Dear Paras,
I have faced a lot of similar issues in the past and maybe these
suggestions can help (or maybe not).
1. Generally visual rendering software (at least paraview) renders data on
quad/hex meshes using triangular polygons. Consequently, when you look at
the color map within a square,
Dear all,
I hope you are well :).
We are currently facing a weird bottle neck. There are some operation which
require us to set a particle property to zero and I think we are doing
something which is not optimal at all. Right now, we loop over the
particles, then we get the properties array
Maybe it is callgrind that is playing tricks on me.
Here is the code :
for (auto particle = particle_handler.begin();
particle != particle_handler.end();
++particle)
{
// Getting properties of particle as local variable
auto particle_properties = particle->get_properties();
// Reinitializing
/17/20 3:50 PM, blais...@gmail.com wrote:
> > Maybe it is callgrind that is playing tricks on me.
> > Here is the code :
> >
> > for (auto particle = particle_handler.begin();
> > particle != particle_handler.end();
> > ++particle)
> > {
> > // Gettin
that be the right approach? If so, I can work on a PR.
On Monday, October 19, 2020 at 10:11:33 a.m. UTC-4 Wolfgang Bangerth wrote:
> On 10/19/20 4:58 AM, blais...@gmail.com wrote:
> > The issue is that this code is being called a lot (in our case every
> > iteration, so 100k to 10M
Dear Ramiro,
You could also take a look at step-70 by Luca and I. It deplays a very
prototype-ish fluid-structure interaction framework using immersed
boundaries. I am sure Luca has progressed a lot on this issue since then.
You can also look at software derived from Deal.II. Our group develops
Be careful about SnappyHexMesh. You can use it to make hex-only meshes, but
it will generate a tesselated mesh (which does not really conform to the
boundary, it is by all means a voxel mesh).
If you fully use Snappy, it will generate a polyhedral mesh with as many as
20 faces per element. This
Hello Jose,
I wish I could help, but I second Wolfgang's question.
Is your code available somewhere? I would be glad to take a look at it and
compare the solutions for the same problems using different formulations. I
would expect that if you fix the issue with boundary conditions (those
>
> Hello Jose,
>> I wish I could help, but I second Wolfgang's question.
>> Is your code available somewhere? I would be glad to take a look at it
>> and compare the solutions for the same problems using different
>> formulations. I would expect that if you fix the issue with boundary
>>
There is a Facebook deal.II account? Now I know what to follow :)!
Cheers!
Bruno
On Tuesday, December 29, 2020 at 12:20:15 p.m. UTC-5 Wolfgang Bangerth
wrote:
> On 12/28/20 10:54 PM, blais...@gmail.com wrote:
> >
> > If you want to see an animation of DEM done using the d
Hello all,
I hope you are all well. This is not strictly a deal.II question, but I
thought I could benefit for the huge amount of expertise present on this
board.
I am currently launching large (at least from my POV) tasks on our HPC
cluster. The task generally contain on the order of 50M to
Dear Timo,
thank you for your answer and your time :)
On Sunday, December 6, 2020 at 9:04:24 p.m. UTC-5 Timo Heister wrote:
> > The task generally contain on the order of 50M to 100M DOFs and are
> transient DNS problems.
>
> With this you are likely at a point where factorizations (even ILU)
Dear Wolgang, thank you for the answers
On Sunday, December 6, 2020 at 8:00:09 p.m. UTC-5 Wolfgang Bangerth wrote:
> On 12/6/20 12:27 PM, blais...@gmail.com wrote:
> >
> > In this case, even using ILU(1) is extremely expensive (e.g. it takes 2X
> more
> > time tha
Dear Timo and Martin,
Thank you very much for the help and advice.
I'll definitely take the time to read the references of Martin and look
into what you are suggesting. Clearly, I need to exploit the structure of
the matrix significantly more to be able to extract more performance out of
the
Thank you all for the help :).
This is always a bit of a lesson in humility where I realise there is just
so much I don't know, and how much out there there is still to learn :)!.
On Monday, December 7, 2020 at 11:52:51 a.m. UTC-5 Wolfgang Bangerth wrote:
> On 12/7/20 6:19 AM, bl
Dear all, I hope you are well.
