date:20200302

Re: [deal.II] Scaling behavior of Matrix-Free test program

2020-03-02 Thread Daniel Arndt

Maxi,

it would likely be interesting to run the STREAM benchmark on these two
systems to see how much memory bandwidth you can hope to get.
I would not be too surprised if that still is the limiting factor for your
test.

Best,
Daniel

Am Mo., 2. März 2020 um 12:17 Uhr schrieb 'Maxi Miller' via deal.II User
Group :

> I wrote a small test program for solving a non-linear equation using the
> RK4-solver implemented in deal.II, and assembling the right hand side using
> the matrix-free framework (code is attached). Afterwards I wanted to check
> the scaling behavior, after it should serve as a base for a larger program.
> Therefore I run several tests both on the development machine (i7-6700)
> with 8 threads and the high-performance machine (E5-2560 v4
> )
> with 24 threads. Both machines were configured for using AVX-extensions in
> deal.II, and the program itself was compiled in release mode.
>
> When running the program in both configurations, I compared the time it
> took for taking the first step in time:
>
> Local machine:
> MPI-ThreadsTBB-ThreadsTime (s)
> 1 8  170
> 2 4  40
> 4 2  20
>
> HPC:
> MPI-ThreadsTBB-ThreadsTime (s)
> 1 24840
> 2 12887
> 4 6  424
> 8 3  41
> 12   2  28
> 24   1  14
>
> I do not fully understand that behavior: Why is the code so much slower on
> the E5 compared to the i7, except for 24 threads? Due to a different clock
> frequency, or newer structure (Broadwell vs Skylake)? Why is the transition
> from 1 MPI thread to 2 MPI threads on the i7 four times faster, but going
> from 2 MPI threads to 4 MPI threads only twice (which is expected)?
> Similarly for the E5: Going from 1 thread to 2 threads does not speed up
> the code at all. Going from two to four threads halves the execution time
> (as expected), but going from four to eight results in a factor of ten. The
> steps afterwards follow the expected pattern again.
>
> Are there any explanations for the observed behavior? And if not, what can
> I do for a deeper investigation?
>
> Thanks!
>
> --
> 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] Scaling behavior of Matrix-Free test program

2020-03-02 Thread 'Maxi Miller' via deal.II User Group

I wrote a small test program for solving a non-linear equation using the 
RK4-solver implemented in deal.II, and assembling the right hand side using 
the matrix-free framework (code is attached). Afterwards I wanted to check 
the scaling behavior, after it should serve as a base for a larger program. 
Therefore I run several tests both on the development machine (i7-6700) 
with 8 threads and the high-performance machine (E5-2560 v4 
)
 
with 24 threads. Both machines were configured for using AVX-extensions in 
deal.II, and the program itself was compiled in release mode.

When running the program in both configurations, I compared the time it 
took for taking the first step in time:

Local machine:
MPI-ThreadsTBB-ThreadsTime (s)
1 8  170
2 4  40
4 2  20

HPC:
MPI-ThreadsTBB-ThreadsTime (s)
1 24840
2 12887
4 6  424
8 3  41
12   2  28
24   1  14

I do not fully understand that behavior: Why is the code so much slower on 
the E5 compared to the i7, except for 24 threads? Due to a different clock 
frequency, or newer structure (Broadwell vs Skylake)? Why is the transition 
from 1 MPI thread to 2 MPI threads on the i7 four times faster, but going 
from 2 MPI threads to 4 MPI threads only twice (which is expected)?
Similarly for the E5: Going from 1 thread to 2 threads does not speed up 
the code at all. Going from two to four threads halves the execution time 
(as expected), but going from four to eight results in a factor of ten. The 
steps afterwards follow the expected pattern again.

Are there any explanations for the observed behavior? And if not, what can 
I do for a deeper investigation?

Thanks!

