Re: [deal.II] Matrix-free: two-point volume fluxes for entropy-stable DG?

[Jack Coughlin]

Martin,

I'm not sure what happened to my previous reply, it seems to have been 
deleted somehow.

I haven't been able to implement the 1D version of this method in deal.ii 
yet, but I did do a prototype in Julia which leads me to believe it's 
simpler than I anticipated. However, one important detail eludes me for the 
deal.ii implementation: how to iterate over one "slice" of a tensor product 
quadrature rule. 
In essence, for a quadrature point $q_{i,j,k}$, the two-point volume flux 
term wants a contribution from all of the quadrature points sharing one 
index, namely all of the points $q_{i,j,m}$ for example.

Would you be able to share a pointer to documentation on how the 
FEEvaluation class numbers the quadrature points in a tensor-product rule? 
If I know that then I believe I can write a hacky loop that does the 
appropriate thing by manually combining the quadrature rule and 
FiniteElement.

Best,
-Jack

On Wednesday, April 24, 2024 at 1:28:07 PM UTC-7 Martin Kronbichler wrote:

> Dear Jack,
>
> Two-point fluxes are something we have not yet included in deal.II. I 
> would be very interested if we could realize this feature. I must admit 
> that I did not yet try to understand the complete formula in the link you 
> provided, but in fact it should be possible to implement this with the 
> internal evaluators used by FEEvaluation very efficiently. Would you be 
> willing to share the FEValues variant, it is enough to provide it in 1D. I 
> did work with the Trixi code before, but did not yet look into the 
> algorithms, so I would be very curious to learn the details. My initial 
> approach would be to encode the full D_split matrix to be fed into the 
> tensor product evaluators in the internal namespace, and then add the 
> respective boundary fluxes. Once we have a basic version, we can think 
> about making the interface nicer.
>
> Best,
> Martin
>
>
> Am 23.04.24 um 17:19 schrieb Jack Coughlin:
>
> I am interested in using the deal.ii matrix-free infrastructure to 
> implement an entropy-stable DG method. The entropy stable family of methods 
> uses an interesting variation, where the volume flux is actually a 
> consistent two-point flux function (similar to the numerical flux). 
>
> I've attached a screenshot of the formula in question, which is taken from 
> this 
> documentation page 
> <https://trixi-framework.github.io/Trixi.jl/stable/tutorials/DGSEM_FluxDiff/#DGSEM-with-flux-differencing>.
>  
> I've also attached a review of the method.
>
> As far as I can tell, to do this you would need to be able to tell a class 
> like FEEvaluation to integrate a given submission only for one test 
> function. I think I can see how to do this integration manually with 
> FEValues, but it would be nice to take advantage of the matrix-free 
> infrastructure if possible.
>
> Thank you,
> -Jack C
>
> -- 
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Re: [deal.II] Matrix-free: two-point volume fluxes for entropy-stable DG?

[Jack Coughlin]

Martin,

I haven't tried implementing it with FEValues yet, but when I do I will 
loop you in.

-Jack

On Wednesday, April 24, 2024 at 1:28:07 PM UTC-7 Martin Kronbichler wrote:

> Dear Jack,
>
> Two-point fluxes are something we have not yet included in deal.II. I 
> would be very interested if we could realize this feature. I must admit 
> that I did not yet try to understand the complete formula in the link you 
> provided, but in fact it should be possible to implement this with the 
> internal evaluators used by FEEvaluation very efficiently. Would you be 
> willing to share the FEValues variant, it is enough to provide it in 1D. I 
> did work with the Trixi code before, but did not yet look into the 
> algorithms, so I would be very curious to learn the details. My initial 
> approach would be to encode the full D_split matrix to be fed into the 
> tensor product evaluators in the internal namespace, and then add the 
> respective boundary fluxes. Once we have a basic version, we can think 
> about making the interface nicer.
>
> Best,
> Martin
>
>
> Am 23.04.24 um 17:19 schrieb Jack Coughlin:
>
> I am interested in using the deal.ii matrix-free infrastructure to 
> implement an entropy-stable DG method. The entropy stable family of methods 
> uses an interesting variation, where the volume flux is actually a 
> consistent two-point flux function (similar to the numerical flux). 
>
> I've attached a screenshot of the formula in question, which is taken from 
> this 
> documentation page 
> <https://trixi-framework.github.io/Trixi.jl/stable/tutorials/DGSEM_FluxDiff/#DGSEM-with-flux-differencing>.
>  
> I've also attached a review of the method.
>
> As far as I can tell, to do this you would need to be able to tell a class 
> like FEEvaluation to integrate a given submission only for one test 
> function. I think I can see how to do this integration manually with 
> FEValues, but it would be nice to take advantage of the matrix-free 
> infrastructure if possible.
>
> Thank you,
> -Jack C
>
> -- 
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see 
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> .
>
>

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Re: [deal.II] Minimal deal.ii application loads many surprising dynamic libraries on macos

[Jack Coughlin]

Wolfgang,

Thank you for the reply, I'm glad to see that the developers are keeping an 
eye on dependencies and startup time.

In my case, I was actually careful to compile deal.ii ONLY against MPI, so 
there are only seven direct deps, mostly from my homebrew installation of 
openmpi. But after figuring out the correct tooling to do this on macos and 
digging a little more, it seems that openmpi's libhwloc is the culprit. 
Once it pulls in Foundation.framework and IOKit.framework, we are really 
off to the races.

It appears that my ubuntu build in a docker container starts up in about 
half the time (also just built against MPI).

-Jack

On Friday, April 19, 2024 at 2:00:29 PM UTC-7 Wolfgang Bangerth wrote:

On 4/18/24 23:29, Jack Coughlin wrote: 
> 
> As I say, I don't understand the issue well enough to know if there is 
> anything I or the deal.ii developers can do about it! In any case, 0.25s 
is a 
> very small price to pay for so much functionality and expressiveness. 

Jack, 
I appreciate the qualification in the last sentence :-) 

I don't have a Mac, so can't repeat the experiment and tell you what these 
~100 libraries are, but I've looked into this on my Linux laptop. There, 
libdeal_II.g.so directly references the following 54 libraries: 

Part of Trilinos: 
libnox.so.13 
libamesos2.so.13 
libtacho.so.13 
libml.so.13 
libifpack.so.13 
libamesos.so.13 
libaztecoo.so.13 
libtrilinosss.so.13 
libtpetra.so.13 
libtpetraclassicnodeapi.so.13 
libepetraext.so.13 
libzoltan.so.13 
libepetra.so.13 
libkokkoskernels.so.13 
libteuchoscomm.so.13 
libteuchosparameterlist.so.13 
libteuchoscore.so.13 
libkokkoscore.so.13 
libsuperlu_dist.so.5 

HDF5: 
libhdf5.so.103 

Part of OpenCASCADE: 
libTKBool.so.11 
libTKBRep.so.11 
libTKernel.so.11 
libTKG3d.so.11 
libTKGeomAlgo.so.11 
libTKGeomBase.so.11 
libTKMath.so.11 
libTKMesh.so.11 
libTKShHealing.so.11 
libTKTopAlgo.so.11 
libTKXSBase.so.11 
libTKIGES.so.11 
libTKSTEP.so.11 
libTKSTL.so.11 

PETSc and SLEPc: 
libslepc.so.3.16 
libpetsc.so.3.16 
libmetis.so 

MPI: 
libmpi_cxx.so.40 
libmpi.so.40 

SUNDIALS: 
libsundials_idas.so.4 
libsundials_arkode.so.4 
libsundials_kinsol.so.5 
libsymengine.so.0.8 

BLAS and LAPACK: 
liblapack.so.3 
libblas.so.3 

p4est: 
libp4est.so.0 
libsc.so.0 

System and compiler libraries: 
libgmp.so.10 
libz.so.1 
libm.so.6 
libstdc++.so.6 
libgcc_s.so.1 
libc.so.6 
ld-linux-x86-64.so.2 

These are all libraries from which deal.II directly utilizes functionality. 
It 
is so many because some of the packages we rely on (notably Trilinos and 
OpenCASCADE) split their functionality into many separate libraries for 
reasons unknown to me. 

Beyond these 54, every executable then pulls in another 27 libraries. These 
are libraries that, directly or indirectly, one of the 57 above references. 
For me, these are: 

More from Trilinos: 
libgaleri-epetra.so.13 
libHYPRE-2.23.0.so 
libkokkoscontainers.so.13 
libteuchosnumerics.so.13 
libteuchosparser.so.13 
libteuchosremainder.so.13 
libthyracore.so.13 
libtriutils.so.13 

More from OpenCASCADE: 
libTKBO.so.11 
libTKG2d.so.11 
libTKPrim.so.11 
libTKSTEP209.so.11 
libTKSTEPAttr.so.11 
libTKSTEPBase.so.11 

More from PETSc: 
libparmetis.so 

More from MPI: 
libmpi_mpifh.so.40 
libopen-pal.so.40 
libopen-rte.so.40 

More compiler libraries: 
libgfortran.so.5 
libgomp.so.1 
libhwloc.so.15 
libquadmath.so.0 

Unclear to me: 
libevent_core-2.1.so.7 
libevent_pthreads-2.1.so.7 
libmvec.so.1 
libudev.so.1 
linux-vdso.so.1 (0x7ffc27ddc000) 


The example you show, libAudioStatistics.dylib, would fall into this last 
category. It would be interesting to see which of the dependencies pulls it 
in. In general, though, from the example above, nearly everything I see is 
there for a fairly good reason. 

I will note that you can very substantially slim down if you trim all of 
the 
dependencies. You can build deal.II without reference to Trilinos, PETSc, 
and 
a lot of other stuff, and it compiles substantially faster and is 
substantially smaller. It will of course also have substantially less 
functionality :-) 

Best 
W. 

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


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[deal.II] Minimal deal.ii application loads many surprising dynamic libraries on macos

[Jack Coughlin]

Hello,

I don't know enough to say whether this is an observation about deal.ii or 
about Mac OSX (or maybe homebrew?), but the compiled binary of step-1 loads 
around 100 system dynamic libraries:

```
$ DYLD_PRINT_LIBRARIES=1 ./step-1.release

```
This includes a bunch of things that seemingly shouldn't be required, such 
as `libAudioStatistics.dylib`, etc.

The reason I care about this is that I think it adds around .25 seconds to 
the application startup time, which is a very minor quality of life hit.

