Ubuntu 16.04 is a very outdated (and unsupported) system. What compiler
version of GCC are you using? (gcc -v)
-- https://www.math.clemson.edu/~heister/
On Tue, May 28, 2024, 09:07 王艺康 wrote:
> Hello, everyone.
> I'm having a problem installing dealii with candi.I'm installing
> dealii-9.5.1
If you use an FESystem, you typically don't need the evaluation done over
all components. Instead, use an FEValuesExtractor and you should have
everything available:
https://www.dealii.org/current/doxygen/deal.II/classFEInterfaceViews_1_1Vector.html
I'd anything is wrong or missing, please open an
in Bergen.
For further information please visit website:
https://pdesoft.org/
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You received
is a SparseMatrix.
Same for the vector. This way, there are no different code paths, different
types, or copies involved.
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From: dealii@googlegroups.com on behalf of Wolfgang
Bangerth
Sent: Monday, December
Bundled TBB compiles just fine in CI on my M1:
https://ci.tjhei.info/job/dealii-osx/job/master/lastSuccessfulBuild/
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Timo Heister
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From: dealii@googlegroups.com on behalf of Matthias
Maier
Sent: Friday, December 1, 2023 3
What compilers are you using? Are you aware of the guide at
https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX ?
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Timo Heister
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From: dealii@googlegroups.com on behalf of Jai
Sent: Friday, December 1, 2023
/dc8e8d348533072bc189f5b52e6e9cd63956a22e/deal.II-toolchain/packages/dealii.package#L355
Rene Gassmoeller has built TACC docker/singularity containers of deal.II and
ASPECT to run on supercomputers, so you can ask him about that option.
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Timo Heister
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Hi Alberto,
Thanks for reporting. I apologize for messing up the server configuration. I
will fix this today or tomorrow.
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From: dealii@googlegroups.com on behalf of Alberto
Salvadori
Sent: Monday
).
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Timo Heister
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From: dealii@googlegroups.com on behalf of Lex Lee
Sent: Wednesday, September 27, 2023 8:15:14 PM
To: deal.II User Group
Subject: [deal.II] Difference between 2 Wasy to Initialize System Matrix in MPI
World
ASPECT. Also, feel free to get in touch if you have
any questions.
Best,
Timo
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com.
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For mailing list/forum option
call, and I'm once again
> recovering the correct residual in the global refinement and adaptive
> refinement cases; no unexpected behavior there.
>
> Thank you,
> Corbin
>
> On Friday, April 7, 2023 at 2:49:48 PM UTC-4 Timo Heister wrote:
>
>> > to my eye, in both cases,
ooglegroups.com.
>
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> em
Corbin,
Do you know if this problem is only present in 1d?
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On Mon, Apr 3, 2023, 18:36 Corbin Foucart wrote:
> Hello everyone, I'm solving a 1D explicit DG-FEM problem and I've
> encountered behavior that I don't understand using MeshWorker: :
It should be as simple as doing
constraints.add_line(y);
Unless you are writing an MPI parallel program. Then you would need to
check if this line can be stored first.
-- https://www.math.clemson.edu/~heister/
On Sun, Mar 12, 2023, 09:17 Wasim Niyaz Munshi ce21d400 <
ce21d...@smail.iitm.ac.in>
m it, send an
> email to dealii+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
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> --
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*
> [packages/stratimikos/adapters/belos/src/CMakeFiles/stratimikosbelos.dir/all]
> Error 2
>
> make: *** [all] Error 2
>
> Failure with exit status: 2
>
> Exit message: There was a problem building trilinos 13-2-0.
>
>
>
>
> Can anyone provide me some way t
;>
>> I do not need hdf5.
>> At least I was not aware that I had it on my old computer.
>>
>> Is there a way to work around the issue?
>>
>> Best
>> Simon
>>
>>
>> Timo Heister schrieb am Di., 3. Jan. 2023, 20:19:
>>>
>>&g
ot;deal.II User Group" group.
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fense.com/v3/__https://groups.google.com/d/msgid/dealii/c1d413d2-3c55-0523-19fd-9f399d1781da*40colostate.edu__;JQ!!PTd7Sdtyuw!Vf-IQx7HQQ5bIq8xBQu1BzCdpZiz9Q3UC6emGlg1Z50xBT-oA9UeUBtyamyADtrTV0zLEZpa0RBQ_lV6CppyxvM$
> .
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nd an
> email to dealii+unsubscr...@googlegroups.com.
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The deal.II project is located a
o this question in the mailing list or the
> documentation. I would like to avoid the workaround suggested here, because I
> need a new copy of the triangulation multiple times during computation.
>
> Thanks,
> Katharina
>
> On Tuesday, September 22, 2015 at 2:00:39
y?
>
> Thank you very much.
