Re: [deal.II] Issue linking GMSH when installing & building dealii 9.4

2022-09-08 Thread Matthew Rich
Thanks for the reply.  I tried building from source a couple times and no
luck. I see tetgen and netgen in the cmake output but not  blas

Anyone do this recently? I have LAPACK debian package but that does not
seem to do the job. I think this is my issue is BLAS is missing but not
sure how to rectify.


*cmake output  for GMSH*
cmake -DENABLE_BUILD_DYNAMIC=1 -DENABLE_BUILD_SHARED=1 -DENABLE_MUMPS=1
-ENABLE_NUMPY=1 -DENABLE_PETSC4PY=1 -DENABLE_OCC_TBB=1 -DENABLE_OPENACC=1
-DENABLE_PETSC=1 -DENABLE_REVOROPT=1 -VERBOSE=1 ../
-- Found 64Bit
-- Found OpenMP
-- Found OpenACC_C: -fopenacc
-- Found OpenACC_CXX: -fopenacc
-- Found OpenACC
-- Found Eigen[contrib]
-- Found Mesh
-- Found Solver
-- Found Post
-- Found Plugins
-- Found Parser
CMake Warning (dev) at /usr/share/cmake-3.18/Modules/FindOpenGL.cmake:305
(message):
  Policy CMP0072 is not set: FindOpenGL prefers GLVND by default when
  available.  Run "cmake --help-policy CMP0072" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

  FindOpenGL found both a legacy GL library:

OPENGL_gl_LIBRARY: /usr/lib/x86_64-linux-gnu/libGL.so

  and GLVND libraries for OpenGL and GLX:

OPENGL_opengl_LIBRARY: /usr/lib/x86_64-linux-gnu/libOpenGL.so
OPENGL_glx_LIBRARY: /usr/lib/x86_64-linux-gnu/libGLX.so

  OpenGL_GL_PREFERENCE has not been set to "GLVND" or "LEGACY", so for
  compatibility with CMake 3.10 and below the legacy GL library will be
used.
Call Stack (most recent call first):
  /usr/share/cmake-3.18/Modules/FindFLTK.cmake:83 (find_package)
  CMakeLists.txt:633 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Could NOT find FLTK (missing: FLTK_LIBRARIES)
-- Found ONELAB
-- Found ONELABMetamodel
-- Found ANN[contrib]
-- Found ALGLIB[contrib]
-- Found DIntegration
-- Found Kbipack
-- GMP not found: Kbipack uses long int
-- Found MathEx[contrib]
-- Found Metis[contrib]
-- Found TetGen/BR
-- Found Voro++[contrib]
-- Found OptHom
-- Found DomHex
-- Found QuadTri
-- Found Blossom
-- Found Netgen
-- Found Bamg
-- Found Hxt
-- Found QuadMeshingTools
-- Found WinslowUntangler
-- Found Gmm[contrib]
-- Found PETSc
-- Found OpenCASCADE version 7.5.1 in /usr/include/opencascade
-- Found OpenCASCADE-CAF
-- Found OpenCASCADE
-- Found Dlopen
-- Found LinuxJoystick
-- Found Revoropt
--
-- Gmsh 4.10.5 has been configured for Linux64-sdk
--
--  * Build options: 64Bit ALGLIB[contrib] ANN[contrib] Bamg Blossom
DIntegration Dlopen DomHex Eigen[contrib] Gmm[contrib] Hxt Kbipack
LinuxJoystick MathEx[contrib] Mesh Metis[contrib] Netgen ONELAB
ONELABMetamodel OpenACC OpenCASCADE OpenCASCADE-CAF OpenMP OptHom PETSc
Parser Plugins Post QuadMeshingTools QuadTri Revoropt Solver TetGen/BR
Voro++[contrib] WinslowUntangler
--  * Build type: RelWithDebInfo
--  * C compiler: /usr/bin/cc
--  * C++ compiler: /usr/bin/c++
--  * Install prefix: /usr/local
--
-- Configuring done
-- Generating done
-- Build files have been written to: /home/mjrich/gmsh-4.10.5

On Thu, 8 Sept 2022 at 13:51, Daniel Arndt  wrote:

