[deal.II] Installation problem using spack

2022-08-09 Thread Marco Nawijn 
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.

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Installation error: (I stripped the path to the package folders from the output 
so it is
 slightly easier to read; in addition I slightly formatted 
the output,
 again for better reading)

'cmake'
'-G'
'Ninja'
'-DCMAKE_INSTALL_PREFIX:STRING=dealii-9.4.0-pditdv3j4dpps4nc5jx4kfj42kfaphms'
'-DCMAKE_BUILD_TYPE:STRING=DebugRelease'
'-DBUILD_TESTING:BOOL=OFF'
'-DCMAKE_INTERPROCEDURAL_OPTIMIZATION:BOOL=OFF'
'-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=ON'
'-DCMAKE_INSTALL_RPATH:STRING=dealii-9.4.0-pditdv3j4dpps4nc5jx4kfj42kfaphms/lib
;dealii-9.4.0-pditdv3j4dpps4nc5jx4kfj42kfaphms/lib64
;arborx-1.1-zbemm6cpbwzbc6k7krso53grucr4fikm/lib
;boost-1.79.0-yulo43tufrk6kqsiigupmm3bktxlosrx/lib
;gsl-2.7.1-6qxuvfmjcopnkiwiqhvfbmngfizuzjy4/lib
;hdf5-1.10.7-v5iwjch4peubuguzhmonjmdg3vxkxdps/lib
;intel-tbb-2020.3-qxolbur3xiql2gma47jkxlvcyexfjpsd/lib
;metis-5.1.0-p7gsmz77yalgrjonfddy35lejrpw6bhf/lib
;netlib-scalapack-2.2.0-2pjpdwlwkht62nb3xwvcc4ug7qunhxus/lib
;oce-0.18.3-3ipfgc77pw27hwrp5bqbcxru2zqvj2vc/lib
;openblas-0.3.20-ih7wyjdf5jdptw3ase6vpwv6ws562jhs/lib
;openmpi-4.1.4-t7algfna2xa4kajv4igfphurkgdggpin/lib
;p4est-2.8-2w57tbexytitual2yrwkvvwg247pb4ct/lib
;petsc-3.17.3-tbou37jct6iwy7dvhz3o7pdvjjnbj7eo/lib
;slepc-3.17.1-ftyxr4kokjjbjs7bw6ea6pnwgcat5hug/lib
;suite-sparse-5.10.1-be64aqdsyjppfvsff3o5pxoiebxqnu32/lib
;symengine-0.9.0-226vwo56e557zv5lgl4lencntm6oinlg/lib
;trilinos-13.0.1-hi6xxic3bbib3dpxde5k3x4cn5f5u44f/lib
;zlib-1.2.12-itsi2i4tzpvkirehmpm4jjffkhtq6ooc/lib
;adol-c-2.7.2-ettinbhhlk2mxftfamwbpw5t44jstkpo/lib64
;arpack-ng-3.8.0-ixbfxtzdlgsbg4srqsxfqttbzs2otwwr/lib64
;assimp-5.2.4-y7f3umvzjviupqd33nmy7x5v3rjtbig4/lib64
;cgal-5.4.1-ikvmqd56pyc6t7vztunay3gyuv4emrpi/lib64
;ginkgo-1.4.0-2li5nizcwch6pc7wq32osy3sb2dafabi/lib64
;muparser-2.2.6.1-zwvhtt2hnul4tpwf7vzgpu4d63fqznqv/lib64
;sundials-6.2.0-wfeuorzp4faj7oluoc4r2upvlomd73kp/lib64
;symengine-0.9.0-226vwo56e557zv5lgl4lencntm6oinlg/lib64'
'-DCMAKE_PREFIX_PATH:STRING=symengine-0.9.0-226vwo56e557zv5lgl4lencntm6oinlg
;mpc-1.2.1-2wfbtlx4n6eetumhkrh7o4oapmemtj4n
;cereal-1.3.2-adcttjetlkihblkiki33v4oejgktdqwi
;sundials-6.2.0-wfeuorzp4faj7oluoc4r2upvlomd73kp
;suite-sparse-5.10.1-be64aqdsyjppfvsff3o5pxoiebxqnu32
;slepc-3.17.1-ftyxr4kokjjbjs7bw6ea6pnwgcat5hug
;petsc-3.17.3-tbou37jct6iwy7dvhz3o7pdvjjnbj7eo
;superlu-dist-7.2.0-s3d5rka6nlilimznjnmkhtiopf6d6ni4
;parmetis-4.0.3-dsixfphfyd7ftl7pf7q2ml3pbq657v6o
;hypre-2.25.0-5dtolxjd5lzm5vfwgfkveztjultvtgjm
;p4est-2.8-2w57tbexytitual2yrwkvvwg247pb4ct
;netlib-scalapack-2.2.0-2pjpdwlwkht62nb3xwvcc4ug7qunhxus
;muparser-2.2.6.1-zwvhtt2hnul4tpwf7vzgpu4d63fqznqv
;metis-5.1.0-p7gsmz77yalgrjonfddy35lejrpw6bhf
;gsl-2.7.1-6qxuvfmjcopnkiwiqhvfbmngfizuzjy4
;gmsh-4.8.4-2o34yusib4chg2ax635pito5czoyapq4
;oce-0.18.3-3ipfgc77pw27hwrp5bqbcxru2zqvj2vc
;intel-tbb-2020.3-qxolbur3xiql2gma47jkxlvcyexfjpsd
;ninja-1.11.0-mx4b5z2d5xs3pr4cunc2fj5hwaneskpm
;hdf5-1.10.7-v5iwjch4peubuguzhmonjmdg3vxkxdps
;ginkgo-1.4.0-2li5nizcwch6pc7wq32osy3sb2dafabi
;cgal-5.4.1-ikvmqd56pyc6t7vztunay3gyuv4emrpi

