paulst / ngstrefftz Goto Github PK

This issue is created as part of the review of the JOSS paper (openjournals/joss-reviews#4135).

The tests do not work out of the box. To run them, I had to:

1. install the package
2. update my environment variables (PYTHONPATH in practice)
3. run the tests with make test

This is fairly cumbersome and unsual and incompatible with most common practices and package managers.

This issue is created as part of the review of the JOSS paper (openjournals/joss-reviews#4135).

The compilation of master branch of NGSTrefftz against the master branch of NGSolve fails. Please find below a complete log.

The README.md file in the top level directory of NGSTrefftz do not seem to mention compatible versions. Would you provide some insights to get started ?

$ cmake ../NGSTrefftz/src/ -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/home/th202608/codes/NGSTrefftz/master/install
-- The C compiler identification is GNU 8.3.0
-- The CXX compiler identification is GNU 8.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Netgen: /home/th202608/codes/NGSolve/master/install/lib/cmake/netgen
-- Found PythonInterp: /usr/bin/python3 (found suitable version "3.7.3", minimum required is "3") 
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.7m.so (found suitable version "3.7.3", minimum required is "3") 
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/x86_64-linux-gnu/libopenblas.so  
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
With 'make install' the python package will be installed to: /home/th202608/codes/NGSTrefftz/master/install
-- Configuring done
-- Generating done
-- Build files have been written to: /home/th202608/codes/NGSTrefftz/master/src/build
th202608@pleiades093:~/codes/NGSTrefftz/master/src/build$ make
Scanning dependencies of target _pytents
[  9%] Building CXX object CMakeFiles/_pytents.dir/home/th202608/codes/NGSTrefftz/master/src/NGSTrefftz/external_dependencies/ngstents/src/python_tents.cpp.o
[ 18%] Building CXX object CMakeFiles/_pytents.dir/home/th202608/codes/NGSTrefftz/master/src/NGSTrefftz/external_dependencies/ngstents/src/tents.cpp.o
/home/th202608/codes/NGSTrefftz/master/src/NGSTrefftz/external_dependencies/ngstents/src/tents.cpp: In member function ‘virtual void GradPhiCoefficientFunction::GenerateCode(ngfem::Code&, ngcore::FlatArray<int>, int) const’:
/home/th202608/codes/NGSTrefftz/master/src/NGSTrefftz/external_dependencies/ngstents/src/tents.cpp:31:3: error: ‘TraverseDimensions’ was not declared in this scope
   TraverseDimensions( dims, [&](int ind, int i, int j) {
   ^~~~~~~~~~~~~~~~~~
/home/th202608/codes/NGSTrefftz/master/src/NGSTrefftz/external_dependencies/ngstents/src/tents.cpp:31:3: note: suggested alternative: ‘SetDimensions’
   TraverseDimensions( dims, [&](int ind, int i, int j) {
   ^~~~~~~~~~~~~~~~~~
   SetDimensions
make[2]: *** [CMakeFiles/_pytents.dir/build.make:76: CMakeFiles/_pytents.dir/home/th202608/codes/NGSTrefftz/master/src/NGSTrefftz/external_dependencies/ngstents/src/tents.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:622: CMakeFiles/_pytents.dir/all] Error 2
make: *** [Makefile:141: all] Error 2

Hi,
I'm trying to build NGSTrefftz from source, but I'm experiencing compile time errors:

  /workspace/ngstents/src/tents.hpp:107:17: error: ‘IVec’ is not a member of ‘ngcore’
    107 |   Array<ngcore::IVec<2,size_t>> felpos;
        |                 ^~~~

See also the failing CI Pipeline.
I think this stems from the specific version of ngstents the git submodule is set to (commit 088d773).
If I checkout the master branch of ngstents, the problem vanishes.

This issue is created as part of the review of the JOSS paper (openjournals/joss-reviews#4135).

The url to NGSolve is invalid in the README.md file

This issue is created as part of the review of the JOSS paper (openjournals/joss-reviews#4135).

It seems that running the tests requires to build NGSTrefftz in a subdirectory of the source directory, as indicated in the README file.

Otherwise, this is seems a terrible practice and is probably incompatible with most package manager, hence the issue.

This issue is created as part of the review of the JOSS paper (openjournals/joss-reviews#4135).

The review implies checking if proper community guidelines are present. Here are the requirements:

Community guidelines: Are there clear guidelines for third parties wishing to

1. Contribute to the software
2. Report issues or problems with the software
3. Seek support

I did not find such guidelines. You may want to have a look at this example from one of my personal projects: https://github.com/thelfer/MFrontGenericInterfaceSupport/blob/master/CONTRIBUTING.md

This issue is created as part of the review of the JOSS paper (openjournals/joss-reviews#4135).

JOSS review criteria imply judging the API documentation (https://joss.readthedocs.io/en/latest/review_criteria.html).

If I am not mistaken, I only saw tutorials, but no pages describing the API.

This issue is created as part of the review of the JOSS paper (openjournals/joss-reviews#4135).

My biggest concern with the paper concerns the following statements:

1. line 19: NGSTrefftz provides a framework to implement Trefftz finite element spaces
2. line 40: The aim of this package is to facilitate research into Trefftz methods and to make them more
   accessible to a broad audience.

My feeling is that the NGSTrefftz currently does not provide an appealing introduction to the Trefftz method (not in the paper, but on the website and a reference to it in the paper) that would make the reader want to give it a try and maybe contribute to your project.

I would have expected to find, for example, a introductive text to the method that would be accessible to standard engineer. A minima, a description of the advantages of the Trefftz method (regarding other methods) would help to explain why "research into Trefftz methods" are important.

I have understood that the main drawback of the Trefftz metho is that it requires knowledge of the PDE to solve, but I did not see how I could extend NGSTrefftz for my particular PDE (example: linear elasticity or hyperelastictity). Shall I go at the C++ level. Shall I use the "general framework to produce Trefftz spaces implicitly" ?

By that, I do mean that one can not expect the interrested user to go through the provided notebooks (unless you're more than lucky).

This issue is created as part of the review of the JOSS paper (openjournals/joss-reviews#4135).

The installation directory of NGSTrefftz is currently as follows:

$ tree -d .
.
├── ngstents
└── ngstrefftz

This structure is not standard and worse, not compatible with the one of NGSolve which installs its python module in lib/python3/dist-packages/.