> Matthew,
>
> I don't know if the missing references are due to missing components in
> your gmsh installation (but I wouldn't be surprised).
> In any way, *"netgen, tetgen and blas support has to be enabled in Gmsh" *
> relates to CMake options when building gmsh from source, e.g.,
> https://gmsh.info/src/gmsh-4.10.5-source.tgz.
> I would try if building gmsh yourself with those dependencies/options
> resolves the issue.
>
> Best,
> Daniel
>
> On Thu, Sep 8, 2022 at 9:48 AM Matthew Rich  wrote:
>
>> Hi all,
>>
>> I was upgrading the 9.4 and I needed to include GMSH for a project I am
>> working on so I can use the API in my dealii code. I am getting the
>> following error despite getting the all clear from CMAKE. How can I fix
>> this , are there version limits on GMSH? I did notice this line*
>> "netgen, tetgen and blas support has to be enabled in Gmsh"  *How does
>> one ensure that? I do not see much in their github readme.
>>
>> *Some details- *
>> On a windows system running dealii in WSL2 under debian. I have built
>> gmsh from source and it is functional by itself, so I feel I did that part
>> right.  I have -DGMSH_DIR set to the root directory of my gmsh installation
>> so ~/gmsh-gmsh-4.10.5 cmake settings when I install dealii
>>
>> *make Error *
>> [ 75%] Linking CXX executable ../bin/step_3_mixed.debug
>> ../lib/libdeal_II.g.so.9.4.0: error: undefined reference to
>> 'gmsh::model::addPhysicalGroup(int, std::vector >
>> const&, int)'
>> ../lib/libdeal_II.g.so.9.4.0: error: undefined reference to
>> 'gmsh::model::mesh::removeDuplicateNodes()'
>> ../lib/libdeal_II.g.so.9.4.0: error: undefined reference to
>> 'gmsh::initialize(int, char**, bool)'
>> collect2: error: ld returned 1 exit status
>> make[2]: *** [examples/CMakeFiles/step_3_mixed.debug.dir/build.make:292:
>> bin/step_3_mixed.debug] Error 1
>> make[1]: *** [CMakeFiles/Makefile2:3926:
>> examples/CMakeFiles/step_3_mixed.debug.dir/al

Re: [deal.II] fe_interface_values but of a tensor quantity

2022-09-08 Thread Wolfgang Bangerth

On 9/8/22 04:40, Abbas wrote:


I want the average of (uu) which is = u1*u1/2 +u2*u2/2 but I don't know 
how to get it.


Do I understand right that u1 and u2 are vectors, and when you say
  u1 * u1
you mean the outer product of a vector with itself, forming a tensor?

Best
 W.

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Issue linking GMSH when installing & building dealii 9.4

2022-09-08 Thread Daniel Arndt
Matthew,

I don't know if the missing references are due to missing components in
your gmsh installation (but I wouldn't be surprised).
In any way, *"netgen, tetgen and blas support has to be enabled in Gmsh" *
relates to CMake options when building gmsh from source, e.g.,
https://gmsh.info/src/gmsh-4.10.5-source.tgz.
I would try if building gmsh yourself with those dependencies/options
resolves the issue.

Best,
Daniel

On Thu, Sep 8, 2022 at 9:48 AM Matthew Rich  wrote:

> Hi all,
>
> I was upgrading the 9.4 and I needed to include GMSH for a project I am
> working on so I can use the API in my dealii code. I am getting the
> following error despite getting the all clear from CMAKE. How can I fix
> this , are there version limits on GMSH? I did notice this line* "netgen,
> tetgen and blas support has to be enabled in Gmsh"  *How does one ensure
> that? I do not see much in their github readme.
>
> *Some details- *
> On a windows system running dealii in WSL2 under debian. I have built gmsh
> from source and it is functional by itself, so I feel I did that part
> right.  I have -DGMSH_DIR set to the root directory of my gmsh installation
> so ~/gmsh-gmsh-4.10.5 cmake settings when I install dealii
>
> *make Error *
> [ 75%] Linking CXX executable ../bin/step_3_mixed.debug
> ../lib/libdeal_II.g.so.9.4.0: error: undefined reference to
> 'gmsh::model::addPhysicalGroup(int, std::vector >
> const&, int)'
> ../lib/libdeal_II.g.so.9.4.0: error: undefined reference to
> 'gmsh::model::mesh::removeDuplicateNodes()'
> ../lib/libdeal_II.g.so.9.4.0: error: undefined reference to
> 'gmsh::initialize(int, char**, bool)'
> collect2: error: ld returned 1 exit status
> make[2]: *** [examples/CMakeFiles/step_3_mixed.debug.dir/build.make:292:
> bin/step_3_mixed.debug] Error 1
> make[1]: *** [CMakeFiles/Makefile2:3926:
> examples/CMakeFiles/step_3_mixed.debug.dir/all] Error 2
> make: *** [Makefile:149: all] Error 2
>
> *CMAKE output *
>
> #  Configured Features (DEAL_II_ALLOW_BUNDLED = ON,
> DEAL_II_ALLOW_AUTODETECTION = ON):
> #  ( DEAL_II_WITH_64BIT_INDICES = OFF )
> #  ( DEAL_II_WITH_ADOLC = OFF )
> #  ( DEAL_II_WITH_ARBORX = OFF )
> #DEAL_II_WITH_ARPACK set up with external dependencies
> #DEAL_II_WITH_ASSIMP set up with external dependencies
> #DEAL_II_WITH_BOOST set up with external dependencies
> #  ( DEAL_II_WITH_CGAL = OFF )
> #DEAL_II_WITH_COMPLEX_VALUES = ON
> #  ( DEAL_II_WITH_CUDA = OFF )
> #  ( DEAL_II_WITH_GINKGO = OFF )
> #DEAL_II_WITH_GMSH set up with external dependencies
> #DEAL_II_WITH_GSL set up with external dependencies
> #DEAL_II_WITH_HDF5 set up with external dependencies
> #DEAL_II_WITH_KOKKOS set up with external dependencies
> #DEAL_II_WITH_LAPACK set up with external dependencies
> #DEAL_II_WITH_METIS set up with external dependencies
> #DEAL_II_WITH_MPI set up with external dependencies
> #DEAL_II_WITH_MUPARSER set up with external dependencies
> #DEAL_II_WITH_OPENCASCADE set up with external dependencies
> #DEAL_II_WITH_P4EST set up with external dependencies
> #DEAL_II_WITH_PETSC set up with external dependencies
> #DEAL_II_WITH_SCALAPACK set up with external dependencies
> #DEAL_II_WITH_SLEPC set up with external dependencies
> #  ( DEAL_II_WITH_SUNDIALS = OFF )
> #  ( DEAL_II_WITH_SYMENGINE = OFF )
> #DEAL_II_WITH_TBB set up with external dependencies
> #DEAL_II_WITH_TRILINOS set up with external dependencies
> #DEAL_II_WITH_UMFPACK set up with external dependencies
> #DEAL_II_WITH_ZLIB set up with external dependencies
> #
> #  Component configuration:
> #  ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
> #DEAL_II_COMPONENT_EXAMPLES
> #  ( DEAL_II_COMPONENT_PACKAGE = OFF )
> #  ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )
> #
> #  Detailed information (compiler flags, feature configuration) can be
> found in detailed.log
> #
> #  Run  $ make info  to print a help message with a list of top level
> targets
> #
> ###
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/mjrich/dealii-9.4.0/build
>
>
> --
> The deal.II project is located at http://www.dealii.org/
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> 
> .
>

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Re: [deal.II] compiling deal.ii 9.4 on wsl error

2022-09-08 Thread jim wo
Daniel
thank you very much,you are so kind,God bless you.
best
qiong

Daniel Arndt  于 2022年9月8日周四 21:41写道:

> Qiong,
>
> It's not sufficient to include deal.II's include files but you need to
> link the library target. Have a look at
> https://www.dealii.org/current/users/cmake_user.html.
>
> Best,
> Daniel
>
>
> On Wed, Sep 7, 2022 at 9:38 PM jim wo  wrote:
>
>> and at the same time, I write the codes and it comes "the
>> deal.II/grid/tria.h not found" I dont konw why
>> best
>> Qiong
>>
>>
>> 在2022年9月8日星期四 UTC+8 09:34:59 写道:
>>
>>> I created a new cmake project on wsl with vscode ,I write the
>>> INCLUDE_DIRETORIES with header file of dealii in the CMakeLists and then
>>> cmake project ,I am not sure if its going to work . But when I make it
>>> comes error as follow
>>> [image: 1662600815935.png]
>>>  best
>>> Qiong
>>> 在2022年9月8日星期四 UTC+8 09:23:08 写道:
>>>
 I did install MPI on wsl
 and I congfigure deal.ii with DEAL_II_WITH_PETSC = ON
 DEAL_II_WITH_P4EST = ON


