Re: [deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

[Matthias Maier]

On Thu, Oct 18, 2018, at 17:48 CDT, David Wells  wrote:

> Hi Chucui,
>
> StraightBoundary was removed in deal.II 9.0; it should not show up in any 
> object files so these errors don't make any sense. Did you use a clean 
> build directory?

Not quite. It got completely removed in the current development version.

In version 9.0.1 it is present in the library. What is surprising though
is the fact that we completely instantiate the class:

grid/tria_boundary.inst.in (on branch dealii-9.0
 18 for (deal_II_dimension : DIMENSIONS; deal_II_space_dimension :  
SPACE_DIMENSIONS)
 19 {   
 
 20 #if deal_II_dimension <= deal_II_space_dimension
 
 21 template class Boundary;
 
 22 template class StraightBoundary; 
 23 #endif  
 
 24 } 

yet, Chucui observes an undefined reference to the constructor. Which is
a bit puzzling.

Chucui, can you please post your full `detailed.log` please? Further,
can you please try to recompile again by (a) unpacking dealii-9.0.1 to a
new directory, and configure and compile in a new build directory?

Best,
Matthias

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[deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

[David Wells]

Hi Chucui,

StraightBoundary was removed in deal.II 9.0; it should not show up in any 
object files so these errors don't make any sense. Did you use a clean 
build directory?

Thanks,
David Wells

On Thursday, October 18, 2018 at 8:27:40 AM UTC-4, chucu...@gmail.com wrote:
>
> Dear all, 
>
> I want to reinstall my deal.ii because I need to run some codes in 
> parallel just like Step-40, step-55 and Step-32, and I choose deal.ii-9.0.1 
> The command lines I use are: 
>
> $cmake ../dealii-9.0.1/dealii-9.0.1  -DDEAL_II_WITH_MPI=ON  
> -DCMAKE_C_COMPILER=/usr/local/mpi3/bin/mpicc  
> -DCMAKE_CXX_COMPILER=/usr/local/mpi3/bin/mpicxx  
> -DCMAKE_Fortran_COMPILER=/usr/local/mpi3/bin/mpifort 
> -DCMAKE_INSTALL_PREFIX=../dealii-9.0.1/build -DMPI_DIR=/usr/local/mpi3 
> -DP4EST_DIR=../p4est/p4est-2.0 -DPETSC_DIR=../new-petsc-3.7.7/petsc-3.7.7 
> -DHDF5_DIR=/usr/lib64/ -DMETIS_DIR=../metis-5.1.0/metis-5.1.0 
> -DDEAL_II_WITH_METIS=ON -DDEAL_II_WITH_HDF5=OFF -DDEAL_II_WITH_PETSC=ON 
> -DDEAL_II_WITH_P4EST=OFF -DDEAL_II_WITH_MPI=ON 
> -DDEAL_II_FORCE_BUNDLED_BOOST=ON-DDEAL_II_ALLOW_AUTODETECTION=ON
>
> $make
>
> $make install
>
> But after "make install", the installation was interupped, and the errors 
> are showed as:
>
> Scanning dependencies of target obj_rol_debug
> [ 82%] Built target obj_rol_debug
> Scanning dependencies of target step-3.release
> [ 82%] Building CXX object 
> examples/CMakeFiles/step-3.release.dir/step-3/step-3.cc.o
> [ 82%] Linking CXX executable ../bin/step-3.release
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<1, 2>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<1, 1>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<3, 3>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<3, 3>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<2, 2>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<2, 3>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<1, 1>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<1, 3>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<1, 2>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<2, 3>::StraightBoundary()'
> ../lib/libdeal_II.so.9.0.1: undefined reference to 
> `dealii::StraightBoundary<2, 2>::StraightBoundary()'
> make[2]: *** [bin/step-3.release] Error 1
> make[1]: *** [examples/CMakeFiles/step-3.release.dir/all] Error 2
> make: *** [all] Error 2
>
> So, I don't what happened and know how to do. Hope some suggestions! 
> Thanks in advance!
>
> Best,
> Chucui
>
>
>
>
>

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[deal.II] deal.II Newsletter #53

[Rene Gassmoeller]

Hello everyone!

