> 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.)
ll get
> the same error.
>
> To be honest, I am not shure how to tackle either apporach.
>
> Thank you very much.
>
> Best regards,
> Gregor
>
>
>
>
>
>
>
>
> Timo Heister schrieb am Samstag, 26. September 2020 um 21:44:05 UTC+2:
>>
>> H
allel file system)
Best,
Timo
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what the assertion checks. I
think that this check is correct. If you want your first block to be
1815 DoFs large, then rows[0].size() needs to be 1815.
How are you creating these IndexSets? I find the function
IndexSet::split_by_block() convenient to use.
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Hi,
I don't quite understand your reasoning for a block with 0 DoFs. Try
removing any rows/columns from your block sparsity pattern and from your
IndexSet's that have size 0. Notice that the number of blocks is
independent of the number of components in your FEM.
Can you post the values for ro
free
multigrid and how far we can scale computations these days.
A recording is now available here:
https://www.youtube.com/watch?v=K2xjCsXnfYI
I hope this is useful for some of you.
Best,
Timo
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You are running out of RAM while compiling. Try compiling without -j if
necessary.
On Sun, Sep 13, 2020, 01:38 Animesh Rastogi IIT Gandhinagar <
animesh.rast...@alumni.iitgn.ac.in> wrote:
>
> Dear Dealii community,
>
> I am reinstalling dealii using candi on my PC. Here is the error, I am
> getti
Take a look at this repository:
https://github.com/dealii/code-gallery
All files should be in there.
On Thursday, September 10, 2020 at 2:08:50 PM UTC-4
animesh...@alumni.iitgn.ac.in wrote:
> Dear All,
>
> I can not access the Readme, parameters and other files from the code
> gallery program
ealii.org/
> For mailing list/forum options, see
> https://groups.google.com/d/forum/dealii?hl=en
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s, the
>>> person(https://github.com/JBlaschke) helping me out asked me to contact the
>>> developers. I would really appreciate your help on this.
>>>
>>> Thank you.
>>>
>>>
>>>
>>>
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II User Group" group.
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automatic
> differentiation tools that
> we have, or to easily write a posteriori error estimators… If anybody is
> looking for a starter project, this may be a very nice one.
Yes, also on my todo list for "some day". :-)
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d 217 billion unknowns (see https://arxiv.org/abs/1907.06696 for
details). See https://aspect.geodynamics.org/ and
https://github.com/geodynamics/aspect/releases/tag/v2.2.0 for more
information about ASPECT.
Best,
Timo
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Hi all,
the videos and slides are now available at https://dealii.org/workshop-2020/
On Monday, May 25, 2020 at 3:53:24 PM UTC-4, Timo Heister wrote:
>
> Hi all,
>
> the information on how to join is now available at
> https://dealii.org/workshop-2020/
>
> Please join
Hi all,
the information on how to join is now available at
https://dealii.org/workshop-2020/
Please join us tomorrow!
Best,
Timo
On Tuesday, May 19, 2020 at 8:40:31 PM UTC-4, Timo Heister wrote:
>
> Hi all,
>
> we would like to announce a one day-deal.II workshop on May 2
Great, can I convince you to send in a pull request with your changes to
deal.II? That would be very much appreciated.
Let us know if you need help with that.
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Hi Julian,
you will need to extend MGTransferPrebuilt::prolongate with support for
user constraints:
https://github.com/dealii/dealii/blob/70455cc1efde9ad0d5ca4295ea5597fc2fa98171/source/multigrid/mg_transfer_prebuilt.cc#L93
This might be as simple as a call to
get_user_constraint_matrix(...).
/workshop-2020/
Best,
Timo and Wolfgang
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Malik,
There is three different directories at play:
1. build directory (this is where you run cmake in)
2. the source directory (this is the deal.II download and contains
CMakeLists.txt and source/ include/, etc.)
3. the install directory
All three directories can be anything you want. For examp
early as January.
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ictor Eijkhout wrote:
>
>
>
> On Oct 5, 2019, at 4:13 PM, Timo Heister wrote:
>
> -D DEAL_II_WITH_MPI=ON \
> -D DEAL_II_CXX_FLAGS="-march=native" \
> -D DEAL_II_WITH_CXX17=OFF \
> -D DEAL_II_WITH_64BIT_INDICES=ON \
> -D DEAL_II_COMPONENT_EXAM
is is with Intel 19.0.5 and intel MPI. You can also run without
64bit indices, but I need it to be able to do large runs with more
than 4 billion DoFs.