I am trying to add checkpointing in our particle code. Particles do not
have a save function, but they have a serialize function, which I think
would be exactly what I need.
However, the function is not documented. It takes as an argument something
of class
?
On Wednesday, December 9, 2020 at 7:13:08 p.m. UTC-5 blais...@gmail.com
wrote:
> I think they will! I feel kind-off dumb not having realized that :)
> Thanks!
> Bruno
>
>
> On Wednesday, December 9, 2020 at 6:06:17 p.m. UTC-5 peterrum wrote:
>
>> Do the following links help?
; -
> https://github.com/dealii/dealii/blob/master/tests/serialization/particle_handler_02.cc
>
> Peter
>
> On Wednesday, 9 December 2020 at 23:15:09 UTC+1 blais...@gmail.com wrote:
>
>> Dear all, I hope you are well.
>> I am trying to add checkpointing in our particle code.
Awesome.
It works perfectly
Thank you all :)!
On Wednesday, December 9, 2020 at 8:10:13 p.m. UTC-5 Wolfgang Bangerth
wrote:
> On 12/9/20 5:32 PM, blais...@gmail.com wrote:
> > I have one tiny question actually.
> > In all tests, the std::ostringstream oss which contains s
Hello Shahab,
I would wait before trying to do some changes. Rene has started looking
more deeply into the particle structure (see
: https://github.com/dealii/dealii/pull/11314) and this will, most likely,
fix your problem.
On Friday, December 4, 2020 at 8:18:11 a.m. UTC-5
Dear Wu,
Have you tried without the dynamic cast? Can you bind the callback of a
regular triangulation?
I must admit I have never tried to use particles with regular triangulation
(and I think that outside of step-19, not much people have done it ).
On Tuesday, December 15, 2020 at 4:49:39
Hello Jose,
I hope you are well.
I was wondering if you had managed to get your code on github or any
sharing service? I would be really interested in comparing how it behaves
with monolothic FEM approaches. This is something that is very relevant to
our research (and on which I would be glad
Dear all,
I hope you are well.
It is me again pestering you all with questions or looking for advice :).
We are currently working on our DEM simulation engine using deal.II
particles features. DEM lead to very chaotic systems (with positive
Lyapunov exponents, like in MD), which means that
Hi Wolfgang,
Thank you for the suggestion. I did not think about it, but testing
statistical properties (center of mass, average velocity, total kinetic
energy) seems like a very sound idea!
If you want to see an animation of DEM done using the deal.II particle
library, you can find one on the
.
>
> Best,
>
> Bruno
>
> On Monday, January 4, 2021 at 3:31:45 PM UTC-5 blais...@gmail.com wrote:
>
>> Dear all,
>> I wish you all an happy new year!
>>
>> One problem we always end up facing with FEM problems is that, as program
>> grow, more
e executed one after each other
> per cell. This means the vtable access cost is small compared to the
> actual work.
> See
>
> https://github.com/geodynamics/aspect/blob/b9add5f53172aac18bdbb19d14ca266e88c491dd/include/aspect/simulator/assemblers/interface.h#L493-L515
>
> On
Dear all,
I would like to bring to you attention the following open tenure track
faculty position at Polyechnique Montréal:
https://www.polymtl.ca/carriere/en/offres-demploi/professor-mechanical-engineering-computational-fluid-dynamics
The position is centered around turbulent CFD in external
Dear all,
I wish you all an happy new year!
One problem we always end up facing with FEM problems is that, as program
grow, more and more features are added to the equations. This leads to
multiple variation of the same equations (for example, Navier-Stokes with
Newtonian and non-Newtonian
Dear all,
I hope you are well.
This is most likely a very simple question, but what would be a good way to
robustly set an AffineConstraint not on a face, but on a single DOF, while
making sure that it is not an hanging node. I'd like to do something
equivalent to what is done by
Thank you Wolfgang, this is exactly what I needed :)
Best
Bruno
On Tuesday, June 22, 2021 at 6:04:42 p.m. UTC-4 Wolfgang Bangerth wrote:
> On 6/22/21 3:12 PM, blais...@gmail.com wrote:
> >
> > This is most likely a very simple question, but what would be a good way
> to
I would second what the other Bruno said. I think the easiest
preconditioner to try would be an ILU preconditioner. You can play with the
fill level (start from 1 and move up from there). Make sure you set your
absolute and relative tolerance to a reasonable level though.