>
> Best regards,
>
> Judy
>
> On Wednesday, September 7, 2022 at 1:40:39 PM UTC-4 Timo Heister wrote:
>>
>> You will need to configure deal.II with HDF5 support, see
>> https://www.dealii.org/developer/readme.html#optional-softw
/
> For mailing list/forum options, see
> https://groups.google.com/d/forum/dealii?hl=en
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> check if a cell is locally owned) and call it right after the mesh is read
> in. Is this enough to ensure that the boundary IDs are set properly, or is
> it safer to use `triangulation_.signals.any_change.connect()`?
>
> Best regards,
> Maurice
>
> Timo Heister schrieb am Freita
Maurice,
Reassigning boundary IDs (or manifold IDs, material IDs) is somewhat tricky
in parallel as they need to stay consistent.
While you would expect the IDs to only matter for locally owned cells, this
is not enough because each process needs to know the correct constraints
for all "locally
-
> Wolfgang Bangerth email: bange...@colostate.edu
> www:
> https://urldefense.com/v3/__http://www.math.colostate.edu/*bangerth/__;fg!!PTd7Sdtyuw!QO7eTW5kBhW7q3_5N54yZsv-uBFuFmPb-34csveLecKNqiHWY-Dvroos6-RjWwuJhwHp3T_urOO
s discussion on the web visit
> https://groups.google.com/d/msgid/dealii/eed5b3fb-2052-44a3-8840-1be2f1484c7a%40Spark.
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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
>
>
ASPECT.
Best,
Timo
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t value (for example
non-homogeneous Dirichlet conditions.
Best,
Timo
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> ht
Hi all,
I am still looking to hire a postdoc and just extended the application
deadline. Please forward this opening to people who might be
interested.
Thanks.
On Tue, Mar 22, 2022 at 10:30 PM Timo Heister wrote:
>
> Hi all,
>
> I am hiring a postdoc to work on the Finite El
brew install cmake open-mpi gcc
>>>>
>>>> Then I install the master version, this time the setup was completed;
>>>> however, when I tried to run step-1 example, this happened:
>>>> [image: Screenshot 2022-03-18 at 12.30.12.png]
>>>
Hi all,
I can not share a recording at this point, sorry.
On Fri, Apr 1, 2022 at 11:48 PM Praveen C wrote:
>
> Is the video of this talk archived somewhere ?
> Thanks
> praveen
>
> On Friday, March 25, 2022 at 10:42:11 PM UTC+5:30 Timo Heister wrote:
>>
>> Hi all,
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
On Fri, Mar 25, 2022 at 1:11 PM Timo Heister wrote:
>
> Hi all,
>
> I would like to announce the following seminar talk in our Clemson
>
instruction
multiple data) vectorization.
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Best,
Timo Heister
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; Dear Timo,
>
> thank you for your answer. Is there any other option for ILU with parallel
> matrices apart of Block Jacobi?
>
> Thank you
> Regards
>
> El martes, 15 de marzo de 2022 a las 18:45:29 UTC+1, Timo Heister escribió:
>>
>> Hi,
>>
>> >
can use -j to use more cores of course).
On Wed, Mar 16, 2022 at 9:42 AM Masoud Ahmadi wrote:
>
> I had removed candi, so I had to reinstall it.
> But again got the same error.
> The requested log file is attached. Please see.
>
>
>
> On Tuesday, 15 March 2022 at 13:0
the original error code is 92.
>
>
>
>
> Thank you very much
>
> Regards,
>
> H
>
> --
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> ---
> You received
ote:
>>
>> 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.
>>
&g
> I attached the log file, please take a look.
>
>
> On Sunday, 13 March 2022 at 19:55:52 UTC Timo Heister wrote:
>
>> What candi git branch are you on? You might need to switch to master to
>> make things work for now.
>>
>> Can you post how you execute
I worked on that.
Interestingly, I didn't see this error in my testing of ASPECT. Are
you saying that a deal.II step like step-32 fails? I think we should
try updating Trilinos first.
Do you want to try 13.2 and see if that works? If not, I will update
the package in candi master when I get to
ctly what is explained in the
> following link, step by step:
> https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX
>
> On Saturday, 12 March 2022 at 16:54:56 UTC Timo Heister wrote:
>
>> Did you make any changes to candi.cfg? Can you also please post how you
>&
fining the mathematical constants (specifically M_PI, M_PI_4, and
>>>> M_SQRT2) in each script that used one (a partial list was added to the
>>>> github issue for this).
>>>>
>>>> Since the install worked I didn't try the older version.
>>>>
>>>>
are subscribed to the Google Groups
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Hi Lorenzo,
I didn't look at your code, but I can help with this:
> however i am not sure how to extract PETSc Vec object from
> PETScWrappers::MPI::Vector without passing from a PETScWrapper::VectorBase.
