Introducing SALOME Smesh module

[supermatrixx]

Hello, everyone,

me and my team would like to introduce the features of the smesh module present in the SALOME platform within SunCAE alongside the present gmsh meshing.

Are there any guidelines on how to proceed (what files to edit, what paths to add, etc.)?

Thank you very much

[gtheler]

Hi supermatrixx. Thanks for your interest and your help.

There is no written guideline, I have some ideas on how to organize the thing which I will explain below. If you think there is a better way, we can discuss and change the current design.

The first and most "important" choice would be the solver. So far we only have FeenoX, but eventually I will add more (candidates are Sparselizard, CalculiX and CodeAster). Each solver has a directory inside solvers, e.g. solvers/feenox. In that directory, there should be a file problem.php that tells SunCAE

1. That this solver is available
2. Which problems it can solve
3. Which meshers it supports

The current problems.php for FeenoX is

register_solver("feenox", "FeenoX", ["mechanical", "heat_conduction"], ["gmsh"]);

So SunCAE can tell that FeenoX can solve mechanical and heat_conduction and that it only supports gmsh.
The first step would be to add salome next to Gmsh so when creating a new case, salome appears in the "mesher" combo in step 5.

The next thing would be to add a directory salome in meshers and try to match the files that already exist for gmsh. Most likely this won't be possible and Salome might need some things that Gmsh does not, and viceversa.

Note that Gmsh is used to import the CAD as well. Probably this can also be done by Salome, but the "new project" step imports the CAD before the user chooses the mesher so maybe there will be a mix of Gmsh and Salome at some point.

Also, each mesher (and solver) can provide a deps.sh script to download all the dependencies when running the root-level deps.sh. Check the feenox and gmsh example.

Please start playing and let me know all the bumps you hit.

[supermatrixx]

Since we use code_aster, he might be the correct candidate for us as a solver.

Let's start developing some features and I'll keep you updated, thank you very much Jeremy.

[gtheler]

Fair enough. I had some ideas about how to use Code Aster as a solver, but probably you guys will do far better.
My only attempt to use CodeAster was a couple of years ago: https://seamplex.com/feenox/tests/nafems/le10/

[gtheler]

Hey @supermatrixx .
I'm trying to compile code aster following my notes from three years ago.
I see in the download page at https://code-aster.org/spip.php?article272 that the latest version is from 2020.
When I do

wget https://www.code-aster.org/FICHIERS/aster-full-src-14.6.0-1.noarch.tar.gz
tar xvzf aster-full-src-14.6.0-1.noarch.tar.gz 
cd aster-full-src-14.6.0
mkdir -p $HOME/aster
python3 setup.py --aster_root=$HOME/aster

It gets stuck in tfel-3.2.1 because the compiler does not like to operate on an output stream with an const char[]:

