > To unsubscribe from this group and stop receiving emails from it, send an 
>>> > email to dealii+un...@googlegroups.com.
>>> > To view this discussion on the web visit 
>>> > https://groups.google.com/d/msgid/dealii/fc6ad924-8776-4fa8-8a6f-5c96c44a0c47n%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/7f7277e9-5279-4bba-9bab-e75afb05986an%40googlegroups.com.



-- 
Timo Heister
http://www.math.clemson.edu/~heister/

-- 
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Re: [deal.II] Error installing dealii by candi on Apple M1

[Timo Heister]

Can you please post
your /Users/masoud/dealii-candi/tmp/build/deal.II-master/detailed.log ?

On Tue, Mar 15, 2022 at 7:18 AM Masoud Ahmadi  wrote:

> Thanks Timo,
>
> I tried to switch to master, but again the same thing happened.
> So, now on the master branch of candi, same error.
> I attached the log file, please take a look.
>
>
> On Sunday, 13 March 2022 at 19:55:52 UTC Timo Heister wrote:
>
>> What candi git branch are you on? You might need to switch to master to
>> make things work for now.
>>
>> Can you post how you execute candi.sh including the first few pages of
>> output?
>>
>> On Sun, Mar 13, 2022, 06:42 Masoud Ahmadi  wrote:
>>
>>> Dear Timo,
>>>
>>> No, I did not change anything; I did exactly what is explained in the
>>> following link, step by step:
>>> https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX
>>>
>>> On Saturday, 12 March 2022 at 16:54:56 UTC Timo Heister wrote:
>>>
>>>> Did you make any changes to candi.cfg? Can you also please post how you
>>>> execute candi.sh (what arguments)?
>>>>
>>>> On Mon, Mar 7, 2022, 12:23 Masoud Ahmadi  wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I am trying to install dealii on a apple ARM M1 OSX, using the
>>>>> following instructor:
>>>>> https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX
>>>>>
>>>>> However, I get the following error:
>>>>>
>>>>>
>>>>> error: use of undeclared identifier 'H5Pset_dxpl_mpio'
>>>>>   status   = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT);
>>>>>  ^
>>>>> /Users/masoud/dealii-candi/tmp/unpack/deal.II-v9.3.3/source/lac/scalapack.cc:3242:63:
>>>>> warning: unused parameter 'filename' [-Wunused-parameter]
>>>>> ScaLAPACKMatrix::load_parallel(const std::string &filename)
>>>>>   ^
>>>>> /Users/masoud/dealii-candi/tmp/unpack/deal.II-v9.3.3/source/lac/scalapack.cc:2861:20:
>>>>> error: use of undeclared identifier 'H5Pset_fapl_mpio'
>>>>>   status = H5Pset_fapl_mpio(plist_id,
>>>>> tmp.grid->mpi_communicator, info);
>>>>>^
>>>>> /Users/masoud/dealii-candi/tmp/build/deal.II-v9.3.3/source/lac/scalapack.inst:10:16:
>>>>> note: in instantiation of member function
>>>>> 'dealii::ScaLAPACKMatrix::save_parallel' requested here
>>>>> template class ScaLAPACKMatrix< double >;
>>>>>^
>>>>> /Users/masoud/dealii-candi/tmp/unpack/deal.II-v9.3.3/source/lac/scalapack.cc:2861:20:
>>>>> error: use of undeclared identifier 'H5Pset_fapl_mpio'
>>>>>   status = H5Pset_fapl_mpio(plist_id,
>>>>> tmp.grid->mpi_communicator, info);
>>>>>^
>>>>> /Users/masoud/dealii-candi/tmp/build/deal.II-v9.3.3/source/lac/scalapack.inst:20:16:
>>>>> note: in instantiation of member function
>>>>> 'dealii::ScaLAPACKMatrix::save_parallel' requested here
>>>>> template class ScaLAPACKMatrix< float >;
>>>>>^
>>>>> 1 warning and 3 errors generated.
>>>>>
>>>>>
>>>>> [image: Screenshot 2022-03-07 at 17.11.39.png]
>>>>> [image: Screenshot 2022-03-07 at 17.15.11.png]
>>>>>
>>>>> --
>>>>> The deal.II project is located at http://www.dealii.org/
>>>>> For mailing list/forum options, see
>>>>> https://groups.google.com/d/forum/dealii?hl=en
>>>>> ---
>>>>> You received this message because you are subscribed to the Google
>>>>> Groups "deal.II User Group" group.
>>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>>> an email to dealii+un...@googlegroups.com.
>>>>> To view this discussion on the web visit
>>>>> https://groups.google.com/d/msgid/dealii/5f96b566-3112-4dda-bb63-86e61b654156n%40googlegroups.com
>>>>> <https://groups.google.com/d/msgid/dealii/5f96b566-3112-4dda-bb63-86e61b654156n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>>> .
>>>>>
>>>> --
>>> The deal.II project is located at http://www.dealii.org/

Re: [deal.II] Error when compiling a deal.II app using Trilinos on Apple M1

[Timo Heister]

I worked on that. 😃

Interestingly, I didn't see this error in my testing of ASPECT. Are
you saying that a deal.II step like step-32 fails? I think we should
try updating Trilinos first.

Do you want to try 13.2 and see if that works? If not, I will update
the package in candi master when I get to it in a couple of days.


On Mon, Mar 14, 2022, 13:25 blais...@gmail.com  wrote:
>
> Dear all,
> Hope you are well
> Using the candi master branch, I succeeded in compiling deal.II using candi. 
> Everything was smooth. I don't know who took care of that, but awesome work.
>
> When trying to compile an example that uses Trilinos (any), I get the 
> following error that arise from an include in Trilinos
>
> Users/blaisb/work/candi/trilinos-release-12-18-1/include/Tpetra_Import_def.hpp:1171:24:
>  error: no member named 'bind1st' in namespace 'std'; did you mean 
> 'boost::container::bind1st'?
>
>std::bind1st (std::equal_to (), -1));
>
>^
>
> /Users/blaisb/work/candi/deal.II-master/include/deal.II/bundled/boost/container/detail/algorithm.hpp:55:24:
>  note: 'boost::container::bind1st' declared here
>
> inline binder1st bind1st(const Func& func, const T& arg)
>
>
>
> Is there a way around this error? Should I try to manually fix it or switch 
> to another trilinos version?
>
> Thanks!
>
> Bruno
>
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see 
> https://groups.google.com/d/forum/dealii?hl=en
> ---
> You received this message because you are subscribed to the Google Groups 
> "deal.II User Group" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to dealii+unsubscr...@googlegroups.com.
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/dealii/fc6ad924-8776-4fa8-8a6f-5c96c44a0c47n%40googlegroups.com.

-- 
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Re: [deal.II] Error installing dealii by candi on Apple M1

[Timo Heister]

What candi git branch are you on? You might need to switch to master to
make things work for now.

Can you post how you execute candi.sh including the first few pages of
output?

On Sun, Mar 13, 2022, 06:42 Masoud Ahmadi  wrote:

> Dear Timo,
>
> No, I did not change anything; I did exactly what is explained in the
> following link, step by step:
> https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX
>
> On Saturday, 12 March 2022 at 16:54:56 UTC Timo Heister wrote:
>
>> Did you make any changes to candi.cfg? Can you also please post how you
>> execute candi.sh (what arguments)?
>>
>> On Mon, Mar 7, 2022, 12:23 Masoud Ahmadi  wrote:
>>
>>> Hi,
>>>
>>> I am trying to install dealii on a apple ARM M1 OSX, using the following
>>> instructor:
>>> https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX
>>>
>>> However, I get the following error:
>>>
>>>
>>> error: use of undeclared identifier 'H5Pset_dxpl_mpio'
>>>   status   = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT);
>>>  ^
>>> /Users/masoud/dealii-candi/tmp/unpack/deal.II-v9.3.3/source/lac/scalapack.cc:3242:63:
>>> warning: unused parameter 'filename' [-Wunused-parameter]
>>> ScaLAPACKMatrix::load_parallel(const std::string &filename)
>>>   ^
>>> /Users/masoud/dealii-candi/tmp/unpack/deal.II-v9.3.3/source/lac/scalapack.cc:2861:20:
>>> error: use of undeclared identifier 'H5Pset_fapl_mpio'
>>>   status = H5Pset_fapl_mpio(plist_id,
>>> tmp.grid->mpi_communicator, info);
>>>^
>>> /Users/masoud/dealii-candi/tmp/build/deal.II-v9.3.3/source/lac/scalapack.inst:10:16:
>>> note: in instantiation of member function
>>> 'dealii::ScaLAPACKMatrix::save_parallel' requested here
>>> template class ScaLAPACKMatrix< double >;
>>>^
>>> /Users/masoud/dealii-candi/tmp/unpack/deal.II-v9.3.3/source/lac/scalapack.cc:2861:20:
>>> error: use of undeclared identifier 'H5Pset_fapl_mpio'
>>>   status = H5Pset_fapl_mpio(plist_id,
>>> tmp.grid->mpi_communicator, info);
>>>^
>>> /Users/masoud/dealii-candi/tmp/build/deal.II-v9.3.3/source/lac/scalapack.inst:20:16:
>>> note: in instantiation of member function
>>> 'dealii::ScaLAPACKMatrix::save_parallel' requested here
>>> template class ScaLAPACKMatrix< float >;
>>>^
>>> 1 warning and 3 errors generated.
>>>
>>>
>>> [image: Screenshot 2022-03-07 at 17.11.39.png]
>>> [image: Screenshot 2022-03-07 at 17.15.11.png]
>>>
>>> --
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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] University cluster installation issue: compilers

[Timo Heister]

Providing Intel compilers with a newer GCC is something the cluster as
admins should be able to do. It is not as easy as just installing GCC, I
would guess.

On Thu, Mar 10, 2022, 12:37 Stephanie Sparks  wrote:

> Bruno,
>
> Thanks for that explanation. I was indeed wondering if there was a way to
> use a newer version of gcc with the Intel compilers.
>
> I'm now trying to figure out how to call icc -gcc-name=/path/to/gcc
> because I can only load the intel/2019.4 or the updated gcc compilers
> independently.
>
> I thought I might try to install gcc locally but that is involved as there
> are many dependencies.
>
> Thanks,
> Stephanie
>
> On Thursday, March 10, 2022 at 7:01:24 AM UTC-7 bruno.t...@gmail.com
> wrote:
>
>> Stephanie,
>>
>> If you are still using the same compiler as before: icc version
>> 19.0.4.243 (gcc version 4.8.5 compatibility) The problem is because of the
>> standard library. The Intel compiler does not have its own standard
>> library, instead it uses the library from gcc. In your case the compiler is
>> icc 19.0 which supports C++14 but the standard library is from gcc 4.8.5
>> which does not support C++14. Usually the way to fix the problem is to load
>> a newer version of gcc, then icc should use the newer standard library.
>> Right now it probably uses the version from the system gcc, which is really
>> old.
>>
>> Best,
>>
>> Bruno
>>
>> On Wednesday, March 9, 2022 at 11:08:39 PM UTC-5 sasp...@asu.edu wrote:
>>
>>> I have a new (related) problem:
>>>
>>> I now can't configure deal.ii (I believe because of the compiler).
>>>
>>> Below is the output and attached is the CMakeOutput.log
>>>
>>> CMake Error at cmake/setup_compiler_flags_gnu.cmake:25 (MESSAGE):
>>>
>>>
>>>   deal.II requires support for features of C++14 that are not present in
>>>
>>>   versions of GCC prior to 5.0.
>>> Call Stack (most recent call first):
>>>   cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
>>>   cmake/setup_compiler_flags.cmake:113 (VERBOSE_INCLUDE)
>>>   cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
>>>   CMakeLists.txt:97 (VERBOSE_INCLUDE)
>>>
>>>
>>> -- Configuring incomplete, errors occurred!
>>> See also
>>> "/home/saspark2/build2/tmp/build/deal.II-v9.3.3/CMakeFiles/CMakeOutput.log".
>>> Failure with exit status: 1
>>> Exit message: There was a problem configuring dealii v9.3.3.
>>>
>>> If you have any suggestions, I'd greatly appreciate the help.
>>>
>>> Thank you,
>>> Stephanie
>>>
>>> On Wednesday, March 9, 2022 at 6:00:35 PM UTC-7 Stephanie Sparks wrote:
>>>
>>>> I was able to install p4est successfully by
>>>>
>>>> (1) setting CFLAGS="-std=c99"
>>>> (2) editing the sc_io.c file per the suggestion on the github issue
>>>> page opened by Wolfgang
>>>> (3) defining the mathematical constants (specifically M_PI, M_PI_4, and
>>>> M_SQRT2) in each script that used one (a partial list was added to the
>>>> github issue for this).
>>>>
>>>> Since the install worked I didn't try the older version.
>>>>
>>>> Thanks all!
>>>>
>>>> On Wednesday, March 9, 2022 at 1:24:09 PM UTC-7 Stephanie Sparks wrote:
>>>>
>>>>> Hi Timo,
>>>>>
>>>>> I get the following:
>>>>>
>>>>> icc version 19.0.4.243 (gcc version 4.8.5 compatibility)
>>>>>
>>>>> I'll try with an older version of p4est now.
>>>>>
>>>>> Stephanie
>>>>>
>>>>> On Wednesday, March 9, 2022 at 10:31:51 AM UTC-7 Timo Heister wrote:
>>>>>
>>>>>> Stephanie,
>>>>>>
>>>>>> What does "icc -v" return for you? I can compile p4est 2.3.2 with icc
>>>>>> version 19.1.1.217
>>>>>>
>>>>>> You can also try an older p4est release like 2.2 instead of having to
>>>>>> fix a bunch of bugs inside the codebase.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Mon, Mar 7, 2022 at 2:57 PM Wolfgang Bangerth <
>>>>>> bang...@colostate.edu> wrote:
>>>>>> >
>>>>>> > On 3/7/22 12:22, Stephanie Sparks wrote:
>>>>>> > >
>>

Re: [deal.II] University cluster installation issue: compilers

[Timo Heister]

Stephanie,

What does "icc -v" return for you? I can compile p4est 2.3.2 with icc
version 19.1.1.217

You can also try an older p4est release like 2.2 instead of having to
fix a bunch of bugs inside the codebase.




