[deal.II] deal.II v8.5.1 released

[Timo Heister]

Hey all,

we just created the 8.5.1 release containing a few bugfixes when
compiling with gcc 7+ or when using a recent boost version. There is
no reason for you to upgrade from 8.5.0 if you don't see these
warnings/errors.

For more infromation: 
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dealii_dealii_releases_tag_v8.5.1=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=-dy8aIOtSz4BOhBPr936uvC-JhbwoFUKC7IzJ4DZmOs=kTGB_Wg6sr5z6YXtDXQHHInXQEhbe_HD0fJNmxEdWNE=
 

Best,
Timo

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

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[deal.II] deal.II Newsletter #1

[Rene Gassmoeller]

Hello everyone!

This is deal.II newsletter #1.
It automatically reports recently merged features and discussions about the 
deal.II finite element library.


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

#4860: Add an assertion. (proposed by bangerth) 
https://github.com/dealii/dealii/pull/4860

#4858: Generalize GridTools::exchange_cell_data_to_ghosts() (proposed by 
bangerth) https://github.com/dealii/dealii/pull/4858

#4857: [WIP] Generalized support points / interpolation (proposed by tamiko) 
https://github.com/dealii/dealii/pull/4857

#4856: Clean up CUDA related files (proposed by masterleinad) 
https://github.com/dealii/dealii/pull/4856

#4855: Express the ghost exchange of DoF indices using 
GridTools::exchange_cell_data_to_ghosts(). (proposed by bangerth) 
https://github.com/dealii/dealii/pull/4855

#4854: minor extension of FullMatrix::cholesky documentation (proposed by 
davydden; merged) https://github.com/dealii/dealii/pull/4854

#4853: Moved Sacado product type header and Sacado tests (proposed by 
jppelteret; merged) https://github.com/dealii/dealii/pull/4853

#4852: IDAInterface (proposed by luca-heltai) 
https://github.com/dealii/dealii/pull/4852

#4849: Fix a markup problem. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/4849

#4848: Improve a couple of error messages that weren't quite clear. (proposed 
by bangerth; merged) https://github.com/dealii/dealii/pull/4848

#4847: Sundials detection. (proposed by luca-heltai; merged) 
https://github.com/dealii/dealii/pull/4847

#4846: CMake: Refactor and fix CUDA configuration (proposed by tamiko) 
https://github.com/dealii/dealii/pull/4846

#4845: [8.5.1] disable gcc warnings (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/4845

#4844: Add NANOFLANN to doxygen. (proposed by luca-heltai; merged) 
https://github.com/dealii/dealii/pull/4844

#4843: Simpify some code. (proposed by bangerth) 
https://github.com/dealii/dealii/pull/4843

#4842: enable CUDA in doxygen (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/4842

#4841: Bugfix: Make library compile with -DWITH_NANOFLANN=ON (proposed by 
tamiko; merged) https://github.com/dealii/dealii/pull/4841

#4840: [8.5.1] remove fallthrough warnings. (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/4840

#4839: [8.5.1] Increase the version number. (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/4839

#4838: [8.5.1] Boost patches for 8.5 (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/4838

#4837: Changelog entry for #4834 (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/4837

#4834: Deprecate constraint_and_return_value in favor of std::enable_if 
(proposed by masterleinad; merged) https://github.com/dealii/dealii/pull/4834

#4833: Avoid warnings related to the deprecation of types_are_equal (proposed 
by masterleinad; merged) https://github.com/dealii/dealii/pull/4833

#4832: [WIP] Further optimize MappingQGeneric for tensor product Quadrature 
(proposed by masterleinad) https://github.com/dealii/dealii/pull/4832

#4831: CMake: Bugfix: Remove SuiteSparse_config PIC test (proposed by tamiko; 
merged) https://github.com/dealii/dealii/pull/4831

#4830: Bugfix: Only run kdtree tests if nanoflann is configured (proposed by 
tamiko; merged) https://github.com/dealii/dealii/pull/4830

#4829: add mesh_loop GMG test (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/4829

#4828: Remove double underscores from include guards. (proposed by drwells; 
merged) https://github.com/dealii/dealii/pull/4828

#4827: Skip a type checking test on older boost versions. (proposed by drwells; 
merged) https://github.com/dealii/dealii/pull/4827

#4826: Make trilinos/precondition more robust (proposed by masterleinad; 
merged) https://github.com/dealii/dealii/pull/4826