 在2022年9月7日星期三 UTC+8 23:03:57 写道:

> Qiong,
>
> What CMake settings did you use to configure deal.II?
> Does your system indeed provide an MPI installation?
>
> Bets,
> Daniel
>
> On Wed, Sep 7, 2022 at 10:22 AM jim wo  wrote:
>
>> Hello,
>> I want to  develop my own project on wsl with deal.ii 9.4.  after
>> make I got this message:
>>
>> In file included from /home/wu/deal_II/include/deal.II/grid/tria.h:20,
>>  from /home/wu/cmakeQuickStart/main.cpp:23:
>> /home/wu/deal_II/include/deal.II/base/config.h:540:12: fatal error:
>> mpi.h: No such file or directory
>>   540 | #  include 
>>   |^~~
>> compilation terminated.
>> thanks for  your help
>>  Qiong
>>
>> --
>> 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
>> ---
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>> Groups "deal.II User Group" group.
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>> send an email to dealii+un...@googlegroups.com.
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>> 
>> .
>>
> --
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>> 
>> .
>>
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[deal.II] Issue linking GMSH when installing & building dealii 9.4

2022-09-08 Thread Matthew Rich
Hi all, 

I was upgrading the 9.4 and I needed to include GMSH for a project I am 
working on so I can use the API in my dealii code. I am getting the 
following error despite getting the all clear from CMAKE. How can I fix 
this , are there version limits on GMSH? I did notice this line* "netgen, 
tetgen and blas support has to be enabled in Gmsh"  *How does one ensure 
that? I do not see much in their github readme. 

*Some details- *
On a windows system running dealii in WSL2 under debian. I have built gmsh 
from source and it is functional by itself, so I feel I did that part 
right.  I have -DGMSH_DIR set to the root directory of my gmsh installation 
so ~/gmsh-gmsh-4.10.5 cmake settings when I install dealii  

*make Error *
[ 75%] Linking CXX executable ../bin/step_3_mixed.debug
../lib/libdeal_II.g.so.9.4.0: error: undefined reference to 
'gmsh::model::addPhysicalGroup(int, std::vector > 
const&, int)'
../lib/libdeal_II.g.so.9.4.0: error: undefined reference to 
'gmsh::model::mesh::removeDuplicateNodes()'
../lib/libdeal_II.g.so.9.4.0: error: undefined reference to 
'gmsh::initialize(int, char**, bool)'
collect2: error: ld returned 1 exit status
make[2]: *** [examples/CMakeFiles/step_3_mixed.debug.dir/build.make:292: 
bin/step_3_mixed.debug] Error 1
make[1]: *** [CMakeFiles/Makefile2:3926: 
examples/CMakeFiles/step_3_mixed.debug.dir/all] Error 2
make: *** [Makefile:149: all] Error 2