On Mon, Mar 7, 2022 at 2:57 PM Wolfgang Bangerth  wrote:
>
> On 3/7/22 12:22, Stephanie Sparks wrote:
> >
> > The #include  declaration did not seem to work; however, as I
> > still get the same error.
> >
> > Should I note this on the github issue?
>
> Yes, please do.
>
> You can just put
> #define M_PI 3.14159265358979323846264338327950288
> anywhere in that file (before the first place where it is used) then.
>
> Best
>   W.
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
> --
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Re: [deal.II] PETSc SNES implementation in deal.ii

[Timo Heister]

Hi Lorenzo,

I didn't look at your code, but I can help with this:

> however i am not sure how to extract PETSc Vec object from 
> PETScWrappers::MPI::Vector without passing from a PETScWrapper::VectorBase.

You should be able to use the conversion operator
https://www.dealii.org/developer/doxygen/deal.II/classPETScWrappers_1_1VectorBase.html#ade5e08d408ee79da10cceb7642bfa1da

PETScWrappers::MPI::Vector x;
Vec px = static_cast(x);

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Re: [deal.II] Re: Cluster installation error with symengine library

[Timo Heister]

Do you have $SYMENGINE_DIR defined in your environment? If yes, "unset
SYMENGINE_DIR" might help.

On Tue, Feb 22, 2022 at 10:08 AM Stephanie Sparks  wrote:
>
> Timo,
>
> I did try to install from scratch and I'm getting the same error:
>
> Could not find the symengine library!
>
> Please ensure that a suitable symengine library is installed on your computer.
>
> I turned off symengine in the candi.cfg file and deleted the installation 
> library so I'm not sure what else to do.
>
> Thanks,
> Stephanie
> On Tuesday, February 15, 2022 at 1:42:34 PM UTC-7 Timo Heister wrote:
>>
>> Sure, the easiest is to start over and delete the whole installation 
>> directory before you run Candi.
>> You can try if it is enough to delete tmp/build/ but I am not sure.
>>
>> On Tue, Feb 15, 2022, 13:49 Stephanie Sparks  wrote:
>>>
>>> Hi Timo,
>>>
>>> I did use candi to re-install without symengine and then when attempting to 
>>> install deal.ii I got an error that symengine library could not be found. 
>>> Is there a way to configure it such that symengine is not necessary for 
>>> deal.ii?
>>>
>>> Thanks,
>>> Stephanie
>>>
>>> On Tuesday, February 8, 2022 at 8:05:01 AM UTC-7 Timo Heister wrote:
>>>>
>>>> Stephanie,
>>>>
>>>> I think you likely don't need some fine, am i right? Just comment out the 
>>>> line for it in the candi.cfg and rerun the setup (you might need to delete 
>>>> the tmp directory).
>>>>
>>>>
>>>> On Tue, Feb 8, 2022, 10:01 Raghunandan Pratoori  wrote:
>>>>>
>>>>> Hi Stephanie,
>>>>>
>>>>> I use a singularity container with deal.ii on my university cluster. I 
>>>>> found it to be much simpler and working on any other cluster tried 
>>>>> without any problems. I suggest you try that as it is a more reliable 
>>>>> solution.
>>>>> Also, if needed, I can give you access to the singularity container I 
>>>>> built on Ubuntu 20.04 with deal.ii v9.3.0
>>>>>
>>>>> Best,
>>>>> Raghunandan.
>>>>>
>>>>> On Tuesday, February 8, 2022 at 8:30:33 AM UTC-6 sasp...@asu.edu wrote:
>>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I am trying to install deal.ii on my university cluster and have been 
>>>>>> successful up to this point; however, when I attempt to run examples I 
>>>>>> get the following error:
>>>>>>
>>>>>> ./step-1: error while loading shared libraries: libsymengine.so.0.7: 
>>>>>> cannot open shared object file: No such file or directory
>>>>>>
>>>>>> I found an entry in the FAQ regarding similar problems with linking 
>>>>>> PETSc and attempted to use that fix but I'm still running into the same 
>>>>>> issue.
>>>>>>
>>>>>> Any help would be greatly appreciated.
>>>>>>
>>>>>> Thanks,
>>>>>> Stephanie
>>>>>
>>>>> --
>>>>> 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 dealii+un...@googlegroups.com.
>>>>> To view this discussion on the web visit 
>>>>> https://groups.google.com/d/msgid/dealii/61bc9eb6-a392-4b3a-836e-37764a389b0an%40googlegroups.com.
>>>
>>> --
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>
> --
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Re: [deal.II] Exporting hdf5 file in a loop

[Timo Heister]

What we do typically in this situation is that we write one visualization
output file per iteration with a different filename. This is done in many
of the examples, especially for time dependent problems.
I don't think there is an easy way to append data to an existing file like
you suggested. This would overwrite existing data. With the hdf5 data, you
can store the mesh only once, assuming it doesn't change. See the
DataOutBase::DataOutFilterFlags.


On Tue, Feb 15, 2022, 15:02 Uclus Heis  wrote:

> Thank you very much for the answer.
> I need to evaluate a high number of frequencies, so in that case I would
> need to have a large number of vectors to track the results, which is not
> optimal in my case.
> Is it any other way to do that? Would be possible to call 
> data_out.add_data_vector()
> and data_out.write_hdf5_parallel() in each iteartion? Would that keep the
> previous written information?
>
> Thank you
>
> El martes, 15 de febrero de 2022 a las 19:43:02 UTC+1, Timo Heister
> escribió:
>
>> The call to data_out.add_data_vector() does not copy the contents of the
>> vector but it just keeps track of it until the data is actually written.
>> You will need to store your solutions in different vectors without
>> touching the old ones.
>>
>> On Tue, Feb 15, 2022, 11:05 Uclus Heis  wrote:
>>
>>> Good afternoon,
>>>
>>> I want to store my results in a hdf5 file using a distributed
>>> implementation. I am computing different frequencies, so I have a loop in
>>> my run() function where I solve for each frequency.  When for example
>>> computing 5 frequencies, I get 5 results with the same value in my hdf5
>>> file, however, the solution vector inside dealii is correct. Can I ask for
>>> help, I do not know what am I doing wrong when exporting the results, my
>>> code looks like the following:
>>>
>>> DataOut data_out;
>>> data_out.attach_dof_handler(dof_handler);
>>> for(int freq_iter=0 ...  )*//solver loop, *
>>> {
>>> ... //*computes the solution per frequency*
>>> string nname = "rb";
>>> string nit = to_string(freq_iter);
>>> string fitame =nname+nit;
>>> data_out.add_data_vector(locally_relevant_solution, fitame);
>>> }
>>> data_out.build_patches();
>>> DataOutBase::DataOutFilterFlags flags(true, true);
>>> DataOutBase::DataOutFilter data_filter(flags);
>>> data_out.write_filtered_data(data_filter);
>>> data_out.write_hdf5_parallel(data_filter, "solution.h5", MPI_COMM_WORLD);
>>>
>>>
>>> Thank you for you time.
>>>
>>> --
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>>> .
>>>
>> --
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Re: [deal.II] Re: Cluster installation error with symengine library

[Timo Heister]

Sure, the easiest is to start over and delete the whole installation
directory before you run Candi.
You can try if it is enough to delete tmp/build/ but I am not sure.

On Tue, Feb 15, 2022, 13:49 Stephanie Sparks  wrote:

> Hi Timo,
>
> I did use candi to re-install without symengine and then when attempting
> to install deal.ii I got an error that symengine library could not be
> found. Is there a way to configure it such that symengine is not necessary
> for deal.ii?
>
> Thanks,
> Stephanie
>
> On Tuesday, February 8, 2022 at 8:05:01 AM UTC-7 Timo Heister wrote:
>
>> Stephanie,
>>
>> I think you likely don't need some fine, am i right? Just comment out the
>> line for it in the candi.cfg and rerun the setup (you might need to delete
>> the tmp directory).
>>
>>
>> On Tue, Feb 8, 2022, 10:01 Raghunandan Pratoori  wrote:
>>
>>> Hi Stephanie,
>>>
>>> I use a singularity container with deal.ii on my university cluster. I
>>> found it to be much simpler and working on any other cluster tried without
>>> any problems. I suggest you try that as it is a more reliable solution.
>>> Also, if needed, I can give you access to the singularity container I
>>> built on Ubuntu 20.04 with deal.ii v9.3.0
>>>
>>> Best,
>>> Raghunandan.
>>>
>>> On Tuesday, February 8, 2022 at 8:30:33 AM UTC-6 sasp...@asu.edu wrote:
>>>
>>>> Hello,
>>>>
>>>> I am trying to install deal.ii on my university cluster and have been
>>>> successful up to this point; however, when I attempt to run examples I get
>>>> the following error:
>>>>
>>>> ./step-1: error while loading shared libraries: libsymengine.so.0.7:
>>>> cannot open shared object file: No such file or directory
>>>>
>>>> I found an entry in the FAQ regarding similar problems with linking
>>>> PETSc and attempted to use that fix but I'm still running into the same
>>>> issue.
>>>>
>>>> Any help would be greatly appreciated.
>>>>
>>>> Thanks,
>>>> Stephanie
>>>>
>>> --
>>> The deal.II project is located at http://www.dealii.org/
>>> For mailing list/forum options, see
>>> https://groups.google.com/d/forum/dealii?hl=en
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>>> .
>>>
>> --
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> .
>

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Re: [deal.II] Exporting hdf5 file in a loop

[Timo Heister]

The call to data_out.add_data_vector() does not copy the contents of the
vector but it just keeps track of it until the data is actually written.
You will need to store your solutions in different vectors without touching
the old ones.

On Tue, Feb 15, 2022, 11:05 Uclus Heis  wrote:

> Good afternoon,
>
> I want to store my results in a hdf5 file using a distributed
> implementation. I am computing different frequencies, so I have a loop in
> my run() function where I solve for each frequency.  When for example
> computing 5 frequencies, I get 5 results with the same value in my hdf5
> file, however, the solution vector inside dealii is correct. Can I ask for
> help, I do not know what am I doing wrong when exporting the results, my
> code looks like the following:
>
> DataOut data_out;
> data_out.attach_dof_handler(dof_handler);
> for(int freq_iter=0 ...  )*//solver loop, *
> {
> ... //*computes the solution per frequency*
> string nname = "rb";
> string nit = to_string(freq_iter);
> string fitame =nname+nit;
> data_out.add_data_vector(locally_relevant_solution, fitame);
> }
> data_out.build_patches();
> DataOutBase::DataOutFilterFlags flags(true, true);
> DataOutBase::DataOutFilter data_filter(flags);
> data_out.write_filtered_data(data_filter);
> data_out.write_hdf5_parallel(data_filter, "solution.h5", MPI_COMM_WORLD);
>
>
> Thank you for you time.
>
> --
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>

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[deal.II] Re: Clemson Computational Math Seminar: Bruno Blais - Feb 4

[Timo Heister]

Hi all,

The recording of the talk is now available at
https://www.youtube.com/watch?v=-qJfml3_HuA

Thanks again, Bruno!