[ 40%] Building CXX object mtest/src/CMakeFiles/TFELMTest.dir/FunctionEvolution.o
[ 40%] Building CXX object mtest/src/CMakeFiles/TFELMTest.dir/Behaviour.o
/tmp/install_tfel.801026/tfel-3.2.1/mtest/src/Behaviour.cxx: In static member function ‘static void mtest::Behaviour::setOptionalMaterialPropertyDefaultValue(mtest::EvolutionManager&, const mtest::EvolutionManager&, const std::string&, mtest::real)’:
/tmp/install_tfel.801026/tfel-3.2.1/mtest/src/Behaviour.cxx:230:13: error: no match for ‘operator<<’ (operand types are ‘std::basic_ostream<char>’ and ‘const char [57]’)
  230 |         log << "Behaviour::setOptionalMaterialPropertiesDefaultValues : "
      |         ~~~ ^~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |         |      |
      |         |      const char [57]
      |         std::basic_ostream<char>
In file included from /usr/include/c++/12/string:53,
                 from /usr/include/c++/12/stdexcept:39,
                 from /tmp/install_tfel.801026/tfel-3.2.1/mtest/src/Behaviour.cxx:14:
/usr/include/c++/12/bits/basic_string.h:3883:5: note: candidate: ‘template<class _CharT, class _Traits, class _Alloc> std::basic_ostream<_CharT, _Traits>& std::operator<<(basic_ostream<_CharT, _Traits>&, const __cxx11::basic_string<_CharT, _Traits, _Alloc>&)’
 3883 |     operator<<(basic_ostream<_CharT, _Traits>& __os,
      |     ^~~~~~~~
/usr/include/c++/12/bits/basic_string.h:3883:5: note:   template argument deduction/substitution failed:
/tmp/install_tfel.801026/tfel-3.2.1/mtest/src/Behaviour.cxx:230:16: note:   mismatched types ‘const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>’ and ‘const char [57]’
  230 |         log << "Behaviour::setOptionalMaterialPropertiesDefaultValues : "
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/ios_base.h:46,
                 from /usr/include/c++/12/streambuf:41,
                 from /usr/include/c++/12/bits/streambuf_iterator.h:35,
                 from /usr/include/c++/12/iterator:66,
                 from /tmp/install_tfel.801026/tfel-3.2.1/include/TFEL/Math/fsarray.hxx:17,
                 from /tmp/install_tfel.801026/tfel-3.2.1/include/TFEL/Math/tmatrix.hxx:22,
                 from /tmp/install_tfel.801026/tfel-3.2.1/mtest/include/MTest/CurrentState.hxx:22,
                 from /tmp/install_tfel.801026/tfel-3.2.1/mtest/src/Behaviour.cxx:20:
/usr/include/c++/12/system_error:279:5: note: candidate: ‘template<class _CharT, class _Traits> std::basic_ostream<_CharT, _Traits>& std::operator<<(basic_ostream<_CharT, _Traits>&, const error_code&)’
  279 |     operator<<(basic_ostream<_CharT, _Traits>& __os, const error_code& __e)
      |     ^~~~~~~~
/usr/include/c++/12/system_error:279:5: note:   template argument deduction/substitution failed:
/tmp/install_tfel.801026/tfel-3.2.1/mtest/src/Behaviour.cxx:230:16: note:   cannot convert ‘"Behaviour::setOptionalMaterialPropertiesDefaultValues : "’ (type ‘const char [57]’) to type ‘const std::error_code&’
  230 |         log << "Behaviour::setOptionalMaterialPropertiesDefaultValues : "
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/memory:77,
                 from /tmp/install_tfel.801026/tfel-3.2.1/mtest/include/MTest/Types.hxx:19,
                 from /tmp/install_tfel.801026/tfel-3.2.1/mtest/include/MTest/CurrentState.hxx:26:
/usr/include/c++/12/bits/shared_ptr.h:70:5: note: candidate: ‘template<class _Ch, class _Tr, class _Tp, __gnu_cxx::_Lock_policy _Lp> std::basic_ostream<_CharT, _Traits>& std::operator<<(basic_ostream<_CharT, _Traits>&, const __shared_ptr<_Tp, _Lp>&)’
   70 |     operator<<(std::basic_ostream<_Ch, _Tr>& __os,
      |     ^~~~~~~~
/usr/include/c++/12/bits/shared_ptr.h:70:5: note:   template argument deduction/substitution failed:
/tmp/install_tfel.801026/tfel-3.2.1/mtest/src/Behaviour.cxx:230:16: note:   mismatched types ‘const std::__shared_ptr<_Tp, _Lp>’ and ‘const char [57]’
  230 |         log << "Behaviour::setOptionalMaterialPropertiesDefaultValues : "
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: *** [mtest/src/CMakeFiles/TFELMTest.dir/build.make:300: mtest/src/CMakeFiles/TFELMTest.dir/Behaviour.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:4232: mtest/src/CMakeFiles/TFELMTest.dir/all] Error 2
make: *** [Makefile:166: all] Error 2
gtheler@tom:/tmp/install_tfel.801026/tfel-3.2.1/build$ 

The next thing I tried was to clone from hg.code.sf.net:

$ hg clone http://hg.code.sf.net/p/codeaster/src codeaster-src
$ cd codeaster-src
$ ./waf configure

It fails to find a mumps header when it is already there

gtheler@tom:~/codigos/3ros/codeaster-src$ ./waf configure
checking environment... executing: ./waf.engine configure --out=build/std --jobs=4
Setting top to                           : /home/old/3ros/codeaster-src 
Setting out to                           : /home/old/3ros/codeaster-src/build/std 
Setting prefix to                        : /home/old/3ros/install/std 
Checking for 'gcc' (C compiler)          : /usr/bin/gcc 
Checking for 'g++' (C++ compiler)        : /usr/bin/g++ 
Checking for 'gfortran' (Fortran compiler) : /usr/bin/gfortran 
Checking for C compiler version          : gcc 12.2.0 
Checking for Fortran compiler version    : gfortran 12.2.0 
fortran link verbose flag                : -v 
Checking for OpenMP flag -fopenmp        : yes 
Checking for program 'python'            : /usr/bin/python3 
Checking for python version >= 3.5.0     : 3.11.2 
python-config                            : /usr/bin/python3-config 
Asking python-config for pyembed '--cflags --libs --ldflags --embed' flags : yes 
Testing pyembed configuration            : yes 
Asking python-config for pyext '--cflags --libs --ldflags' flags : yes 
Testing pyext configuration              : yes 
Checking for python module 'numpy'       : 1.26.4 
Checking for numpy include               : ['/home/gtheler/.local/lib/python3.11/site-packages/numpy/core/include'] 
Checking for python module 'asrun'       : not found 
Getting platform                         : ASTER_PLATFORM_LINUX64 
Checking for library m                   : yes 
Checking for library z                   : yes 
Checking for number of cores             : 1 
Checking for program 'ldd'               : /usr/bin/ldd 
Checking library blas                    : yes (openblas) 
Checking for a program using blas/lapack : yes 
Detected math libraries                  : ['openblas'] 
Setting libm after files                 : nothing done 
Checking for library hdf5                : not found 
Checking for library med                 : not found 
Checking for library metis               : yes 
Checking for header metis.h              : yes 
Checking metis version                   : 5.1.0 
Checking for smumps_struc.h              : no 
The configuration failed
(complete log in /home/old/3ros/codeaster-src/build/std/config.log)
check your environment or use --disable-mumps
gtheler@tom:~/codigos/3ros/codeaster-src$ ls /usr/include/smumps_struc.h 
/usr/include/smumps_struc.h
gtheler@tom:~/codigos/3ros/codeaster-src$ 

Any help?