This is deal.II newsletter #53.
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:

#7360: Replace non-prefixed macros (proposed by masterleinad) 
https://github.com/dealii/dealii/pull/7360

#7359: Add test for SphericalManifold (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/7359

#7358: Refactored FESeries to allow spacedim template for FECollection. 
(proposed by marcfehling; merged) https://github.com/dealii/dealii/pull/7358

#7356: Changelong entry for #7063 (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/7356

#7354: Update comments of two functions. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/7354

#7353: Avoid DEAL_II_COMPILER_CUDA_AWARE inside objects (proposed by 
masterleinad; merged) https://github.com/dealii/dealii/pull/7353

#7351: Document the various *_accessor typedefs at their source. (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/7351

#7350: Improve wording of a doc string. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/7350

#7349: Restrict non_matching/coupling_07 (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/7349

#7348: Avoid warnings in ad_drivers.h (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/7348

#7347: Replace ConstraintMatrix by AffineConstraints in tests (proposed by 
masterleinad; merged) https://github.com/dealii/dealii/pull/7347

#7346: Fix failing Sacado tests (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/7346

#7343: Use the infinitive form of verbs in the first sentence of doc strings. 
(proposed by bangerth; merged) https://github.com/dealii/dealii/pull/7343

#7342: Americanize the ADHelperResidualLinearization class name (proposed by 
jppelteret; merged) https://github.com/dealii/dealii/pull/7342

#7340: Add tests to check compilation of functions / classes with AD numbers 
(proposed by jppelteret; merged) https://github.com/dealii/dealii/pull/7340

#7339: Refactor check for registered tapes (proposed by jppelteret; merged) 
https://github.com/dealii/dealii/pull/7339

#7338: Add tests for cell-level ADHelper classes (proposed by jppelteret; 
merged) https://github.com/dealii/dealii/pull/7338

#7337: Introduced 'compare_for_cell_domination'. Refactored 
'compare_for_face_domination'. (proposed by marcfehling) 
https://github.com/dealii/dealii/pull/7337

#7336: Fix step-16 (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/7336

#7330: ScaLAPACKMatrix: improve documentation (proposed by BenBrands; merged) 
https://github.com/dealii/dealii/pull/7330

#7327: Added cell->is_locally_owned() in project_boundary_values_div_conforming 
(proposed by JonMatthewsFCAS; merged) https://github.com/dealii/dealii/pull/7327

#7230: Allow omitting std::complex instantiations (proposed by masterleinad; 
merged) https://github.com/dealii/dealii/pull/7230

#6978: AD Helpers: Add helper for residual linearisation (cell-level) (proposed 
by jppelteret; merged) https://github.com/dealii/dealii/pull/6978


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

#7357: SphericalManifold inaccurate/broken (opened) 
https://github.com/dealii/dealii/issues/7357

#7355: switch hp_cell_weights_03.cc to Zoltan (opened) 
https://github.com/dealii/dealii/issues/7355

#7352: Underlinkage in quick tests with GSL (opened) 
https://github.com/dealii/dealii/issues/7352

#7345: scalapack_06c fails with Intel MKL (opened) 
https://github.com/dealii/dealii/issues/7345

#7344: BOOST_SERIALIZATION_USABLE fails: the test program crashes (opened and 
closed) https://github.com/dealii/dealii/issues/7344

#7341: Modernise step-33 (opened and closed) 
https://github.com/dealii/dealii/issues/7341

#7331: Problems with step-16 (closed) 
https://github.com/dealii/dealii/issues/7331

#7318: Tests: Changing the floating point environment in tests without setting 
FENV_ACCESS results in undefined behavior (closed) 
https://github.com/dealii/dealii/issues/7318