On Mon, Jan 31, 2022 at 2:56 PM Timo Heister  wrote:
>
> Hi all,
>
> I would like to announce the following seminar talk in our Clemson
> Computational Math seminar that is related to deal.II. If you are
> interested, feel free to join using the zoom link below.
>
> Date and time: Friday, Feb 4 at 11:15am Eastern time
> Speaker: Bruno Blais (Polytechnique Montréal)
> Title: Lethe: Open-source FEM-based CFD and CFD-DEM models for the
> simulation, design and optimization of chemical processes
>
> Zoom link: https://clemson.zoom.us/j/96402109287
>
> Abstract:
> Chemical process plants generally consist of a combination of multiple
> unit operations which all
> have a specific purpose: separating components, facilitating a
> chemical reaction, mixing,
> transferring energy from one fluid to another, moving fluids. The
> design of these operations is still
> mostly based on design heuristics which lead to significant challenges
> when designing new chemical
> processes or scaling-up existing ones. These challenges are
> exacerbated by the occurrence of
> turbulence, the complex rheology of the fluid or the presence of
> multiple phases such as a fluid (gas
> or liquid) and solid particles. Computational Fluid Dynamics (CFD) for
> the fluid phase, the Discrete
> Element Method (DEM) for granular material, and their combination
> (CFD-DEM) enable us to
> predict the dynamics of these unit operations. This requires
> high-performance robust models for
> which the components (linear solver, finite element formulation) are
> tailored to the application.
>
> In this talk, we introduce a new open-source CFD, DEM and CFD-DEM
> software: Lethe. Lethe is built
> upon the well-established deal.II library. It leverages deal.II not
> only for its state of the art FEM
> capabilities, but it also makes extensive usage of its
> high-performance particle tracking module for
> its DEM solver. We present four very different examples that highlight
> the challenges that the
> chemical engineering community face and that can be addressed through
> simulations:
> - The mixing of shear-thinning fluids.
> - The prediction of early turbulent flows.
> - The flow of powder.
> - The solid-fluid flow in a fluidized bed reactor.
>
> For each of these examples, we discuss the mathematical formulation
> that we use within Lethe as
> well as the technical challenges faced when developing the models. We
> conclude by providing a
> high-level perspective of the direction in which we are heading, the
> challenges that we are currently
> facing and the key lessons that have been learned through this
> endeavor to develop a
> CFD/DEM/CFD-DEM software.
>
> Best,
> Timo
>
> --
> Timo Heister
> http://www.math.clemson.edu/~heister/



-- 
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Re: [deal.II] DataOut class only offers 6 digit output for double type?

[Timo Heister]

huyanzhuo,

We compute and then output data inside DataOut as float (32 bit
floating point) and not as double (64bit). Float has an accuracy of
approximately 7 decimal digits, so your number would be roughly
1647.999 but it happens to be rounded up to 1648.000.
I am afraid there is no easy way to change this because this is
hard-coded inside DataOut. It is in the Patch class if you are
curious:
https://www.dealii.org/developer/doxygen/deal.II/structDataOutBase_1_1Patch.html#a366bf92bcc2b667586d630455953d911

Normally, this should be enough for visualization.

On Tue, Feb 8, 2022 at 4:58 PM huyanzhuo  wrote:
>
> I'm using the 8.5.1 version.
> As the theme side, i gives a vector to a  DataOut object, the type of 
> the vector entry is double, with 15 effective digit. But there is only 6 
> digit when write to a file (vtk or gpl). My vector is around  1647.99932, 
> the result write into the file is 1648. How can i improve the presion of the 
> result in file?
>
> --
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Re: [deal.II] Solution mismatch (FullMatrix vs. PETScWrappers::MPI::SparseMatrix)

[Timo Heister]

> *L_operator(local_dof_indices[i],local_dof_indices[j]) =
cell_matrix(i,j);*

*This looks incorrect, because global pairs of indices will happen more
than once in a normal assembly (with a continuous finite element). You have
to add the contribution using +=.*


On Tue, Feb 8, 2022, 16:52 Hermes Sampedro  wrote:

>
> Dear Wolfgang,
>
> Thank you for the clarification. In that case, I am missing some operation
> somewhere...
>
> Let me clarify what I am doing. Apart from building the system_matrix, I
> save the operator L in the assembling process. But I did not do any
> distribute_local_to_global nor compress to that operator, as I do for the
> system matrix. Is that wrong?
>
>
> 
> *for (const auto &cell : dof_handler.active_cell_iterators())*
> * if (cell->is_locally_owned())*
> *{*
> * for (unsigned int i = 0; i < dofs_per_cell; ++i)*
> * { ..*
> * for (unsigned int j = 0; j < dofs_per_cell; ++j)*
> * {. .*
> * cell_matrix(i, j)= *
> * *
> * L_operator(local_dof_indices[i],local_dof_indices[j]) =
> cell_matrix(i,j);*
> * }*
> * }*
>
> * cell->get_dof_indices(local_dof_indices);*
> * constraints.distribute_local_to_global(cell_matrix,*
> * cell_rhs,*
> * local_dof_indices,*
> * system_matrix,*
> * system_rhs);*
> *}*
> *system_matrix.compress(VectorOperation::add);*
> *system_rhs.compress(VectorOperation::add);*
>
> 
>
> I checked the content of the matrics by solving a very small case. I found
> that indeed system_matrix is different to the saved operator L.  Do you
> have any suggestion where the different is coming from? Both are taken from
> the same assembling, the difference is that system_matrix applies 
> *distribute_local_to_global()
> and compress().*
>
> Thank you again.
> Regards
> El martes, 8 de febrero de 2022 a las 22:22:37 UTC+1, Wolfgang Bangerth
> escribió:
>
>> On 2/8/22 09:06, Hermes Sampedro wrote:
>> >
>> > I checked that in both cases, the operators/system_matrix have the same
>> > values just in the assemble_system() function. I was wondering if there
>> > is something internally that change somehow the systme_matrix. I can
>> see
>> > that after checking the values of the operators I have the following
>> > lines which I am not sure if there is something happening:
>>
>> No functions in deal.II touch your linear system unless you specifically
>> call a function that takes a matrix or vector as argument. So, if you
>> have the distribute_local_to_global() call for one type of matrix, you
>> need to call it for the other kind of matrix as well. But these
>> functions do not internally store some kind of magic pointer to the
>> matrix and right hand side so that at some later point, when you're not
>> watching, they do something nefarious to your matrix :-)
>>
>> My suggestion would be to make sure that before the solve, the two
>> matrices and corresponding right hand sides are the same. This is often
>> awkward if the objects are large, but you can test this by outputting
>> the norm of these objects.
>>
>> Then check that the solution is also the same. My guess is that for some
>> reason, either the matrix or the rhs are different.
>>
>> Best
>> W.
>>
>> --
>> 
>> Wolfgang Bangerth email: bang...@colostate.edu
>> www: http://www.math.colostate.edu/~bangerth/
>>
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> 
> .
>

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Re: [deal.II] Re: Cluster installation error with symengine library

[Timo Heister]

Stephanie,

I think you likely don't need some fine, am i right? Just comment out the
line for it in the candi.cfg and rerun the setup (you might need to delete
the tmp directory).


On Tue, Feb 8, 2022, 10:01 Raghunandan Pratoori  wrote:

> Hi Stephanie,
>
> I use a singularity container with deal.ii on my university cluster. I
> found it to be much simpler and working on any other cluster tried without
> any problems. I suggest you try that as it is a more reliable solution.
> Also, if needed, I can give you access to the singularity container I
> built on Ubuntu 20.04 with deal.ii v9.3.0
>
> Best,
> Raghunandan.
>
> On Tuesday, February 8, 2022 at 8:30:33 AM UTC-6 sasp...@asu.edu wrote:
>
>> Hello,
>>
>> I am trying to install deal.ii on my university cluster and have been
>> successful up to this point; however, when I attempt to run examples I get
>> the following error:
>>
>> ./step-1: error while loading shared libraries: libsymengine.so.0.7:
>> cannot open shared object file: No such file or directory
>>
>> I found an entry in the FAQ regarding similar problems with linking PETSc
>> and attempted to use that fix but I'm still running into the same issue.
>>
>> Any help would be greatly appreciated.
>>
>> Thanks,
>> Stephanie
>>
> --
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>

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[deal.II] Clemson Computational Math Seminar: Bruno Blais - Feb 4

[Timo Heister]

Hi all,

I would like to announce the following seminar talk in our Clemson
Computational Math seminar that is related to deal.II. If you are
interested, feel free to join using the zoom link below.

Date and time: Friday, Feb 4 at 11:15am Eastern time
Speaker: Bruno Blais (Polytechnique Montréal)
Title: Lethe: Open-source FEM-based CFD and CFD-DEM models for the
simulation, design and optimization of chemical processes

Zoom link: https://clemson.zoom.us/j/96402109287

Abstract:
Chemical process plants generally consist of a combination of multiple
unit operations which all
have a specific purpose: separating components, facilitating a
chemical reaction, mixing,
transferring energy from one fluid to another, moving fluids. The
design of these operations is still
mostly based on design heuristics which lead to significant challenges
when designing new chemical
processes or scaling-up existing ones. These challenges are
exacerbated by the occurrence of
turbulence, the complex rheology of the fluid or the presence of
multiple phases such as a fluid (gas
or liquid) and solid particles. Computational Fluid Dynamics (CFD) for
the fluid phase, the Discrete
Element Method (DEM) for granular material, and their combination
(CFD-DEM) enable us to
predict the dynamics of these unit operations. This requires
high-performance robust models for
which the components (linear solver, finite element formulation) are
tailored to the application.

In this talk, we introduce a new open-source CFD, DEM and CFD-DEM
software: Lethe. Lethe is built
upon the well-established deal.II library. It leverages deal.II not
only for its state of the art FEM
capabilities, but it also makes extensive usage of its
high-performance particle tracking module for
its DEM solver. We present four very different examples that highlight
the challenges that the
chemical engineering community face and that can be addressed through
simulations:
- The mixing of shear-thinning fluids.
- The prediction of early turbulent flows.
- The flow of powder.
- The solid-fluid flow in a fluidized bed reactor.

For each of these examples, we discuss the mathematical formulation
that we use within Lethe as
well as the technical challenges faced when developing the models. We
conclude by providing a
high-level perspective of the direction in which we are heading, the
challenges that we are currently
facing and the key lessons that have been learned through this
endeavor to develop a
CFD/DEM/CFD-DEM software.

Best,
Timo

-- 
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Re: [deal.II] Introduction and request for feedback

[Timo Heister]

Hi Macro,

Thanks for getting in touch. I don't have much to say about your plan,
but I can comment on the following:

> As a final note, I am a big fan of open source software. Therefore, I am fully
> committed to contribute whatever I develop back to the Deal II community
> including examples/tests/documentation and so on. For example, one of the 
> first
> things on my list is to expand on the Abaqus input file reader. I have some
> ideas in this area that I would like to pitch if there is any interest.

Great, we are always happy to get contributions! See
https://github.com/dealii/dealii/wiki/Contributing to get started and
feel free to ask for help.

> Another
> practical thing I can contribute to is testing the compilation of Deal II with
> different versions of libraries. For example, Deal II will not compile out of 
> the
> box with newer TBB versions.

There has been progress on supporting the new oneTBB in the last 2 weeks, see
https://github.com/dealii/dealii/pull/13031
https://github.com/dealii/dealii/pull/12958
and things should work already or soon, I think.

> But I also get a fair amount of warnings of array
> bounds that (the compiler thinks) are not correct.

If you see them on deal.II master, feel free to create an issue at
https://github.com/dealii/dealii/issues or try to fix them and submit
a pull request.

Best,
Timo

-- 
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[deal.II] Re: online deal.II workshop: Friday, June 18

[Timo Heister]

Hi all,

I finally got around cutting and uploading the workshop recordings.
The first half is now available on youtube, see
https://dealii.org/workshop-2021/ for the links.

Best,
Timo

On Wed, Jun 16, 2021 at 10:50 AM Timo Heister  wrote:
>
> Hi all,
>
> This is a quick reminder that our one-day workshop will happen this Friday. 
> We hope to see you there and celebrate the 9.3 release with us!
>
> The information on how to join the meeting via Zoom is now available at
> https://dealii.org/workshop-2021/
>
> Best,
> Timo
>
>
>
>
>
>
>
> On Wed, Jun 2, 2021 at 11:35 AM Timo Heister  wrote:
> >
> > Hi all,
> >
> > We would like to announce a one-day deal.II workshop on June 18, 2021
> > with several talks about recent developments in the library, the 9.3
> > release, and interesting user projects. The talks will be available
> > live using zoom and available as a video at a later time.
> >
> > For more information including a schedule, please see:
> > https://dealii.org/workshop-2021/
> >
> > Information on how to join will be made available closer to the date.
> > We hope to see you there!
> >
> > Best,
> > Timo and the deal.II developers
> >
> > --
> > Timo Heister
> > http://www.math.clemson.edu/~heister/
>
>
>
> --
> Timo Heister
> http://www.math.clemson.edu/~heister/



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Re: [deal.II] Re: MPI error while running inside a Docker container

[Timo Heister]

>> David
> >>
> >> --
> >> The deal.II project is located at http://www.dealii.org/
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> >
> > --
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Re: [deal.II] Inaccurate convergence rate using ParsedConvergenceTable class

[Timo Heister]

FunctionParser uses a finite difference approximation for the gradient. I
think this is explained in the class documentation.
This explains the results you see...