In fact, I can't see how to create a dealii binary that starts in less than 
around a quarter second:
```
minimal.cc:
int main() {
return 0;
}

CMakeLists:
add_executable(minimal minimal.cc)
deal_ii_setup_target(minimal)

$ time builds/jackc-macos/minimal
builds/jackc-macos/minimal  0.24s user 0.01s system 98% cpu 0.255 total
```

As I say, I don't understand the issue well enough to know if there is 
anything I or the deal.ii developers can do about it! In any case, 0.25s is 
a very small price to pay for so much functionality and expressiveness.

Thank you,
-Jack

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[deal.II] Received signal SIGSEGV, Segmentation fault

[Smith Jack]

Hello, I am trying to compile DEAL.II on a server. There is no error in the 
compilation, but when I try to run an example, segmentation fault occurs.
I create a environment by conda, in this environment, I installed 
gcc, gxx， gfortan, make, cmake, lapack, blas, scalapack, petsc, symengine
I also compiled SUNDIALS, Trilinos, p4est by myself. Trilinos depends on 
two others libraries, NETCDF and MATIO, I also compiled them by myself. 
Everything seemed to be fine. But when I run the example, I got the error:

(gdb) r
Starting program: 
/work5/luandong/softwares/dealii-9.5.1/examples/step-1/step-1.debug
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
[New Thread 0x2aaaf6efd700 (LWP 100087)]
[New Thread 0x2aaaf70fe700 (LWP 100088)]
[New Thread 0x2aaaff2ff700 (LWP 100089)]
[New Thread 0x2aab0f500700 (LWP 100090)]
[New Thread 0x2aab0f701700 (LWP 100091)]
[New Thread 0x2aab1f902700 (LWP 100092)]
[New Thread 0x2aab27b03700 (LWP 100093)]

Thread 1 "step-1.debug" received signal SIGSEGV, Segmentation fault.
0x2aaac5a3089f in __static_initialization_and_destruction_0 () at 
/home/luandong/data-copy/download/dealii-9.5.1/include/deal.II/base/mpi.h:1732
1732  mpi_type_id_for_type = internal::MPIDataTypes::mpi_type_id(
(gdb) q
A debugging session is active.

Inferior 1 [process 99962] will be killed.

Quit anyway? (y or n) y

Is that because the program use the library "libthread_db.so" ? 
If I use ldd program to see which *so libraries are linked to the program, 
I get 

ldd ./step-1.debug | grep lib64 | grep -v Trilinos | grep -v sundials
libdl.so.2 => /lib64/libdl.so.2 (0x2b026da1)
librt.so.1 => /lib64/librt.so.1 (0x2b028782e000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x2b028871f000)
libm.so.6 => /lib64/libm.so.6 (0x2b0288964000)
libc.so.6 => /lib64/libc.so.6 (0x2b028fd1d000)
/lib64/ld-linux-x86-64.so.2 (0x2b0246f78000)
libresolv.so.2 => /lib64/libresolv.so.2 (0x2b0292e89000)

There are some libraries which are the default libraries of the linux. Do I 
have to install them in my conda environment ?

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[deal.II] How to use a numerical boundary condition in deal.II

[Smith Jack]

Hello:
I want to know how to use a numerical boundary condition in deal.II. For 
example, I want to solve a set of diffusion equations:
\partial c_1 / \partial t = d_1 \partial c_1^2 / \partial x^2
\partial c_2 / \partial t = d_2 \partial c_2^2 / \partial x^2
on the one dimensional domain [0, L].
At the right boundary, the Dirichlet boundary condition is applied: c_1(x = 
L, t) = c_{10},  c_2(x = L, t) = c_{20}.
At the left boundary, the flux of c_1, c_2 is set by:
*\partial c_1 / \partial x  (x = 0, t) = r_1(c_1, c_2)*
*\partial c_2 / \partial x  (x = 0, t) = r_2(c_1, c_2)*
Here, r1 r2 are reactions rates solved by an ODE solver. Then how to use 
such a boundary condition ? There is no analytic expression for r1 and r2. 
I can only get them numerically. [image: 屏幕截图 2023-12-16 095822.jpg]

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Re: [deal.II] Compiling release 9.5.0

[Jack Urombo]

Here is the detailed log.

On Sat, 8 Jul 2023 at 17:37, Matthias Maier  wrote:

> Hi,
>
> Would you mind to also send us the "detailed.log" file located in your
> build directory?
>
> Best,
> Matthias
>
>
>
> On Sat, Jul  8, 2023, at 03:16 CDT, jack urombo  wrote:
>
> > The new release has this error on compiling.
> >
> > [ 10%] Building CXX object
> > bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/tbb/ar
> > ena.cpp.o
> > In file included from
> > /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/s
> > cheduler_common.h:43,
> > from
> > /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/s
> > cheduler.h:24,
> > from
> > /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/a
> > rena.cpp:23:
> > /home/
> ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:266:2
> > 0: error: declaration of ‘tbb::task& tbb::internal::task_prefix::task()’
> > changes meaning o
> > f ‘task’ [-Wchanges-meaning]
> >  266 | tbb::task& task() {return
> > *reinterpret_cast(this+1);}
> >  |^~~~
> > /home/
> ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:225:9
> > : note: used here to mean ‘class tbb::task’
> >  225 | task* next_offloaded;
> >  | ^~~~
> > /home/
> ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:33:7
> :
> > note: declared here
> >   33 | class task;
> >  |   ^~~~
> > make[2]: ***
> > [bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/build.make:90:
> > bund
> > led/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/tbb/arena.cpp.o]
> Error
> > 1
> > make[1]: *** [CMakeFiles/Makefile2:1782:
> > bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_de
> > bug.dir/all] Error 2
> > make: *** [Makefile:136: all] Error 2
> >
> >
> >
> > --
> >
> >
> >
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[deal.II] Compiling release 9.5.0

[jack urombo]

The new release has this error on compiling.

[ 10%] Building CXX object 
bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/tbb/ar
ena.cpp.o 
In file included from 
/home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/s
cheduler_common.h:43, 
from 
/home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/s
cheduler.h:24, 
from 
/home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/a
rena.cpp:23: 
/home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:266:2
0: error: declaration of ‘tbb::task& tbb::internal::task_prefix::task()’ 
changes meaning o
f ‘task’ [-Wchanges-meaning] 
 266 | tbb::task& task() {return 
*reinterpret_cast(this+1);} 
 |^~~~ 
/home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:225:9
: note: used here to mean ‘class tbb::task’ 
 225 | task* next_offloaded; 
 | ^~~~ 
/home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:33:7:
note: declared here 
  33 | class task; 
 |   ^~~~ 
make[2]: *** 
[bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/build.make:90: 
bund
led/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/tbb/arena.cpp.o] Error 
1 
make[1]: *** [CMakeFiles/Makefile2:1782: 
bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_de
bug.dir/all] Error 2 
make: *** [Makefile:136: all] Error 2



-- 




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Re: [deal.II] Re: Dimension Mismatch

[jack urombo]

I am halfway there, after taking Wolfgang's correction.  Now the program is 
running, but runs into trouble later with error:

--- 
An error occurred in line <1333> of file 
 in 
function 
   constexpr ArrayElementType& 
dealii::internal::TensorSubscriptor::subscript(ArrayElementType*, un
signed int, std::integral_constant) [with ArrayElementType = 
dealii::Tensor<0, 2, double>;
int dim = 2] 
The violated condition was:  
   static_cast::type)>:: type>(i) < static_cast::type)>:: type>(dim) 
Additional information:  
   Index 2 is not in the half-open range [0,2). 

Stacktrace: 
--- 
#0  ./oldroyd_bn: Viscoelastic::ExactSolution<2>::gradient(dealii::Point<2, 
double> const&, unsigned
int) const 
#1  /usr/local/share/dealii/lib/libdeal_II.g.so.9.3.2: dealii::Function<2, 
double>::vector_gradient(
dealii::Point<2, double> const&, std::vector, 
std::allocator > >&) const 
#2  /usr/local/share/dealii/lib/libdeal_II.g.so.9.3.2: dealii::Function<2, 
double>::vector_gradient_
list(std::vector, std::allocator > > const&, std::
vector, 
std::allocator > >, st
d::allocator, 
std::allocator >
> > >&) const 
#3  /usr/local/share/dealii/lib/libdeal_II.g.so.9.3.2: double 
dealii::VectorTools::internal::integra
te_difference_inner<2, 2, double>(dealii::Function<2, double> const&, 
dealii::VectorTools::NormType 
const&, dealii::Function<2, double> const*, dealii::UpdateFlags, double, 
unsigned int, dealii::Vecto
rTools::internal::IDScratchData<2, 2, double>&) 
#4  /usr/local/share/dealii/lib/libdeal_II.g.so.9.3.2:  
#5  /usr/local/share/dealii/lib/libdeal_II.g.so.9.3.2: void 
dealii::VectorTools::integrate_differenc
e<2, dealii::BlockVector, dealii::Vector, 
2>(dealii::Mapping<2, 2> const&, dealii::D
oFHandler<2, 2> const&, dealii::BlockVector const&, 
dealii::Function<2, dealii::BlockVector<
double>::value_type> const&, dealii::Vector&, dealii::Quadrature<2> 
const&, dealii::VectorTo
ols::NormType const&, dealii::Function<2, double> const*, double) 
#6  ./oldroyd_bn: Viscoelastic::StokesProblem<2>::output_results(unsigned 
int) 
#7  ./oldroyd_bn: Viscoelastic::StokesProblem<2>::run() 
#8  ./oldroyd_bn: main 
 

make[3]: *** [CMakeFiles/run.dir/build.make:71: CMakeFiles/run] Aborted 
(core dumped) 
make[2]: *** [CMakeFiles/Makefile2:116: CMakeFiles/run.dir/all] Error 2 
make[1]: *** [CMakeFiles/Makefile2:123: CMakeFiles/run.dir/rule] Error 2 
make: *** [Makefile:137: run] Error 2 
ju.rom.bo@MathW15Linux:/home/jurombo/binaires/dealii/nnf/nnewton/oldroyd_b_stab>
 





On Wednesday, 8 March 2023 at 06:19:28 UTC+2 Wolfgang Bangerth wrote:

>
> Jack:
> You are creating a Function=Function<7>, but that is not 
> right. 
> The template argument denotes the number of components of the *input* 
> vector 
> 'x' for which you want to evaluate 'f(x)'. It does not denote the number 
> of 
> *output* vector components. It should only be ComponentSelectFunction.
>
> Best
> W.
>
> On 3/7/23 20:38, jack urombo wrote:
> > *** Caution: EXTERNAL Sender ***
> > 
> > Took a brief hiatus. and managed to pass a huddle following Marc's 
> suggestion.
> > 
> > Now I have set to construct convergence tables for the polymer flow 
> problem I 
> > am solving. It involves solving a Stokes Problem for velocity and 
> pressure 
> > (u,p), (size dim+1)  and the Constitutive Equations for the stress 
> tensor tau, 
> > (size dim*dim). The solution has 7 components for dim=2.
> > To calculate the errors, I need the exact solution [(u,p), tau], ( size 
> dim +1 
> > + dim*dim). To pick the correct component I use the 
> ComponentSelectFunction:
> > 
> > constComponentSelectFunction
> > 
> > velocity_mask(std::make_pair(0,dim),dim*dim+dim+1);
> > 
> > constComponentSelectFunction
> > 
> > pressure_mask(dim,dim+3);
> > 
> > constComponentSelectFunction
> > 
> > stress_mask(std::pair(dim+3,dim*dim+dim+1),dim*dim+dim+1);
> > 
> > Now the errors that I am getting are:
> > 
> > 
> /home/jurombo/binaires/dealii/nnf/nnewton/oldroyd_b_stab/oldroyd_bn.cc:951:43:error:
>  
> no matching fu
> > nction for call to ‘integrate_difference(dealii::MappingQ<2, 2>&, 
> > dealii::DoFHandler<2, 2>&, dealii:
> > :BlockVector&, Viscoelastic::ExactSolution<7>&, 
> > dealii::Vector&, dealii::QGauss<7>&,
> > dealii::VectorTools::NormType, const dealii::ComponentSelectFunction<7, 
> > double>*)’
> >  951 | Vect

[deal.II] Re: Dimension Mismatch

[jack urombo]

The code is attached this message.

On Wednesday, 8 March 2023 at 05:38:43 UTC+2 jack urombo wrote:

> Took a brief hiatus. and managed to pass a huddle following Marc's 
> suggestion.
>
> Now I have set to construct convergence tables for the polymer flow 
> problem I am solving. It involves solving a Stokes Problem for velocity and 
> pressure (u,p), (size dim+1)  and the Constitutive Equations for the stress 
> tensor tau, (size dim*dim). The solution has 7 components for dim=2. 
> To calculate the errors, I need the exact solution [(u,p), tau], ( size 
> dim +1 + dim*dim). To pick the correct component I use the 
> ComponentSelectFunction:
>
> const ComponentSelectFunction
>
> velocity_mask(std::make_pair(0, dim), dim*dim+dim+1);
>
> const ComponentSelectFunction
>
> pressure_mask (dim, dim+3);
>
> const ComponentSelectFunction
>
> stress_mask(std::pair(dim+3, dim*dim+dim+1), dim*dim+dim+1);
> Now the errors that I am getting are: 
>
>
> /home/jurombo/binaires/dealii/nnf/nnewton/oldroyd_b_stab/oldroyd_bn.cc:951:43:
>  error: 
> no matching fu
> nction for call to ‘integrate_difference(dealii::MappingQ<2, 2>&, 
> dealii::DoFHandler<2, 2>&, dealii:
> :BlockVector&, Viscoelastic::ExactSolution<7>&, 
> dealii::Vector&, dealii::QGauss<7>&,
> dealii::VectorTools::NormType, const dealii::ComponentSelectFunction<7, 
> double>*)’ 
>  951 | VectorTools::integrate_difference (mapping, dof_handler, 
>  | ~~^~ 
>  952 |solution, 
>  |~ 
>  953 |exact_solution, 
>  |~~~ 
>  954 |cellwise_errors, 
>  | 
>  955 |quadrature, 
>  |~~~ 
>  956 | 
>VectorTools::H1_seminorm, 
>  |
> ~ 
>  957 |_mask); 
>  |~~~ 
>
> /usr/local/share/dealii/include/deal.II/numerics/vector_tools_integrate_difference.h:143:3:
>  note: 
> ca
> ndidate: ‘template spacedim> void dealii::VectorTools:
> :integrate_difference(const dealii::Mapping&, const 
> dealii::DoFHandler
>
> &, const InVector&, const dealii::Function InVector::value_type>&, OutVector&, co
> nst dealii::Quadrature&, const NormType&, const 
> dealii::Function*, double)’ 
>  143 |   integrate_difference( 
>  |   ^~~~ 
>
> /usr/local/share/dealii/include/deal.II/numerics/vector_tools_integrate_difference.h:143:3:
>  note: 
>   
> template argument deduction/substitution failed: 
>
> /home/jurombo/binaires/dealii/nnf/nnewton/oldroyd_b_stab/oldroyd_bn.cc:951:43:
>  note: 
>   deduced confl
> icting values for non-type parameter ‘spacedim’ (‘2’ and ‘7’) 
>  951 | VectorTools::integrate_difference (mapping, dof_handler, 
>  | ~~^~ 
>  952 |solution, 
>  |~ 
>  953 |exact_solution, 
>  |~~~ 
>  954 |cellwise_errors, 
>  | 
>  955 |quadrature, 
>  |~~~ 
>  956 | 
>VectorTools::H1_seminorm, 
>  |
> ~ 
>  957 |_mask); 
>  |~~~ 
>
> /usr/local/share/dealii/include/deal.II/numerics/vector_tools_integrate_difference.h:160:3:
>  note: 
> ca
> ndidate: ‘template spacedim> void dealii::VectorTools:
> :integrate_difference(const dealii::DoFHandler&, const 
> InVector&, const dealii::Funct
> ion&, OutVector&, const 
> dealii::Quadrature&, const Nor
> mType&, const dealii::Function*, double)’
>
> The issues seem to be emanating from the form of the *exact_solution *and 
> how 

[deal.II] Re: Dimension Mismatch

[jack urombo]

Took a brief hiatus. and managed to pass a huddle following Marc's 
suggestion.

Now I have set to construct convergence tables for the polymer flow problem 
I am solving. It involves solving a Stokes Problem for velocity and 
pressure (u,p), (size dim+1)  and the Constitutive Equations for the stress 
tensor tau, (size dim*dim). The solution has 7 components for dim=2. 
To calculate the errors, I need the exact solution [(u,p), tau], ( size dim 
+1 + dim*dim). To pick the correct component I use the 
ComponentSelectFunction:

const ComponentSelectFunction

velocity_mask(std::make_pair(0, dim), dim*dim+dim+1);

const ComponentSelectFunction

pressure_mask (dim, dim+3);

const ComponentSelectFunction

stress_mask(std::pair(dim+3, dim*dim+dim+1), dim*dim+dim+1);
Now the errors that I am getting are: 

/home/jurombo/binaires/dealii/nnf/nnewton/oldroyd_b_stab/oldroyd_bn.cc:951:43: 
error: 
no matching fu
nction for call to ‘integrate_difference(dealii::MappingQ<2, 2>&, 
dealii::DoFHandler<2, 2>&, dealii:
:BlockVector&, Viscoelastic::ExactSolution<7>&, 
dealii::Vector&, dealii::QGauss<7>&,
dealii::VectorTools::NormType, const dealii::ComponentSelectFunction<7, 
double>*)’ 
 951 | VectorTools::integrate_difference (mapping, dof_handler, 
 | ~~^~ 
 952 |solution, 
 |~ 
 953 |exact_solution, 
 |~~~ 
 954 |cellwise_errors, 
 | 
 955 |quadrature, 
 |~~~ 
 956 |VectorTools::H1_seminorm, 
 |~ 
 957 |_mask); 
 |~~~ 
/usr/local/share/dealii/include/deal.II/numerics/vector_tools_integrate_difference.h:143:3:
 note: 
ca
ndidate: ‘template 
void dealii::VectorTools:
:integrate_difference(const dealii::Mapping&, const 
dealii::DoFHandler
&, const InVector&, const dealii::Function&, OutVector&, co
nst dealii::Quadrature&, const NormType&, const 
dealii::Function*, double)’ 
 143 |   integrate_difference( 
 |   ^~~~ 
/usr/local/share/dealii/include/deal.II/numerics/vector_tools_integrate_difference.h:143:3:
 note: 
  
template argument deduction/substitution failed: 
/home/jurombo/binaires/dealii/nnf/nnewton/oldroyd_b_stab/oldroyd_bn.cc:951:43: 
note: 
  deduced confl
icting values for non-type parameter ‘spacedim’ (‘2’ and ‘7’) 
 951 | VectorTools::integrate_difference (mapping, dof_handler, 
 | ~~^~ 
 952 |solution, 
 |~ 
 953 |exact_solution, 
 |~~~ 
 954 |cellwise_errors, 
 | 
 955 |quadrature, 
 |~~~ 
 956 |VectorTools::H1_seminorm, 
 |~ 
 957 |_mask); 
 |~~~ 
/usr/local/share/dealii/include/deal.II/numerics/vector_tools_integrate_difference.h:160:3:
 note: 
ca
ndidate: ‘template 
void dealii::VectorTools:
:integrate_difference(const dealii::DoFHandler&, const 
InVector&, const dealii::Funct
ion&, OutVector&, const 
dealii::Quadrature&, const Nor
mType&, const dealii::Function*, double)’

The issues seem to be emanating from the form of the *exact_solution *and 
how the components are selected.
Ant suggestions on resolving this?

----
On Monday, 6 February 2023 at 03:11:19 UTC+2 wrote:

Hello Jack,

the error message is quite descriptive and tells you that something is off 
with the number of components of your Function object:

*The violated condition was:  exact_solution.n_components == 
n_components*

Check line 200 of your code:
ExactSolution () : Function(dim+1) {}

You call the constructor for Function with 3 components (since dim=2 in 
your case). However, your implementation returns 7 components. Make sure 
that you call the

[deal.II] Dimension Mismatch

[jack urombo]

i am using the implimenation by  Jaekwang Kim to model polymer flows. The 
major change that I want to do is to output convergence tables like in 
Step-7 and Step-22, which means I have to have an ExactSolution.