#4825: KDTree class. (proposed by luca-heltai; merged) 
https://github.com/dealii/dealii/pull/4825

#4824: Add mesh_loop parallel test and improve MPILogInitAll (proposed by 
tjhei; merged) https://github.com/dealii/dealii/pull/4824

#4823: fix tests/meshworker/mesh_loop_* (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/4823

#4822: Better document what the ghost DoF index exchange does. (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/4822

#4821: Reverse template arguments to 
parallel::GridTools::exchange_cell_data_to_ghosts() (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/4821

#4820: LogStream: Remove timestamp machinery and memory_consumption (proposed 
by tamiko; merged) https://github.com/dealii/dealii/pull/4820

#4819: Deprecate types_are_equal. (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/4819

#4817: Make DoFAccessor::set_active_fe_index() a 'const' function. (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/4817

#4816: Document the default argument for the 

[deal.II] deal.II automated newsletter

[Rene Gassmoeller]

Hello everyone,

In a recent meeting with many of the developers of deal.II we came up
with the idea that it would be a nice feature to create an automated
weekly newsletter about the current development of the library. Since
this development mostly happens on Github, but for many users getting
hundreds of Github notifications is not helpful such a newsletter could
summarize the significant advances without cluttering everyone's inbox
too much. Note that this would be an automated newsletter to make sure
it is not dependent on somebody "having the time" to write one, and thus
there is no distinction in important vs. less important topics. It is
simply a way to keep an overview over the development and to give some
credit to all the contributors who constantly offer to spend some of
their time to improve deal.II further.

I already created such a newsletter for the deal.II based geodynamic
modelling software ASPECT (http://aspect.dealii.org/), and therefore
volunteered to take over this task for deal.II as well. In case you are
interested in the format of such a newsletter you can find the latest
ASPECT newsletter here:
http://lists.geodynamics.org/pipermail/aspect-devel/2017-August/001955.html

The first newsletter for deal.II will be out later today, and will
likely be somewhat longer than average, because it includes the activity
during the developer meeting, but on average we expect the newsletter to
cover around 20-30 pull requests/issues per week with one line per PR/issue.

Hopefully this newsletter will prove useful to some of you. I am open to
suggestions and feedback about the format, content or frequency of the
newsletter. Just let me know by answering to this thread.


Best regards,

Rene


-- 
Rene Gassmoeller
http://www.math.colostate.edu/~gassmoel/

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[deal.II] Re: advection equation weak form in tutorial 9

[Jaekwang Kim]

Thanks, now I clearly understand what's going on!

Jaekwang 

On Monday, August 14, 2017 at 3:08:18 PM UTC-5, Jaekwang Kim wrote:
>
> Hi, all 
>
> I am little bit confused by weak form for advection problem written in 
> step-9 tutorial 
>
> in the its tutorial, in the middle of the line, it says that... 
>
> I am little bit unsure the red-marked form, 
>
> From the whole boundary integral, we put inflow case, to the right hand 
> side, and remaining part on left-hand-side is cases other than inflow 
> condition 
>
> so I thought, this should be.. 
>
>
> 
>  
>
> the left hand side term is boundary that is not inflow case... 
>
> I saw similar expression, in Dr. Bangerth video lecture 31, on hyperbolic 
> equation, here his weak form also marked 'not inflow boundary' remaining in 
> left hand side and inflow case, with boundary value description went to RHS 
> 
>
> . I am not sure i am just confusing some of indication... .. 
>
>
> thanks !
>
>
>
>
>
>
>
>
>
> This is a point we made in the introduction of step-3 
> . There, we 
> argued that to avoid this very kind of problem, one should get in the habit 
> of always multiplying with test functions *from the left* instead of from 
> the right to obtain the correct matrix right away. In order to obtain the 
> form of the linear system that we need, it is therefore best to rewrite the 
> weak formulation to 
>
> (vh+δβ⋅∇vh,β⋅∇uh)Ω*−(β⋅nvh,uh**)**∂**Ω**−*=(vh+δβ⋅∇vh,f)Ω−(β⋅nvh,g)∂Ω−
>
> and then to obtain
>
>

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[deal.II] GridRefinement::refine_and_coarsen_optimize

[j . l . boltersdorf]

We struggle to find out how to use 
GridRefinement::refine_and_coarsen_optimize (documentation 
)
 
appropriately. We couldn't find an application in one of the deal.ii 
tutorials, so we felt free to contact this mailing list. 