On Sun, Aug 8, 2021, 15:15 Marco Feder  wrote:

> Ciao Luca!
>
> > Can you check if you get the same results with this order?
> Yes, the rates are the same.
>
> > Are you calling `error_from_exact` with mapping as a first argument?
> Yes
>
> Actually, I've fixed the issue after reading this:
> > If the Solution class implements the Gradient, then
> ParsedConvergenceTable should use that.
>
> Indeed, I realised I wrote:
> error_table.error_from_exact(mapping, dof_handler, solution,
> *exact_solution*);
>
> where exact_solution is a FunctionParser<*dim*> which will be
> initialised with the expression of the analytical solution, so it doesn't
> give any info about the Gradient. Instead, if I replace exact_solution in
> the last argument with the "classical" Solution() (so that there's
> also an implementation of Gradient) I have my expected rates. Apparently it
> wasn't using the Gradient function.
>
> However, looking at the source code and in the documentation of
> integrate_difference, I don't see how the H^1 norm was computed without
> having an implementation of the Gradient. I would expect to see an
> exception asking for its implementation. Was it using some FD-like
> approximation or am I missing something?
>
>
> Thanks,
> Marco
>
>
> Il giorno domenica 8 agosto 2021 alle 18:52:03 UTC+2 luca@gmail.com
> ha scritto:
>
>> The other option is that you are not calling the `error_from_exact`
>> function that takes a mapping argument, but the one without it, and your
>> boundary cells are introducing some error due to a worse mapping…. Are you
>> calling `error_from_exact` with mapping as a first argument?
>>
>> Luca
>>
>> Il giorno 8 ago 2021, alle ore 6:49 PM, Luca Heltai 
>> ha scritto:
>>
>> 
>>
>> Ciao Marco,
>>
>> I was expanding step-12
>>  using a
>> manufactured solution to check the order p in H^1 (and p+1 in L^2) norm on
>> a uniformly refined mesh for the DG upwind method. I've used the
>> ParsedConvergenceTable with a parameter file as described in the docs. As
>> Rate_key I'm using the DoFs, while as Rate_mode I have reduction_rate_log2.
>>
>> With p=1 and p=2 everything is fine. But if I set the finite element
>> degree to 3, then the H^1 convergence rate decreases, as you can see in the
>> attached image.
>> 
>>
>>
>> Is it possible that you are using different quadrature rules in the two
>> cases? Your image shows a deterioration of the error on the order of 1e-8
>> for H1, and 1e-12 for L2, which is very close to machine precision.
>>
>> Internally the parsed convergence table does the exact same thing you
>> wrote explicitly. (If you check the source code, you’ll see that it calls
>> integrate_difference and compute_global_error for each error type you
>> specify in the parameter file).
>>
>> This, however, doesn't happen if I use a classical ConvergenceTable.
>> Namely, I first compute the local error in each cell, and then the global
>> error in the classical way:
>>
>> VectorTools::integrate_difference(mapping,dof_handler,solution, Solution<
>> *dim*>(),H1_error_per_cell, QGauss<*dim*
>> >(fe->tensor_degree()+1),VectorTools::H1_norm);
>>
>> *const* *double* H1_error =
>> VectorTools::compute_global_error(triangulation, H1_error_per_cell,
>> VectorTools::H1_norm); //assuming I provided also the gradient method for
>> the Solution class
>>
>>
>> Does anyone have any idea why this is happening? My guess was that while
>> computing the H^1 *semi-*norm the ParsedConvergenceTable class does some
>> approximation to compute the gradient from the exact solution
>> expression and hence that could be the source of the issue. Conversely, in
>> the "ConvergenceTable" way I do define explicitly the gradient of the exact
>> solution in the Solution class.
>>
>>
>> If the Solution class implements the Gradient, then
>> ParsedConvergenceTable should use that.
>>
>> You are calling “error_from_exact” of that class, right?
>>
>> This is where it is called:
>>
>>
>> https://www.dealii.org/current/doxygen/deal.II/parsed__convergence__table_8h_source.html
>>
>> Line 621. As you see, the quadrature rule used is a Gauss formula of
>> order (dh.get_fe().degree+1)*2.
>>
>> Can you check if you get the same results with this order?
>>
>> L.
>>
>> --
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Re: [deal.II] Debug multithread code

[Timo Heister]

It sounds like (I don't know what code you are running) that you use
something like WorkStream::run or mesh_loop that calls your assemble
function.
Stepping into this function should be possible (assuming you have deal.II
installed in a way that gdb can find the source code). What happens if you
step into it?
Of course this is a more complicated situation than a simple step-3
assembly loop. I would probably add a breakpoint inside the function of
interest...


On Thu, Aug 5, 2021, 21:01 Michael Lee  wrote:

> Yes, I'm in debug mode. I mean I cannot step over one line each time or
> step into a function. I have to set a lot of breakpoints to stop the
> program at these lines.
>
> On Aug 5, 2021, at 6:16 PM, Timo Heister  wrote:
>
> 
> What do you mean by "cannot do step debug"? Are you compiling in debug
> mode?
>
> On Thu, Aug 5, 2021, 18:34 Michael Li  wrote:
>
>> I put *MultithreadInfo::set_thread_limit(**1**)* in *main* function, but
>> still cannot do step debug in the function
>>
>> *assemble_neumann_contribution_one_cell. *Am I doing something wrong?
>>
>>
>>
>>
>>
>>
>>
>> *From: *Timo Heister 
>> *Sent: *Thursday, August 5, 2021 1:19 PM
>> *To: *dealii@googlegroups.com
>> *Subject: *Re: [deal.II] Debug multithread code
>>
>>
>>
>> Take a look at set_thread_limit:
>>
>> https://www.dealii.org/current/doxygen/deal.II/classMultithreadInfo.html
>>
>> As you can see, you can also control it using an environment variable, so
>> you don't have to recompile.
>>
>>
>>
>> On Thu, Aug 5, 2021, 13:36 Michael Lee  wrote:
>>
>> Hi,
>>
>>
>>
>> I find it's difficult to debug multithread code on a multiple-core
>> computer. Sometimes it does not step into a function (I'm using vscode +
>> wsl). Does deal.II use all the cores available? For the sake of debug, how
>> can I limit the cores used? Is there a way to debug the code just like
>> series one?
>>
>>
>>
>> Regards,
>>
>> Michael
>>
>> --
>> The deal.II project is located at http://www.dealii.org/
>> For mailing list/forum options, see
>> https://groups.google.com/d/forum/dealii?hl=en
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>> .
>>
>> --
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>> .
>>
>>
>>
>> --
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>>
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Re: [deal.II] Debug multithread code

[Timo Heister]

What do you mean by "cannot do step debug"? Are you compiling in debug mode?

On Thu, Aug 5, 2021, 18:34 Michael Li  wrote:

> I put *MultithreadInfo::set_thread_limit(**1**)* in *main* function, but
> still cannot do step debug in the function
>
> *assemble_neumann_contribution_one_cell. *Am I doing something wrong?
>
>
>
>
>
>
>
> *From: *Timo Heister 
> *Sent: *Thursday, August 5, 2021 1:19 PM
> *To: *dealii@googlegroups.com
> *Subject: *Re: [deal.II] Debug multithread code
>
>
>
> Take a look at set_thread_limit:
>
> https://www.dealii.org/current/doxygen/deal.II/classMultithreadInfo.html
>
> As you can see, you can also control it using an environment variable, so
> you don't have to recompile.
>
>
>
> On Thu, Aug 5, 2021, 13:36 Michael Lee  wrote:
>
> Hi,
>
>
>
> I find it's difficult to debug multithread code on a multiple-core
> computer. Sometimes it does not step into a function (I'm using vscode +
> wsl). Does deal.II use all the cores available? For the sake of debug, how
> can I limit the cores used? Is there a way to debug the code just like
> series one?
>
>
>
> Regards,
>
> Michael
>
> --
> The deal.II project is located at http://www.dealii.org/
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> .
>
> --
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> .
>
>
>
> --
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> .
>

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[deal.II] ASPECT v2.3.0 released

[Timo Heister]

Hi all,

We recently released version 2.3.0 of ASPECT, the Advanced Solver for
Problems in Earth's ConvecTion, which is built on deal.II.

See https://aspect.geodynamics.org/ and
https://github.com/geodynamics/aspect/releases/tag/v2.3.0 for more
information about ASPECT.

Best,
Timo

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Re: [deal.II] Debug multithread code

[Timo Heister]

Take a look at set_thread_limit:
https://www.dealii.org/current/doxygen/deal.II/classMultithreadInfo.html
As you can see, you can also control it using an environment variable, so
you don't have to recompile.

On Thu, Aug 5, 2021, 13:36 Michael Lee  wrote:

> Hi,
>
> I find it's difficult to debug multithread code on a multiple-core
> computer. Sometimes it does not step into a function (I'm using vscode +
> wsl). Does deal.II use all the cores available? For the sake of debug, how
> can I limit the cores used? Is there a way to debug the code just like
> series one?
>
> Regards,
> Michael
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see
> https://groups.google.com/d/forum/dealii?hl=en
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> 
> .
>

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[deal.II] Re: online deal.II workshop: Friday, June 18

[Timo Heister]

Hi all,

This is a quick reminder that our one-day workshop will happen this Friday.
We hope to see you there and celebrate the 9.3 release with us!

The information on how to join the meeting via Zoom is now available at
https://dealii.org/workshop-2021/

Best,
Timo







On Wed, Jun 2, 2021 at 11:35 AM Timo Heister  wrote:
>
> Hi all,
>
> We would like to announce a one-day deal.II workshop on June 18, 2021
> with several talks about recent developments in the library, the 9.3
> release, and interesting user projects. The talks will be available
> live using zoom and available as a video at a later time.
>
> For more information including a schedule, please see:
> https://dealii.org/workshop-2021/
>
> Information on how to join will be made available closer to the date.
> We hope to see you there!
>
> Best,
> Timo and the deal.II developers
>
> --
> Timo Heister
> http://www.math.clemson.edu/~heister/



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Re: [deal.II] Re: online deal.II workshop: Friday, June 18

[Timo Heister]

Hi David,

Yes, it might take some time for me to edit and upload, but I will
make the talks available.

On Mon, Jun 14, 2021 at 3:09 AM 'David' via deal.II User Group
 wrote:
>
> Hi Timo,
>
> short question: will the workshop afterwards be available on YouTube 
> analogous to the last workshop?
>
> Regards,
> David
> On Wednesday, 2 June 2021 at 17:36:08 UTC+2 Timo Heister wrote:
>>
>> Hi all,
>>
>> We would like to announce a one-day deal.II workshop on June 18, 2021
>> with several talks about recent developments in the library, the 9.3
>> release, and interesting user projects. The talks will be available
>> live using zoom and available as a video at a later time.
>>
>> For more information including a schedule, please see:
>> https://dealii.org/workshop-2021/
>>
>> Information on how to join will be made available closer to the date.
>> We hope to see you there!
>>
>> Best,
>> Timo and the deal.II developers
>>
>> --
>> Timo Heister
>> http://www.math.clemson.edu/~heister/
>
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[deal.II] online deal.II workshop: Friday, June 18

[Timo Heister]

Hi all,

We would like to announce a one-day deal.II workshop on June 18, 2021
with several talks about recent developments in the library, the 9.3
release, and interesting user projects. The talks will be available
live using zoom and available as a video at a later time.

For more information including a schedule, please see:
https://dealii.org/workshop-2021/

Information on how to join will be made available closer to the date.
We hope to see you there!

Best,
Timo and the deal.II developers

-- 
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Re: [deal.II] Bug in FEInterfaceValues?

[Timo Heister]

Hi Corbin,

Indeed, the following code:

sd.fe_interface_values.reinit(cell, face_index);

initializes the object as a boundary face. You need to pass the two
neighboring cells to the other reinit() function.