The code is encountering an error because the dimension of the solutions do 
not match at a some point when generating output:

























*An error occurred in line <820> of file 

 
in functionvoid 
dealii::VectorTools::internal::do_integrate_difference(const 
dealii::hp::MappingCollection&, const 
dealii::DoFHandler&, const InVector&, const 
dealii::Function&, OutVector&, 
const dealii::hp::QCollection&, const dealii::VectorTools::NormType&, 
const dealii::Function*, double) [with int dim = 2; int spacedim 
= 2; InVector = dealii::BlockVector; OutVector = 
dealii::Vector; typename InVector::value_type = double] The 
violated condition was:  exact_solution.n_components == n_components 
Additional information:  Dimension 3 not equal to 7. Stacktrace: 
--- #0  /usr/local/share/dealii/lib/libdeal_II.g.so.9.3.2:  #1 
 /usr/local/share/dealii/lib/libdeal_II.g.so.9.3.2: void 
dealii::VectorTools::integrate_difference<2, dealii::BlockVector, 
dealii::Vector, 2>(dealii::Mapping<2, 2> const&, 
dealii::DoFHandler<2, 2> const&, dealii::BlockVector const&, 
dealii::Function<2, dealii::BlockVector::value_type> const&, 
dealii::Vector&, dealii::Quadrature<2> const&, 
dealii::VectorTools::NormType const&, dealii::Function<2, double> const*, 
double) #2  ./oldroyd_bn: 
Viscoelastic::StokesProblem<2>::output_results(unsigned int) #3 
 ./oldroyd_bn: Viscoelastic::StokesProblem<2>::run() #4  ./oldroyd_bn: main 
*
I have checked the ExactSolution in the code to try and figure wher the 
error is occurring without success.
Can anyone point me the direction to look. 

-- 




The information in this message is confidential and legally
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It is intended solely for the addressee(s). Access to this message
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or damage arising in any 
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// Developed by Jaekwang Kim
// Welcome to the world of viscoelastic fluids
// Coding from 18th May ~
// Viscoelastic Models 
// Oldroyd B model 
// Upper Convective Maxwel polymer(UCM) + a Newtonian solvent
// Mixed Finite Element (also called viscous formulation) will be considered
// (a) Starting from large viscous contribution from a Newtonian Solvent 
// (b) Low Wissenberg Number
// (c) Stabilization Method 
// (d) Be careful on the LBB condition; Continuous Discretization of T_tensor?
//what is the convention of grad_u_[0][1] ?

#include 
#include 
#include 
#include 
#include 

#include 
#include 
#include 
#include  // CG used for viscous flow
#include  //Matrix solver for transport equation, unsymmetric matrix
#include 
#include 
#include 
#include 
#include 

#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 

#include 
#include 
#include 
#include 

#include 
#include 
#include 
#include 

#include 
#include 
#include 
#include 
#include 
#include 

#include 
#include 
#include 

#include "headers/post_processor.h"
#include "headers/precondition.h"
#include "headers/bcfunctions.h"
#include "headers/fluidclass.h"
#include "headers/flowclass.h"

namespace Viscoelastic
{
  using namespace dealii;

  template 
  class StokesProblem
  {
  public:
StokesProblem (const unsigned int degree);
void run ();

  private:

void read_mesh ();
void setup_dofs ();
void setup_bc_constraints ();
void assemble_stokes (); 		 // Flow system
void solve_stokes ();  		 // Solve with CG
void 

Re: [deal.II] 3D Periodic BCs

[jack urombo]

After following Dan's advice the following exception is now thrown
















* Exception on 
processing:    An 
error occurred in line <595> of file 
 in functionvoid 
RMHD::Entities::VectorBoundaryConditions::set_neumann_bc(dealii::types::boundary_id,
 
const std::shared_ptr >&, bool) [with int 
dim = 3; dealii::types::boundary_id = unsigned int] The violated condition 
was:  !this->closed() Additional information:  The boundary 
conditions have already been closed 
 Aborting! 
 *


On Friday, 8 July 2022 at 00:17:17 UTC+2 d.arnd...@gmail.com wrote:

> Jack,
>
> step-45 https://www.dealii.org/current/doxygen/deal.II/step_45.html 
> provides an example for dealing with periodic boundary conditions. Even 
> though it's a 2D example, the interface is the same in 3D. 
>
> Assuming that the arguments for your set_periodic_boundary_condition 
> function are similar to the ones for GridTools::collect_periodic_faces and 
> you use a unit cube with standard coloring, you probably want to call it 
> with arguments 0,1,0 and 2,3,1 respectively.
>
> Best,
> Daniel
>
> On Thu, Jul 7, 2022 at 1:56 PM jack urombo  wrote:
>
>> I am trying to set periodic boundary conditions for a 3D problem like 
>>
>>
>>
>>
>> *velocity->set_periodic_boundary_condition(0, 1, 2);  
>> velocity->set_periodic_boundary_condition(2, 3, 1);  
>> pressure->set_periodic_boundary_condition(0, 1, 2);  
>> pressure->set_periodic_boundary_condition(2, 3, 1);*
>>
>> The boundary conditions are not matching and that i triggering errors.
>>
>> How do you set the period BCs in 3D.
>>
>> The information in this message is confidential and legally privileged. 
>> It is intended solely for the addressee(s). Access to this message by 
>> anyone else is unauthorized. If received in error, please accept our 
>> apologies and notify the sender immediately. You must also delete the 
>> original message from your machine. If you are not the intended recipient, 
>> any use, disclosure, copying, distribution or action taken in reliance of 
>> it, is prohibited and may be unlawful. The information, attachments, 
>> opinions or advice contained in this email are not the views or opinions of 
>> Harare Institute of Technology, its subsidiaries or affiliates. Although 
>> this email and any attachments are believed to be free of any virus or 
>> other defects which might affect any computer or IT system into which they 
>> are received, no responsibility is accepted by Harare Institute of 
>> Technology and/or its subsidiaries for any loss or damage arising in any 
>> way from the receipt or use thereof.
>>
>> -- 
>> 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/5eaf4f26-00dd-4e6d-841d-4a22e2328fb1n%40googlegroups.com
>>  
>> <https://groups.google.com/d/msgid/dealii/5eaf4f26-00dd-4e6d-841d-4a22e2328fb1n%40googlegroups.com?utm_medium=email_source=footer>
>> .
>>
>
-- 




The information in this message is confidential and legally
privileged. 
It is intended solely for the addressee(s). Access to this message
by 
anyone else is unauthorized. If received in error, please accept our 
apologies
and notify the sender immediately. You must also delete the 
original message
from your machine. If you are not the intended recipient, 
any use, disclosure,
copying, distribution or action taken in reliance of 
it, is prohibited and may
be unlawful. The information, attachments, 
opinions or advice contained in this
email are not the views or opinions of 
Harare Institute of Technology, its
subsidiaries or affiliates. Although 
this email and any attachments are
believed to be free of any virus or 
other defects which might affect any
computer or IT system into which they 
are received, no responsibility is
accepted by Harare Institute of 
Technology and/or its subsidiaries for any loss
or damage arising in any 
way from the receipt or use thereof.

-- 
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see 
https://groups.google.c

[deal.II] 3D Periodic BCs

[jack urombo]

I am trying to set periodic boundary conditions for a 3D problem like 




*velocity->set_periodic_boundary_condition(0, 1, 2);  
velocity->set_periodic_boundary_condition(2, 3, 1);  
pressure->set_periodic_boundary_condition(0, 1, 2);  
pressure->set_periodic_boundary_condition(2, 3, 1);*

The boundary conditions are not matching and that i triggering errors.

How do you set the period BCs in 3D.

-- 




The information in this message is confidential and legally
privileged. 
It is intended solely for the addressee(s). Access to this message
by 
anyone else is unauthorized. If received in error, please accept our 
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and notify the sender immediately. You must also delete the 
original message
from your machine. If you are not the intended recipient, 
any use, disclosure,
copying, distribution or action taken in reliance of 
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[deal.II] Re: MPI and Docker

[jack urombo]

 I am running dealii in Docker container and because of issue to do with 
using filesystem under c++17 i have:
 
*[  0%] Building CXX object 
source/CMakeFiles/rotatingMHD.dir/problem_class.cc.o *









*/home/dealii/rotmhd/source/problem_class.cc: In constructor 
‘RMHD::Problem::Problem(const 
RMHD::RunTimeParameters::ProblemBaseParameters&)’: 
/home/dealii/rotmhd/source/problem_class.cc:185:13: error: 
‘std::filesystem’ has not been declared  185 |   if 
(!std::filesystem::exists(prm.graphical_output_directory) &&  | 
^~ /home/dealii/rotmhd/source/problem_class.cc:190:12: 
error: ‘std::filesystem’ has not been declared  190 | 
  std::filesystem::create_directories(prm.graphical_output_directory); 
 |^~ make[2]: *** 
[source/CMakeFiles/rotatingMHD.dir/build.make:206: 
source/CMakeFiles/rotatingMHD.dir/problem_class.cc.o] Error 1*

Does the dealii Docker container support c++17? 

On Friday, 31 December 2021 at 21:44:54 UTC+2 luca@gmail.com wrote:

> This happened to me when I forgot to call `DEAL_II_SETUP_TARGET` from the 
> CMakeLists.txt. Did you resolve this issue?
>
> On Tuesday, December 14, 2021 at 9:54:42 AM UTC+1 jack urombo wrote:
>
>> The current docker image is not finding mpi.h
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *[ 50%] Building CXX object CMakeFiles/cdr.dir/cdr.cc.o In file included 
>> from /usr/include/deal.II/base/conditional_ostream.h:19, 
>> from /home/dealii/dealii/cdr/cdr.cc:1: 
>> /usr/include/deal.II/base/config.h:490:12: fatal error: mpi.h: No such file 
>> or directory  490 | #  include   |^~~ 
>> compilation terminated. make[2]: *** [CMakeFiles/cdr.dir/build.make:63: 
>> CMakeFiles/cdr.dir/cdr.cc.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:76: 
>> CMakeFiles/cdr.dir/all] Error 2 make: *** [Makefile:84: all] Error 2 
>> dealii@cdab72233c4c:~/dealii/cdr$ *
>>
>
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Re: [deal.II] step-35 in modified

[jack urombo]

I want to generate convergence table for the modified step-35 for a couple 
of velocity and pressure error norms.
The problem seems to emanate from my definition of the errors in 
*process_output()   
*template.
The message is:

