#7282: 9.0.1 release (closed) https://github.com/dealii/dealii/issues/7282

#7260: dealii-9.0.0 wrongly detects the PETSc version: 3.10.1 is detected as 
3.0.1.0 (closed) https://github.com/dealii/dealii/issues/7260

#316: Document iterators at the place where they are typedef'ed (closed) 
https://github.com/dealii/dealii/issues/316

#304: Use lower_bound more intelligently (closed) 
https://github.com/dealii/dealii/issues/304


A list of all major changes since the last release can be found at 
https://www.dealii.org/developer/doxygen/deal.II/changes_after_8_5_0.html.


Thanks for being part of the community!


Let us know about questions, problems, bugs or just share your experience by 
writing to dealii@googlegroups.com, or by opening issues or pull requests at 

[deal.II] Re: Computing min and max eigenvalues

[Michał Wichrowski]

W dniu czwartek, 18 października 2018 17:59:40 UTC+2 użytkownik Bruno 
Turcksin napisał:
>
> Michal,
>
> Have you tried to use ARPACK to get the smallest eigenvalues? That's what 
> we are doing in one of our code and it works pretty well. We have a patch 
> here 
> 
>  
> so that you don't need to provide the inverse of the operator to use 
> ARPACK. You still need to provide a mass matrix but it's no used.
>
> Best,
>
> Bruno
>

Thanks a lot!
In the meantime, I found that  I was probably using the wrong solver to get 
inverse (the system may be not SPD) using GMRes resulted in a 
significant speedup. However, I still have strange results, including the 
smallest eigenvalue being larger than the largest one. I think using ARPACK 
instead of my own code will solve the problem, thank you.
Michał

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[deal.II] Re: Several questions about mesh generation and distributed triangulations

[Pascal Kraft]

I am by the way aware of the parrallel::distributed::Triangulation 
constructor which accepts another Triangulation as an argument - however 
this calls repartitioning and is therefore no solution to the problem.
Also weights could be passed to influence the partitioning, but determining 
weights such that the partitioning is exactly the one I want would be hard 
and it would depend massively on the algorithm used to compute the 
partitioning which should be kept as a black box. This would also be a very 
error-prone workaround.

Am Donnerstag, 18. Oktober 2018 13:54:13 UTC+2 schrieb Pascal Kraft:
>
> I will try to be as short as possible - if more details are required feel 
> free to ask. Also I offer to submit all mesh generation code I create in 
> the future, since others might have similar needs at some point.
>
> I work on a 3d mesh with purely axis-parallel edges. The mesh is a 2d-mesh 
> (say in x and y direction) extruded to 3d (z-direction). Due to the scheme 
> I use it is required, that the distributed version of this mesh be 
> distributed as intervals along the z-axis ( process 0 has all cells with 
> cell->center()[2] in [0,1], process 1 has all cells with cell->center()[2] 
> in (1,2] and so on.)
> What I did originally was simply generating a mesh consisting of 
> n_processes cells, let that mesh be auto partitioned, then turning 
> partitioning off and then using global refinement of marked cells to 
> generate the right structure inside these cells for each processor. This 
> however feels like a very elaborate workaround and the lack of anisotropic 
> refinement for distributed meshes is a heavy restriction here. However, 
> this seemed to be a feasible workaround for the time being.
> Recently a new problem has arisen however: For the construction of a 
> blockwise, parallel preconditioner for a sweeping method I now need 
> codimension 1 meshes of the process-to-process mesh-interfaces (again a 
> simple copy of the theoretical 2D-mesh, which was extruded to generate the 
> 3d mesh, if that were possible) because I need nodal and Nedelec-elements 
> on these 2D-interfaces for the computation of some integrals.
> So my questions would be:
> 1. given a 2D-mesh, what is the easiest way to get a distributed 
> 3d-extrusion with the partitioning described above?  (auto-partitioning 
> generates balls in this mesh, not cuboids with z-orthogonal 
> process-to-process interfaces) One suggestion for a function here would be 
> a function to transform a shared to a distributed mesh because on a shared 
> mesh I could set the subdomain Ids and then just call that function when 
> I'm done
> 2. say I have a layer of faces in that mesh (in the interior) and I need 
> nedelec elements and nodal elements on these faces (codimension 1) to 
> evaluate their shape function and gradients in quadrature points of a 
> 2D-quadrature on the faces. What is the best way to do this? (if it was a 
> boundary I could give a boundary id and call 
> GridGenerator::extract_boundary_mesh but it's not always on the boundary.
> 3. There is a description on how to manually generate a mesh which seems 
> easy enough in my case. How does this work for a distributed mesh? Is the 
> only version to generate a mesh and then auto-partition or can I somehow 
> define the partitioning in the generation phase similar to the way I could 
> set subdomain Ids in a shared parallel mesh?
> 4. What can I do to extend the exising functionality? Since the memory 
> consumtion of my (and most likely most codes) is low during mesh 
> generation, first generating a shared mesh and then distributing it would 
> not be a problem (compared to keeping the shared mesh during computation 
> when the matrices and vectors also take up a lot of the memory). Do you 
> consider such a function "easy" to implement?
>
> Thank you for your time!
> Pascal
>
>
>