On Thursday, April
In addition to what Wolfgang said.
If you want to add radiation boundary condition, the first step would be to
implement a general robin condition. You can see radiation BC following
Stefan law as a non-linear Robin BCs. Once you have a non-linear heat
equation solver ready that works with
I most likely copied this mistake from the regular Cylinder and did not
think of it when I coded the subdivided cylinder.
Alex, if you feel comfortable, you could go ahead and make a PR following
Wolfgang's suggestion. Otherwise, I'll gladly look into it this week :)
Best
BRuno
On Friday, June
In addition,
Step-77 does not compile with the Sundials 3.1.0 distributed with candi.
The following error is obtained at run time in debug mode:
An error occurred in line <427> of file
in function
unsigned int
Dear all,
I hope you are well.
I am currently trying to solve an advection-diffusion equation at very,
very high Péclet number. I first implemented a GLS-stabilized continuous
Galerkin solution, it works well, but clearly I think a DG approach would
be immensely better here.
The issue is that
Good to know.
Let me read the documentation a bit and I could try to come up with a PR.
Maybe this is something we could discuss? I'd be glad to help in improving
DG methods :)
On Thursday, March 11, 2021 at 4:29:04 p.m. UTC-5 Wolfgang Bangerth wrote:
> On 3/11/21 10:14 PM, bl
tests, and
> submit the PR. Sorry. I will try to pick this up again in the next few
> days.
>
> On Fri, Mar 12, 2021 at 12:26 PM Wolfgang Bangerth
> wrote:
> >
> > On 3/11/21 11:10 PM, blais...@gmail.com wrote:
> > > Let me read the documentation a bit and I coul
Dear Michal,
We have a post-doc position available in my group regarding deal.II and
topology optimisation for conformal cooling.
Please send an email to bruno.bl...@polymtl.ca if you are interested :)!
Best
Bruno
On Saturday, April 17, 2021 at 6:44:44 p.m. UTC-4 mtwich...@gmail.com wrote:
>
This issue is now fixed by a PR merged yesterday.
Best
Bruno
On Monday, June 28, 2021 at 6:40:04 a.m. UTC-4 alexanderc...@gmail.com
wrote:
> Hi Bruno,
>
> Sure, I can try making a PR this week.
>
> Best,
> Alex
>
> On Sunday, June 27, 2021 at 9:36:50 p.m. UTC+2 blais...
Dear Truong,
My understanding is that the triangulation in deal.II works like a
quad/oct-forest.That is, the mesh that is generated or read serves as the
forest and each cell is a tree. Consequently, it is not possible to coarsen
a mesh more than it's initial configuration.
For a lot of meshes
would lead to a cleaner design.
You are right that this is already very well documented in the
GridTools::transform() documentation :). I need to learn to read the
documentation a bit more before asking :)
On Wednesday, August 4, 2021 at 10:11:03 a.m. UTC-4 Wolfgang Bangerth wrote:
> On 8/4/21 6
Peter this is what I suspected :).
Is that not a bit of an ill-defined behavior for the triangulations?
Shouldnt the manifolds also translate themselves when the triangulation is
translated?
Clearly, it is possible to reset the manifold every time the triangulation
is moved, but this becomes a
Dear Richard,
I have used valgrind's callgrind tool extensively in the past and it works
quite well.
It seems Intel VTune is free now. I have used it a lot in the last two
months to optimize our code and I have found it work very, very well. We
managed to improve some functions tremendously
Dear Pushkar,
Deal.II supports simplex meshes, you can look at the documentation :
https://www.dealii.org/current/doxygen/deal.II/group__simplex.html
Consequently, you can import a 2D triangular mesh made with GMSH, or you
can transform a quad mesh generated by deal.II into a simplex mesh.
Best
component that was deprecated in Trilinos 13.0.1
Thanks for the help! I really appreciate it.
