[deal.II] Re: 2D circular mesh extrusion

[Hadi Morovvatju]

Hello again,

Thank you so much for your help. Yes, you're totally right. The lethe code 
is accessible :)

On Friday, 15 September 2023 at 15:04:19 UTC+3:30 blais...@gmail.com wrote:

> Dear Hadi,
> The Lethe code to generate all of these cylinders is fully available only. 
> Might as well just reuse it :)
> Everything starts here:
> https://github.com/lethe-cfd/lethe/blob/master/source/core/grids.cc#L162
>
> This should help you reproduce these kind of grids
>
>
>
> On Thursday, September 14, 2023 at 11:45:51 a.m. UTC-4 
> hadimor...@gmail.com wrote:
>
>> Hi,
>> I hope you-all are doing okay. Btw I'm new to deal.ii and C++. Actually 
>> I'm trying to generate 3D cylinder-shaped grid, fully structured hex mesh 
>> as depicted in lethe documentation (attached to post). It seems that 
>> refining a 3D hyper_cube would produce the target grids. So I successfully 
>> generated 2D mesh which shaped as a circular surface (attached to post). 
>> Then tried out extruding it, but it comes up that refined mesh is not 
>> allowed to get extruded, according to deal.ii manual. I'm also a bit 
>> confused about setting multiple manifolds to specific faces of the grid. 
>> Honestly I tried a lot, but was not so successful. I'm gonna attach target 
>> mesh images (4 different mesh types) and my 2D generated meshes. If anyone 
>> could provide any help to reach target 3D meshes, it would be greatly 
>> appreciated. 
>> Thank you
>>
>> *grids in lethe documentation:*
>> [image: lethe.PNG]
>>
>> *And here are 2D meshes I generated:*
>>
>>
>>

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Re: [deal.II] Re: question about hybrid MPI and TBB thread parallelism

[Bruno Turcksin]

Timo,

You will get vastly different results in debug and release modes for two 
reasons. First, the compiler generates much faster code in release mode 
compared to debug. Second, there are a lot of checks inside deal.II that 
are only enabled in debug mode. This is great when you develop your code 
because it helps you catch bugs early but it makes your code much slower. 
In general, you want to develop your code in debug mode but your production 
run should be done in release.

Best,

Bruno

On Friday, September 15, 2023 at 1:53:59 PM UTC-4 Tim hyvärinen wrote:

hi, Marc,

Thank you for the reply.

I compiled the lib with debug mode, didn't try the optimized version. 
I didn't think this could be a significant issue, but I infer optimized lib 
could improve performance alot based on your question. 

Sincerely,
Timo

On Fri, Sep 15, 2023 at 8:21 PM Marc Fehling  wrote:

Hello Tim,

> Yet, even though it is universally believed to be superior in terms of 
convergence properties, it is not widely used because it is often believed 
to be difficult to implement. One way to address this belief is to provide 
well-tested, easy to use software that provides this kind of functionality. 


Just to make sure: did you compile the deal.II library and your code in 
Optimized 
mode/Release mode 
?

Best,
Marc

On Friday, September 15, 2023 at 3:17:39 AM UTC-6 Tim hyvärinen wrote:

Dear dealii community and developers,

I have used dealii framework (9.3.x) a while on HPC machine. My project 
involves solving vector-valued nonlinear PDE with nine components.
Currently, I've implemented damping newton iteration with GMRES+AMG 
preconditioner with MPI on distributed memory architecture. 

A simple timing tells me the assembly process of system-matrix takes 99% of 
the whole running time in every newton iteration. I guess there are
a lot of idle cpu times during assembly because I don't take advantage of 
thread parallelism yet.

So here is my question, which tutorial steps demonstrate how to 
implement the mpi-thread hybrid parallelism. I've found step-48 is talking 
about this, but 
I wonder are there any other tutorial programs to look at? I also wonder if 
any of you guys have suggestions about mpi+thread parallelism under
dealii framework?

Sincerely,
Timo Hyvarinen 

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.

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Re: [deal.II] Re: question about hybrid MPI and TBB thread parallelism

[timo Hyvärinen]

hi, Marc,

Thank you for the reply.

I compiled the lib with debug mode, didn't try the optimized version.
I didn't think this could be a significant issue, but I infer optimized lib
could improve performance alot based on your question.