On Tue, Apr 13, 2021 at 11:08 PM Corbin Foucart
 wrote:
>
> I took a look at the unit tests for FEInterfaceValues in 
> tests/feinterface/fe_interface_values_0*.cc, and found that the following 
> modification to the code in the face loop, changing how reinit and the 
> boundary check is done:
>
> for ( cell loop)
>   for ( face loop)
>   ...
>
>   // detect top face
>   if (nrml[0][1] > 0 && !(cell->at_boundary(face_index)))
>   {
> std::cout << std::endl;
> sd.fe_interface_values.reinit(cell,
>   face_index,
>   numbers::invalid_unsigned_int,
>   cell->neighbor(face_index),
>   
> cell->neighbor_of_neighbor(face_index),
>   numbers::invalid_unsigned_int);
>...
>
> sd.fe_interface_values.get_fe_face_values(1).get_function_values(field, 
> uhat_qpt);
>}
>
> Works fine at getting the values from the other side of the interface. 
> Perhaps I used the reinit(...) function incorrectly.
>
> Best,
> Corbin
>
>
> On Tue, Apr 13, 2021 at 9:56 PM Corbin Foucart  
> wrote:
>>
>> Hello all,
>>
>> I have found an unexpected behavior in using the FEInterfaceValues object. 
>> Namely, it seems that a line like,
>>
>> fe_interface_values.get_fe_face_values(1).get_function_values(...);
>>
>> returns the following error
>>
>> > The violated condition was:
>> > cell_index == 0 || !at_boundary()
>> > Additional information:
>> > You are on a boundary, so you can only ask for the first FEFaceValues 
>> > object.
>>
>> ...if the cell is on a boundary, but the face is an interior face.
>>
>> I've attached code for a small test case illustrating the issue. It consists 
>> of a 2x2 2D mesh, and attempts to use FEInterfaceValues to get field values 
>> from the cell "above".
>>
>> Is this indeed a bug, or am I misunderstanding the intended usage of 
>> FEInterfaceValues? I'm using deal.II, version 9.2.0.
>>
>> Best,
>> Corbin
>>
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Re: [deal.II] HDF5 output on multiple nodes at HPC cluster

[Timo Heister]

Great to hear. Was it a standard NFS filesystem that produced the failures?

On Tue, Apr 13, 2021 at 4:03 AM 'Christian Burkhardt' via deal.II User
Group  wrote:
>
> Thanks for your quick answer.
> The problem persisted for the parallel vtu output.
> Changing the file system where the output is written to, to a xfs solved the 
> problem. Sorry for the inconvinience, but we are quite new to cluster systems.
>
> Thanks,
> Christian
>
> Timo Heister schrieb am Montag, 12. April 2021 um 18:37:32 UTC+2:
>>
>> Christian,
>>
>> What kind of filesystem is this file written to? Does our parallel vtu
>> output that also uses MPI IO work correctly? (step-40 with grouping
>> set to a single file)
>>
>> On Mon, Apr 12, 2021 at 12:15 PM 'Christian Burkhardt' via deal.II
>> User Group  wrote:
>> >
>> > Hi everyone,
>> >
>> > we installed dea...@9.2.0 on our HPC cluster (centos7) using spack and the 
>> > intel compilers 
>> > (dea...@9.2.0%in...@19.0.4~assimp~petsc~slepc~ginkgo~adol-c+mpi^intel-mpi^intel-mkl^boost).
>> > When running our code, which uses hdf5 for output, on the front node and 
>> > when submitting it via the batch script everything works fine as long as 
>> > we run on a single node (up to 40 cores).
>> > As soon as we increase the node number above 1 (eg 41 cores) the code 
>> > fails.
>> > We were able to reproduce the problem with an adapted version of step-40 
>> > of the dealii tutorials that outputs using hdf5 (see attached step-40).
>> > The restriction to 32 MPI Processes for the output was bypassed by setting 
>> > the limit to 42.
>> > The code can overwrite existing files (created during a previous run with 
>> > 40 processes or less and 1 node), but crashes when new files are to be 
>> > created with the following error message, which is related to the hdf5 
>> > output:
>> >
>> > ...
>> > HDF5-DIAG: Error detected in HDF5 (1.8.21) MPI-process 41:
>> > #000: H5F.c line 520 in H5Fcreate(): unable to create file
>> > major: File accessibilty
>> > minor: Unable to open file
>> > #001: H5Fint.c line 990 in H5F_open(): unable to open file: time = Mon Apr 
>> > 12 11:25:30 2021
>> > , name = 'Solution_0.h5', tent_flags = 13
>> > major: File accessibilty
>> > minor: Unable to open file
>> > #002: H5FD.c line 991 in H5FD_open(): open failed
>> > major: Virtual File Layer
>> > minor: Unable to initialize object
>> > #003: H5FDmpio.c line 1057 in H5FD_mpio_open(): MPI_File_open failed
>> > major: Internal error (too specific to document in detail)
>> > minor: Some MPI function failed
>> > #004: H5FDmpio.c line 1057 in H5FD_mpio_open(): File does not exist, error 
>> > stack:
>> > ADIOI_UFS_OPEN(39): File Solution_0.h5 does not exist
>> > major: Internal error (too specific to document in detail)
>> > minor: MPI Error String
>> > ...
>> >
>> > The file mentioned in the error message is still created, but remains 
>> > empty (file size 0)
>> > (see testRunMPI.e1448739 for the full error message).
>> > We tried different hdf5 versions (1.10.7, 1.8.21).
>> > We also looked into https://github.com/choderalab/yank/issues/1165 and 
>> > tried setting the environment variable "HDF5_USE_FILE_LOCKING=FALSE" which 
>> > didn't alter the outcome.
>> > As our configuration includes MPI "WITH_MPI=ON" the issue 
>> > https://github.com/dealii/dealii/issues/605 is about something different, 
>> > right?
>> >
>> > In the tutorial description it is mentioned that a limitation of 16 
>> > processors was chosen because such large examples have problems being 
>> > visualised.
>> > Is there a general rule of thumb that states graphical output for DOF 
>> > numbers over a certain threshold are unfeasible?
>> >
>> > Any help is much appreciated.
>> >
>> > Christian
>> >
>> > --
>> > 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.
>> > To view this discussion on the web visit 
>&

Re: [deal.II] HDF5 output on multiple nodes at HPC cluster

[Timo Heister]

Christian,

What kind of filesystem is this file written to? Does our parallel vtu
output that also uses MPI IO work correctly? (step-40 with grouping
set to a single file)

On Mon, Apr 12, 2021 at 12:15 PM 'Christian Burkhardt' via deal.II
User Group  wrote:
>
> Hi everyone,
>
> we installed dealii@9.2.0 on our HPC cluster (centos7) using spack and the 
> intel compilers 
> (dealii@9.2.0%intel@19.0.4~assimp~petsc~slepc~ginkgo~adol-c+mpi^intel-mpi^intel-mkl^boost).
> When running our code, which uses hdf5 for output, on the front node and when 
> submitting it via the batch script everything works fine as long as we run on 
> a single node (up to 40 cores).
> As soon as we increase the node number above 1 (eg 41 cores) the code fails.
> We were able to reproduce the problem with an adapted version of step-40 of 
> the dealii tutorials that outputs using hdf5 (see attached step-40).
> The restriction to 32 MPI Processes for the output was bypassed by setting 
> the limit to 42.
> The code can overwrite existing files (created during a previous run with 40 
> processes or less and 1 node), but crashes when new files are to be created 
> with the following error message, which is related to the hdf5 output:
>
> ...
> HDF5-DIAG: Error detected in HDF5 (1.8.21) MPI-process 41:
>   #000: H5F.c line 520 in H5Fcreate(): unable to create file
> major: File accessibilty
> minor: Unable to open file
>   #001: H5Fint.c line 990 in H5F_open(): unable to open file: time = Mon Apr 
> 12 11:25:30 2021
> , name = 'Solution_0.h5', tent_flags = 13
> major: File accessibilty
> minor: Unable to open file
>   #002: H5FD.c line 991 in H5FD_open(): open failed
> major: Virtual File Layer
> minor: Unable to initialize object
>   #003: H5FDmpio.c line 1057 in H5FD_mpio_open(): MPI_File_open failed
> major: Internal error (too specific to document in detail)
> minor: Some MPI function failed
>   #004: H5FDmpio.c line 1057 in H5FD_mpio_open(): File does not exist, error 
> stack:
> ADIOI_UFS_OPEN(39): File Solution_0.h5 does not exist
> major: Internal error (too specific to document in detail)
> minor: MPI Error String
> ...
>
> The file mentioned in the error message is still created, but remains empty 
> (file size 0)
> (see testRunMPI.e1448739 for the full error message).
> We tried different hdf5 versions (1.10.7, 1.8.21).
> We also looked into https://github.com/choderalab/yank/issues/1165 and tried 
> setting the environment variable "HDF5_USE_FILE_LOCKING=FALSE" which didn't 
> alter the outcome.
> As our configuration includes MPI "WITH_MPI=ON" the issue 
> https://github.com/dealii/dealii/issues/605 is about something different, 
> right?
>
> In the tutorial description it is mentioned that a limitation of 16 
> processors was chosen because such large examples have problems being 
> visualised.
> Is there a general rule of thumb that states graphical output for DOF numbers 
> over a certain threshold are unfeasible?
>
> Any help is much appreciated.
>
> Christian
>
> --
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Re: [deal.II] Using FEInterfaceValues with FESystems?

[Timo Heister]

Bruno, I already have a working implementation of the extractors on my
machine. I just didn't get the time to clean up, write tests, and
submit the PR. Sorry. I will try to pick this up again in the next few
days.

On Fri, Mar 12, 2021 at 12:26 PM Wolfgang Bangerth
 wrote:
>
> On 3/11/21 11:10 PM, blais...@gmail.com wrote:
> > Let me read the documentation a bit and I  could try to come up with a PR.
> > Maybe this is something we could discuss? I'd be glad to help in improving 
> > DG
> > methods :)
>
> Happy to discuss in whatever venue you propose!
>
> Start by looking at the FEValuesViews::Scalar class. We'd need a corresponding
> FEInterfaceValuesViews::Scalar class. Once you know how the former operates,
> you will probably be able to see how the latter needs to be implemented. I
> foresee a lot of copy-paste of small functions where the only change is in the
> 2-3 line bodies.
>
> Best
>   Wolfgang
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
> --
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Re: [deal.II] Tags and Communicators

[Timo Heister]

I see additional problems with separate communicators per object:
1. For me it is unclear how operations that involve more than one
object should communicate. For example, a mat-vec has 2 vectors (src,
dst) and a matrix and as such 3 communicators. Of course you can make
an arbitrary choice here, but this doesn't seem clean to me.
2. MPI_comm_dup can involve communication and as such can be slow for
large processor counts. Not sure you want to always pay the price for
that. I remember at least one MPI implementation that does an
allreduce (or something worse than that).
3. The number of communicators can be quite limited, see [1]

[1] see https://www.mcs.anl.gov/~thakur/papers/mpi-million.pdf

On Thu, Feb 18, 2021 at 12:19 PM Wolfgang Bangerth
 wrote:
>
>
> > One fix that I have found (PETSc does this) is to assign every object its
> > own duplicated communicator which can then keep track of its own tags with
> > MPI's own get and set attributes functions.
>
> Sometime back in the day (in the 2005-2010 range) I spent an inordinate amount
> of time going through every class that receives a communicator in some way or
> other in the constructor or a reinit() call, and had that class duplicate the
> communicator in the way you mention (Utilities::MPI::duplicate_communicator()
> does that). You can probably still find those patches if you look long enough.
>
> The reason I did this was primarily because I wanted to have one added layer
> of security. If for some reason one process does not participate in a
> collective communication, you should get a deadlock, whereas you would either
> get funny errors or just completely unreliable results if that process
> proceeds to the next communication on the same communicator. Right now, in
> practice, all communication happens on MPI_COMM_WORLD.
>
> But, after spending a good amount of time to duplicate all of these
> communicators (probably several days of work), I spent *an even larger amount
> of time* to track down what was quite likely the worst-to-find bug I have ever
> worked on. It only manifested in a crash after a program had been running for
> many hours, and small changes to the program made the bug move to unrelated
> pieces of the code but not make it appear any earlier in the run time of the
> program.
>
> In the end, what it boiled down is that the MPI implementation I was using was
> only able to provide 64k different communicators and if you asked for the
> 64k+1'st communicator, it just crashed. In programs that do thousands of time
> steps and allocate a few vectors for temp operations in each time step, you'd
> get there in a matter of hours.
>
> I had sort of expected that MPI implementations recycle released
> communicators, and I would expect that that's what they do today, but they
> didn't back then. So after all of this time spent, I ripped out the
> duplication of communicators again. You can probably also find that patch in
> the repository and, with some luck, you might even be able to revert it if you
> allow some fuzz in indentation etc. It would certainly be interesting to try
> this again.
>
> I'm still in favor of this approach. It's conceptually the right thing, it
> would help uncover bugs, and it is *necessary* if you want to do things
> multithreaded. (All of the MPI implementations have reentrant public
> interfaces these days, but we can't use them unless you also duplicate
> communicators somewhere.) But I would first want to try with a small test
> program whether that is scalable to very large numbers of communicators -- I
> think we would quite easily run into millions of communicators with this
> approach if programs run long enough, though of course only a rather small
> number would be live at any given time.
>
> Best
>   W.
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
> --
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-- 
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On Fri, Feb 19, 2021 at 3:54 PM Wolfgang Bangerth
 wrote:
>
> On 2/19/21 1:31 PM, Wells, David wrote:
> >

Re: [deal.II] Unable to visualise high order polynomial variation in ParaView

[Timo Heister]

One thing that might not be obvious is that it is not enough to have a 
manifold id for boundary faces. You need to assign a manifold to the cells 
as well.