Best
Bruno
On Friday, October 29, 2021 at 8:38:57 a.m. UTC-4 Wolfgang Bangerth wrote:
> On 10/29/21 5:10 AM, blais...@gmail.com wrote:
> >
> > Is Adelus a Trilinos component that is m
d/CMakeFiles/CMakeTmp'
gmake: *** [Makefile:121: cmTC_be568/fast] Error 2
Hopefully I find a solution from there :)!
On Thursday, October 28, 2021 at 11:20:42 p.m. UTC-4 Wolfgang Bangerth
wrote:
> On 10/28/21 8:02 PM, blais...@gmail.com wrote:
> >
> > However, whenever I run CMAKE
hitecture
> extensions are supported on the target CPU. I most often use
> "-march=native" unless I'm cross-compiling on a different CPU compared to
> where the code is eventually executed.
>
> Best,
> Martin
> On 29.10.21 12:47, blais...@gmail.com wrote:
>
>
gt;
> Possible solution from the second issue: use `-DBUILD_SHARED_LIBS:BOOL=OFF`
> or add -undefined dynamic_lookup to CMAKE_CXX_FLAGS
>
> Best,
>
> Bruno
> On Friday, October 29, 2021 at 9:41:01 AM UTC-4 Wolfgang Bangerth wrote:
>
>> On 10/29/21 7:10 AM, blais...
Dear All,
I hope you are well.
I am trying to compile deal.II on a new cluster in Canada called Narval
(named after another cute whale, we love those up north). It uses the
following versions of the core library that we need:
gcc/9.3.0
openmpi/4.0.3
trilinos/13.0.1
parmetis/4.0.3
p4est/2.2
Hi Martin,
Multiple IDEs work very well with Deal.II. As long as your IDE has good
CMAKE support, compiling deal.II with it is a joke.
Some IDEs which me and my colleagues have found work very well in the
present case:
- Jetbrains CLION (this one is not free, but for a reason I don't
understand
and how to find neighbor particles, I was
> looking for a way to access neighbor particles, something like the one that
> is used for the cell in step-68 "particle->get_surrounding_cell()".
>
> Thanks
> Hassan
>
> On Saturday, February 12, 2022 at 6:27:09 AM U
Pleasure was all mine.
Thanks for the invite.
I consider myself quite lucky to be part of such a vibrant, open and
constructive community :)!
On Friday, February 11, 2022 at 4:57:39 p.m. UTC-5 Timo Heister wrote:
> Hi all,
>
> The recording of the talk is now available at
>
:42:53 p.m. UTC-4 Wolfgang Bangerth wrote:
> On 3/14/22 11:24, blais...@gmail.com wrote:
> >
> *Users/blaisb/work/candi/trilinos-release-12-18-1/include/Tpetra_Import_def.hpp:1171:24:
>
>
> > **error: **no member named 'bind1st' in namespace 'std'; did you mean
> &
Dear all,
Hope you are well
Using the candi master branch, I succeeded in compiling deal.II using
candi. Everything was smooth. I don't know who took care of that, but
awesome work.
When trying to compile an example that uses Trilinos (any), I get the
following error that arise from an include
a.m. UTC-4 blais...@gmail.com wrote:
> Step-32 worked. I think there was an issue with the way I set-up my dylib.
> I'll investigate, but it seems that since I was able to run step-32 with
> MPI, I should be ok on my side also :)
> I'll keep you informed if this pops up again.
>
Dear all,
Are you interested in the environment and on harnessing renewable energies
in chemical processes? Do you have a keen interest in fluid dynamics and
computational fluid dynamics? Do you love using deal.II ? Are you
interested in multiphase flows?
We have a very interesting opening
Dear all,
I hope you are well?
It seems MuParser does not, by default, allow for the use of the error
function (erf). We are solving a Stefan problem right now and I'd like to
be able to compare the solution to the analytical one to make a unit test
out of it. Regrettably, the analytical
Awesome,
I'll make a PR for it.