-- 
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/* -
 *
 * Copyright (C) 2009 - 2019 by the deal.II authors
 *
 * This file is part of the deal.II library.
 *
 * The deal.II library is free software; you can use it, redistribute
 * it, and/or modify it under the terms of the GNU Lesser General
 * Public License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 * The full text of the license can be found in the file LICENSE.md at
 * the top level directory of deal.II.
 *
 * -
 *
 * Author: Wolfgang Bangerth, Texas A University, 2009, 2010
 * Timo Heister, University of Goettingen, 2009, 2010
 */
#include 
#include 
#include 
#include 

#include 

#include 
#include 
#include 
#include 

#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 

#include 
#include 
#include 

#include 
#include 
#include 

#include 
#include 
#include 

#include 
#include 
#include 

#include 
#include 
#include 

#include 

#include 
#include 

#include 
#include 

constexpr double time_step = 0.01;

constexpr unsigned int fe_degree= 3;
constexpr unsigned int n_q_points_1d= fe_degree + 2;
using Number= double;
constexpr unsigned int n_components			= 2;
constexpr unsigned int refinement_degree	= 6;

constexpr bool use_scale_function = true;
constexpr bool use_threads = use_scale_function;

namespace Step40
{
	using namespace dealii;

	using vector_t = LinearAlgebra::distributed::Vector;

	void print_vector(const vector_t _vector, const std::string ){
		std::ofstream data_out(filename);
		for(size_t i = 0; i < input_vector.size(); ++i)
			data_out << input_vector(i) << '\n';
		data_out.close();
	}

	template 
	class LaplaceOperator
	{
	public:
		static constexpr unsigned int n_quadrature_points_1d = n_points_1d;

		LaplaceOperator() : computing_times(6), local_time(0.){

		};

		void reinit(const Mapping &   mapping,
	const DoFHandler _handler,
	const AffineConstraints _node_constraints);

		void print_computing_times() const;

		void apply(const double  current_time,
   const vector_t ,
   vector_t &  dst) const;

		void

[deal.II] deal.II Newsletter #112

2020-03-02 Thread Rene Gassmoeller

Hello everyone!

This is deal.II newsletter #112.
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:

#9592: CI: github action: test 64bit indices (proposed by tjhei) 
https://github.com/dealii/dealii/pull/9592

#9591: Fix two 64 bit warnings by converting to long long unsigned (proposed by 
kronbichler) https://github.com/dealii/dealii/pull/9591

#9590: Eliminate two places with unsigned long long int (proposed by 
kronbichler) https://github.com/dealii/dealii/pull/9590

#9589: Fix compile error of GeometryInfo::unit_tangential_vectors on clang-4/5 
(proposed by kronbichler; merged) https://github.com/dealii/dealii/pull/9589

#9587: Follow up to #9581 (proposed by bangerth) 
https://github.com/dealii/dealii/pull/9587

#9586: Introduce types::global_cell_index. (proposed by bangerth) 
https://github.com/dealii/dealii/pull/9586

#9585: use global_cell_index in many places (proposed by tjhei) 
https://github.com/dealii/dealii/pull/9585

#9584: CI: Jenkins: set -x and set -e (proposed by tjhei) 
https://github.com/dealii/dealii/pull/9584

#9583: CI: remove check_doxygen as we do this in Travis (proposed by tjhei; 
merged) https://github.com/dealii/dealii/pull/9583

#9582: Improve indentation of Jenkinsfile (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/9582

#9581: Use uint64_t instead of 'unsigned long long int'. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/9581

#9580: Add rank 2 tensor orthogonalization function (proposed by MFraters) 
https://github.com/dealii/dealii/pull/9580

#9579: Add GeometryInfo::unit_tangential_vectors (proposed by kronbichler; 
merged) https://github.com/dealii/dealii/pull/9579

#9578: doxygen: replace DEAL_II_CONSTEXPR (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/9578

#9576: Add assert to MGLevelGlobalTransfer (proposed by peterrum; merged) 
https://github.com/dealii/dealii/pull/9576

#9575: documentation: improve level_ghost_owners (proposed by tjhei) 
https://github.com/dealii/dealii/pull/9575

#9574: Add AnonymousConsensusAlgorithmProcess (proposed by peterrum; merged) 
https://github.com/dealii/dealii/pull/9574

#9572: improve documentation of MGTransferMatrixFree::interpolate_to_mg() 
(proposed by nfehn; merged) https://github.com/dealii/dealii/pull/9572

#9571: amend FGMRES documentation (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/9571

#9570: doxygen: do not remove multiline code comments (proposed by tjhei; 
merged) https://github.com/dealii/dealii/pull/9570

#9569: doxygen: skip license header in step-xxb (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/9569

#9568: fix 64bit overflow in refine_and_coarsen_fixed_number (proposed by 
tjhei; merged) https://github.com/dealii/dealii/pull/9568