On Wednesday, January 20, 2021 at 11:49:59 AM UTC-5 luca@gmail.com 
wrote:

> Did you call
>
> data_out.build_patches(mapping, 
> subdivisions,DataOut::curved_inner_cells);
>
> with subdivisions > 1?
>
> L.
>
> > On 20 Jan 2021, at 12:06, vachanpo...@gmail.com  
> wrote:
> > 
> > Dear all,
> > 
> > I have a working code that outputs pvtu/vtu files for visualisation.
> > 
> > I have read the wiki page for writing and visualising high order output. 
> Currently, I only have straight-edge quadrilaterals so I the only change I 
> have made to my code is to update VtkFlags and set them in the DataOut 
> object (as below). Please correct me if I am missing anything here.
> > 
> > DataOutBase::VtkFlags flags;
> > flags.write_higher_order_cells = true;
> > data_out.set_flags(flags);
> > 
> > However, the output of this modified code still produces linear 
> variation when visualised. I have also set the Nonlinear Subdivision Level 
> in paraview accordingly. But is seems to produce no change.
> > 
> > What am I missing?
> > 
> > Thanking in anticipation
> > Vachan
> > 
> > -- 
> > The deal.II project is located at http://www.dealii.org/
> > For mailing list/forum options, see 
> https://groups.google.com/d/forum/dealii?hl=en
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> .
>
>

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Re: [deal.II] FEInterfaceValues

[Timo Heister]

> If this is correct, do you see a way to circumvent the TRILINOS problem I am 
> facing?

If you need entries i,j in the sparsity pattern and none of the
make_*_sparsity_pattern() function apply, you will need to add them
manually. This should be as simple as following the same logic you are
using in the assembly, where you identify DoF indices (you called them
local_interface_dof_indices) and you add them using

dsp.add(i,j)

where i and j are all indices in local_interface_dof_indices.


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Re: [deal.II] Re: Slepc Solver Dimension error

[Timo Heister]

Hi Zachary,

It is difficult for many of us to find the time to debug problems from
our users like this, I hope you understand. May I suggest that you
look into this problem in more detail by yourself first? Have you used
a debugger to see where the error occurred exactly? Do you understand
what the error message is telling you? Can you simplify the problem
further? How many MPI ranks do you need to see the problem?

If you suspect a bug in deal.II, we will be happy to look into it,
especially if you can provide a minimal example that shows the
problem.

On Thu, Jan 7, 2021 at 8:17 PM Zachary 42!  wrote:
>
> Sorry, forgot the file!
>
> --
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>
>
>
>
> > On Jan 7, 2021, at 7:15 PM, Zachary 42!  wrote:
> >
> > Hi everyone,
> >
> > I get a “sum of local lengths 32 does not equal global length 128” PETSC 
> > error in the following test file.  It dies at the eigensolver.solve step.  
> > I tried to use the test and tutorial programs but to no avail.  Still 
> > wrapping my head around the logic so please excuse me.
> >
> > Thank you,
> >
> > Zachary
> >
> >
>
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Re: [deal.II] Re: Tips on writing "versatile" assembly function

[Timo Heister]

What I forgot to say:
We used to have something like

if (use_anisotropic_viscosity==true)
  cell(i,j) += viscosity_tensor * 
else
  cell(i,j) += viscosity_constant * 

and improved the performance by making two separate assemblers (note
that there is no function call/vtable lookup here, just an "if"). I
don't remember how big the difference was, so I went back and found
the PR:
https://github.com/geodynamics/aspect/pull/2139
Rene claims 25% fewer instructions.



On Tue, Jan 5, 2021 at 4:48 PM blais...@gmail.com  wrote:
>
> Hi Timo,
>
> I understand. It makes a lot of sense.
> Thanks!
> Bruno
>
> On Tuesday, January 5, 2021 at 4:34:19 p.m. UTC-5 Timo Heister wrote:
>>
>> Hi Bruno,
>>
>> We mitigate the performance problem by making the decision per cell in 
>> ASPECT:
>> We have a set of "assemblers" that are executed one after each other
>> per cell. This means the vtable access cost is small compared to the
>> actual work.
>> See
>> https://github.com/geodynamics/aspect/blob/b9add5f53172aac18bdbb19d14ca266e88c491dd/include/aspect/simulator/assemblers/interface.h#L493-L515
>>
>> On Tue, Jan 5, 2021 at 4:28 PM blais...@gmail.com  wrote:
>> >
>> > Bruno,
>> >
>> > Thanks, you are right. As always, measure first and then optimize after. 
>> > No point in optimising stuff that costs nothing...
>> >
>> >
>> > On Tuesday, January 5, 2021 at 3:15:06 p.m. UTC-5 bruno.t...@gmail.com 
>> > wrote:
>> >>
>> >> Bruno,
>> >>
>> >> If you are worry about the cost of looking up though the vtable, I think 
>> >> that you are stuck using template. So either use 2 or 3 and CRTP. But 
>> >> first of all, I think that you should profile your code and verify that 
>> >> this is a problem. There is no point in spending time refactoring your 
>> >> code, if your are going to gain less than 1%...
>> >>
>> >> Best,
>> >>
>> >> Bruno
>> >>
>> >> On Monday, January 4, 2021 at 3:31:45 PM UTC-5 blais...@gmail.com wrote:
>> >>>
>> >>> Dear all,
>> >>> I wish you all an happy new year!
>> >>>
>> >>> One problem we always end up facing with FEM problems is that, as 
>> >>> program grow, more and more features are added to the equations. This 
>> >>> leads to multiple variation of the same equations (for example, 
>> >>> Navier-Stokes with Newtonian and non-Newtonian viscosity, etc.). In 
>> >>> turn, this leads to assembly functions for the non-linear systems of 
>> >>> equations which branch out to multiple possibilities.
>> >>>
>> >>> I was wondering what is the best approach to deal with multiple 
>> >>> "switches" in an assembly function. The naïve approach would be to use 
>> >>> if conditions, but I have a feeling that if they appear down in the 
>> >>> assembly (for example the loop on dofs), this would lead to 
>> >>> significantly higher assembly cost because the loops would spend time 
>> >>> just checking if.
>> >>>
>> >>> From experience, I have seen the following approaches:
>> >>> 1- If or switches in the assembly routine. Simplest/most versatile way, 
>> >>> but adds significant overhead
>> >>> 2- Template the assembly function with the parameters. I think this 
>> >>> would lead to zero additional cost, but as the number of parameters 
>> >>> grows, this can become more and more complex since the various 
>> >>> possibilities have to be known at compile time.
>> >>> 3- Use generic interface objects for common elements (for example a 
>> >>> viscosity class to calculate viscosity, etc.) and use inheritance to 
>> >>> specialise the model. I think this could be inefficient because of the 
>> >>> need to extensively look up through the vtable.
>> >>>
>> >>> What is the general consensus in the deal.II community on this problem? 
>> >>> What's the best way to deal with multiple possibilities in the same 
>> >>> assembly function? I would be very interested in hearing the perspective 
>> >>> of the ASPECT author since it has such a large range of sub models.
>> >>>
>> >>>
>> > --
>> > The deal.II project is located at http://www.dealii.org/
>> > For mailing list/forum options, see

Re: [deal.II] Re: Tips on writing "versatile" assembly function

[Timo Heister]

Hi Bruno,

We mitigate the performance problem by making the decision per cell in ASPECT:
We have a set of "assemblers" that are executed one after each other
per cell. This means the vtable access cost is small compared to the
actual work.
See
https://github.com/geodynamics/aspect/blob/b9add5f53172aac18bdbb19d14ca266e88c491dd/include/aspect/simulator/assemblers/interface.h#L493-L515

On Tue, Jan 5, 2021 at 4:28 PM blais...@gmail.com  wrote:
>
> Bruno,
>
> Thanks, you are right. As always, measure first and then optimize after. No 
> point in optimising stuff that costs nothing...
>
>
> On Tuesday, January 5, 2021 at 3:15:06 p.m. UTC-5 bruno.t...@gmail.com wrote:
>>
>> Bruno,
>>
>> If you are worry about the cost of looking up though the vtable, I think 
>> that you are stuck using template. So either use 2 or 3 and CRTP. But first 
>> of all, I think that you should profile your code and verify that this is a 
>> problem. There is no point in spending time refactoring your code, if your 
>> are going to gain less than 1%...
>>
>> Best,
>>
>> Bruno
>>
>> On Monday, January 4, 2021 at 3:31:45 PM UTC-5 blais...@gmail.com wrote:
>>>
>>> Dear all,
>>> I wish you all an happy new year!
>>>
>>> One problem we always end up facing with FEM problems is that, as program 
>>> grow, more and more features are added to the equations. This leads to 
>>> multiple variation of the same equations (for example, Navier-Stokes with 
>>> Newtonian and non-Newtonian viscosity, etc.). In turn, this leads to 
>>> assembly functions for the non-linear systems of equations which branch out 
>>> to multiple possibilities.
>>>
>>> I was wondering what is the best approach to deal with multiple "switches" 
>>> in an assembly function. The naïve approach would be to use if conditions, 
>>> but I have a feeling that if they appear down in the assembly (for example 
>>> the loop on dofs), this would lead to significantly higher assembly cost 
>>> because the loops would spend time just checking if.
>>>
>>> From experience, I have seen the following approaches:
>>> 1- If or switches in the assembly routine. Simplest/most versatile way, but 
>>> adds significant overhead
>>> 2- Template the assembly function with the parameters. I think this would 
>>> lead to zero additional cost, but as the number of parameters grows, this 
>>> can become more and more complex since the various possibilities have to be 
>>> known at compile time.
>>> 3- Use generic interface objects for common elements (for example a 
>>> viscosity class to calculate viscosity, etc.) and use inheritance to 
>>> specialise the model. I think this could be inefficient because of the need 
>>> to extensively look up through the vtable.
>>>
>>> What is the general consensus in the deal.II community on this problem? 
>>> What's the best way to deal with multiple possibilities in the same 
>>> assembly function? I would be very interested in hearing the perspective of 
>>> the ASPECT author since it has such a large range of sub models.
>>>
>>>
> --
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Re: [deal.II] Coming back to dealii after a long time

[Timo Heister]

> However, I installed it before upgrading my Mac OS from Mojave 10.14.6 to 
> Catalina 10.15.7.
> Do you think this could be the reason for the error?

I doubt it, but I am not that familiar with the OSX side of things.

> but my xcode version is still version 10, do you think this matters?

I also think that this doesn't matter and does not explain the error.

> Processor: 2.9 GHz Dual-Core Intel Core i7

That must be a quite old machine and might explain the issues you
have. If the current .dmg does not work, I fear you will need to
install deal.II in a different way. See
https://github.com/dealii/dealii/wiki/Getting-deal.II for some
guidance.


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Re: [deal.II] Coming back to dealii after a long time

[Timo Heister]

Hi Wakil,

> make[3]: *** [CMakeFiles/run] Illegal instruction: 4

This is due to the library (or a dependency) having been compiled on a
newer processor architecture than the one you are using. Can you
please check that you use the latest dealii-9.2.0-v3.dmg from
https://www.dealii.org/download.html ? I think we fixed this issue a
while ago.

If this is the case, what kind of processor/mac do you have?

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Re: [deal.II] Using Dealii to developing aa finite element software on Windows

[Timo Heister]

Hi Amir,

deal.II 9.1 requires c++11
deal.II 9.2 requires c++11
deal.II 9.3 will require c++14

Your only choice would be to use an older version of deal.II but I
would strongly suggest updating your compilers instead.