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Re: [deal.II] Ghost layers in Parallell Computation

[Wolfgang Bangerth]

On 10/17/18 10:33 PM, Sunder Dasika wrote:
> Thank you. I would be very happy if it could be implemented.

You may have misunderstood -- I was trying to suggest that *you* implement it 
:-) deal.II is an open source volunteer project. We don't have the manpower to 
implement everything our users would like to have, and as a project greatly 
profit by users implementing things that then flow into the library. But we 
would be happy to provide feedback and help!

Best
  W.

-- 

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

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[deal.II] Computing min and max eigenvalues

[Michał Wichrowski]

Dear all,
I need to compute the minimum and maximum eigenvalues of the matrix-free 
operator (vmult is only available ). For the largest eigenvalue, I'm using 
the power method, but I have some problems with minimal eigenvalue. The 
condition number of the operator is close to 1, so I tried using the power 
method on inverse obtained by CG. This solution is time-consuming and for 
some cases I got strange results.
I have seen that CG can output eigenvalues: 
  solver_outer.connect_eigenvalues_slot( [](const std::vector<  double > & 
vec)->void { std::cout<< "  "

[deal.II] After "make install", there are some Errors when install Deal.II-9.0.1

[chucui1016]

Dear all, 

I want to reinstall my deal.ii because I need to run some codes in parallel 
just like Step-40, step-55 and Step-32, and I choose deal.ii-9.0.1 
The command lines I use are: 

$cmake ../dealii-9.0.1/dealii-9.0.1  -DDEAL_II_WITH_MPI=ON  
-DCMAKE_C_COMPILER=/usr/local/mpi3/bin/mpicc  
-DCMAKE_CXX_COMPILER=/usr/local/mpi3/bin/mpicxx  
-DCMAKE_Fortran_COMPILER=/usr/local/mpi3/bin/mpifort 
-DCMAKE_INSTALL_PREFIX=../dealii-9.0.1/build -DMPI_DIR=/usr/local/mpi3 
-DP4EST_DIR=../p4est/p4est-2.0 -DPETSC_DIR=../new-petsc-3.7.7/petsc-3.7.7 
-DHDF5_DIR=/usr/lib64/ -DMETIS_DIR=../metis-5.1.0/metis-5.1.0 
-DDEAL_II_WITH_METIS=ON -DDEAL_II_WITH_HDF5=OFF -DDEAL_II_WITH_PETSC=ON 
-DDEAL_II_WITH_P4EST=OFF -DDEAL_II_WITH_MPI=ON 
-DDEAL_II_FORCE_BUNDLED_BOOST=ON-DDEAL_II_ALLOW_AUTODETECTION=ON