[deal.II] Component dof index

2022-08-09 Thread Uclus Heis 
Dear all, 

Is it possible to obtain the index of the total dof distribution for each 
component?

I work with two components, having a 2*N size system and I need to know 
where in my solution vector is each component.

I found functions like *count_dofs_per_component* or* ComponentMask *however, 
I can not find a option to obtain the index position of the components in 
the dof vector.

Thank you

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[deal.II] Stiffness Matrix

2022-08-09 Thread Prashanth 
Hey Everone,

I have recently started studying FEM and I have some basic doubts. Hope I 
can get some clarity here.
 
1. Is the stiffness matrix defined for element or node? In a simple truss 
with 2 linear elements, we calculate the stiffness matrix for K(1,1), K 
(1,2), K(2,1), K(2,2). In K(e,n): e is the element number and n is the node 
number. So is the stiffness matrix defined for node or element?

2. How is the order of Stiffness matrix calculated? 

3. Does the stiffness matrix only depends on geometry and material? are 
there any other factors?

4. Why is the load vector not symmetrical? In a simple truss with 2 linear 
elements, why is F(1,2) not equal to F(2,1)?  F(e,n): e is the element 
number and n is the node number.


Thanks and Regards,
Prashanth Setty

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Re: [deal.II] FEInterfaceValues and hp::FECollection

2022-08-09 Thread Simon Sticko 

Hi,

Unfortunately no-one has implemented FEInterfaceValues for hp yet (I think it 
would be great if someone did). The only workaround I know is to NOT use 
FEInterfaceValues and instead:

1. Use 2 hp::FEFaceValues objects, one initialized with cell 0 and one 
initialized with cell 1.

2. Split the jump term in 4 terms: [u][v] = u_0*v_0 - u0*v_1 - u_1*v_0 + u_1*v_1

3. Assemble each term in a separate local matrix (A_00, A_01, A_10, A_11), where

   A_01 - Rows correspond to local dofs on cell 0, columns to local dofs on 
cell 1.

4. Use global_dof_indices of cell 0 and cell 1 to map each local matrix to the 
global matrix.

Best,
Simon



On 09/08/2022 00:58, Marco Feder wrote:

Dear all,

I'm using an hp::FECollection object to describe different FE spaces in my 
grid. In particular, I'm in the following scenario:

x- - - - - -x
|             |
|     0      |
|             |
x - - F - -x
|             |
|     1      |
|             |
x- - - - - -x

On cell number 0 I have a FESystem with FE_Q(1) and FE_Q(1), which corresponds 
to fe_collection[0].
On cell number 1, I have again a FESystem with FE_Q(1) and FE_Nothing, 
corresponding to fe_collection[1].

I need to compute the jump [d_n u_h]_F, being F the face shared by the two 
cells. Unfortunately, I can't find a proper way to initialize FEInterfaceValues 
so that it understands that I need the jump of the first components only. 
Indeed, if I use fe_collection[0] (or fe_collection[1]) as first argument in 
the constructor, I have a runtime error in reinit(cell) saying (as expected):

/    The FiniteElement you provided to FEValues and the FiniteElement that
     belongs to the DoFHandler that provided the cell iterator do not
     match./
/
/
since we have different spaces on cell0 and cell1. Is there a possible 
workaround to this?

Best,
Marco

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.


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Re: [deal.II] Installation problem using spack

2022-08-09 Thread Daniel Arndt 
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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> You received this message because you are subscribed to the Google Groups
> "deal.II User Group" group.
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> https://groups.google.com/d/msgid/dealii/7383fcc8-af66-438f-b363-3aa1c9032d5en%40googlegroups.com
> 
> .
>

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Re: [deal.II] Installation problem using spack

2022-08-09 Thread 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
>> --- 
>> 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/7383fcc8-af66-438f-b363-3aa1c9032d5en%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [deal.II] Component dof index

2022-08-09 Thread Wolfgang Bangerth 

On 8/9/22 06:22, Uclus Heis wrote:


Is it possible to obtain the index of the total dof distribution for each 
component?


I work with two components, having a 2*N size system and I need to know where 
in my solution vector is each component.


You want to look at DoFTools::extract_dofs(). It returns the indices of those 
DoFs that correspond to one or several solution components.