On Wednesday, February 16, 2022 at 11:33:58 p.m. UTC-5 Wolfgang Bangerth
wrote:
> On 2/16/22 20:16, blais...@gmail.com wrote:
> >
> > It seems MuParser does not, by default, allow for the use of the error
> > function (erf). We are sol
.
>
> Thanks,
> Hassan
>
> On Sunday, February 13, 2022 at 6:21:42 PM UTC+3:30 blais...@gmail.com
> wrote:
>
>> Dear Hassan,
>> There is no way to do that directly in Deal.II
>> Lethe adds two classes to achieve this using a coarse and then a fine
>> contact d
If I may suggest, at that point, I would ask you what you are trying to
specifically achieve?
If you want to build an SPH code from scratch, this is definitely possible
to do using deal.II particle classes (esp. with the exchange and update
ghosts functionalities), but this will require a lot
You had me scared there for a moment.
Looking forward to this :)!
On Friday, March 25, 2022 at 1:15:31 p.m. UTC-4 Timo Heister wrote:
> Hi all,
>
> I am sorry for messing up the title. The talk is of course given on
> Monday by Matthias as written in the body of the email.
>
> Best,
> Timo
>
>
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,
It seems your deal.II was configured without UMFPACK.
Can you give us more information about which operating system you are using
and under which conditions you are installing the library? This would
greatly help us helping you debug.
Most likely you will need to reinstall deal.II with UMFPACK
Dear all,
I hope you are well.
We have three fully-funded PhD positions open in my group that we are
aiming to fill for the Summer 2024 or Fall 2025 semester. They all concern
the computer-assisted design of sustainable chemical reactors. This
concerns reactors which use alternative energy
Dear all,
I hope you are well.
I was wondering if there was anything specific that had to be done to
enable deal.II to leverage AVX and AVX512 instructions on intel processors?
By default, it seems that on my intel machine, these vectorization
instructions are not detected, e.g.:
-- Performing
Changing to Fe1 really alters the solution, so consequently the kelly error
estimator will also give you a different error estimation and thus a
different mesh adaptation.
If your mesh adaptation is based on an error estimator, altering the finite
element interpolation order will alter the
If you need any help, feel free to reach out to the deal.II community, we
are always glad to help
On Sunday, November 5, 2023 at 10:37:42 a.m. UTC-5 M. Bakry wrote:
> Dear Wolfgang,
>
> thanks very much for your answer. I think I will give it a try when I
> find some time. Non-C1 manifolds
Thank you very much for pointing this reference out.
It is highly helpful and I think the community really appreciate you making
all these efforts to not only move science forward, but teach it in a
better fashion :)
On Thursday, August 4, 2022 at 9:47:36 p.m. UTC-4 Wolfgang Bangerth wrote:
>
Dear all, I hope you are all doing fine :)!
I am trying to do some quick testing of something and this would require me
applying a zero constraint to a set of cells which have a specific material
id. I could surely do that from the weak form, but I was wondering if there
was a way to do it
relevant) dofs to the AffineConstraints object with add_line().
>
> Best,
> Daniel
>
> On Mon, Oct 31, 2022 at 8:36 AM blais...@gmail.com
> wrote:
>
>> Dear all, I hope you are all doing fine :)!
>>
>> I am trying to do some quick testing of something an
There might be many things that can be done to improve the speed of this
function. You can ask yourselve the following question as guidance:
- Does the function allocate memory?
- Could it be inlined?
- Are you calling the function inside the DOF loops or inside the
quadrature loop?
Then I
I am a bit surprised that your assembly is really 100x more expensive than
your linear solver.
Maybe your assembly code is not optimized?
For example, I try to avoid doing as much work as possible during the
double loop over DOFs which is the inner most loop. Sometimes
pre-calculating things
Dear all,
I hope you are well.
I know that P4est as a partitioner has limitations compared to other
approaches like Metis or Scotch. However, I was wondering if there was
anyway to penalize the partitioner in order to generate the smaller valence
that is possible? Sometimes we end up with
Can you tell us a bit more about what you have tried? For example, in the
limit of low Re (say Re=0.1 or Re=1) does your non-linear solver converge?
Have you tried making a manufactured solution to get your convergence order
to see if everything is all fine?