So far, we have assumed it's supposed to be used as a follow-up to another 
refinement strategy, e.g. GridRefinement::refine_and_coarsen_fixed_number 
to optimize the new refinement. 
However, this approach resulted in an error when it tried to refine a cell 
previously flagged for coarsening: 

An error occurred in line <3085> of 
file
in function

void dealii::CellAccessor::set_refine_flag(dealii::RefinementCase) const [with int
dim = 2; int spacedim = 2]

The violated condition was:

!coarsen_flag_set()

Additional information:

(none)



Looking at its source code, the function does not set coarsen flags at all 
despite being named refine_and_coarsen_optimize, so we initially thought it 
mighty only be applicable as an iterative procedure to find a suitable mesh 
like in tutorial step-6. However, if we understood correctly, Thomas 
Richter implemented this algorithm for his PhD thesis on time-dependent 
problems, which, in our opinion, would also require mesh coarsening during 
simulations. 

We'd be hugely grateful if someone with more experience could tell us how 
to use refine_and_coarsen_optimize correctly. 

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[deal.II] Re: about deal.II with CUDA C programming acceleration

[Bruno Turcksin]

Chih-Che,

The CUDA support in deal.II is very new. It is only in the development 
version of deal (https://github.com/dealii/dealii). You can see our current 
development plan here https://github.com/dealii/dealii/projects/2 Right 
now, we have support for vector and partial support for matrix-free (a good 
place to see the capabilities is the test suite 
https://github.com/dealii/dealii/tree/master/tests/cuda). I would advise 
you to wait for this PR https://github.com/dealii/dealii/pull/4846 to be 
merged before your try to install deal with CUDA. This PR makes it a lot 
easier to install deal with CUDA. If you want to work on CUDA, you should 
work on something that you like / is of interest to you. If you want to 
help our existing effort, you can pick something from this list 
https://github.com/dealii/dealii/issues/4399. I am working on the first 
item but let me know if you find anything else interesting, I can help you 
implementing it.

If you have any questions, please ask. We are looking for people to help us 
with CUDA.

Best,

Bruno

On Monday, August 14, 2017 at 7:56:45 AM UTC-4, Chih-Che Chueh wrote:
>
> Dear deal.II developers and users,
>
> Recently, I spent some spare time assimilating CUDA C programming in the 
> last few months, and I already know very well how to use CUDA stream 
> events to let CPU and kernel (GPU) execution work asynchronously with 
> efficiently overlapping data transfer between CPU and GPU, how to use 
> shared memory to ensure global memory coalescing efficiently, how to map 
> threads to matrix elements either using CARTESIAN x, y, z or a row/column 
> mapping in GPU, as well as how to use shared memory to enhance data 
> reuse. Most importantly, for actual practice, we have a GPU accelerator 
> (i.e. NVIDIA Tesla K40) that was bought last year. I plan to use the CUDA C 
> programming to deal with big data or image identification with artificial 
> intelligence (deep learning) for atmospheric data.
>
> Anyway, I am writing to ask if I could get involved with a deal.II project 
> of people who are working on asynchronous adaptive mesh refinement for 
> acceleration or other performance improvement in deal.II with CUDA C 
> programming.
>
> Thanks!
>
> Sincerely,
>
> Chih-Che
>

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[deal.II] Research Associate Position, Helmut Schmidt Univ. Hamburg

['Uwe Köcher' via deal . II User Group]

Applications are invited to a full Research Associate Position at the
Helmut Schmidt University Hamburg in the fields of numerical analysis
and/or high performance computing at PhD or Postdoc level.

Teaching in German language is mandatory.

Full details can be found at:
https://www.hsu-hh.de/jobs/index_LvhPrRPv2FqPDClB.html

The position will be filled as soon as possible. 

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[deal.II] Explanation of right hand side in example 33?

['Maxi Miller' via deal.II User Group]

I try to follow the math in example 33, but am not fully able to understand 
how the right hand side is included. According to my understanding, I have 
the function/vector G, multiply it with the test function z, and integrate 
over both over the whole area. After there are no derivatives included, I 
do not have to do any reformulations. Why do I then still end up with an 
integral over both (G\cdot z), but integrated over the border?
Thanks!

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