#9567: CI: run matrix_free tests (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/9567

#9566: Deprecate another function in DoFTools. (proposed by bangerth) 
https://github.com/dealii/dealii/pull/9566

#9565: Enable refreshing of MatrixFree geometry data for changed mapping 
(proposed by kronbichler) https://github.com/dealii/dealii/pull/9565

#9564: Make assertions to track state in FEEvaluation debug-only (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/9564

#9562: Replace std::endl in include and source folder [WIP] (proposed by 
peterrum) https://github.com/dealii/dealii/pull/9562

#9561: Avoid using std::endl over '\n'. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/9561

#9560: Handle special case for PolarManifold::normal_vector (proposed by 
gassmoeller) https://github.com/dealii/dealii/pull/9560

#9559: Update documentation of SphericalManifold::normal_vector. (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/9559

#9549: changelog entry for 64bit fixes (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/9549

#9542: CI: run checkdoxygen.py for each PR (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/9542

#9541: checkdoxygen.py cleanup (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/9541

#9521: Remove one newline at beginning of timer statistics (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/9521


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

#9588: Compilation failes for DEAL_II_WITH_64BIT_INDICES="ON" (opened) 
https://github.com/dealii/dealii/issues/9588

#9577: constexpr vs DEAL_II_CONSTEXPR (opened) 
https://github.com/dealii/dealii/issues/9577

#9573: Improve documentation/asserts of MGTransferMatrixFree build() usage 
(opened) https://github.com/dealii/dealii/issues/9573

#9563: Assert -> AssertThrow in release tests with FEEvaluation (opened and 
closed) https://github.com/dealii/dealii/issues/9563

#9554: incorrect text transformation of inline

Re: [deal.II] Step-57

2020-03-02 Thread hussan zeb

Dear Arndt

Thank you for your email. i want to modified the geometry cavity to cylinder

Best   Zeb

On Mon, Mar 2, 2020 at 4:12 PM hussan zeb  wrote:

> Yes i want to change the geometry of the problem to cylinder
>
> On Mon, 2 Mar 2020, 16:08 Daniel Arndt,  wrote:
>
>> Hussan,
>>
>> Do you observe this problem with the unmodified step-57 or did you change
>> anything?
>> What does the full backtrace look like (running gdb)?
>>
>> Best,
>> Daniel
>>
>> Am Mo., 2. März 2020 um 09:42 Uhr schrieb hussan zeb <
>> zebhuss...@gmail.com>:
>>
>>> how can resolve this error in step-57,
>>> Scanning dependencies of target step-57
>>> [ 33%] Building CXX object CMakeFiles/step-57.dir/step-57.cc.o
>>> [ 66%] Linking CXX executable step-57
>>> [ 66%] Built target step-57
>>> [100%] Run step-57 with Debug configuration
>>> grid refinements: 0
>>> viscosity: 0.1
>>> Number of active cells: 432
>>> Number of degrees of freedom: 4188 (3696 + 492)
>>> FGMRES steps: 0
>>> The residual of initial guess is 0
>>>
>>>
>>> 
>>> Exception on processing:
>>>
>>> 
>>> An error occurred in line <534> of file
>>> 
>>> in function
>>> std::pair::active_cell_iterator,
>>> dealii::Point >
>>> dealii::GridTools::{anonymous}::find_active_cell_around_point_tolerance(const
>>> dealii::Mapping&, const MeshType&, const
>>> dealii::Point&, const std::vector&, double) [with int dim =
>>> 2; MeshType = dealii::DoFHandler; int spacedim = 2; typename MeshType>> spacedim>::active_cell_iterator =
>>> dealii::TriaActiveIterator>> 2>, false> >]
>>> The violated condition was:
>>> best_cell.first.state() == IteratorState::valid
>>> Additional information:
>>> The point <0.5 0.42> could not be found inside any of the subcells
>>> of a coarse grid cell.
>>> 
>>>
>>> Aborting!
>>> 
>>> CMakeFiles/run.dir/build.make:57: recipe for target 'CMakeFiles/run'
>>> failed
>>> make[3]: *** [CMakeFiles/run] Error 1
>>> CMakeFiles/Makefile2:195: recipe for target 'CMakeFiles/run.dir/all'
>>> failed
>>> make[2]: *** [CMakeFiles/run.dir/all] Error 2
>>> CMakeFiles/Makefile2:202: recipe for target 'CMakeFiles/run.dir/rule'
>>> failed
>>> make[1]: *** [CMakeFiles/run.dir/rule] Error 2
>>> Makefile:170: recipe for target 'run' failed
>>> make: *** [run] Error 2
>>> zeb@kutta:~/deal/examples/step-57> make run
>>>
>>> --
>>> 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/8a6dd884-c75b-4a05-a119-48e22ca0a3c1%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
>> ---
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>> "deal.II User Group" group.
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>> email to dealii+unsubscr...@googlegroups.com.
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>> https://groups.google.com/d/msgid/dealii/CAOYDWbLsFxCfm041Ks0CCOxxbcMv2Spd0ncHfCNYQhJKu%3DJabA%40mail.gmail.com
>> 
>> .
>>
>