*[ 50%] Building CXX object CMakeFiles/step-35a.dir/step-35a.cc.o 
/home/jurombo/binaires/dealii/nse/step-35a/step-35a.cc: In member function 
‘void Step35a::NavierStokesProjection::compute_errors(unsigned int)’: 
/home/jurombo/binaires/dealii/nse/step-35a/step-35a.cc:1941:40: error: 
‘vL2_error’ was not declared in this scope 1941 | 
convergence_table.add_value("vL2", vL2_error);  | 
   ^ 
/home/jurombo/binaires/dealii/nse/step-35a/step-35a.cc:1942:40: error: 
‘vH1_error’ was not declared in this scope 1942 | 
convergence_table.add_value("vH1", vH1_error);  | 
   ^ 
/home/jurombo/binaires/dealii/nse/step-35a/step-35a.cc:1943:44: error: 
‘vLinfty_error’ was not declared in this scope 1943 | 
convergence_table.add_value("vLinfty", vLinfty_error);  | 
   ^ 
/home/jurombo/binaires/dealii/nse/step-35a/step-35a.cc:1944:40: error: 
‘pL2_error’ was not declared in this scope; did you mean ‘perror’? 1944 | 
convergence_table.add_value("pL2", pL2_error);  | 
   ^  | 
   perror 
/home/jurombo/binaires/dealii/nse/step-35a/step-35a.cc:1945:40: error: 
‘pH1_error’ was not declared in this scope; did you mean ‘perror’? 1945 | 
convergence_table.add_value("pH1", pH1_error);  | 
   ^  | 
   perror 
/home/jurombo/binaires/dealii/nse/step-35a/step-35a.cc:1946:44: error: 
‘pLinfty_error’ was not declared in this scope 1946 | 
convergence_table.add_value("pLinfty", pLinfty_error);  | 
   ^ make[2]: *** 
[CMakeFiles/step-35a.dir/build.make:76: 
CMakeFiles/step-35a.dir/step-35a.cc.o] Error 1 make[1]: *** 
[CMakeFiles/Makefile2:90: CMakeFiles/step-35a.dir/all] Error 2 make: *** 
[Makefile:91: all] Error 2 
jurombo@MathW15Linux:~/binaires/dealii/nse/step-35a> *

I need suggestions on how to properly define or indications of where I 
getting wrong. 
The code is attached.
On Saturday, 5 March 2022 at 05:42:26 UTC+2 jack urombo wrote:

> Yeah this:
>   
>
>
> *scratch.fe_val_vel.reinit(std::get<0> (*SI));  
> scratch.fe_val_pres.reinit(std::get<1> (*SI));  std::get<0> 
> (*SI)->get_dof_indices(data.vel_local_dof_indices);  std::get<1> 
> (*SI)->get_dof_indices(data.pres_local_dof_indices);*
>
> On Saturday, 5 March 2022 at 01:02:42 UTC+2 Wolfgang Bangerth wrote:
>
>> On 3/4/22 14:37, jack urombo wrote:
>> > **
>> > 
>> > Does this replace all the four instances of *std::get *or just the 
>> > last two?
>>
>> All of the ones where you call
>> std::get<...>(SI.iterators)
>>
>> Best
>> W.
>>
>> -- 
>> 
>> Wolfgang Bangerth email: bang...@colostate.edu
>> www: http://www.math.colostate.edu/~bangerth/
>>
>
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Re: [deal.II] step-35 in modified

[jack urombo]

Yeah this:
  


*scratch.fe_val_vel.reinit(std::get<0> (*SI));  
scratch.fe_val_pres.reinit(std::get<1> (*SI));  std::get<0> 
(*SI)->get_dof_indices(data.vel_local_dof_indices);  std::get<1> 
(*SI)->get_dof_indices(data.pres_local_dof_indices);*

On Saturday, 5 March 2022 at 01:02:42 UTC+2 Wolfgang Bangerth wrote:

> On 3/4/22 14:37, jack urombo wrote:
> > **
> > 
> > Does this replace all the four instances of *std::get *or just the 
> > last two?
>
> All of the ones where you call
> std::get<...>(SI.iterators)
>
> Best
> W.
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>

-- 




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Re: [deal.II] step-35 in modified

[jack urombo]

Does this replace all the four instances of *std::get *or just the last 
two?

On Friday, 4 March 2022 at 22:39:14 UTC+2 Wolfgang Bangerth wrote:

> On 3/4/22 12:12, jack urombo wrote:
> > /
> >   std::get<0> (SI.iterators)->get_dof_indices 
> (data.vel_local_dof_indices);
> >   std::get<1> (SI.iterators)->get_dof_indices 
> > (data.pres_local_dof_indices);/
>
> The code you are basing yours own is apparently built on an old version 
> of deal.II. I believe that you need to write this as
> std::get<0> (*SI)->get_dof_indices
> now.
>
> Best
> W.
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>

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Re: [deal.II] step-35 in modified

[jack urombo]

Still working on modified step-35, but now starting the modification by 
Muhammad Mohebujjaman.

https://github.com/Mohebujjaman/Projection-Method-for-NSE

I want to resolve the issue of the iterators defined here:






















*template voidNavierStokesProjection::assemble_one_cell_of_gradient (const 
IteratorPair ,InitGradScratchData 
,InitGradPerTaskData ){  
scratch.fe_val_vel.reinit (std::get<0> (SI.iterators));  
scratch.fe_val_pres.reinit (std::get<1> (SI.iterators));  std::get<0> 
(SI.iterators)->get_dof_indices (data.vel_local_dof_indices);  std::get<1> 
(SI.iterators)->get_dof_indices (data.pres_local_dof_indices);  
data.local_grad = 0.;  Vector rhs_vector (dim);for (unsigned 
int q=0; q On 8/4/21 4:20 AM, SebG wrote:
> > 
> > a colleague and I have also worked with step-35 and we programmed a 
> > parallelized version whose layout is similar to that of step-32. 
> Currently, 
> > the code is not suitable to be directly used as a tutorial, but, if you 
> are 
> > interested, we could refactor it and send it through github as a 
> step-35b.
>
> Maybe a better option would be the code gallery:
> https://dealii.org/code-gallery
> It would relatively straightforward to get it in there.
>
> Over the past few years, we've started to think of the tutorial more in 
> terms 
> as a place where we *teach deal.II*, and so we tried to focus on programs 
> that 
> illustrate specific aspects of deal.II rather than just a landing pad for 
> general deal.II-based programs. The latter should go into the code gallery 
> instead. Want to give that a try?
>
> Best
> W.
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>
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errors
Description: Binary data

[deal.II] MPI and Docker

[jack urombo]

The current docker image is not finding mpi.h











*[ 50%] Building CXX object CMakeFiles/cdr.dir/cdr.cc.o In file included 
from /usr/include/deal.II/base/conditional_ostream.h:19, 
from /home/dealii/dealii/cdr/cdr.cc:1: 
/usr/include/deal.II/base/config.h:490:12: fatal error: mpi.h: No such file 
or directory  490 | #  include   |^~~ 
compilation terminated. make[2]: *** [CMakeFiles/cdr.dir/build.make:63: 
CMakeFiles/cdr.dir/cdr.cc.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:76: 
CMakeFiles/cdr.dir/all] Error 2 make: *** [Makefile:84: all] Error 2 
dealii@cdab72233c4c:~/dealii/cdr$ *

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Re: [deal.II] Docker and Eclipse

[jack urombo]

Managed to install from  the latest git repo and it went perfectly well:

MathW15Lnx:/home/jurombo/Downloads/dealii/build # make test 
Running quicktests... 
Test project /home/jurombo/Downloads/dealii/build/tests/quick_tests 
 Start  1: step.debug 
 Start  2: step.release 
 Start  3: affinity.debug 
 Start  4: tbb.debug 
1/10 Test  #4: tbb.debug    Passed   22.25 sec 
 Start  5: taskflow.debug 
2/10 Test  #3: affinity.debug ...   Passed   22.71 sec 
 Start  6: lapack.debug 
3/10 Test  #2: step.release .   Passed   24.02 sec 
 Start  7: umfpack.debug 
4/10 Test  #1: step.debug ...   Passed   28.17 sec 
 Start  8: arpack.debug 
5/10 Test  #5: taskflow.debug ...   Passed7.62 sec 
 Start  9: boost_zlib.debug 
6/10 Test  #6: lapack.debug .   Passed8.39 sec 
 Start 10: gmsh.debug 
7/10 Test  #7: umfpack.debug    Passed   14.48 sec 
8/10 Test  #9: boost_zlib.debug .   Passed8.85 sec 
9/10 Test #10: gmsh.debug ...   Passed9.46 sec 
10/10 Test  #8: arpack.debug .   Passed   13.42 sec 

100% tests passed, 0 tests failed out of 10 

Total Test time (real) =  41.59 sec 
Built target test



On Wednesday, 6 October 2021 at 02:00:41 UTC+2 Wolfgang Bangerth wrote:

>
> Andrew,
>
> > I am running dealii on Docker, and now would like to debug my projects 
> using 
> > Eclipse.
> > 
> > 1. How do you that so that Eclipse recognise the dealii that is in a 
> container 
> > and work in sync?
>
> I don't actually know how to do that, but you could presumably just run 
> Eclipse in the container as well.
>
>
> > Why I am not running a compiled dealii is because I am getting//this 
> error 
> > with log ending:
> > 
> > 
> //usr/lib64/gcc/x86_64-suse-linux/11/../../../../x86_64-suse-linux/bin/ld: 
> > 
> CMakeFiles/step_3_simplex.debug.dir/doxygen/step_3_simplex.cc.o:(.data.rel.ro._ZTVN6dealii13FiniteElementILi2ELi2EE16InternalDataBaseE[_ZTVN6dealii13FiniteElementILi2ELi2EE16InternalDataBaseE]+0x20):
>  
>
> > undefined reference to `dealii::FiniteElement<2, 
> > 2>::InternalDataBase::memory_consumption() const'//
>
> This looks like a bug to me. Can you try whether this patch help?
> https://github.com/dealii/dealii/pull/12793
>
> Best
> W.
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>
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[deal.II] Docker and Eclipse

[andrew jack urombo]

I am running dealii on Docker, and now would like to debug my projects 
using Eclipse.


