Gemini3d

* Option to disable TLS verification (discourage unless your computer has broken certificates, just for debugging) -DCMAKE_TLS_VERIFY=off. Default is TLS verify on
* Option to fall back to unmaintained Zlib 1.x. Zlib 2.x works on most systems and is significantly faster for compressed HDF5 operations. -Dzlib_legacy=on. Default is to use Zlib 2.x
* check that TLS working from CMake before downloading to avoid confusing errors when user's CMake doesn't have SSL or TLS certificates are broken.

gemini3d.run: correct behavior on Windows. Also in general allow running from same directory or other directory.

HDF5 is crucial to Gemini3D functionality. We overhauled how HDF5 is found and linked via h5fortran. To help make Gemini3D more robust build overall, we now require CMake >= 3.19 to build Gemini3D.

To run the full Gemini3D self-tests required CMake >= 3.20 as before. Intel compilers also require CMake >= 3.20 in general.

A recent CMake release (usually the latest) is available almost instantly by:

sh
cmake -P gemini3d/scripts/install_cmake.cmake

Since CMake >= 3.20 is required for Intel compilers and to reduce maintenance burden due to numerous features added in CMake 3.20, full features of Gemini3D self-tests now requires CMake >= 3.20. Gemini3d can still build and run some unit tests with CMake >= 3.13. For best robustness of build and test, we recommended CMake >= 3.20.

Features added:

* add ability to expand environment variables into paths in config.nml. This is a more robust / general method than fixed absolute paths in config.nml. For example, `GEMINI_SIMROOT` starting a path in config.nml tells Gemini to read environment variable GEMINI_SIMROOT and inject it there
* improve gemini3d.compare considerably, covering more quantities and adding ability to use Python or Matlab to plot differences detected
* use newer Glow version that corrects bugs leading to NaN in output data
* gemini3d.run frontend: more effective at finding low-level gemini.bin
* added ability to `ctest -R download` to one-time download test reference data for systems that are normally offline
* ExternalProject: use better options to avoid constantly rebuilding external libraries
* Mumps >= 5.4.0 uses an enhanced build technique with better source code traceability

Use ExternalProject instead of FetchContent for project scope separation and flexibility. This has recently become performant via enhancements to CMake ExternalProject.

Turn TLS verification for all Git and Download operations

Find MPIexec more robustly

write more metadata for easier simulation reading


Full Gemini3D functionality continues to require CMake >= 3.19. Intel Fortran requires Cmake >= 3.20. Please run
sh
cmake -P scripts/install_cmake.cmake

if you have old CMake

* default build to Release (-O3 typically) for significantly faster runtime, in case you weren't using CMake preset
* MSIS: don't use HDF5 compact dataset, as larger sims will exceed 64K dataset size
* gemini3d.run: improve auto-CPU detection and warn if mpiexec not specified, as incompatible MPIexec can cause frozen runs

* gemini3d.run -plan: print MPI image count on own line for tool parsing
* scripts/CMakeLists.txt to build and install prereq packages
* read_dnew2d: adapt to proper and workaround read
* gemini3d.run: apple M1 workaround CPU count
* ctest labels
* improve mumps link robustness
* h5fortran: fix findhdf5
* h5fortran 3.6.5 self-find HDF5
* mat_gemini v4.1.6