On Sun, Dec 27, 2020 at 12:09 AM amir kiani  wrote:
>
> Hello.
> Recently I started to learn finite element programming.
> By surfing the net, I came to C++ and Deal.ii.
> One of my concerns in using Deal.ii and C++ is about any possible future 
> limitations.
> By reading tutorials on the website of Deal.ii, I realized that using Deal.ii 
> directly on windows is experimentally supported.
> Now my main question:
> As presented on the Deal.ii Website, If I build Deal.ii via each approach 
> (and in any operating system like Linux), Can I use classes and libraries of 
> Deal.ii in other C++ programs? Consider I want to use Deal.ii features in 
> C++03 with Visual Studio 2008 on Windows 7.
> Because I am working on developing an existing software, I am restricted to 
> use this standard of C++ and this version of Visual Studio.
> I appreciate all answers in advance
>
> --
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Re: [deal.II] FEInterfaceValues

[Timo Heister]

Alberto,

>  I would like to associate to each gauss point on the interface, identified 
> by the command
>   const auto &q_points = fiv.get_quadrature_points();
>  the values of the unknown fields at the two faces of the two cells that form 
> the interface itself.
>  It should not be too difficult I think.
>  Perhaps I should use

Currently, FEInterfaceValues does not have support for
get_function_values() directly but this is something I am planning to
do soon.

Your code looks reasonable, but I think you can use the existing
FEFaceValues objects inside the FEInterfaceValues like

feiv.get_fe_face_values(0).get_function_values(...)
feiv.get_fe_face_values(1).get_function_values(...)


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[deal.II] new publication about the design of the deal.II library published

[Timo Heister]

Hi all,

I would like to bring your attention to the publication

The deal.II finite element library: design, features, and insights
Computers & Mathematics with Applications, vol. 81, pages 407-422, 2021.
https://doi.org/10.1016/j.camwa.2020.02.022

that just got published. As a user/developer of deal.II, I think you
might find it to be an interesting read.

Thank you for being part of this great community and happy holidays.

Best,
Timo (and co-authors)


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Re: [deal.II] FEInterfaceValues

[Timo Heister]

Alberto,

> I would like to have a few more details on the class FEInterfaceValues.
> since it is my feeling that  FEInterfaceValues
> might be conveniently used for interfaces, even out of DG methods.

Yes, I would think so.

> Specifically I'd like to figure out if this notion can be used without 
> recurring to the MeshWorker::mesh_loop,
> which I am not quite confident at present.

Note that we are not using the MeshWorker machinery but a single
function that contains the loops over the cells. The code of the
function is "relatively" easy to understand and you will appreciate
the logic for the following things you would have to deal with when
looping manually:
- assembling from the finer cell for interfaces with adaptive refinement
- correctly handling each facet once (or twice if desired) even in parallel
- handling of periodic boundaries

> I'd like to play autonomously with the class FEInterfaceValues
> but unfortunately I cannot grasp the notion of subface, which is apparently
> required by the reinit as in step 12:
>  fe_iv.reinit(cell, f, sf, ncell, nf, nsf);

With adaptivity you will need to pass the subface as returned by
neighbor_of_coarser_neighbor, otherwise it is
numbers::invalid_unsigned_int. See
https://github.com/dealii/dealii/blob/691ff4907964605dd21e94f06c880786af2cd612/tests/feinterface/fe_interface_values_03.cc#L94-L100
and
https://github.com/dealii/dealii/blob/691ff4907964605dd21e94f06c880786af2cd612/tests/feinterface/fe_interface_values_02.cc#L88-L93

> Can anyone address me some reading on this notion and how it is dealt with
> by the MeshWorker::mesh_loop ?

Take a look at the tests in tests/feinterface/:
https://github.com/dealii/dealii/tree/master/tests/feinterface

Many of them use FEInterfaceValues directly on a small test mesh.

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Re: [deal.II] Re: Gmsh support on Deal.II Virtualbox image

[Timo Heister]

This has nothing to do with DEAL_II_WITH_GMSH. That feature is only
required if you use functionality from the Gmsh namespace
(https://www.dealii.org/developer/doxygen/deal.II/namespaceGmsh.html).
The error message

The violated condition was:
in
Additional information:
An input/output error has occurred.

occurs when the .msh file is not found. Does the file exist in the
current folder?


On Tue, Dec 15, 2020 at 1:48 PM Aaditya Lakshmanan
 wrote:
>
> Hi,
>   You probably also need to supply the flag -DDEAL_II_WITH_GMSH=ON in the 
> cmake line.
>
> Best,
> Aaditya
>
> On Tuesday, December 15, 2020 at 1:21:00 PM UTC-5 husain.u...@gmail.com wrote:
>>
>>
>> Hello Deal.II community,
>> I am working on deal.II via the VM image (release 9.1.1). I am having 
>> trouble reading the .msh file. I even tried running running step 49 and 
>> received this error:
>>
>> 
>> Exception on processing:
>>
>> 
>> An error occurred in line <1408> of file 
>>  in function
>> void dealii::GridIn::read_msh(std::istream&) [with int 
>> dim = 2; int spacedim = 2; std::istream = std::basic_istream]
>> The violated condition was:
>> in
>> Additional information:
>> An input/output error has occurred. There are a number of reasons why 
>> this may be happening, both for reading and writing operations.
>>
>> If this happens during an operation that tries to read data: First, you may 
>> be trying to read from a file that doesn't exist or that is not readable 
>> given its file permissions. Second, deal.II uses this error at times if it 
>> tries to read information from a file but where the information in the file 
>> does not correspond to the expected format. An example would be a truncated 
>> file, or a mesh file that contains not only sections that describe the 
>> vertices and cells, but also sections for additional data that deal.II does 
>> not understand.
>>
>> If this happens during an operation that tries to write data: you may be 
>> trying to write to a file to which file or directory permissions do not 
>> allow you to write. A typical example is where you specify an output file in 
>> a directory that does not exist.
>> 
>>
>> Aborting!
>> 
>>
>> I checked the detailed.log file and found DEAL_II_WITH_GMSH is OFF.
>> I also tried to install the latest version of gmsh (4.7.1) and ran the cmake 
>> command for deal ii installation with -DGMSH_DIR=/path/to/gmsh added to it. 
>> But it gives me warning
>>
>> CMake Warning:
>>   Manually-specified variables were not used by the project:
>>
>> GMSH_DIR
>>
>> Can someone please suggest if I am missing anything here?
>
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Re: [deal.II] Suggestions for "cheap" distributed preconditioner for transient systems?

[Timo Heister]

> If I understand correctly,  you mean formulating the problem using a 
> BlockMatrix and a BlockVector, then preconditioning each matrix of the block 
> independently?

Correct. You perform a block LU decomposition by hand and use that as
your preconditioner. Then approximate the blocks as best as you can.
The advantage is that you can exploit PDE specifics:
- lumping of mass matrices
- AMG/GMG for laplace-like operators
- ILU/Jacobi for mass matrix-like operators
- spectrally-equivalent matrices to approximate Schur complements
- and more

We have many tutorial steps that teach this (but not precisely for
your problem).

> I guess this would be best achieved using the linear operators within deal.II 
> right?

Not necessarily. See step-55 and step-57 for example. The linear
operator framework helps, especially to define implicit operators
(step-20), but is not required.

> What would be the added benefit of that? I would presume that since each 
> block have more "coherent units", this would at least to a better 
> conditioning of the final system, but is there anything else there?

I doubt you can get optimal preconditioners (in the sense of cost
independent of h and other problem parameters) without exploiting
PDE-specifics.


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Re: [deal.II] Suggestions for "cheap" distributed preconditioner for transient systems?

[Timo Heister]

> The task generally contain  on the order of 50M to 100M DOFs and are 
> transient DNS problems.

With this you are likely at a point where factorizations (even ILU)
not work very well. Even if you can afford a Block ILU, you likely run
on 100+ cores, which means the quality of the preconditioner will
deteriorate quite a lot just based on the number of processors. You
likely need something that puts more effort into the parallel aspect.

> Our solver : Either GMRES or BiCGStab. In our case it seems GMRES is a bit 
> faster (around 20%) because the iterations are cheaper. I have tried all of 
> the solvers in the TrilinosWrappers except FGMRES actually.

My general advice is to work on the preconditioner to have a method in
the 10-40 iterations range. Then, it doesn't really matter which
Krylov method you use. Just use FGMRES (if you need flexibility), CG
(for SPD), MINRES (for symmetric), or GMRES (for everything else).
Switching between different Krylov methods is unlikely to make a big
difference unless you are in the 100k+ core range or need too many
iterations.

> Our current preconditioner : ILU(0)
> Element order : Q2-Q2, Q3-Q3 or Q4-Q4.

Are you just applying ILU to the whole system? My general advice is to
exploit the block structure of your PDE first and then apply ILU or
AMG to individual blocks. Time dependent Navier-Stokes with small time
steps is a relatively easy case. Let me know if you want more details.


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Re: [deal.II] Periodic Boundary conditions on Step-3 tutorial with dim != spacedim

[Timo Heister]

> Thank you for your reply. Yeah, I would definitely like try and make it work. 
> So, what I did was, I made some small changes in the file 
> 'dof_tools_constraints.inst.in '.
> I just added spacedim loop for the first two 'for loop' blocks.

Yes, this is probably all that is needed.

> Although the build was successful, I am not sure how to check if its 
> implemented correctly or not.

I would typically go about this in the following ways:
1. Look over the implementation and think about if the operations make sense.
2. Create a small test, run it, and make sure you are not running into
Assert/crashes.
3. Set up a test problem where you can verify that things work correctly.

It sounds like you should be able to make 2) and 3) work with the
modified step-3 that you posted.

 One more slightly basic question, do I need to build all the other
files if I only changed this one file? Does it not detect that only
one file was changed? This is the way one goes about changing stuff
right?

If you run "make", we automatically detect everything that needs to be
rebuilt and do exactly that. You might need a "make install" as well,
depending on how you specify the location of your deal.II library.

> Also, I will be sure to put a pull request if it works.

Awesome! Let us know if you need help at any point.



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Re: [deal.II] Periodic Boundary conditions on Step-3 tutorial with dim != spacedim

[Timo Heister]

Hi Malhar,

if you look at
https://github.com/dealii/dealii/blob/a56c8585863b774de9dce5f7dd5c334ef56f3a51/source/dofs/dof_tools_constraints.inst.in#L69

you can see that it is only instantiated for
DoFHandler
meaning only for dim=spacedim (the second argument is the default right now).

Instead, we would need to move the instantiation down into a loop that
has two loops over dim and instantiate it for all pairs like it is
done for
https://github.com/dealii/dealii/blob/a56c8585863b774de9dce5f7dd5c334ef56f3a51/source/dofs/dof_tools_constraints.inst.in#L123

Do you want to try if you can make this work? I am not sure if the
implementation will work correctly, but we can check that in a second
step.
If this works, we would appreciate a pull request from you to fix this!

Best,
Timo



On Sun, Nov 22, 2020 at 4:11 PM Malhar T.  wrote:
>
> Hello All !
>
> I was trying the step-3 with periodic boundary conditions and dim = 2 and 
> spacedim = 3. The main reason behind this is I want to test periodic boundary 
> conditions for dim != spacedim. I have tested the code for dim = spacedim = 2 
> and the periodic boundary conditions and it works (never mind the results for 
> now !). I have also tested the code for dim = 2 and spacedim = 3 without 
> periodic boundary conditions and it works too. But only when I add periodic 
> conditions for that case, the issue arises.
>
> I got the following error,
>
> error: undefined reference to 'void 
> dealii::DoFTools::make_periodicity_constraints<2, 3, 
> double>(dealii::DoFHandler<2, 3> const&, unsigned int, unsigned int, unsigned 
> int, dealii::AffineConstraints&, dealii::ComponentMask const&, 
> double)'
> collect2: error: ld returned 1 exit status
> make[2]: *** [CMakeFiles/step1.dir/build.make:139: step1] Error 1
> make[1]: *** [CMakeFiles/Makefile2:76: CMakeFiles/step1.dir/all] Error 2
> make: *** [Makefile:84: all] Error 2
>
> The version that I am using is 9.3.0-pre. Although I am not really great at 
> C++ but according to the template and source, it should have worked, but I 
> could not find anything here. I tried running it without template arguments 
> or with only '2' as a template argument, but couldn't make it work. I have 
> attached the code which I have tried, and also the code dim = 2 and spacedim 
> = 3 without periodic boundary conditions. Any help will be greatly 
> appreciated.
>
> Thank You
>
> --
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Re: [deal.II] Re: parallel::distributed::Triangulation: Wrong level n_dofs after

[Timo Heister]

Hi Mathias,

Awesome. This looks correct to me. Would you be interested in creating
a pull request to fix this in the master version?