You should be able to use the conversion operator
e library!
>
> Please ensure that a suitable symengine library is installed on your computer.
>
> I turned off symengine in the candi.cfg file and deleted the installation
> library so I'm not sure what else to do.
>
> Thanks,
> Stephanie
> On Tuesday, February 15,
t keep the
> previous written information?
>
> Thank you
>
> El martes, 15 de febrero de 2022 a las 19:43:02 UTC+1, Timo Heister
> escribió:
>
>> The call to data_out.add_data_vector() does not copy the contents of the
>> vector but it just keeps track of it until the da
symengine and then when attempting
> to install deal.ii I got an error that symengine library could not be
> found. Is there a way to configure it such that symengine is not necessary
> for deal.ii?
>
> Thanks,
> Stephanie
>
> On Tuesday, February 8, 2022 at 8:05:01 AM UTC-7 Timo Heist
The call to data_out.add_data_vector() does not copy the contents of the
vector but it just keeps track of it until the data is actually written.
You will need to store your solutions in different vectors without touching
the old ones.
On Tue, Feb 15, 2022, 11:05 Uclus Heis wrote:
> Good
Hi all,
The recording of the talk is now available at
https://www.youtube.com/watch?v=-qJfml3_HuA
Thanks again, Bruno!
On Mon, Jan 31, 2022 at 2:56 PM Timo Heister wrote:
>
> Hi all,
>
> I would like to announce the following seminar talk in our Clemson
> Computation
ups.google.com/d/msgid/dealii/db91c18b-7e9b-4aa0-9a81-3e93e1f3df2an%40googlegroups.com.
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You re
> *L_operator(local_dof_indices[i],local_dof_indices[j]) =
cell_matrix(i,j);*
*This looks incorrect, because global pairs of indices will happen more
than once in a normal assembly (with a continuous finite element). You have
to add the contribution using +=.*
On Tue, Feb 8, 2022, 16:52 Hermes
Stephanie,
I think you likely don't need some fine, am i right? Just comment out the
line for it in the candi.cfg and rerun the setup (you might need to delete
the tmp directory).
On Tue, Feb 8, 2022, 10:01 Raghunandan Pratoori wrote:
> Hi Stephanie,
>
> I use a singularity container with
lessons that have been learned through this
endeavor to develop a
CFD/DEM/CFD-DEM software.
Best,
Timo
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Hi all,
I finally got around cutting and uploading the workshop recordings.
The first half is now available on youtube, see
https://dealii.org/workshop-2021/ for the links.
Best,
Timo
On Wed, Jun 16, 2021 at 10:50 AM Timo Heister wrote:
>
> Hi all,
>
> This is a quick reminder that
; To unsubscribe from this group and stop receiving emails from it, send an
> >> email to dealii+unsubscr...@googlegroups.com.
> >> To view this discussion on the web visit
> >> https://groups.google.com/d/msgid/dealii/368cf5ae-ac31-4883-91f2-8ef1b794a684n%40googlegroups.
FunctionParser uses a finite difference approximation for the gradient. I
think this is explained in the class documentation.
This explains the results you see...
On Sun, Aug 8, 2021, 15:15 Marco Feder wrote:
> Ciao Luca!
>
> > Can you check if you get the same results with this order?
> Yes,
; step into a function. I have to set a lot of breakpoints to stop the
> program at these lines.
>
> On Aug 5, 2021, at 6:16 PM, Timo Heister wrote:
>
>
> What do you mean by "cannot do step debug"? Are you compiling in debug
> mode?
>
> On Thu, Aug 5
bution_one_cell. *Am I doing something wrong?
>
>
>
>
>
>
>
> *From: *Timo Heister
> *Sent: *Thursday, August 5, 2021 1:19 PM
> *To: *dealii@googlegroups.com
> *Subject: *Re: [deal.II] Debug multithread code
>
>
>
> Take a look at s
Hi all,
We recently released version 2.3.0 of ASPECT, the Advanced Solver for
Problems in Earth's ConvecTion, which is built on deal.II.
See https://aspect.geodynamics.org/ and
https://github.com/geodynamics/aspect/releases/tag/v2.3.0 for more
information about ASPECT.
Best,
Timo
--
Timo
Take a look at set_thread_limit:
https://www.dealii.org/current/doxygen/deal.II/classMultithreadInfo.html
As you can see, you can also control it using an environment variable, so
you don't have to recompile.
On Thu, Aug 5, 2021, 13:36 Michael Lee wrote:
> Hi,
>
> I find it's difficult to debug
at 11:35 AM Timo Heister wrote:
>
> Hi all,
>
> We would like to announce a one-day deal.II workshop on June 18, 2021
> with several talks about recent developments in the library, the 9.3
> release, and interesting user projects. The talks will be available
> live using zoom and
e last workshop?