1. How do you that so that Eclipse recognise the dealii that is in a 
container and work in sync?


Why I am not running a compiled dealii is because I am getting//this 
error with log ending:


//usr/lib64/gcc/x86_64-suse-linux/11/../../../../x86_64-suse-linux/bin/ld: 
CMakeFiles/step_3_simplex.debug.dir/doxygen/step_3_simplex.cc.o:(.data.rel.ro._ZTVN6dealii13FiniteElementILi2ELi2EE16InternalDataBaseE[_ZTVN6dealii13FiniteElementILi2ELi2EE16InternalDataBaseE]+0x20): 
undefined reference to `dealii::FiniteElement<2, 
2>::InternalDataBase::memory_consumption() const'//

//collect2: error: ld returned 1 exit status//
//make[2]: *** 
[examples/CMakeFiles/step_3_simplex.debug.dir/build.make:110: 
bin/step_3_simplex.debug] Error 1//
//make[1]: *** [CMakeFiles/Makefile2:3814: 
examples/CMakeFiles/step_3_simplex.debug.dir/all] Error 2//

//make: *** [Makefile:136: all] Error 2//
//MathW15Lnx:/home/jurombo/Downloads/dealii-9.3.0/build # /

2. How do I fix this compile error?

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Re: [deal.II] step-35 in modified

[andrew jack urombo]

The error I am trying to have suggestions to fix is:

//home/dealii/dealii/examples/step-35a/step-35a.cc: In member function 
‘void Step35a::NavierStokesProjection::refine_mesh(unsigned int, 
unsigned int)’://
///home/dealii/dealii/examples/step-35a/step-35a.cc:1057:5: error: there 
are no arguments to ‘setup_system’ that depend on a template parameter, 
so a declaration of ‘setup_system’ must be available [-fpermissive]//

// 1057 | setup_system();//
//  | ^~~~//
///home/dealii/dealii/examples/step-35a/step-35a.cc:1057:5: note: (if 
you use ‘-fpermissive’, G++ will accept your code, but allowing the use 
of an undeclared name is deprecated)//
///home/dealii/dealii/examples/step-35a/step-35a.cc:1059:32: error: 
‘previous_solution’ was not declared in this scope//
// 1059 | solution_trans.interpolate(previous_solution, 
output_results);//

//  |    ^//
///home/dealii/dealii/examples/step-35a/step-35a.cc:1060:5: error: 
‘constraints’ was not declared in this scope//

// 1060 | constraints.distribute(output_results);//
//  | ^~~//
///home/dealii/dealii/examples/step-35a/step-35a.cc: At global scope://
///home/dealii/dealii/examples/step-35a/step-35a.cc:1071:8: error: no 
declaration matches ‘void 
Step35a::NavierStokesProjection::process_solution(unsigned int)’//
// 1071 |   void NavierStokesProjection::process_solution(const 
unsigned int cycle)//

//  |    ^~~//
///home/dealii/dealii/examples/step-35a/step-35a.cc:1071:8: note: no 
functions named ‘void 
Step35a::NavierStokesProjection::process_solution(unsigned int)’//
///home/dealii/dealii/examples/step-35a/step-35a.cc:437:9: note: ‘class 
Step35a::NavierStokesProjection’ defined here//

//  437 |   class NavierStokesProjection//
//  | ^~//
//make[3]: *** [CMakeFiles/step-35a.dir/build.make:63: 
CMakeFiles/step-35a.dir/step-35a.cc.o] Error 1//

/

On 11/07/2021 21:24, Wolfgang Bangerth wrote:

On 7/10/21 4:23 AM, andrew jack urombo wrote:


I have attached the  amended code here, and would like suggestions on 
how to make it work.


The error is that at line 1050 /"a function is expected at ,..." /


Andrew,
the line in question is this one, in the middle of a comment:

    // Now everything is ready, so do the refinement and recreate the DoF
    // structure on the new grid, and finally initialize the matrix 
structures

    // and the new vectors in the 
     function. Next, we
    // actually perform the interpolation of the solution from old to new
    // grid. The final step is to apply the hanging node constraints 
to the

    // solution vector, i.e., to make sure that the values of degrees of

It complains about the '' part, which is simply not valid C++ -- 
this is meant to be a part of the commentary, not the code itself. 
Just comment it out.


Best
 W.



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[deal.II] step-35 in modified

[andrew jack urombo]

Hie.

I am working on flow problems with a model based on the NSE.  The
project involves using adaptive finite elementts, and first steps
are  to:

1) have a mesh adapting strategy

2) compute errors

3) obtain convergence rates

I am basing these on the dealii step-35 and have attached my
attempt to implement these 3 , and  would you to point in the
right direction.

I have attached the  amended code here, and would like suggestions on 
how to make it work.


The error is that at line 1050 /"a function is expected at ,..."
/

How do you implement this in an amendment to step-35?

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dealii@e98618c54d0b:~/examples/step-35a$ make
[ 50%] Building CXX object CMakeFiles/step-35a.dir/step-35a.cc.o
/home/dealii/examples/step-35a/step-35a.cc: In member function ‘void 
Step35a::NavierStokesProjection::refine_mesh(unsigned int, unsigned int)’:
/home/dealii/examples/step-35a/step-35a.cc:1050:5: error: expected 
primary-expression before ‘<’ token
 1050 |  function. Next, we
  | ^
/home/dealii/examples/step-35a/step-35a.cc:1050:6: error: expected 
primary-expression before ‘/’ token
 1050 |  function. Next, we
  |  ^
/home/dealii/examples/step-35a/step-35a.cc:1050:7: error: ‘code’ was not 
declared in this scope
 1050 |  function. Next, we
  |   ^~~~
/home/dealii/examples/step-35a/step-35a.cc:1050:13: error: ‘function’ was not 
declared in this scope
 1050 |  function. Next, we
  | ^~~~
/home/dealii/examples/step-35a/step-35a.cc:1050:13: note: suggested 
alternatives:
In file included from /usr/include/c++/9/functional:59,
 from /usr/include/c++/9/pstl/glue_algorithm_defs.h:13,
 from /usr/include/c++/9/algorithm:71,
 from /usr/include/trilinos/Teuchos_ConfigDefs.hpp:98,
 from /usr/include/trilinos/Teuchos_PromotionTraits.hpp:45,
 from 
/usr/include/trilinos/Sacado_Fad_Exp_GeneralFadTraits.hpp:139,
 from /usr/include/trilinos/Sacado.hpp:52,
 from /usr/local/include/deal.II/base/numbers.h:145,
 from /usr/local/include/deal.II/base/config.h:494,
 from /usr/local/include/deal.II/base/parameter_handler.h:20,
 from /home/dealii/examples/step-35a/step-35a.cc:26:
/usr/include/c++/9/bits/std_function.h:128:11: note:   ‘std::function’
  128 | class function;
  |   ^~~~
In file included from /usr/include/boost/function/function_base.hpp:38,
 from /usr/include/boost/function/detail/prologue.hpp:17,
 from /usr/include/boost/function.hpp:30,
 from /usr/include/boost/signals2/signal.hpp:18,
 from /usr/include/boost/signals2.hpp:19,
 from /usr/local/include/deal.II/base/mpi.h:26,
 from /usr/local/include/deal.II/base/aligned_vector.h:24,
 from /usr/local/include/deal.II/base/table.h:21,
 from 
/usr/local/include/deal.II/lac/block_sparsity_pattern.h:25,
 from /usr/local/include/deal.II/lac/sparsity_tools.h:24,
 from /usr/local/include/deal.II/base/graph_coloring.h:25,
 from 

[deal.II] adaptive mesh refinement for Navier Stokes

[andrew jack urombo]

I am working on a adaptive finite elements for flows. For starters I 
want to base my simulation on Step 35 and introduce the refine_mesh( )  
like in Step 26 to it:


See attached code snippet.

When I make I get the error message:

/[ 50%] Building CXX object CMakeFiles/step-35a.dir/step-35a.cc.o//
///home/dealii/examples/step-35a/step-35a.cc: In member function ‘void 
Step35a::NavierStokesProjection::refine_mesh(unsigned int, unsigned 
int)’://
///home/dealii/examples/step-35a/step-35a.cc:1057:5: error: there are no 
arguments to ‘setup_system’ that depend on a template parameter, so a 
declaration of ‘setup_system’ must be available [-fpermissive]//

// 1057 | setup_system();//
//  | ^~~~//
///home/dealii/examples/step-35a/step-35a.cc:1057:5: note: (if you use 
‘-fpermissive’, G++ will accept your code, but allowing the use of an 
undeclared name is deprecated)//
///home/dealii/examples/step-35a/step-35a.cc:1059:32: error: 
‘previous_solution’ was not declared in this scope//
// 1059 | solution_trans.interpolate(previous_solution, 
output_results);//

//  |    ^//
///home/dealii/examples/step-35a/step-35a.cc:1060:5: error: 
‘constraints’ was not declared in this scope//

// 1060 | constraints.distribute(output_results);//
//  | ^~~//
//make[2]: *** [CMakeFiles/step-35a.dir/build.make:63: 
CMakeFiles/step-35a.dir/step-35a.cc.o] Error 1//
//make[1]: *** [CMakeFiles/Makefile2:272: CMakeFiles/step-35a.dir/all] 
Error 2//

//make: *** [Makefile:84: all] Error 2//
//dealii@cd3db784d9d2:~/examples/step-35a$ ^C//
/

Anyone with any idea how to fix this, or have implemented a similar 
problem in dealii.


Thank you.



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  template 
  void NavierStokesProjection::refine_mesh(const unsigned int min_grid_level,
  const unsigned int max_grid_level)
  {
Vector estimated_error_per_cell(triangulation.n_active_cells());

KellyErrorEstimator::estimate(
  dof_handler_velocity,
  dof_handler_pressure,
  QGauss(deg + 1),
  std::map *>(),
  output_results,
  estimated_error_per_cell);
GridRefinement::refine_and_coarsen_fixed_fraction(triangulation,
  estimated_error_per_cell,
  0.6,
  0.4);

if (triangulation.n_levels() > max_grid_level)
  for (const auto  :
   triangulation.active_cell_iterators_on_level(max_grid_level))
cell->clear_refine_flag();
for (const auto  :
 triangulation.active_cell_iterators_on_level(min_grid_level))
  cell->clear_coarsen_flag();

/***/

 SolutionTransfer solution_trans(dof_handler_velocity, dof_handler_pressure);

Vector previous_velocity;
previous_velocity = fe_velocity;
triangulation.prepare_coarsening_and_refinement();
solution_trans.prepare_for_coarsening_and_refinement(previous_velocity);

Vector previous_pressure;
previous_pressure = fe_pressure;
triangulation.prepare_coarsening_and_refinement();
solution_trans.prepare_for_coarsening_and_refinement(previous_pressure);

/***/

 

[deal.II] Example not Compiling in deallii on Docker

[Jack Urombo]

I have installed dealii on docker and when itry t run the examples i get 
the error below. What am i doing wrong?



