Re: [deal.II] installation fails with intel/19.0.5

[Daniel Arndt]

Victor,


But I’m still not finishing the cmake.
>
> So there is a ton of
> ...
> What do those mean? Are they fatal or is that only cmake discovering
> what’s available and what not?
>

No, these are not fatal. We just check for the dependencies to enable.
Again, what is the full output when running CMake? Does it create a
Makefile you can run via 'make'?

Best,
Daniel

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[deal.II] Using interpolate_boundary_conditions

[Amy Kaczmarowski]

Hi,

I'm attempting to apply a displacement boundary condition on a surface in 
my problem.  However, I would like the direction of the displacement of 
each point on the surface to depend on its direction from some point (for 
example the origin).  Imagine a balloon inflating where the displacement 
direction is from the center of the balloon.  My thought was to use a 
function similar to the example boundary conditions in step 23 but extended 
for 3 dimensions.  I defined the following class in my code:

template 
class BoundaryValuesU : public Function{
  public:
virtual void vector_value(const Point & p, Vector &values) 
const override
  {
double xpos, ypos, zpos;
xpos = p[0];
ypos = p[1];
if (dim==3){zpos=p[2];}
else {zpos=0.0;}
values[0] 
= 
xpos/std::pow(std::pow(xpos,2.0)+std::pow(ypos,2.0)+std::pow(zpos,2.0),0.5)*0.1;
values[1] 
= 
ypos/std::pow(std::pow(xpos,2.0)+std::pow(ypos,2.0)+std::pow(zpos,2.0),0.5)*0.1;
values[2] 
= 
zpos/std::pow(std::pow(xpos,2.0)+std::pow(ypos,2.0)+std::pow(zpos,2.0),0.5)*0.1;
return; 
}
  };

Then I apply the boundary conditions in the following way to the surface 
with boundary id 2:

std::vector uBC (3, true);
BoundaryValuesU boundary_values_u_function;
VectorTools::interpolate_boundary_values (dof_handler, 2, 
boundary_values_u_function, constraints, uBC);

However, when I attempt to run with this case I get the following error:

An error occurred in line <2263> of file 

 
in function
void 
dealii::VectorToolsdo_interpolate_boundary_values(const 
M_or_MC &, const DoFHandlerType &, const 
std::map *, 
std::less, std::allocator *>>> &, std::map, std::allocator>> &, const dealii::ComponentMask &) [with dim = 3, spacedim = 
3, number = double, DoFHandlerType = dealii::DoFHandler, M_or_MC = 
dealii::Mapping]
The violated condition was:
n_components == i->second->n_components
Additional information:
Dimension 3 not equal to 1.

Is there a way I am supposed to be initializing n_components in the class 
to make this work?  Or is this just the wrong way to be doing this?

Thank you.

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Re: [deal.II] installation fails with intel/19.0.5

[Victor Eijkhout]

On Sep 30, 2019, at 5:29 PM, Marc Fehling 
mailto:m.fehl...@fz-juelich.de>> wrote:

DDEAL_II_HAVE_FLAG_Wimplicit_fallthrough=0

Hm. Turns out I had an explicit c++14 in my compiler specification. At least 
now I don’t get that fallthrough message anymore.

But I’m still not finishing the cmake.

So there is a ton of

%%
-- Include 
/admin/build/admin/rpms/frontera/BUILD/dealii-9.1.1/cmake/configure/configure_scalapack.cmake
-- SCALAPACK_LIBRARY not found! Call:
-- FIND_LIBRARY(SCALAPACK_LIBRARY NAMES scalapack scalapack-openmpi 
scalapack-pvm scalapack-mpi scalapack-mpich scalapack-mpich2 scalapack-lam 
HINTS PATH_SUFFIXES lib lib64 lib)
--   SCALAPACK_LIBRARIES: *** Required variable "SCALAPACK_LIBRARY" set to 
NOTFOUND ***
--   SCALAPACK_LINKER_FLAGS:
-- Could NOT find SCALAPACK
-- DEAL_II_WITH_SCALAPACK has unmet external dependencies.
%%

reports. What do those mean? Are they fatal or is that only cmake discovering 
what’s available and what not?

Victor.

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[deal.II] Re: About Darcy-Brinkman-Forchheimer equation discretization

[Bruno Blais]

Hello, 

It depends of the value of the Reynolds number and the gradients of K with 
respect to x or t, but generally the last two terms do not generally pose 
problems. The first additional term to the right leads to a mass matrix, 
which is well conditioned.
The second term itself is trickier. If you want to use an analytical 
Jacobian formulation and Newton's method, you will need to calculate the 
Frechet derivative of the velocity magnitude. You can also use a Picard 
iteration for this term, which will greatly simplify the expression of the 
Jacobian at the cost more Newton iteration.
Issues generally arise when you have jumps the value of K in space. Then 
generally it is better to use some sort of upwinding to prevent 
oscillations in the velocity field (i.e SUPG).