[supermatrixx]

Hi jeremy,

• Since a couple of years the code_aster team has moved to gitlab https://gitlab.com/codeaster/src , on the official website https://code-aster.org/spip.php?rubrique21 you will find older versions of the code. The first advice is to use the official gitlab for the updated source code.

• Information on how to compile the updated source code can be found at the following link https://gitlab.com/codeaster-opensource-documentation/opensource-installation-development.

• I will now answer your question. We in my team decided to compile code_aster MPI inside a singularity container. We have version 17.0.13 available.
  Would the container also be OK for your case, or do you want to compile it bare-metal?
  Because if so, I could provide you with the .def file or the .sif directly.

All the best for the holidays :)

[gtheler]

Thanks @supermatrixx . I cloned from gitlab. Side question: how do people know they have to use gitlab if it does not say so in the website?

I could not understand the intructions in the link from the second bullet. Don't they have something like "if you want to compile do this: apt-get install whatever; configure; make?

First time I hear about singularity contents. I assume they are similar to docker containers. If so, then I'm afraid I won't like them (I don't like docker). I'd keep old-fashioned bare-metal instructions.

So far, with the new gitlab, I run ./waf configure and cannot get past parmetis

[...]
Checking metis version                   : 5.1.0 
Checking for library parmetis            : yes 
Checking parmetis version                : can not get version 
The configuration failed
(complete log in /home/old/3ros/src/build/mpi/config.log)
gtheler@tom:~/codigos/3ros/src$ 

The thing is that the test program is

#include <stdio.h>
#include <parmetis.h>
int main(void) {
    printf("PARMETISVER: %d.%d.%d", PARMETIS_MAJOR_VERSION, PARMETIS_MINOR_VERSION,
           PARMETIS_SUBMINOR_VERSION);
    return 0;
}

but parmetis from Debian stable has this in parmetis.h

#ifndef SCOTCH_PARMETIS_VERSION
#define SCOTCH_PARMETIS_VERSION     3             /* ParMeTiS API version is 3 by default */
#endif /* SCOTCH_PARMETIS_VERSION */

#if (SCOTCH_PARMETIS_VERSION == 3)
#ifndef SCOTCH_METIS_PREFIX                       /* With "SCOTCH_" prefix, names already defined */
int                         METISNAMEU (ParMETIS_V3_NodeND) (const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, MPI_Comm * const);

int                         METISNAMEU (ParMETIS_V3_PartGeomKway) (const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const float * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const float * const, const float * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, MPI_Comm * const);
int                         METISNAMEU (ParMETIS_V3_PartKway) (const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const float * const, const float * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, MPI_Comm * const);
#endif /* SCOTCH_METIS_PREFIX            */
#endif /* (SCOTCH_PARMETIS_VERSION == 3) *

so I'm stuck.

Happy new year!

[supermatrixx]

1. Answers concerning the choice to move to gitlab can be found in the official code_aster forum (https://forum.code-aster.org/public/) and we are also in contact with the development team.

2. code_aster requires a number (many) of prerequisites to be compiled, including e.g. blas, lapack, metis, parmetis, etc.
   You have to compile all these prerequisites manually before you can compile the code source. The source of the prerequisites can be found here: https://www.code-aster.org/FICHIERS/prerequisites/codeaster-prerequisites-20240327-oss.tar.gz

Read the instructions here: https://gitlab.com/codeaster-opensource-documentation/opensource-installation-development/-/blob/main/devel/changelog.md

3. The official development team recommends compiling code_aster inside a singularity container to ease installation. Since my team and I operate inside an HPC, we preferred to pursue this container route to make local compilation less of a hassle.

If you have any doubts write to me, I will be happy to answer you :)

[gtheler]

Hey, thanks for answering.

1. Fair enough. It seems we (i.e. me and the aster devs) have different opinions about what "prerequisites" mean. To me it is apt-get install whatever-you-need. BTW, most of the time, paraphrasing the Beatles, PETSc is all you need.
2. I am used to provide dependencies for computational software, so I already had everything you mention. But this waf thing refused to detect Debian's parmetis.
3. I'm not looking for "ease of installation" but for "flexible (and I would add reasonable) compilation." Anyway, having to deal with containers is something I was expecting anyway. I should flow with the current at some point.

Thank you.