Thanks,
Timo

On Mon, Nov 2, 2020 at 1:14 PM mathias@posteo.de
 wrote:
>
> Hello again,
>
> I guess I have found the problem in dof_handler_policy.cc: In line 4565 the 
> n_global_dofs is set to the n_dofs(), not to the n_dofs(level).
> Changing this fixes the problem for me.
> I have created a commit in my dealii fork, where you can see it.
>
> Greetings
>
> Mathias
> mathias@posteo.de schrieb am Montag, 2. November 2020 um 18:06:27 UTC+1:
>>
>>
>> Hello,
>>
>> I'm working with MultiGrid on a parallel::distributet::Triangulation and 
>> want to reorder the DoFs for the individual levels.
>>  After doing e.g. a Cuthill_McKee reordering I realised that the 
>> MGTools::make_sparsity_pattern() function throws an assertion in line 602:
>>
>> Assert(sparsity.n_rows() == n_dofs, ExcDimensionMismatch(sparsity.n_rows(), 
>> n_dofs));
>>
>> A simple test shows that indeed the number of level DoFs gets somehow 
>> changed during the reordering. I have attached a simple test, based on a 
>> deal.II test.
>> The problem doesn't occur If one uses a normal (not parallel) triangulation.
>> I'm still looking for the root cause of the problem, maybe someone has an 
>> idea here?
>>
>> Greetings
>>
>> Mathias
>
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Re: [deal.II] dealii installation issue on NERSC Cori

[Timo Heister]

>Thanks for you suggestion. I tested step-1 and step-2 again and they ran 
> successfully after I set the number of OpenMP threads to 1. I only plan plan 
> on running MPI codes without any multi-threading. The BLAS implementation I 
> am using is a part of the Intel MKL library which is already present within 
> one of the default modules which loads intel compilers and intel 
> implementations of other commonly used libraries. Would you recommend using 
> another BLAS implementation or install one manually?

No, just make sure you set OMP_NUM_THREADS=1 in your job script.

> Installing deal.ii on the Cori system was definitely a bit convoluted since 
> even the original cmake and make install had to be run on the compute node, 
> and that was an extremely slow process taking a few hours to complete even 
> with make -j64 install(unlike the login nodes where the entire thing would be 
> done in about 30 minutes). In one of their(NERSC) 
> presentations(https://www.nersc.gov/assets/Uploads/06-Compiling-Codes.pdf, 
> slide 14) they do recommend swapping a haswell module with mic-knl module and 
> compiling on login nodes whenever possible(slide 20). That's what I had tried 
> earlier and did so again yesterday, and then running step-1(interactively on 
> a compute node) yielded the following error :

Yes, while I have no experience with working on system like this, I am
not surprised that this is challenging.

> make[3]: *** No rule to make target '/usr/lib64/libopenblas.so', needed by 
> 'step-1'. Stop.

That means this library is missing on the compute node.

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Re: [deal.II] dealii installation issue on NERSC Cori

[Timo Heister]

Can you try setting

export OMP_NUM_THREADS=1

before running any of the examples?

If you are planning on running MPI-only codes, you don't need to use
OpenMP in your BLAS implementation.


On Sun, Oct 25, 2020 at 7:25 PM Aaditya Lakshmanan
 wrote:
>
> Hi Timo,
>I cleaned the previous installation and started with a fresh build. This 
> time after a compilation and installation(with MPI, LAPACK, P4EST and PETSC), 
> trying to run examples/step-1 in the installation directory :
>
> cmake .
> make -j16
>
> ran successfully after which
>
> make run
>
> resulted in the following output :
>
> [ 66%] Built target step-1
> [100%] Run step-1 with Debug configuration
>
> OpenBLAS Warning : The number of CPU/Cores(272) is beyond the limit(256). 
> Terminated.
> make[3]: *** [CMakeFiles/run.dir/build.make:58: CMakeFiles/run] Error 1
> make[2]: *** [CMakeFiles/Makefile2:174: CMakeFiles/run.dir/all] Error 2
> make[1]: *** [CMakeFiles/Makefile2:181: CMakeFiles/run.dir/rule] Error 2
> make: *** [Makefile:157: run] Error 2
>
> Regarding your questions and suggestions, the libdeal_ii.g.so file is about 
> 1.6GB. Do you know what the above error signifies? Thank you.
>
> Best,
> Aaditya
>
>
>
> On Sunday, October 25, 2020 at 2:10:21 PM UTC-4 Timo Heister wrote:
>>
>> > Seems like there might then be some issue with the LAPACK, P4EST or PETSC 
>> > installation I am using.
>>
>> I doubt it, when looking at this error:
>>
>> >> /usr/bin/ld: 
>> >> /global/project/projectdirs/m2360/packagesCPFE/dealii_install/lib/libdeal_II.g.so:
>> >>  file not recognized: file truncated
>>
>> This sounds like the linking of the .so file failed. Can you take a
>> look at this file (check the size?)? You can try deleting the file and
>> running "make install" again. Maybe the last linker step failed?
>> If this does not help, maybe try the release mode examples as well.
>>
>>
>>
>>
>> --
>> Timo Heister
>> http://www.math.clemson.edu/~heister/
>
> --
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Re: [deal.II] dealii installation issue on NERSC Cori

[Timo Heister]

> Seems like there might then be some issue with the LAPACK, P4EST or PETSC 
> installation I am using.

I doubt it, when looking at this error:

>> /usr/bin/ld: 
>> /global/project/projectdirs/m2360/packagesCPFE/dealii_install/lib/libdeal_II.g.so:
>>  file not recognized: file truncated

This sounds like the linking of the .so file failed. Can you take a
look at this file (check the size?)? You can try deleting the file and
running "make install" again. Maybe the last linker step failed?
If this does not help, maybe try the release mode examples as well.




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Re: [deal.II] Re: Pressure-correction scheme: Behaviour of the H1 norm on the Taylor-Green vortex

[Timo Heister]

> From my understanding, the lowest bound of the error on each norm is set 
> either by the spatial or the temporal discretization. I was kind of expecting 
> that the L2- and H1-Norms share a similar spatial and time dependence, i.e. 
> that each field reaches its lowest bound simultaneously, and that they do so 
> with a similar convergence rate evolution. Stated differently, they start 
> with an order of convergence which remains constant for a given time step 
> range. After reaching a small time step size, the convergence order tends to 
> zero as the lowest bound of the error is reached.

I don't support this idea. If you take the Taylor-Green vortex for
example, the velocity decays with exp(-2 nu t), while the pressure
decays with the square of that term. Why do you expect error from your
pressure-correction scheme and your error from the time discretization
to converge in the same way? Note that they are not completely
independent of course.

> Furthermore, for the Taylor-Green vortex I am using periodic boundary 
> conditions on all boundaries which rules out the corner singularities which 
> plague the pressure-correction scheme. The solution in itself is smooth, so I 
> had not thought the error of the boundary layer could have had such an effect 
> on the H1-Norm.

I am not convinced that this completely eliminates all influence of
the pressure-correction scheme. I assume that it still gives an O(dt)
additional error (or maybe something higher order depending on your
scheme).



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Re: [deal.II] dealii installation issue on NERSC Cori

[Timo Heister]

Running the tests seems to have triggered a rebuild of deal.iII. Can you
try running some of the tutorial steps instead?

On Fri, Oct 23, 2020, 17:05 Aaditya Lakshmanan 
wrote:

> Hi Wolfgang,
>I tried compiling, installing and running the deal.ii tests
> interactively on a KNL compute node. Both compilation and installation were
> seemingly successful but all the tests failed. I have attached the output
> from make test in the file *test_output.txt*. An example error looks like
> the following :
> 2/11 Test  #1: step.debug ...***Failed  265.99 sec
> gmake[6]: *** write jobserver: Invalid argument.  Stop.
> gmake[6]: *** Waiting for unfinished jobs
> gmake[6]: *** write jobserver: Invalid argument.  Stop.
> gmake[5]: *** [CMakeFiles/Makefile2:10829:
> tests/quick_tests/CMakeFiles/step.debug.run.dir/rule] Error 2
> gmake[4]: *** [Makefile:3700: step.debug.run] Error 2
> Test step.debug: BUILD
> ===   OUTPUT BEGIN
> ===
> step.debug: BUILD failed. Output:
> [  0%] Built target obj_sundials_inst
> [ 21%] Built target obj_physics_elasticity_inst
> [ 30%] Built target obj_dofs_inst
> [ 25%] Built target obj_matrix_free_inst
> [ 23%] Built target obj_amd_global_debug
> [ 34%] Built target obj_umfpack_DI_TRIPLET_MAP_NOX_debug
> [ 30%] Built target obj_differentiation_ad_inst
> [ 34%] Built target obj_multigrid_inst
> [ 59%] Built target obj_physics_inst
> [ 59%] Built target obj_non_matching_inst
> [ 59%] Built target obj_gmsh_inst
> [ 34%] Built target obj_distributed_inst
> [ 34%] Built target kill-step.debug-OK
> [ 34%] Built target obj_muparser_debug
> [ 34%] Built target obj_umfpack_DL_SOLVE_debug
> [ 59%] Built target obj_numerics_inst
> [ 59%] Built target obj_boost_system_debug
> [ 59%] Built target obj_umfpack_DL_STORE_debug
> [ 59%] Built target obj_umfpack_DL_TRIPLET_MAP_NOX_debug
> [ 59%] Built target obj_umfpack_DL_TRIPLET_MAP_X_debug
> [ 59%] Built target obj_umfpack_DI_TSOLVE_debug
> [ 78%] Built target obj_base_inst
> [ 78%] Built target obj_grid_inst
> [ 59%] Built target obj_umfpack_DI_SOLVE_debug
> [ 34%] Built target obj_amd_int_debug
> [ 59%] Built target obj_algorithms_inst
> [ 59%] Built target obj_meshworker_inst
> [ 59%] Built target obj_hp_inst
> [ 78%] Built target obj_particle_inst
> [ 59%] Built target obj_differentiation_sd_inst
> [ 59%] Built target obj_opencascade_inst
> [ 78%] Built target obj_lac_inst
> [ 59%] Built target obj_amd_long_debug
> [ 59%] Built target obj_umfpack_DL_TSOLVE_debug
> [ 59%] Built target obj_umfpack_DI_STORE_debug
> [ 59%] Built target obj_umfpack_DL_TRIPLET_NOMAP_X_debug
> [ 59%] Built target obj_umfpack_DI_TRIPLET_MAP_X_debug
> [ 59%] Built target obj_umfpack_DI_TRIPLET_NOMAP_X_debug
> [ 59%] Built target obj_umfpack_GENERIC_debug
> [ 78%] Built target obj_umfpack_DL_ASSEMBLE_debug
> [ 59%] Built target obj_umfpack_DI_ASSEMBLE_debug
> [ 84%] Built target obj_fe_inst
>
>
> step.debug: **BUILD failed***
>
> ===OUTPUT END
>  ===
> Expected stage PASSED - aborting
> CMake Error at
> /global/project/projectdirs/m2360/packagesCPFE/dealii/cmake/scripts/run_test.cmake:140
> (MESSAGE):
>   *** abort
>
>
> Best,
> Aaditya
>
> On Friday, October 23, 2020 at 2:00:00 AM UTC-4 Aaditya Lakshmanan wrote:
>
>> Hi Wolfgang,
>>Thanks for your suggestion. I just checked that the Cori login nodes
>> are Haswell processors while the compute nodes on which I wish to run
>> simulations eventually are KNL processors(certain modules are also with
>> that intention). I will use idev to access the compute nodes interactively
>> and try the build, installation and testing phases again.
>>
>> Best,
>> Aaditya
>>
>> On Thursday, October 22, 2020 at 11:29:38 PM UTC-4 Wolfgang Bangerth
>> wrote:
>>
>>>
>>> Aaditya,
>>> is NERSC Cori a machine where the front-end node runs a different
>>> processor/system than the compute nodes? If so, you're building a
>>> library for
>>> the compute nodes, and the tests are also built for the compute nodes.
>>> But
>>> you're trying to run the test executables on the front-end node -- which
>>> might
>>> help explain the error you see.
>>>
>>> Best
>>> W.
>>>
>>>
>>> On 10/22/20 7:52 PM, Aaditya Lakshmanan wrote:
>>> > Hi Everyone,
>>> >I have been trying to install deal.ii on the NERSC Cori System and
>>> after a
>>> > seemingly successful cmake and make install, make test yields failure
>>> for all
>>> > the tests setup. I briefly detail the procedure I followed and the
>>> outputs and
>>> > errors obtained.
>>> >
>>> > As a pre-requisite I installed p4est using the setup script(with some
>>> > modifications) and petsc manually with the configure.py script and
>>> appropriate
>>> > settings. The following modules were loaded :
>>> >
>>> > Currently Loaded Modulefiles:
>>> >   1) modules/3.2.11.4  5) craype-network-aries
>>> 9)
>>> > PrgEnv-intel/6.0.5   13) valgrin