Sincerely,
Timo

On Fri, Sep 15, 2023 at 8:21 PM Marc Fehling  wrote:

> Hello Tim,
>
> > Yet, even though it is universally believed to be superior in terms of
> convergence properties, it is not widely used because it is often believed
> to be difficult to implement. One way to address this belief is to provide
> well-tested, easy to use software that provides this kind of functionality.
>
> Just to make sure: did you compile the deal.II library and your code in 
> Optimized
> mode/Release mode
> ?
>
> Best,
> Marc
>
> On Friday, September 15, 2023 at 3:17:39 AM UTC-6 Tim hyvärinen wrote:
>
>> Dear dealii community and developers,
>>
>> I have used dealii framework (9.3.x) a while on HPC machine. My project
>> involves solving vector-valued nonlinear PDE with nine components.
>> Currently, I've implemented damping newton iteration with GMRES+AMG
>> preconditioner with MPI on distributed memory architecture.
>>
>> A simple timing tells me the assembly process of system-matrix takes 99%
>> of the whole running time in every newton iteration. I guess there are
>> a lot of idle cpu times during assembly because I don't take advantage of
>> thread parallelism yet.
>>
>> So here is my question, which tutorial steps demonstrate how to
>> implement the mpi-thread hybrid parallelism. I've found step-48 is talking
>> about this, but
>> I wonder are there any other tutorial programs to look at? I also wonder
>> if any of you guys have suggestions about mpi+thread parallelism under
>> dealii framework?
>>
>> Sincerely,
>> Timo Hyvarinen
>>
> --
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> 
> .
>

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[deal.II] Re: question about hybrid MPI and TBB thread parallelism

[Marc Fehling]

Hello Tim,

> A simple timing tells me the assembly process of system-matrix takes 99% 
of the whole running time in every newton iteration.

Just to make sure: did you compile the deal.II library and your code in 
Optimized 
mode/Release mode 
?

Best,
Marc


On Friday, September 15, 2023 at 3:17:39 AM UTC-6 Tim hyvärinen wrote:

> Dear dealii community and developers,
>
> I have used dealii framework (9.3.x) a while on HPC machine. My project 
> involves solving vector-valued nonlinear PDE with nine components.
> Currently, I've implemented damping newton iteration with GMRES+AMG 
> preconditioner with MPI on distributed memory architecture. 
>
> A simple timing tells me the assembly process of system-matrix takes 99% 
> of the whole running time in every newton iteration. I guess there are
> a lot of idle cpu times during assembly because I don't take advantage of 
> thread parallelism yet.
>
> So here is my question, which tutorial steps demonstrate how to 
> implement the mpi-thread hybrid parallelism. I've found step-48 is talking 
> about this, but 
> I wonder are there any other tutorial programs to look at? I also wonder 
> if any of you guys have suggestions about mpi+thread parallelism under
> dealii framework?
>
> Sincerely,
> Timo Hyvarinen 
>

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[deal.II] Re: question about hybrid MPI and TBB thread parallelism

[Marc Fehling]

Hello Tim,

> Yet, even though it is universally believed to be superior in terms of 
convergence properties, it is not widely used because it is often believed 
to be difficult to implement. One way to address this belief is to provide 
well-tested, easy to use software that provides this kind of functionality. 

Just to make sure: did you compile the deal.II library and your code in 
Optimized 
mode/Release mode 
?

Best,
Marc

On Friday, September 15, 2023 at 3:17:39 AM UTC-6 Tim hyvärinen wrote:

> Dear dealii community and developers,
>
> I have used dealii framework (9.3.x) a while on HPC machine. My project 
> involves solving vector-valued nonlinear PDE with nine components.
> Currently, I've implemented damping newton iteration with GMRES+AMG 
> preconditioner with MPI on distributed memory architecture. 
>
> A simple timing tells me the assembly process of system-matrix takes 99% 
> of the whole running time in every newton iteration. I guess there are
> a lot of idle cpu times during assembly because I don't take advantage of 
> thread parallelism yet.
>
> So here is my question, which tutorial steps demonstrate how to 
> implement the mpi-thread hybrid parallelism. I've found step-48 is talking 
> about this, but 
> I wonder are there any other tutorial programs to look at? I also wonder 
> if any of you guys have suggestions about mpi+thread parallelism under
> dealii framework?
>
> Sincerely,
> Timo Hyvarinen 
>

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[deal.II] deal.II Newsletter #267

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

Hello everyone!