/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/dealii-9.1.1-kbq6c5p67nir5zwpx5lbevwutndfivxz/share/deal.II/examples/step-6/CMakeFiles/CMakeTmp/testCCompiler.c

  try_compile() works only for enabled languages.  Currently these are:

C CXX

  See project() command to enable other languages.
Call Stack (most recent call first):
  CMakeLists.txt:38 (PROJECT)


-- Check for working C compiler: /usr/bin/cc -- broken
CMake Error at 
/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/cmake-3.14.4-7gmvmpryqyfj5m42vt5qj5tb27tw7un6/share/cmake-3.14/Modules/CMakeTestCCompiler.cmake:56
 
(file):
  file failed to open for writing (No such file or directory):


/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/dealii-9.1.1-kbq6c5p67nir5zwpx5lbevwutndfivxz/share/deal.II/examples/step-6/CMakeFiles/CMakeError.log
Call Stack (most recent call first):
  CMakeLists.txt:38 (PROJECT)


CMake Error at 
/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/cmake-3.14.4-7gmvmpryqyfj5m42vt5qj5tb27tw7un6/share/cmake-3.14/Modules/CMakeTestCCompiler.cmake:60
 
(message):
  The C compiler

"/usr/bin/cc"

  is not able to compile a simple test program.

  It fails with the following output:



  

  CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
  CMakeLists.txt:38 (PROJECT)


-- Configuring incomplete, errors occurred!
CMake Error: Cannot open file for write: 
/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/dealii-9.1.1-kbq6c5p67nir5zwpx5lbevwutndfivxz/share/deal.II/examples/step-6/CMakeCache.txt.tmp
CMake Error: : System Error: Permission denied
CMake Error: Unable to open cache file for save. 
/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/dealii-9.1.1-kbq6c5p67nir5zwpx5lbevwutndfivxz/share/deal.II/examples/step-6/CMakeCache.txt
CMake Error: : System Error: Permission denied
dealii@85f866bfa019:/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/dealii-9.1.1-kbq6c5p67nir5zwpx5lbevwutndfivxz/share/deal.II/examples/step-6$
 
^C
dealii@85f866bfa019:/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/dealii-9.1.1-kbq6c5p67nir5zwpx5lbevwutndfivxz/share/deal.II/examples/step-6$
 


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Re: [deal.II] Re: Problems in solving two PDE systems using MPI+Thread parallel computing

[Jack]

Hi Prof. Wolfgang,

 

Many thanks!

 

Originally, I suspected that when solving two linear systems simultaneously 
by two threads would reduce time. But now it seems that this idea increases 
the complexity of communication between MPI communicators and coding, and 
also not surely to decrease computing time. I’m not going to try this idea 
at present. When I’m free, I will test its feasibility and post here the 
result.

 

Thank you very much!


All my best wishes,


Jack

在 2017年5月24日星期三 UTC+8上午1:59:17，Wolfgang Bangerth写道：
>
>
> Jack, 
>
> > “The way to do this is to clone the MPI communicator you use for your 
> > overall 
> > problem once for each linear system. ” 
> > 
> > That means for my problem I have to copy the Vector and Matrix of one 
> > linear system（either the thermal diffusion or stokes flow） to another 
> > Vector and Matrix which are built with a clone of present communicator 
> > before starting a thread to solve this linear system. 
> > 
> > And then I have to copy the solution of this linear system to the 
> > targeted Vector which is built using the present MPI communicator for 
> > assembling systems. 
>
> That seems too complicated. Just set up the linear system (=matrix, 
> vectors) with a different communicator from the beginning. 
>
>
> > By the way is it possible to copy Vector and Matrix of TrilinosWrappers 
> > to another ones those are initialized with another MPI communicator? 
>
> I don't remember. It is certainly nor a usual operation. You'll have to 
> investigate whether copying also copies the communicator or not by 
> looking at the actual source. 
>
> It is not common to solve linear systems on different threads in 
> parallel when using MPI. I don't want to say that that is not a good 
> idea -- it seems like a good idea for sure because it can hide some of 
> the latency associated with MPI communication, but it is not usually 
> done. I suspect that you will not save much time compared to just 
> solving the two linear systems one after the other. 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>

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Re: [deal.II] Re: Problems in solving two PDE systems using MPI+Thread parallel computing

[Jack]

Hi Prof. Wolfgang，


Thanks so much！


“The way to do this is to clone the MPI communicator you use for your 
overall 
problem once for each linear system. ”

That means for my problem I have to copy the Vector and Matrix of one 
linear system（either the thermal diffusion or stokes flow） to another 
Vector and Matrix which are built with a clone of present communicator 
before starting a thread to solve this linear system.

 

And then I have to copy the solution of this linear system to the targeted 
Vector which is built using the present MPI communicator for assembling 
systems.

 

By the way is it possible to copy Vector and Matrix of TrilinosWrappers to 
another ones those are initialized with another MPI communicator?

 

Thanks,

 

All best，

 

Jack

在 2017年5月22日星期一 UTC+8下午9:50:32，Wolfgang Bangerth写道：
>
>
> Jack, 
> unrelated to the question about versions of MPI libraries, when you solve 
> two 
> linear systems on separate threads, you need to pay attention that the two 
> solvers (and all associated objects such as matrices, vectors, etc) use 
> separate MPI communicators. Otherwise you will have the two solvers send 
> messages on the same communicator at the same time, and this is certain to 
> lead to trouble. 
>
> The way to do this is to clone the MPI communicator you use for your 
> overall 
> problem once for each linear system. This way, each linear system uses its 
> own 
> communication channel, and one solver can not get in the way of the other. 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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[deal.II] Re: Problems in solving two PDE systems using MPI+Thread parallel computing

[Jack]

Hi Bruno,

 

I appreciated it very much for your responses.

 

The Matrices and Vectors are of TrilinosWrappers, the solvers should use 
MPI, too. I used the OpenMPI 1.8.1. The release date is Apr 22 2014, later 
than the post on the Github. I initialized the MPI as following

try

{

 using namespace dealii;

 using namespace problem;

 Utilities::MPI::MPI_InitFinalize mpi_initialization (argc, argv,

numbers::invalid_unsigned_int);

 Problem<2> app;

 app.infofile = argv[1];

 app.run ();

}

So, It seems this error is because I called two functions which use MPI 
during solving thermal diffusion and stokes flow equations.

 According to this post https://github.com/open-mpi/ompi/issues/1081

 “It turns out that if one tries to use Open MPI with MPI THREAD MULTIPLE 
(at least master) and actually has multiple threads making concurrent MPI 
calls, one gets a flood of messages of the following ilk:

opal_libevent2022_event_base_loop: reentrant invocation. Only one 
event_base_loop can run on each event_base at once.

showing up in stderr.

This needs to be fixed before release of v2.x”

I should update my OpenMPI to the latest version and such problem will be 
avoided and I do not need to change my code for initialization of MPI and 
TBB myself?

 

Thanks for your kind help!

 

Regards,


Jack

在 2017年5月19日星期五 UTC+8下午8:25:55，Bruno Turcksin写道：
>
> Jack,
>
> are your solvers using MPI?  This looks similar to this problem 
> https://github.com/open-mpi/ompi/issues/1081 Which version of MPI are you 
> using? How do you initialize MPI? MPI_InitFinalize set 
> MPI_THREAD_SERIALIZED which "tells MPI that 
> we might use several threads but never call two MPI functions at the same 
> time." This is not want you want if your solvers use MPI. Then you need to 
> initialize MPI and TBB yourself and use MPI THREAD MULTIPLE.
>
> Best,
>
> Bruno
>
> On Friday, May 19, 2017 at 3:52:39 AM UTC-4, Jack wrote:
>>
>> Dear all,
>>
>>  
>>
>> I’m trying to solve the thermal diffusion and Stokes flow problem 
>> simultaneously, similar to the step-32. I opened two threads to solve 
>> thermal diffusion and Stokes equations during solving by linear solvers 
>> (the former is solved by CG solver and the latter is solved by GMRES 
>> solver) after assembling the matrices and RHS. I encountered a problem when 
>> I using parallel computing in combination with distributed and shared 
>> memory.
>>
>>  The code is like following:
>>
>>
>> assemble_thermal_diffusion_system();
>>
>> assemble_stokes_flow_system ();
>>
>> Threads::Task task =
>>
>> Threads::new_task (::solve_thermal_diffsuion, *this);
>>
>> solve_stokes_flow ();
>>
>> task.join();
>>
>>
>> The program ran successfully with single process and showed a high 
>> performance of thread parallel computing, unfortunately, when I ran the 
>> program using several processes I got following error. I have googled this 
>> error and can not find any solution. Could someone help me?
>>
>> Thanks in advance!
>>
>>  
>> [warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only 
>> one event_base_loop can run on each event_base at once.
>>
>> [warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
>> event_base_loop can run on each event_base at once.
>>
>> [warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
>> event_base_loop can run on each event_base at once.
>>
>> [warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
>> event_base_loop can run on each event_base at once.
>>
>> [warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
>> event_base_loop can run on each event_base at once.
>>
>> [warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
>> event_base_loop can run on each event_base at once.
>>
>> [warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
>> event_base_loop can run on each event_base at once.
>>
>> [warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
>> event_base_loop can run on each event_base at once.
>>
>> [warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
>> event_base_loop can run on each event_base at once.
>>
>> [warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
>> event_base_loop can run on each event_base at once.
>>
>> [warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
>> event_base_loop can run on each event_base at once.

[deal.II] Problems in solving two PDE systems using MPI+Thread parallel computing

[Jack]

Dear all,

 

I’m trying to solve the thermal diffusion and Stokes flow problem 
simultaneously, similar to the step-32. I opened two threads to solve 
thermal diffusion and Stokes equations during solving by linear solvers 
(the former is solved by CG solver and the latter is solved by GMRES 
solver) after assembling the matrices and RHS. I encountered a problem when 
I using parallel computing in combination with distributed and shared 
memory.

 The code is like following:


assemble_thermal_diffusion_system();

assemble_stokes_flow_system ();

Threads::Task task =

Threads::new_task (::solve_thermal_diffsuion, *this);

solve_stokes_flow ();

task.join();


The program ran successfully with single process and showed a high 
performance of thread parallel computing, unfortunately, when I ran the 
program using several processes I got following error. I have googled this 
error and can not find any solution. Could someone help me?

Thanks in advance!

 
[warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
event_base_loop can run on each event_base at once.

[warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
event_base_loop can run on each event_base at once.

[warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
event_base_loop can run on each event_base at once.

[warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
event_base_loop can run on each event_base at once.

[warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
event_base_loop can run on each event_base at once.

[warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
event_base_loop can run on each event_base at once.

[warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
event_base_loop can run on each event_base at once.

[warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
event_base_loop can run on each event_base at once.

[warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
event_base_loop can run on each event_base at once.

[warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
event_base_loop can run on each event_base at once.

[warn] opal_libevent2021_event_base_loop: reentrant invocation.  Only one 
event_base_loop can run on each event_base at once.


Thank you very much.

 

Best,

 

Jack

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[deal.II] It seems that parallel::distributed::SolutionTransfer does not support hp::DoFHandler, how can I transfer solution after mesh changed

[Jack]

Dear all,

 

I’m trying to using hp::DoFHandler to solve my problems. It seems that this 
type of dof handler does not work for solution transfer during parallel 
distributed computing. So is there any way to transfer solution after 
refining and coarsening of mesh when using hp::DoFHandler?

 

Many thanks!

 

Best,

 

Jack

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[deal.II] Re: Crack propagation

[Jack]

Hi Daniel,

Thank you very much!

Regards,

Jack

在 2017年5月14日星期日 UTC+8下午5:07:26，Daniel Arndt写道：
>
> Jack,
>
> have a look at https://github.com/tjhei/cracks
>
> Best,
> Daniel
>
> Am Freitag, 12. Mai 2017 07:57:06 UTC+2 schrieb Jack:
>>
>> Hi S. A. Mohseni,
>>
>> I'm also interested on the cracking mechanics, where is such an example 
>> for crack propagation ? 
>>
>> Thanks !
>>
>> 在 2017年3月30日星期四 UTC+8下午9:13:16，Seyed Ali Mohseni写道：
>>>
>>> Dear Timo Heister and Thomas Wick,
>>>
>>> I am trying to run your phase-field crack propagation example, namely 
>>> the single edge notched tension test, with less than 9 Gauss points. 
>>> Hence, the fe variable is initialized using FE_Q(degree) where 
>>> degree cannot be 0. This means degree should always be >1 here in order to 
>>> make things work, but how can one compute the examples with 1 or 4 Gauss 
>>> points? Is the code not suited for what I am trying to achieve or where are 
>>> the parts I have to change in order to make it work for less integration 
>>> points. To be honest, I don't even see the point of having 9 integration 
>>> points for a 4-noded quadrilateral or am I overseeing something?
>>>
>>> Thank you in advance.
>>>
>>> Kind regards,
>>> S. A. Mohseni  
>>>
>>

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[deal.II] Re: Crack propagation

[Jack]

Hi S. A. Mohseni,

I'm also interested on the cracking mechanics, where is such an example for 
crack propagation ? 

Thanks !

在 2017年3月30日星期四 UTC+8下午9:13:16，Seyed Ali Mohseni写道：
>
> Dear Timo Heister and Thomas Wick,
>
> I am trying to run your phase-field crack propagation example, namely the 
> single edge notched tension test, with less than 9 Gauss points. 
> Hence, the fe variable is initialized using FE_Q(degree) where degree 
> cannot be 0. This means degree should always be >1 here in order to make 
> things work, but how can one compute the examples with 1 or 4 Gauss points? 
> Is the code not suited for what I am trying to achieve or where are the 
> parts I have to change in order to make it work for less integration 
> points. To be honest, I don't even see the point of having 9 integration 
> points for a 4-noded quadrilateral or am I overseeing something?
>
> Thank you in advance.
>
> Kind regards,
> S. A. Mohseni  
>

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Re: [deal.II] Re: New: step-57

[Jack]

Hi Timo,
Thanks for your help.

I have presented the formulations for time-dependent NS equations in the 
way you have done in step-57. Is it reasonable or you have a better 
suggestion? 

Thanks very much for your advices and help.








在 2017年3月26日星期日 UTC+8下午10:03:27，Timo Heister写道：
>
> >> Is it possible to extend your code to time dependent Navier-Stokes 
> >> equations? 
>
> Certainly, but one could also start from one of the Stokes examples. I 
> don't know if starting from step-57 is the best approach for you, 
> because one would typically use a stable linearized time stepping 
> method instead of solving the nonlinear system using Newton's method 
> in each timestep. An example would be linearized BDF2 for example. 
>

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[deal.II] Re: New: step-57

[Jack]

Hi Daniel,

 

Thanks for your prompt help.

I'm trying to solve the instationary incompressible Navier-Stokes equations 
at not very high Reynolds number(~100). It seems that this kind of fluid 
should be described by Navier-Stokes flow instead of Stokes flow(Re<<1)[1].

 

The "Vector-Valued" method I mean solving the Navier-Stokes equations using 
the same form of velocity as in step-22, step-32 rather than as "scalar" 
variables like in step-35 using the projection method. The step-22, step-32 
are for stokes flow but not for Navier-Stokes flow.

I have tried to extend them to solve Navier-Stokes equations by adding the 
convection term into the left hand matrix but always failed.

 

Thanks very much!


Regards,

 

Jack

[1] https://en.wikipedia.org/wiki/Stokes_flow

在 2017年3月26日星期日 UTC+8下午5:45:48，Daniel Arndt写道：
>
> Jack,
>
> Is it possible to extend your code to time dependent Navier-Stokes 
>>> equations?
>>>
>>> I want to solve the unsteady Navier-Stokes equations using the 
>>> *Vector-Valued* method, but I did not get any good idea from the 
>>> tutorial examples (step-22, step-32, etc.) for Stokes flow.
>>>
>> The velocity in the Stokes and Navier-Stokes equations is vector-valued, 
> but what exactly do you mean by "vector-valued method"?
> step-22 considers the stationary Stokes equations and so does step-32. 
> Basically, you just have to add a time discretization to your equations. 
> Have a look at the examples that deal with time-dependent problems [1]. 
> E.g. step-26[2] considers the heat equation using theta-time stepping 
> scheme and might be a good starting point. Step-35[3] uses a projection 
> method in combination with a BDF(2) time discretization to solve for the 
> instationary Navier-Stokes equations.
>
> Best,
> Daniel
>
> [1] https://www.dealii.org/8.4.1/doxygen/deal.II/Tutorial.html
> [2] https://www.dealii.org/8.4.1/doxygen/deal.II/step_26.html
> [3] https://www.dealii.org/8.4.1/doxygen/deal.II/step_35.html
>

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[deal.II] Re: New: step-57

[Jack]

Hi Daniel,

 

Thanks for your prompt help.

I'm trying to solve the instationary incompressible Navier-Stokes equations 
at not very high Reynolds number(~100). It seems that this kind of fluid 
should be described by Navier-Stokes flow instead of Stokes flow(Re<<1)[1].

 

The "Vector-Valued" method I mean solving the Navier-Stokes equations using 
the same form of velocity as in step-22, step-32 rather than as "scalar" 
variables like in step-35 using the projection method. The step-22, step-32 
are for stokes flow but not for Navier-Stokes flow.

I have tried to extend them to solve Navier-Stokes equations by adding the 
convection term into the left hand matrix but always failed.

 

Thanks very much!


Regards,

 

Jack



在 2017年3月26日星期日 UTC+8下午5:45:48，Daniel Arndt写道：
>
> Jack,
>
> Is it possible to extend your code to time dependent Navier-Stokes 
>>> equations?
>>>
>>> I want to solve the unsteady Navier-Stokes equations using the 
>>> *Vector-Valued* method, but I did not get any good idea from the 
>>> tutorial examples (step-22, step-32, etc.) for Stokes flow.
>>>
>> The velocity in the Stokes and Navier-Stokes equations is vector-valued, 
> but what exactly do you mean by "vector-valued method"?
> step-22 considers the stationary Stokes equations and so does step-32. 
> Basically, you just have to add a time discretization to your equations. 
> Have a look at the examples that deal with time-dependent problems [1]. 
> E.g. step-26[2] considers the heat equation using theta-time stepping 
> scheme and might be a good starting point. Step-35[3] uses a projection 
> method in combination with a BDF(2) time discretization to solve for the 
> instationary Navier-Stokes equations.
>
> Best,
> Daniel
>
> [1] https://www.dealii.org/8.4.1/doxygen/deal.II/Tutorial.html
> [2] https://www.dealii.org/8.4.1/doxygen/deal.II/step_26.html
> [3] https://www.dealii.org/8.4.1/doxygen/deal.II/step_35.html
>

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[deal.II] Re: New: step-57

[Jack]

>
> Dear Timo,
>
 

> It is a very good example for solving Navier-Stokes equations.
>
> Is it possible to extend your code to time dependent Navier-Stokes 
> equations?
>
> I want to solve the unsteady Navier-Stokes equations using the 
> *Vector-Valued* method, but I did not get any good idea from the tutorial 
> examples (step-22, step-32, etc.) for Stokes flow.
>
> Thanks very much for your help!
>
>  
>
> Jack
>

在 2017年2月11日星期六 UTC+8上午12:47:34，Timo Heister写道：
>
> I am happy to announce that we added a new tutorial program: 
>
> The new tutorial program step-57 (contributed by Liang Zhao and Timo 
> Heister) shows how to solve the stationary, incompressible 
> Navier-Stokes equations using Newton's method. The program features 
> block linear solvers for the saddle point problem and adaptive mesh 
> refinement. The benchmark problem is the famous lid-driven cavity 
> test. 
>
> -- 
> Timo Heister 
> http://www.math.clemson.edu/~heister/ 
>

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Re: [deal.II] Re: Problems in handling the userdata of Distributed Triangulation

[Jack]

Hi Denis,

Thanks.

Yes, that’s right. For distributed MPI parallel computing, this is a big 
problem.

 

I have just learned deal.II for less than three months, so I’m still new. 
And also I’m not working on numerical mathematics, so it is difficult for 
me to solve such problem but I will try. If I figure out this problem I 
will post it to the forum. If you have made some progress on this problem, 
please tell me promptly.

 

Thanks so much.


Cheers,


Jack

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[deal.II] Re: Problems in handling the userdata of Distributed Triangulation

[Jack]

Dear Jean，

 

Thanks so much for your suggestions. I’m really very happy for such new 
development.

 

I understand that using the CellDataStorage and 
TransferableQuadraturePointData classes  is better than user_pointer when 
the mesh requires coarsening and refining. 

*Yet I do not understand how can I read the data of a neighbor quadrature 
point that happens to in a ghost cell. Could you give me some clues?*

 

Thanks!

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