>
> Regards,
> David
> On Wednesday, 2 June 2021 at 17:36:08 UTC+2 Timo Heister wrote:
>>
>> Hi all,
>>
>> We would like to announce a one-day deal.II workshop on June 18, 2021
>> with several talks about recent developments in the library, the
including a schedule, please see:
https://dealii.org/workshop-2021/
Information on how to join will be made available closer to the date.
We hope to see you there!
Best,
Timo and the deal.II developers
--
Timo Heister
http://www.math.clemson.edu/~heister/
--
The deal.II project is located
on the web visit
>> https://groups.google.com/d/msgid/dealii/22813e93-5959-4244-aa45-1652d3e8c7b8n%40googlegroups.com.
>
> --
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e the output is written to, to a xfs solved the
> problem. Sorry for the inconvinience, but we are quite new to cluster systems.
>
> Thanks,
> Christian
>
> Timo Heister schrieb am Montag, 12. April 2021 um 18:37:32 UTC+2:
>>
>> Christian,
>>
>> What kind of fil
receiving emails from it, send an
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roup.
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htt
One thing that might not be obvious is that it is not enough to have a
manifold id for boundary faces. You need to assign a manifold to the cells
as well.
On Wednesday, January 20, 2021 at 11:49:59 AM UTC-5 luca@gmail.com
wrote:
> Did you call
>
> data_out.build_patches(mapping,
>
ic you are
using in the assembly, where you identify DoF indices (you called them
local_interface_dof_indices) and you add them using
dsp.add(i,j)
where i and j are all indices in local_interface_dof_indices.
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g emails from it, send an
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--
The deal.II projec
t makes a lot of sense.
> Thanks!
> Bruno
>
> On Tuesday, January 5, 2021 at 4:34:19 p.m. UTC-5 Timo Heister wrote:
>>
>> Hi Bruno,
>>
>> We mitigate the performance problem by making the decision per cell in
>> ASPECT:
>> We have a set of "assemblers
ssembly function? I would be very interested in hearing the perspective of
>>> the ASPECT author since it has such a large range of sub models.
>>>
>>>
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>
way. See
https://github.com/dealii/dealii/wiki/Getting-deal.II for some
guidance.
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Timo Heister
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You received this
org/download.html ? I think we fixed this issue a
while ago.
If this is the case, what kind of processor/mac do you have?
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ng emails from it, send an
> email to dealii+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/dealii/a4df4788-b1c4-44e6-97c1-b06b6912554dn%40googlegroups.com.
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Timo Heister
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The d
EInterfaceValues like
feiv.get_fe_face_values(0).get_function_values(...)
feiv.get_fe_face_values(1).get_function_values(...)
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oper of deal.II, I think you
might find it to be an interesting read.
Thank you for being part of this great community and happy holidays.
Best,
Timo (and co-authors)
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For mailing
EInterfaceValues directly on a small test mesh.
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of cost
independent of h and other problem parameters) without exploiting
PDE-specifics.
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You
you just applying ILU to the whole system? My general advice is to
exploit the block structure of your PDE first and then apply ILU or
AMG to individual blocks. Time dependent Navier-Stokes with small time
steps is a relatively easy case. Let me know if you want more details.
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Timo Heister
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u specify the location of your deal.II library.
> Also, I will be sure to put a pull request if it works.
Awesome! Let us know if you need help at any point.
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eceived this message because you are subscribed to the Google Groups
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> make[3]: *** No rule to make target '/usr/lib64/libopenblas.so', needed by
> 'step-1'. Stop.
That means this library is missing on the compute node.
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For mailing list/forum opt
1.6GB. Do you know what the above error signifies? Thank you.
>
> Best,
> Aaditya
>
>
>
> On Sunday, October 25, 2020 at 2:10:21 PM UTC-4 Timo Heister wrote:
>>
>> > Seems like there might then be some issue with the LAPACK, P4EST or PETSC
>> > install
cognized: file truncated
This sounds like the linking of the .so file failed. Can you take a
look at this file (check the size?)? You can try deleting the file and
running "make install" again. Maybe the last linker step failed?
If this does not help, maybe try the release mode examples
maybe something higher order depending on your
scheme).
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You received this message because
Running the tests seems to have triggered a rebuild of deal.iII. Can you
try running some of the tutorial steps instead?
On Fri, Oct 23, 2020, 17:05 Aaditya Lakshmanan
wrote:
> Hi Wolfgang,
>I tried compiling, installing and running the deal.ii tests
> interactively on a KNL compute node.
> On another note, I remember having a discussion about this with Timo Heister
> at the deal.II workshop in 2019. Maybe Timo has ideas on this? I know he is
> quite the expert on algorithms to solve the Stokes / Navier-Stokes equations
> (e.g. his paper on the grad-div scheme, etc.)
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