This is deal.II newsletter #267.
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:

#15990: Simplify some code. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/15990

#15986: Add QGaussRadau quadrature formula + tests (proposed by jpthiele; 
merged) https://github.com/dealii/dealii/pull/15986

#15983: Matrix-free: Split up evaluation_kernels.h into cell and face parts 
(proposed by kronbichler; merged) https://github.com/dealii/dealii/pull/15983

#15982: [WIP] Introduce FERemoteEvaluation (proposed by jh66637) 
https://github.com/dealii/dealii/pull/15982

#15981: Matrix-free FEEvaluation: Avoid indirection in call to sum 
factorization (proposed by kronbichler; merged) 
https://github.com/dealii/dealii/pull/15981

#15980: Optimize arithmetic operations for Raviart-Thomas elements (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/15980

#15978: Bump actions/checkout from 3 to 4 (proposed by dependabot[bot]; merged) 
https://github.com/dealii/dealii/pull/15978

#15977: Fix address boundary error in FEInterfaceValues::get_update_flags() 
(proposed by simonsticko; merged) https://github.com/dealii/dealii/pull/15977

#15976: Do not use deprecated extract_locally_* functions in library. (proposed 
by marcfehling; merged) https://github.com/dealii/dealii/pull/15976

#15974: Implement AlignedVector::shrink_to_fit() (proposed by bergbauer) 
https://github.com/dealii/dealii/pull/15974

#15973: Update the count_lines.sh script. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/15973

#15972: Implement StridedArrayView (proposed by bergbauer) 
https://github.com/dealii/dealii/pull/15972

#15971: Optimize FEPointEvaluation/NM::MappingInfo (proposed by bergbauer) 
https://github.com/dealii/dealii/pull/15971

#15970: Augment error message for clang-format. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/15970

#15969: Add a reference to an article. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/15969

#15968: Allow comparison of IndexSet objects against default-constructed 
objects. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/15968

#15967: Avoid using a deprecated function. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/15967

#15966: Mark deprecated functions with DEAL_II_DEPRECATE_EARLY. (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/15966

#15965: Matrix-free shape info: Generate face orientation table for R-T 
(proposed by kronbichler; merged) https://github.com/dealii/dealii/pull/15965

#15964: Matrix-free for Raviart-Thomas: Test correct interpolation (non-affine) 
(proposed by kronbichler; merged) https://github.com/dealii/dealii/pull/15964

#15963: FE_PolyTensor: Only request dof_sign_change if necessary (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/15963

#15962: Remove static declaration from a few tests (proposed by kronbichler; 
merged) https://github.com/dealii/dealii/pull/15962

#15961: Add step-87: Tutorial on RemotePointEvaluation (proposed by mschreter) 
https://github.com/dealii/dealii/pull/15961

#15960: Update shasum for clang-format mac. (proposed by luca-heltai; merged) 
https://github.com/dealii/dealii/pull/15960

#15954: Another attempt to fix compile warning (proposed by kronbichler; 
merged) https://github.com/dealii/dealii/pull/15954

#15952: Added another test for limit_p_level_difference(). (proposed by 
marcfehling; merged) https://github.com/dealii/dealii/pull/15952

#15951: Matrix-free evaluation of Raviart-Thomas: major restructuring (proposed 
by kronbichler; merged) https://github.com/dealii/dealii/pull/15951

#15930: FEValues: Allow checking for cell similarities in multi-threaded mode 
(proposed by masterleinad; merged) https://github.com/dealii/dealii/pull/15930


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

#15989: Regression tester regressed e8073d (opened) 
https://github.com/dealii/dealii/issues/15989

#15988: Further optimize AffineConstraints::distribute() with partitioners. 
(opened) https://github.com/dealii/dealii/issues/15988

#15987: Add check in AffineConstraints that user provided index set arguments 
when running in parallel. (opened) https://github.com/dealii/dealii/issues/15987

#15985: Make transfinite interpolation more accessible (opened) 
https://github.com/dealii/dealii/issues/15985

#15984: Step-12 Solver should use SolverGMRES (opened) 
https://github.com/dealii/dealii/issues/15984

#15979: Tpetra wrapper (opened) https://github.com/dealii/dealii/issues/15979

#15975: Fix hard-to-read code in dof_renumbering.cc. (opened and closed) 
https://github.com/dealii/dealii/issues/15975

#15931: Regression tester regressed 166861 (closed) 
https://github.com/dealii/dealii/issues/15931

#15894: 

Re: [deal.II] question about hybrid MPI and TBB thread parallelism

[timo Hyvärinen]

Hi, Wolfgang,
Thank you for your reply and suggestion.

Your're right, I didn't conduct profiling yet. My commonly used test setup
is 1 node (128 cores) with 128 tasks on it, 99% of assembly time came from
this type of run.
It's a bit surprising for me to be suggested not to use thread, but I
believe it should be a significant experience. I will do profiling first
and then talk in this thread later.

