Re: [deal.II] Open source finite element preprocessor

[Marco Nawijn]

Hi,

Maybe Trame is an option for you?
You have to build something yourself, but a lot of the complexity is hidden.

https://kitware.github.io/trame/

Marco

On Wed, Jan 18, 2023, 4:05 PM Kaushik Das  wrote:

> Hi all,
> I have been using deal.ii for a while. I would like to create a simple but
> customized preprocessor for my deal.ii application.
>
> Please suggest any customizable open-source FE analysis preprocessor that
> I can use as a base to build on.
>
> I am looking for something that will visualize 3D geometry, and have some
> basic picking (registering x,y,z of mouse clicks), and UI functionality.
> This UI will write a prm file that can then be sent to deal.ii.
>
> I am looking for something that is dealii_parameter_gui + 3D geometry
> visualization + mousing click picking.
>
> I am not looking for a mesh generator. I generate mesh using deal.ii
> functionality. I am not looking for a post-processor or results visualizer,
> I am very happy to use ParaView for post-processing.
>
> Thank you very much for your help.
> Kaushik
>
> --
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> 
> .
>

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Re: [deal.II] Installation problem using spack

[Marco Nawijn]

Hi Wolfgang,

No, I didn't check. I was just running a few example programs that were 
compiled during the installation process.
However, I believe it is a good exercise for me to see if I can find the 
bug :). So, I will give it a try and report back if I find anything or get 
stuck.

Marco


On Monday, August 15, 2022 at 4:03:00 PM UTC+2 Wolfgang Bangerth wrote:

> On 8/15/22 00:50, Marco Nawijn wrote:
> > 
> > Just for information, when you run the example with MPI on 1 processor 
> (so -np 
> > 1), the process runs fine. Any value >1 results in this error. The error 
> > itself makes sense because it requests a massive amount of memory (I am 
> > running on a laptop at the moment). A quick fix (based on what I found 
> on the 
> > internet) is to downgrade the version of Metis. However, ideally for 
> Deal-II 
> > newbies using straightforward laptops/workstations, it would be nice to 
> just 
> > run `spack install dealii` and it just works.
> > 
> > If there is anything I can do to help, I am more than willing to.
>
> The question is whether METIS' excessive memory allocation is because of a 
> bug 
> in METIS, or because we call it in a way it doesn't expect. Did your 
> search 
> for the source of the error indicate anything to this effect?
>
> Best
> W.
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>

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Re: [deal.II] Installation problem using spack

[Marco Nawijn]

Hi Jean-Paul,

I can confirm that the patch works like a charm. Thanks!

I now run into another issue, when running step-17. It fails with the 
following message:
  ***Memory allocation failed for SetupCtrl: maxvwgt. Requested size: 
137438953480 bytes

I did a quick search on the internet and it seems to be related to Metis 
5.1.0.

Just for information, when you run the example with MPI on 1 processor (so 
-np 1), the process runs fine. Any value >1 results in this error. The 
error itself makes sense because it requests a massive amount of memory (I 
am running on a laptop at the moment). A quick fix (based on what I found 
on the internet) is to downgrade the version of Metis. However, ideally for 
Deal-II newbies using straightforward laptops/workstations, it would be 
nice to just run `spack install dealii` and it just works. 

If there is anything I can do to help, I am more than willing to.

Kind regards,

Marco

  

On Thursday, August 11, 2022 at 9:30:41 PM UTC+2 Jean-Paul Pelteret wrote:

> Hi Marco,
>
> I've open a PR in Spack (https://github.com/spack/spack/pull/32079) that 
> backports the patches that we added to the development version to 9.4. Feel 
> free to try it and provide some feedback as to whether or not it works for 
> you.
>
> Best,
> Jean-Paul
>
> On Thursday, August 11, 2022 at 7:50:46 AM UTC+2 marco@colosso.nl 
> wrote:
>
>> Hi Daniel and Timo,
>>
>> Thanks for the feedback. The bug indeed seems to be the problem, since 
>> the spack HDF5 package is definitely build with MPI support. I first 
>> thought it was because by default spack doesn't seem to build HDF5 with C++ 
>> support, but that did not help (of course now I know why).
>>
>> Building without HDF5 would be an option for me for the short term, but I 
>> will first try to see if I can get it working.
>>
>> Again, I am pretty impressed by the spack. It works like a charm and it 
>> provides a lot of flexibility.
>>
>> Kind regards,
>>
>> Marco
>>
>> On Tuesday, August 9, 2022 at 7:27:38 PM UTC+2 Timo Heister wrote:
>>
>>> 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 wi

Re: [deal.II] Installation problem using spack

[Marco Nawijn]

Hi Daniel and Timo,

Thanks for the feedback. The bug indeed seems to be the problem, since the 
spack HDF5 package is definitely build with MPI support. I first thought it 
was because by default spack doesn't seem to build HDF5 with C++ support, 
but that did not help (of course now I know why).