-- 
Hussan Zeb
Department of  Mathematics
Hazara University

-- 
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/* -
 *
 * Copyright (C) 2008 - 2019 by the deal.II authors
 *
 * This file is part of the deal.II library.
 *
 * The deal.II library is free software; you can use it, redistribute
 * it, and/or modify it under the terms of the GNU Lesser General
 * Public License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 * The full text of the

Re: [deal.II] Step-57

2020-03-02 Thread hussan zeb

Yes i want to change the geometry of the problem to cylinder

On Mon, 2 Mar 2020, 16:08 Daniel Arndt,  wrote:

> Hussan,
>
> Do you observe this problem with the unmodified step-57 or did you change
> anything?
> What does the full backtrace look like (running gdb)?
>
> Best,
> Daniel
>
> Am Mo., 2. März 2020 um 09:42 Uhr schrieb hussan zeb  >:
>
>> how can resolve this error in step-57,
>> Scanning dependencies of target step-57
>> [ 33%] Building CXX object CMakeFiles/step-57.dir/step-57.cc.o
>> [ 66%] Linking CXX executable step-57
>> [ 66%] Built target step-57
>> [100%] Run step-57 with Debug configuration
>> grid refinements: 0
>> viscosity: 0.1
>> Number of active cells: 432
>> Number of degrees of freedom: 4188 (3696 + 492)
>> FGMRES steps: 0
>> The residual of initial guess is 0
>>
>>
>> 
>> Exception on processing:
>>
>> 
>> An error occurred in line <534> of file
>> 
>> in function
>> std::pair::active_cell_iterator,
>> dealii::Point >
>> dealii::GridTools::{anonymous}::find_active_cell_around_point_tolerance(const
>> dealii::Mapping&, const MeshType&, const
>> dealii::Point&, const std::vector&, double) [with int dim =
>> 2; MeshType = dealii::DoFHandler; int spacedim = 2; typename MeshType> spacedim>::active_cell_iterator =
>> dealii::TriaActiveIterator> 2>, false> >]
>> The violated condition was:
>> best_cell.first.state() == IteratorState::valid
>> Additional information:
>> The point <0.5 0.42> could not be found inside any of the subcells of
>> a coarse grid cell.
>> 
>>
>> Aborting!
>> 
>> CMakeFiles/run.dir/build.make:57: recipe for target 'CMakeFiles/run'
>> failed
>> make[3]: *** [CMakeFiles/run] Error 1
>> CMakeFiles/Makefile2:195: recipe for target 'CMakeFiles/run.dir/all'
>> failed
>> make[2]: *** [CMakeFiles/run.dir/all] Error 2
>> CMakeFiles/Makefile2:202: recipe for target 'CMakeFiles/run.dir/rule'
>> failed
>> make[1]: *** [CMakeFiles/run.dir/rule] Error 2
>> Makefile:170: recipe for target 'run' failed
>> make: *** [run] Error 2
>> zeb@kutta:~/deal/examples/step-57> make run
>>
>> --
>> 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/8a6dd884-c75b-4a05-a119-48e22ca0a3c1%40googlegroups.com
>> 
>> .
>>
> --
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> 
> .
>

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Re: [deal.II] Step-57

2020-03-02 Thread Daniel Arndt

Hussan,

Do you observe this problem with the unmodified step-57 or did you change
anything?
What does the full backtrace look like (running gdb)?