RE=200 can be quite heavy for
Dear Kumar,
You can monitor the processes using your OS to verify that.
If you are loading a relatively large triangulation, this will be very
apparent since the memory footprint of one process will be significantly
larger. Even a quick "top" will enable you to see this.
Best
Bruno
On
What I would suggest is to not use GCC, but instead use the clang compiler
native with the Mac M1.
At least this is how I did it on my apple M1 macbook pro computer
On Thursday, April 6, 2023 at 6:25:13 a.m. UTC-4 malve...@gmail.com wrote:
> Good afternoon.
> I’m truly sorry to bother you, but
It is maybe unrelated, but as far as I remember, OpenFOAM supports mesh
adaptivity. It is maybe not as efficient (and does not include dynamic load
balancing) like deal.II does, but I would first start with that.
Otherwise, you would need to go through the VTK file format or write your
own
In addition to Wolfgang's answer. Here are some suggestions.
1. You system is not symmetric. Consequently, it is not a viable idea to
use the CG linear solver
(see https://en.wikipedia.org/wiki/Conjugate_gradient_method). As
suggested, using something like GMRES would be a better idea for your
Dear Vinayak,
The particle class is very flexible. You can see it as a Lagrangian
container of information for whatever you may need to store information
for. I don't foresee any challenges with your approach except if you need
to maintain some sort of connectivity between the particles. If you
> else
>>> cell(i,j) += viscosity_constant *
>>>
>>> and improved the performance by making two separate assemblers (note
>>> that there is no function call/vtable lookup here, just an "if"). I
>>> don't remember how big the difference was, so I went ba
Dear Lance,
It would be easier if you posted the PDE you wish to solve and it's weak
form. This would enable us to help you write the Jacobian for it.
Currently, it is difficult to fully understand what you are trying to
achieve.
Best
Bruno
On Monday, July 24, 2023 at 4:13:21 p.m. UTC-4
+1 Paul, god is this script fun
On Thursday, August 10, 2023 at 7:18:48 p.m. UTC-4 Paul A. Patience wrote:
> Hello everyone,
>
> Last year I wrote a script to indent PRM files [1] in the Lethe project
> [2]. You may find it useful.
>
> It can be used to recursively indent all PRM files in
n clusters to be sure the right code gets generated. For example GCC
> lists the available architectures to specify here:
>
> https://gcc.gnu.org/onlinedocs/gcc/x86-Options.html
>
> Best,
> Martin
>
>
> On 04.05.23 14:52, blais...@gmail.com wrote:
>
> Dear all,
Dear all,
Hope you are well.
I have tried a few ways to enable AVX instructions (which I think my 12th
Gen Intel(R) Core(TM) i9-12900K) should support, yet I am always unable to
do so. At the Cmake configuration step, the AVX steps all fails whereas the
SSE ones succeed.
How can I remedy this
In addition to what Wolfgang wrote,
Sometimes the OS will map the cores of a CPU in the following order:
Physical-Logical-Physical-Logical-Physical-Logical etc.
Consequently, if your processor supports hyperthreading through the use of
logical core, running with core 0-1 means you are essentially
Dear David,
The Digital Alliance of Canada (Compute Canada) has deal.II on their
cluster through the use of the module system:
https://docs.alliancecan.ca/wiki/Available_software
You could reach out to them and ask them for their module file. They are
generallly very chill.
If you need help
Dear Jack,
Interesting you took a look at this. I was always wondering why lethe takes
forever to start on my ARM M1 Mac compared to on a regular Linux desktop.
Seems you figured it out...
However, I am unsure of the solution for this.
Orthogonally to this, have you ever managed to have cmake
Dear Yufei,
We need more information
What is not working? Is it compiling? Are the results different? In how are
they different?
Could you please state the entire weak formulation of your problem and the
implementation of said weak formulation (e.g. a code snipper of just the
assembler).
On
Glad you found the issue :)
Subtles things often make differences which are hard to capture!
On Tuesday, May 7, 2024 at 10:33:58 a.m. UTC-4 Sean Carney wrote:
> Update -- the question had an obvious answer!
>
> The reason for the discrepancy was simply the order of quadrature used.
> =D
>
>
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