Building without HDF5 would be an option for me for the short term, but I 
will first try to see if I can get it working.

Again, I am pretty impressed by the spack. It works like a charm and it 
provides a lot of flexibility.

Kind regards,

Marco

On Tuesday, August 9, 2022 at 7:27:38 PM UTC+2 Timo Heister wrote:

> 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
>>>  
>>> <https://groups.google.com/d/msgid/dealii/7383fcc8-af66-438f-b363-3aa1c9032d5en%40googlegroups.com?utm_medium=email_source=footer>
>>> .
>>>
>>

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[deal.II] Installation problem using spack

[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] Introduction and request for feedback

[Marco Nawijn]

Dear All,

Let me first quickly introduce myself. My name is Marco Nawijn, I am 49 
years
old and I hold a masters degree in aerospace engineering. I have many years 
of
practical experience in the application of the finite element method in the
field of mechanics (plasticity, buckling, damage initiation and progression 
in
composites and so on). I did have a fair amount of theoretical background 
back
in the day, but this certainly needs some refreshing. I do have a pretty 
solid
background in Python/C/C++ programming although I don't have a formal 
education
in these areas. I am currently the manager of the engineering department of
Rondal (https://rondal.com) where we design sailing systems for super yachts
using commercial FSI (SailPack) and FE (Strand7) packages.

Since a long time however, I feel the urge to open the FE black box so to 
speak
and get more control/insight/understanding of the FE field (theory, 
limitations,
practical issues, solvers and so on). After googling around every now and 
than,
I stumbled across Deal II. And although, a lot of the mathematics is still
daunting for me, I really like the quality of the code itself, the available
reference documentation, the lecture series and the volume of examples and 
their
in-depth explanations. Up to this point in time, I have been lurking 
around, but
I decided to get my hands and feet dirty and dive in. Before I do so 
however, I
would like to kindly ask for some feedback on what my plans are. The reason 
I
ask is because I am afraid that what I want may not exactly align with the 
Deal
II objectives.

What I basically would like to do is, gradually (months/years) develop the
necessary functionality to analyse and optimize our sailing systems. The 
list of
topics I am interested in includes (but is not limited to):
 - Linear elastic static analysis of the rig (mast, spreaders, standing 
rigging)
   using 1D elements (beam, truss);
 - Linear buckling analysis of the rig;
 - Non-linear buckling analysis (account for effect of cable tensioning on
   buckling behaviour);
 - Linear elastic static analysis of the mast using 2D/3D orthotropic 
elements;
 - Linear buckling analysis of the mast using 2D/3D orthotropic elements;
 - Detailed stress analysis of composites (ply-by-ply modelling of 
composite,
   visco-elastic modelling of matrix materials);
 - Calculation of the pressure distribution of a sail using a potential flow
   solver.
 - FSI analysis of rig (flow generates pressure on the sail which deforms 
the
   mast which alters the shape of the sail which alters the pressure
  distribution and so on)

So basically what I would like to do is use as much functionality as 
possible
from Deal II, implement what is missing and build practical analysis tools 
out
of it.

Does this make sense?

In terms of a timeline, I will probably start by myself in my own spare time
untill I am able to do the beam analysis (first 3 bullet points). This 
allows me
to get enough experience in working with Deal II to also guide master/PHD
students. From that point on, some of the additional work will than
probably/hopefully be done in cooperation with master/PHD students.

As a final note, I am a big fan of open source software. Therefore, I am 
fully
committed to contribute whatever I develop back to the Deal II community
including examples/tests/documentation and so on. For example, one of the 
first
things on my list is to expand on the Abaqus input file reader. I have some
ideas in this area that I would like to pitch if there is any interest. 
Another
practical thing I can contribute to is testing the compilation of Deal II 
with
different versions of libraries. For example, Deal II will not compile out 
of the
box with newer TBB versions. But I also get a fair amount of warnings of 
array
bounds that (the compiler thinks) are not correct. So if there is an 
interest to
test different configurations (accessible to mortals, because I do not have
access to a supercomputing cluster) I am more than happy to get my hands 
dirty.

Any thoughts/ideas/feedback?

Marco

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