Sincerely,
Timo


On Fri, Sep 15, 2023 at 3:51 PM Wolfgang Bangerth 
wrote:

> On 9/15/23 03:17, timo Hyvärinen wrote:
> >
> > So here is my question, which tutorial steps demonstrate how to
> implement the
> > mpi-thread hybrid parallelism. I've found step-48 is talking about this,
> but
> > I wonder are there any other tutorial programs to look at? I also wonder
> if
> > any of you guys have suggestions about mpi+thread parallelism under
> > dealii framework?
>
> Timo:
> If your code already works, then the usual suggestion would be to use one
> MPI
> process per core, and to not use thread-parallelism at all. In that case,
> you
> should be using all cores equally.
>
> There is an often-repeated observation that one can not optimize a code
> without first profiling it. From your question, it sounds like you are not
> entire sure why assembly is taking so long. I think it is likely that
> whatever
> solution you try will not be successful unless you first find out why it
> really is taking this long. I would run the code on one MPI process first
> and
> see whether assembly is taking 99% there as well. If that's the case, use
> valgrind's callgrind to figure out why. If it's not taking 99% on one MPI
> process, then you've got another riddle to solve.
>
> Best
>   W.
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>
> --
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> .
>

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Re: [deal.II] question about hybrid MPI and TBB thread parallelism

[Wolfgang Bangerth]

On 9/15/23 03:17, timo Hyvärinen wrote:


So here is my question, which tutorial steps demonstrate how to implement the 
mpi-thread hybrid parallelism. I've found step-48 is talking about this, but
I wonder are there any other tutorial programs to look at? I also wonder if 
any of you guys have suggestions about mpi+thread parallelism under

dealii framework?


Timo:
If your code already works, then the usual suggestion would be to use one MPI 
process per core, and to not use thread-parallelism at all. In that case, you 
should be using all cores equally.


There is an often-repeated observation that one can not optimize a code 
without first profiling it. From your question, it sounds like you are not 
entire sure why assembly is taking so long. I think it is likely that whatever 
solution you try will not be successful unless you first find out why it 
really is taking this long. I would run the code on one MPI process first and 
see whether assembly is taking 99% there as well. If that's the case, use 
valgrind's callgrind to figure out why. If it's not taking 99% on one MPI 
process, then you've got another riddle to solve.


Best
 W.

--

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


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[deal.II] Re: 2D circular mesh extrusion

[blais...@gmail.com]

Dear Hadi,
The Lethe code to generate all of these cylinders is fully available only. 
Might as well just reuse it :)
Everything starts here:
https://github.com/lethe-cfd/lethe/blob/master/source/core/grids.cc#L162

This should help you reproduce these kind of grids



On Thursday, September 14, 2023 at 11:45:51 a.m. UTC-4 hadimor...@gmail.com 
wrote:

> Hi,
> I hope you-all are doing okay. Btw I'm new to deal.ii and C++. Actually 
> I'm trying to generate 3D cylinder-shaped grid, fully structured hex mesh 
> as depicted in lethe documentation (attached to post). It seems that 
> refining a 3D hyper_cube would produce the target grids. So I successfully 
> generated 2D mesh which shaped as a circular surface (attached to post). 
> Then tried out extruding it, but it comes up that refined mesh is not 
> allowed to get extruded, according to deal.ii manual. I'm also a bit 
> confused about setting multiple manifolds to specific faces of the grid. 
> Honestly I tried a lot, but was not so successful. I'm gonna attach target 
> mesh images (4 different mesh types) and my 2D generated meshes. If anyone 
> could provide any help to reach target 3D meshes, it would be greatly 
> appreciated. 
> Thank you
>
> *grids in lethe documentation:*
> [image: lethe.PNG]
>
> *And here are 2D meshes I generated:*
>
>
>

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[deal.II] question about hybrid MPI and TBB thread parallelism

[timo Hyvärinen]

Dear dealii community and developers,

I have used dealii framework (9.3.x) a while on HPC machine. My project
involves solving vector-valued nonlinear PDE with nine components.
Currently, I've implemented damping newton iteration with GMRES+AMG
preconditioner with MPI on distributed memory architecture.

A simple timing tells me the assembly process of system-matrix takes 99% of
the whole running time in every newton iteration. I guess there are
a lot of idle cpu times during assembly because I don't take advantage of
thread parallelism yet.

So here is my question, which tutorial steps demonstrate how to
implement the mpi-thread hybrid parallelism. I've found step-48 is talking
about this, but
I wonder are there any other tutorial programs to look at? I also wonder if
any of you guys have suggestions about mpi+thread parallelism under
dealii framework?

Sincerely,
Timo Hyvarinen

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