On Sat, Oct 5, 2019 at 11:10 AM Victor Eijkhout
wrote:
>
>
>
> On Oct 5, 2019, at 9:27 AM, Timo Heister wrote:
>
> Otherwise I ha
sion on the web visit
> https://groups.google.com/d/msgid/dealii/CAOYDWbJdQ8%2BEbCREUCJ8VXgCoZP3qYatkvg%3DQ%2BT5PU%3DufwYufg%40mail.gmail.com.
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https://grou
r earlier, but that time I forgot the final
> compress()-call before calling set_zero().
>
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JxW(q)
There are a few exceptions like get_function_values() that depend on
the quadrature weights, but if you only want to do assembly, this hack
should work.
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f you
struggle with this, you should probably go back and work through the
first tutorials.
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You r
for (unsigned int d=0; d hessian_phi_v =
fe.shape_hessian_component(i, k, d);
Mii += dx *
(hessian_phi_v.trace * hessian_phi_v.trace);
You are missing curly braces: the way you wrote it, the Mii assignment
is not done inside the loop.
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in the zero constraints.
I don't understand. You need boundary conditions in
nonzero_constraints and zero_constraints for all boundaries. The
reason for these two sets is that one is used for the initial solve,
while the second one is used for the Newton updates.
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but I
remember writing a debug function that checks if a ConstraintMatrix is
consistent in parallel. This was a while back, but I can try to find
it.
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put, the values are not
> associated with the right dof.
well, how do you obtain that vector and where is the data coming from?
You probably want to use something like VectorTools::interpolate() to
get a finite element vector of whatever function you have. This you
can then send to DataOut.
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> If I use your user element, I have to use OPEN MPI? now I have some issues
> with Open MPI in Deal.ii
What do you mean by "user element"? The example code in question
requires deal.II to be configured with MPI. What vendor you use
(OpenMPI, MPICH, ...) is up to you.
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equal to 1 and so ignoring
them is easier.
2. One could also zero out the constrained rows after the fact.
3. Did we rip out the support for removing the constrained entries
from the matrix completely?
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>> Then you have to simplify your problem as much as possible until we
>> can reproduce it.
>
> I am not sure of the best way to do it, as a have a rather large program and
> I need it to build the system matrix. In your experience, saving the
> matrices
> to files and then just load them would be
> Do you know how this version of NetCDF was installed? Do you need it? If
> not, can you uninstall it?
or do
cmake -D DEAL_II_WITH_NETCDF=OFF
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ble residual
> in the similar way the matrix and rhs is assembled in step 40.
You assemble it like a RHS and then set constrained entries to zero.
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f course. That is the whole point of AL. Without it, the mass matrix
is only a good approximation if the viscosity term is dominant (small
Re).
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> However I still do not understand what that line in the documentation means.
> Maybe it is a leftover?
Yes it probably is. Thanks for pointing that out. I just submitted a
fix here:
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dealii_dealii_pull_5453&d=DwIBaQ&c=Ngd-ta5yRYsqeU
> I'm using clang+gfortran. I have not tried using gcc for everything, but I
> could give it a shot if you think it would be worth it.
No, I was just curious. I don't have a strong preference for either.
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thanks, Wolfgang.
>> 1. How can I translate between generalized_support_point j and
>> dof_per_cell index k? For example FE_DGRaviartThomas<2>(1) has 9
>> generalized_support_points but 12 dofs_per_cell.
>
> You can't. There is no obvious relationship between the two for
> *generalized* support po
rmation I can extract from the FE about the degrees of
freedom or support points in this case?
Thanks.
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ning into, I doubt that this
is the case here.
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tion be varying throughout the course of the
> simulation)?
I would probably reply with "not very easy" but I let others with more
experience jump in.
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;
>>
>>
>> ___
>> Aspect-devel mailing list
>> aspect-de...@geodynamics.org
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5o
od performance especially if your problem is not
Laplace-like.
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> I tried
> to use the same trick as in step-22, where an InnerPreconditioner was
> defined to switch between SparseDirectUMFPACK in 2D and SparseILU in 3D.