Best
 Wolfgang


--

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   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Stiffness Matrix

2022-08-09 Thread Wolfgang Bangerth 

On 8/9/22 06:53, Prashanth wrote:
1. Is the stiffness matrix defined for element or node? In a simple truss with 
2 linear elements, we calculate the stiffness matrix for K(1,1), K (1,2), 
K(2,1), K(2,2). In K(e,n): e is the element number and n is the node number. 
So is the stiffness matrix defined for node or element?


Prashant,
you seem to be stuck on a very specific notation that I assume you have from a 
book or course you took. Since I don't know what the source of that notation 
is, it's hard for me to tell you what K(2,1) etc corresponds to -- you'll have 
to check how your reference defines this.


But you may want to take a look at step-3 and step-4, for example, where we 
first build a dense representation of the stiffness matrix contribution of a 
specific element, say A_K(i,j) where K is the element and i,j are local 
indices of the degrees of freedom that live on that cell. And then we add 
these local contributions into the global stiffness matrix A(i,j) where i,j 
are global indices of degrees of freedom.


(We number indices starting at zero, as is common in C++. You may need to take 
that into account when translating your notation.)




2. How is the order of Stiffness matrix calculated?


There is an enumeration of all degrees of freedom. How they are enumerated is 
not particularly important.



3. Does the stiffness matrix only depends on geometry and material? are there 
any other factors?


It depends on the differential operator.


4. Why is the load vector not symmetrical? In a simple truss with 2 linear 
elements, why is F(1,2) not equal to F(2,1)?  F(e,n): e is the element number 
and n is the node number.


Why should it?

Best
 W.

--

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   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] fourth-order referential deviatoric tensor Dev_P: why is 'S' used in the definition?

2022-08-09 Thread Wolfgang Bangerth 

On 8/8/22 15:11, Simon Wiesheier wrote:

grafik.png
grafik.png
The only place I use Dev_P is to compute the above double contractions ('P' in 
the above is what dealii returns as Dev_P)
As you can see, the fourth order tangent C_bar consists of outer products of 
second order symmetric tensors:
boldsymbol 'I' is the second order unit tensor, C_bar is a symmetric second 
order tensor, and blackboard 'I' is the general fourth order unit tensor,

the deltas are just scalars.

In my opinion, the double contractions 'P : outer_product(C_bar, C_bar)' and 
'P : I' produce different results if the fourth order symmetric unit tensor 
'S' is used to define 'P' .

The same holds also for doing the double contractions with P_T.
Correct?


Not being a nonlinear mechanics person, I'll have to defer to someone else 
with more knowledge about these matters :-(


Best
 W.

--

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   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Matrix-free DG with h-adaptive mesh refinement

2022-08-09 Thread Wolfgang Bangerth 

On 8/8/22 02:44, M. Bänsch wrote:

*** Caution: EXTERNAL Sender ***

Dear community,

I am currently trying to implement h-adaptive mesh refinement into step-67 (by 
adding a refine_grid() functionality). As references I looked into step-31 
, 
step-33 
, 
the previous question for step-59 
 
and the distributed::SolutionTransfer documentation.
I tried to adapt the approach in the SolutionTransfer documentation 
 
so that it matches what I see in the references.



Unfortunately, I get the following error:

-
The violated condition was:
     (data_range.size() % bytes_per_entry == 0)
Additional information:
     This exception -- which is used in many places in the library -- usually 
indicates that some condition which the author of the code thought must be 
satisfied at a certain point in an algorithm, is not fulfilled. An example 
would be that the first part of an algorithm sorts elements of an array in 
ascending order, and a second part of the algorithm later encounters an 
element that is not larger than the previous one.


There is usually not very much you can do if you encounter such an exception 
since it indicates an error in deal.II, not in your own program. Try to come 
up with the smallest possible program that still demonstrates the error and 
contact the deal.II mailing lists with it to obtain help.

-

The previous question basically achieved what I am trying to implement but the 
additional functionality that comes with step-59's setup_system() call takes 
care of all the interpolation etc.


I have the feeling that I misunderstood something in the documentation (for 
example replacing the interpolated_solution part. Would someone be able to 
tell me if I made a mistake with adapting the documentation to what I have.
Is there also some mistake on my part since I need another structure 
for LinearAlgebra::distributed::Vector (instead of the TrilinosWrappers 
vectors from the documentation)?


Any help would be much appreciated.


It's hard to say what the reason is without having a small test case that 
shows the issue. Since the issue happens during solution transfer, it is 
almost certainly not something related to whether or not you build solutions.


As is generically the case, it is easiest to find the problem if you reduce 
the program that produces the error to something as minimal as possible -- 
just throw out everything that can be thrown out. Do you think you can come up 
with such a program?


Separately (and almost certainly unrelated): Did you mean to reinit() the 
'solution' variable twice here?

```
  LinearAlgebra::distributed::Vector old_solution;
  old_solution.reinit(locally_owned_dofs,
locally_relevant_dofs,
MPI_COMM_WORLD);
  old_solution = solution;
  soltrans.prepare_for_coarsening_and_refinement(old_solution);

  solution.reinit(locally_owned_dofs, MPI_COMM_WORLD);
  soltrans.interpolate(solution);
```

Best
 W.


--

Wolfgang Bangerth  email: bange...@colostate.edu