$make

$make install

But after "make install", the installation was interupped, and the errors 
are showed as:

Scanning dependencies of target obj_rol_debug
[ 82%] Built target obj_rol_debug
Scanning dependencies of target step-3.release
[ 82%] Building CXX object 
examples/CMakeFiles/step-3.release.dir/step-3/step-3.cc.o
[ 82%] Linking CXX executable ../bin/step-3.release
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<1, 2>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<1, 1>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<3, 3>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<3, 3>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<2, 2>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<2, 3>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<1, 1>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<1, 3>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<1, 2>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<2, 3>::StraightBoundary()'
../lib/libdeal_II.so.9.0.1: undefined reference to 
`dealii::StraightBoundary<2, 2>::StraightBoundary()'
make[2]: *** [bin/step-3.release] Error 1
make[1]: *** [examples/CMakeFiles/step-3.release.dir/all] Error 2
make: *** [all] Error 2

So, I don't what happened and know how to do. Hope some suggestions! Thanks 
in advance!

Best,
Chucui




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[deal.II] Several questions about mesh generation and distributed triangulations

[Pascal Kraft]

I will try to be as short as possible - if more details are required feel 
free to ask. Also I offer to submit all mesh generation code I create in 
the future, since others might have similar needs at some point.

I work on a 3d mesh with purely axis-parallel edges. The mesh is a 2d-mesh 
(say in x and y direction) extruded to 3d (z-direction). Due to the scheme 
I use it is required, that the distributed version of this mesh be 
distributed as intervals along the z-axis ( process 0 has all cells with 
cell->center()[2] in [0,1], process 1 has all cells with cell->center()[2] 
in (1,2] and so on.)
What I did originally was simply generating a mesh consisting of 
n_processes cells, let that mesh be auto partitioned, then turning 
partitioning off and then using global refinement of marked cells to 
generate the right structure inside these cells for each processor. This 
however feels like a very elaborate workaround and the lack of anisotropic 
refinement for distributed meshes is a heavy restriction here. However, 
this seemed to be a feasible workaround for the time being.
Recently a new problem has arisen however: For the construction of a 
blockwise, parallel preconditioner for a sweeping method I now need 
codimension 1 meshes of the process-to-process mesh-interfaces (again a 
simple copy of the theoretical 2D-mesh, which was extruded to generate the 
3d mesh, if that were possible) because I need nodal and Nedelec-elements 
on these 2D-interfaces for the computation of some integrals.
So my questions would be:
1. given a 2D-mesh, what is the easiest way to get a distributed 
3d-extrusion with the partitioning described above?  (auto-partitioning 
generates balls in this mesh, not cuboids with z-orthogonal 
process-to-process interfaces) One suggestion for a function here would be 
a function to transform a shared to a distributed mesh because on a shared 
mesh I could set the subdomain Ids and then just call that function when 
I'm done
2. say I have a layer of faces in that mesh (in the interior) and I need 
nedelec elements and nodal elements on these faces (codimension 1) to 
evaluate their shape function and gradients in quadrature points of a 
2D-quadrature on the faces. What is the best way to do this? (if it was a 
boundary I could give a boundary id and call 
GridGenerator::extract_boundary_mesh but it's not always on the boundary.
3. There is a description on how to manually generate a mesh which seems 
easy enough in my case. How does this work for a distributed mesh? Is the 
only version to generate a mesh and then auto-partition or can I somehow 
define the partitioning in the generation phase similar to the way I could 
set subdomain Ids in a shared parallel mesh?
4. What can I do to extend the exising functionality? Since the memory 
consumtion of my (and most likely most codes) is low during mesh 
generation, first generating a shared mesh and then distributing it would 
not be a problem (compared to keeping the shared mesh during computation 
when the matrices and vectors also take up a lot of the memory). Do you 
consider such a function "easy" to implement?

Thank you for your time!
Pascal


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