> However I found that SparseILU won't work even when in small 2D cases. To
> verify this I tried to replace the SparseDirectUMFPACK in step-5
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emonstrate how to do this.
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Timo Heister
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> What do you mean "manually"? I downloaded .deb from ubuntu and installed
> through ubuntu software manage system. do you mean that I should command
> line to get the package and to install?
Yes, you should use the official ubuntu/debian package manager if at
all possible. You can use "apt" or "
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> Thanks for your reply. I did install mpich_3.2-7_amd64.deb before.
Why do you install a .deb manually? This is likely the reason for your problems.
You also didn't answer my question, do you have more than one MPI
package installed? Please check "dpkg -l | grep mpi" and make sure you
don't have
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> But do I need to call it again after calling .set_zero()?
No. It falls under "all other operations".
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Timo Heister
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On Tue, Oct 10, 2017 at 3:49 PM, 'Maxi Miller' via deal.II User Group
wrote:
> I am coming out of a loop where I am doing
> hanging_node_constraints.distribute_local_to_global(cell_residual,
> local_dof_indices, local_residual);
Do you compress() your vectors (and matrices) after this? It needs t
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> Isn't the 'distribute'-line doing exactly that? Or is that a mistake?
No, set_zero() will set the entries to zero, distribute() will set
them to their correct nonzero entry.
Also, how small are the errors that you are getting when it levels off?
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> I can try to submit to the queue, rather then just using the head node. Do
> you think this might help?
Yes, that is typically a good way to behave on a shared resource.
Maybe long/big running processes are killed on the login node on this
machine.
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> My question: Does it matter if I use centos7.platform instead
> of the linux_cluster.platform?
If it works for you, then all is well of course. You should check the
deal.II installation by doing something like:
cd tmp/build/deal*/
make test
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Timo Heister
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> Now my question. Does deal.ii allow to consider Qn x Qn as an "inner"
> vector-valued FE space and inject this as replacement for RTn, thereby
> ending up in blocks (n_u, n_u), (n_u, n_p), and (n_p, n_u) and use Qn-1 as
> replacement for DG ending up in blocks (n_u, n_p), (n_p, n_u), and (n_p,
>
ectMUMPS::solve(const
> dealii::PETScWrappers::MatrixBase&, dealii::PETScWrappers::VectorBase&,
> const dealii::PETScWrappers::VectorBase&)
I assume that you either did not set the MPI communicator in the mumps
object or you set it to something invalid.
On Mon, Sep 25, 2017
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Timo Heister
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Oh, even easier would be creating a 2d cylinder and then using
GridGenerator::extrude_triangulation()
On Tue, Sep 19, 2017 at 1:47 PM, Timo Heister wrote:
> If you are just interested in a cylinder with more than a single
> layer, it might be easier to make k copies of the cylinder, shift
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> template
> void Pa_Preconditioner::
> vmult(LA::MPI::BlockVector &dst, const LA::MPI::BlockVector &src) const
> {
> SolverControl cn;
> PetScWrappers::SparseDirectMUMPS solver(cn,mpi_communicator);
> solver.set_symmetric_mode(true);
> solver.solve(B,dst.block(0),src.block(0));
> solver.solve(B,ds
PS type;
You have to use PETScWrappers::SparseDirectMUMPS here
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Timo Heister
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set breakpoint pending auto
> [linux-lb8c:17949] 1 more process has sent help message help-mpi-api.txt /
> mpi-abort
> [linux-lb8c:17949] Set MCA parameter "orte_base_help_aggregate" to 0 to see
> all help / error messages
>
> at the same line (.distribute())
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same units, etc.). Otherwise you might need to rescale and/or do
something more clever. We discuss some strategies in the paper
High Accuracy Mantle Convection Simulation through Modern Numerical
Methods. II: Realistic Models and Problems
Geophys J Int, 2017, 210, 833-851.
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Ti
plementation in distributed/tria.cc
for inspiration. Note that this will break if you have periodic
boundary conditions.
Let us know if this lets you run with patch_level_1
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Timo Heister
http://www.math.clemson.edu/~heister/
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For
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and issues linked in
there.
One workaround for now might be to switch to a shared::Triangulation.
Best,
Timo
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you want to ignore
dependencies in system directories) and we should try to fix it.
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Timo Heister
http://www.math.clemson.edu/~heister/
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