On Friday, 27 September 2019 22:41:22 UTC-4, FU wrote:
>
> Hi，
> I want to solve the problem about Darcy-Brinkman-Forchheimer equations, 
> but don't know how to discretizate this equation.
>
> [image: Darcy equation.png]
>
> This equation has a similar N-S equation. But the discretization of the 
> last item of the equation and the programming statements are somewhat 
> unclear.
>
>
> Yours，
>
> FU
>

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Re: [deal.II] installation fails with intel/19.0.5

[Marc Fehling]

On Monday, September 30, 2019 at 11:01:45 PM UTC+2, Victor Eijkhout wrote:
>
>
>
> On Sep 30, 2019, at 3:23 PM, Marc Fehling  > wrote:
>
> Victor, have you tried disabling C++17 support? Maybe that'll do the 
> trick...
>
>
> cmake option please?
>
> (is there a list of all cmake options for your build process?)
>
> My best guess was:
>
> -DDEAL_II_WITH_CXX17=OFF
>

Your guess was indeed correct :) You'll find a list of cmake attributes for 
deal.II in the documentation here 
.
 

>
> and that got me to:
>
> 
> Run Build Command:"/usr/bin/gmake" "cmTC_8b681/fast"
> /usr/bin/gmake -f CMakeFiles/cmTC_8b681.dir/build.make 
> CMakeFiles/cmTC_8b681.dir/build
> gmake[1]: Entering directory `/tmp/dealii-build/CMakeFiles/CMakeTmp'
> Building CXX object CMakeFiles/cmTC_8b681.dir/src.cxx.o
> /opt/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/icpc   
>  -DDEAL_II_HAVE_FLAG_Wimplicit_fallthrough=0   -Wimplicit-fallthrough=0 -o 
> CMakeFiles/cmTC_8b681.dir/src.cxx.o -c 
> /tmp/dealii-build/CMakeFiles/CMakeTmp/src.cxx
> icpc: command line warning #10148: option '-W=implicit-fallthrough=0' not 
> supported
> Linking CXX executable cmTC_8b681
> /opt/apps/cmake/3.13.4/bin/cmake -E cmake_link_script 
> CMakeFiles/cmTC_8b681.dir/link.txt --verbose=1
> /opt/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/icpc   
> -DDEAL_II_HAVE_FLAG_Wimplicit_fallthrough=0-rdynamic 
> CMakeFiles/cmTC_8b681.dir/src.cxx.o  -o cmTC_8b681
> gmake[1]: Leaving directory `/tmp/dealii-build/CMakeFiles/CMakeTmp'
>
> Source file was:
> int main() { return 0; }
> Performing C++ SOURCE FILE Test DEAL_II_HAVE_FLAG_Wno_nested_anon_types 
> failed with the following output:
> Change Dir: /tmp/dealii-build/CMakeFiles/CMakeTmp
>
> Run Build Command:"/usr/bin/gmake" "cmTC_b3b8f/fast"
> /usr/bin/gmake -f CMakeFiles/cmTC_b3b8f.dir/build.make 
> CMakeFiles/cmTC_b3b8f.dir/build
>
> %%%
>
> which does not look fatal to me. It’s only a warning.
>

Yes, these are only warnings.

I am confused about Intel19's state on the fallthrough flag: They say that 
it is implemented on their website 
,
 
but it seems that they just prepared it according to this statement 
? Or 
is it just the 'implicit fallthrough' feature that Intel19 is not capable 
off.

Would you mind to try enabling C++17 support but disabling the implicit 
fallthrough feature by providing "-DDEAL_II_WITH_CXX17=ON 
-DDEAL_II_HAVE_FLAG_Wimplicit_fallthrough=0" to cmake? If this fails, I 
think it would be best to keep C++17 disabled for now...

Best,
Marc

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Re: [deal.II] installation fails with intel/19.0.5

[Marc Fehling]

On Friday, September 27, 2019 at 11:24:12 PM UTC+2, Wolfgang Bangerth wrote:

>
> Didn't we recently merge a patch where ICC reported that it understands 
> C++17, but doesn't in fact support this attribute? Does that ring a bell 
> for anyone? 
>

Intel published a list of all C++17 features that their Intel19 compiler 
features here 

.

We had an issue with Intel19 not understanding class template argument 
deduction (CTAD), which has been fixed via this patch 
.

Victor, have you tried disabling C++17 support? Maybe that'll do the 
trick...

Best,
Marc

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[deal.II] Re: Issue with boost serialization and spack?

[Konrad Simon]

Thank you, Denis. I use a pretty stupid (but simple) workaround: I setup 
and compile deal.ii myself since all dependencies are compiled and use the 
cmake command used by spack. That works. And I do not get the serialization 
error.

However, now my code runs on the machine I installed it on. But once I use 
slurm to distribute the job across nodes I get "illegal instruction" erros. 
Frustrating.

Nevertheless, thanks for your hint.

Best,
Konrad

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