Best,
Daniel

Am Mo., 2. März 2020 um 09:42 Uhr schrieb hussan zeb :

> how can resolve this error in step-57,
> Scanning dependencies of target step-57
> [ 33%] Building CXX object CMakeFiles/step-57.dir/step-57.cc.o
> [ 66%] Linking CXX executable step-57
> [ 66%] Built target step-57
> [100%] Run step-57 with Debug configuration
> grid refinements: 0
> viscosity: 0.1
> Number of active cells: 432
> Number of degrees of freedom: 4188 (3696 + 492)
> FGMRES steps: 0
> The residual of initial guess is 0
>
>
> 
> Exception on processing:
>
> 
> An error occurred in line <534> of file
> 
> in function
> std::pair::active_cell_iterator,
> dealii::Point >
> dealii::GridTools::{anonymous}::find_active_cell_around_point_tolerance(const
> dealii::Mapping&, const MeshType&, const
> dealii::Point&, const std::vector&, double) [with int dim =
> 2; MeshType = dealii::DoFHandler; int spacedim = 2; typename MeshType spacedim>::active_cell_iterator =
> dealii::TriaActiveIterator 2>, false> >]
> The violated condition was:
> best_cell.first.state() == IteratorState::valid
> Additional information:
> The point <0.5 0.42> could not be found inside any of the subcells of
> a coarse grid cell.
> 
>
> Aborting!
> 
> CMakeFiles/run.dir/build.make:57: recipe for target 'CMakeFiles/run' failed
> make[3]: *** [CMakeFiles/run] Error 1
> CMakeFiles/Makefile2:195: recipe for target 'CMakeFiles/run.dir/all' failed
> make[2]: *** [CMakeFiles/run.dir/all] Error 2
> CMakeFiles/Makefile2:202: recipe for target 'CMakeFiles/run.dir/rule'
> failed
> make[1]: *** [CMakeFiles/run.dir/rule] Error 2
> Makefile:170: recipe for target 'run' failed
> make: *** [run] Error 2
> zeb@kutta:~/deal/examples/step-57> make run
>
> --
> 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.
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> email to dealii+unsubscr...@googlegroups.com.
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> https://groups.google.com/d/msgid/dealii/8a6dd884-c75b-4a05-a119-48e22ca0a3c1%40googlegroups.com
> 
> .
>

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[deal.II] Step-57

2020-03-02 Thread hussan zeb

how can resolve this error in step-57, 
Scanning dependencies of target step-57
[ 33%] Building CXX object CMakeFiles/step-57.dir/step-57.cc.o
[ 66%] Linking CXX executable step-57
[ 66%] Built target step-57
[100%] Run step-57 with Debug configuration
grid refinements: 0
viscosity: 0.1
Number of active cells: 432
Number of degrees of freedom: 4188 (3696 + 492)
FGMRES steps: 0
The residual of initial guess is 0



Exception on processing: 


An error occurred in line <534> of file 
 
in function
std::pair::active_cell_iterator, 
dealii::Point > 
dealii::GridTools::{anonymous}::find_active_cell_around_point_tolerance(const 
dealii::Mapping&, const MeshType&, const 
dealii::Point&, const std::vector&, double) [with int dim = 
2; MeshType = dealii::DoFHandler; int spacedim = 2; typename MeshType::active_cell_iterator = 
dealii::TriaActiveIterator, false> >]
The violated condition was: 
best_cell.first.state() == IteratorState::valid
Additional information: 
The point <0.5 0.42> could not be found inside any of the subcells of a 
coarse grid cell.


Aborting!

CMakeFiles/run.dir/build.make:57: recipe for target 'CMakeFiles/run' failed
make[3]: *** [CMakeFiles/run] Error 1
CMakeFiles/Makefile2:195: recipe for target 'CMakeFiles/run.dir/all' failed
make[2]: *** [CMakeFiles/run.dir/all] Error 2
CMakeFiles/Makefile2:202: recipe for target 'CMakeFiles/run.dir/rule' failed
make[1]: *** [CMakeFiles/run.dir/rule] Error 2
Makefile:170: recipe for target 'run' failed
make: *** [run] Error 2
zeb@kutta:~/deal/examples/step-57> make run

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Re: [deal.II] Scaling behavior of Matrix-Free test program

[deal.II] Scaling behavior of Matrix-Free test program

[deal.II] deal.II Newsletter #112

Re: [deal.II] Step-57

Re: [deal.II] Step-57

Re: [deal.II] Step-57

[deal.II] Step-57

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