Underworld2: Python Geodynamics Modelling for Desktop, HPC and Cloud

Release 2.11.0 []

Changes:

• Enabled user defined Gauss integration swarms for all systems.
• Update docker base images: switch to ubuntu(20.04), update petsc(3.1.4) & mpich(3.3.2), other tweaks.
• Cleaner Python compile time configuration.
• Add runtime check for solver availability (for example, 'mumps'). Also add test for check.

Docker image changes:

• Update base image.
• Updated to PETSc 3.15.1
• Updated to MPICH 3.4.2
• Removed petsc4py.
• Switched /opt to ugo+rwx to allow users to install Python packages.

New:

• Model for EBA convection, based on King et al. (2010) benchmarks. See docs/test/14_Convection_EBA.ipynb
• Mesh/MeshVariable/Swarm/SwarmVariable objects now support loading and saving of units information, as well as additional attributes. For usage examples, see docs/test/mesh_aux.py and docs/test/swarm_aux.py.
• Added underworld.function.count() method, which counts function calls.
• Conda binaries available via underworldcode conda channel conda install -c underworldcode underworld2
• Added underworld.function.count() method, which counts function calls.
• Added GADI install/run scripts @ ./docs/install_guides/nci_gadi/
• Updated pull request related documentation and added template.

Fixes:

• Updates for SCons4.1.
• Fix bug where multiple solvers added multiple preconditioners.
• H5py v3 is more strict in allowed indexing array shapes. Updated our structures to accomodate.
• Tester uses jupyter-nbconvert which no longer defaults to Python. Update to explicitly select Python.
• Switched h5 file save to mode "w" instead of "a" as append mode resulted in data from previous datasets (with identical name) not being removed from file, and file sizes therefore growing unnecessarily.