*CMAKE output *

#  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, 
DEAL_II_ALLOW_AUTODETECTION = ON):
#  ( DEAL_II_WITH_64BIT_INDICES = OFF )
#  ( DEAL_II_WITH_ADOLC = OFF )
#  ( DEAL_II_WITH_ARBORX = OFF )
#DEAL_II_WITH_ARPACK set up with external dependencies
#DEAL_II_WITH_ASSIMP set up with external dependencies
#DEAL_II_WITH_BOOST set up with external dependencies
#  ( DEAL_II_WITH_CGAL = OFF )
#DEAL_II_WITH_COMPLEX_VALUES = ON
#  ( DEAL_II_WITH_CUDA = OFF )
#  ( DEAL_II_WITH_GINKGO = OFF )
#DEAL_II_WITH_GMSH set up with external dependencies
#DEAL_II_WITH_GSL set up with external dependencies
#DEAL_II_WITH_HDF5 set up with external dependencies
#DEAL_II_WITH_KOKKOS set up with external dependencies
#DEAL_II_WITH_LAPACK set up with external dependencies
#DEAL_II_WITH_METIS set up with external dependencies
#DEAL_II_WITH_MPI set up with external dependencies
#DEAL_II_WITH_MUPARSER set up with external dependencies
#DEAL_II_WITH_OPENCASCADE set up with external dependencies
#DEAL_II_WITH_P4EST set up with external dependencies
#DEAL_II_WITH_PETSC set up with external dependencies
#DEAL_II_WITH_SCALAPACK set up with external dependencies
#DEAL_II_WITH_SLEPC set up with external dependencies
#  ( DEAL_II_WITH_SUNDIALS = OFF )
#  ( DEAL_II_WITH_SYMENGINE = OFF )
#DEAL_II_WITH_TBB set up with external dependencies
#DEAL_II_WITH_TRILINOS set up with external dependencies
#DEAL_II_WITH_UMFPACK set up with external dependencies
#DEAL_II_WITH_ZLIB set up with external dependencies
#
#  Component configuration:
#  ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
#DEAL_II_COMPONENT_EXAMPLES
#  ( DEAL_II_COMPONENT_PACKAGE = OFF )
#  ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF )
#
#  Detailed information (compiler flags, feature configuration) can be 
found in detailed.log
#
#  Run  $ make info  to print a help message with a list of top level 
targets
#
###
-- Configuring done
-- Generating done
-- Build files have been written to: /home/mjrich/dealii-9.4.0/build


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Re: [deal.II] compiling deal.ii 9.4 on wsl error

2022-09-08 Thread Daniel Arndt
Qiong,

It's not sufficient to include deal.II's include files but you need to link
the library target. Have a look at
https://www.dealii.org/current/users/cmake_user.html.

Best,
Daniel


On Wed, Sep 7, 2022 at 9:38 PM jim wo  wrote:

> and at the same time, I write the codes and it comes "the
> deal.II/grid/tria.h not found" I dont konw why
> best
> Qiong
>
>
> 在2022年9月8日星期四 UTC+8 09:34:59 写道:
>
>> I created a new cmake project on wsl with vscode ,I write the
>> INCLUDE_DIRETORIES with header file of dealii in the CMakeLists and then
>> cmake project ,I am not sure if its going to work . But when I make it
>> comes error as follow
>> [image: 1662600815935.png]
>>  best
>> Qiong
>> 在2022年9月8日星期四 UTC+8 09:23:08 写道:
>>
>>> I did install MPI on wsl
>>> and I congfigure deal.ii with DEAL_II_WITH_PETSC = ON
>>> DEAL_II_WITH_P4EST = ON
>>>
>>>
>>> 在2022年9月7日星期三 UTC+8 23:03:57 写道:
>>>
 Qiong,

 What CMake settings did you use to configure deal.II?
 Does your system indeed provide an MPI installation?

 Bets,
 Daniel

 On Wed, Sep 7, 2022 at 10:22 AM jim wo  wrote:

> Hello,
> I want to  develop my own project on wsl with deal.ii 9.4.  after make
> I got this message:
>
> In file included from /home/wu/deal_II/include/deal.II/grid/tria.h:20,
>  from /home/wu/cmakeQuickStart/main.cpp:23:
> /home/wu/deal_II/include/deal.II/base/config.h:540:12: fatal error:
> mpi.h: No such file or directory
>   540 | #  include 
>   |^~~
> compilation terminated.
> thanks for  your help
>  Qiong
>
> --
> 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.
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> 
> .
>
 --
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> 
> .
>

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[deal.II] fe_interface_values but of a tensor quantity

2022-09-08 Thread Abbas
I am using DG elements and if I want to query the average of my vector 
solution across the interface I can do something like :
  std::vector> old_velocity_averages(n_q_points);
  
fe_iv[velocities].get_average_of_function_values(solution_np0,old_velocity_averages);
which gives me the average of u=u1/2+u2/2

I want the average of (uu) which is = u1*u1/2 +u2*u2/2 but I don't know how 
to get it. 
 
I am stuck and will take any hints. Should I inherit the fe_interface class 
and implement my own function?   

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