Regression test gold standard v23

Update output_hdf5 test gold file to include SparseDeallocCount which was added in #1073, include two-tree test gold files required for the new regression tests in #1071, and include boundary exchange gold files for the test added in #1047.

Regression test gold standard v22

Update gold files for sparse_advection to account for the fixed shape of the sparse scalar fields.

Release 24.03

Release 24.03

Date: 2024-03-21

Added (new features/APIs/variables/...)

• [PR 852] Add Mesh version of UserWorkBeforeOutput
• [PR 998] tensor indices added to sparse pack
• [PR 999] Add a post-initialization hook
• [PR 987] New tasking infrastructure and capabilities
• [PR 969] New macro-based auto-naming of profiling regions and kernels
• [PR 981] Add IndexSplit
• [PR 983] Add Contains to SparsePack
• [PR 968] Add per package registration of boundary conditions
• [PR 948] Add solver interface and update Poisson geometric multi-grid example
• [PR 996] Remove dynamic allocations from swarm particle creation

Changed (changing behavior/API/variables/...)

• [PR 973] Multigrid performance upgrades

Fixed (not changing behavior/API/variables/...)

• [PR1023] Fix broken param of a scalar bool
• [PR1012] Remove accidentally duplicated code
• [PR992] Allow custom PR ops with sparse pools
• [PR988] Fix bug in neighbor finding routine for small, periodic, refined meshes
• [PR986] Fix bug in sparse boundary communication BndInfo cacheing
• [PR978] remove erroneous sparse check

Infrastructure (changes irrelevant to downstream codes)

• [PR 1017] Make regression tests more verbose on failure
• [PR 1007] Split template instantiations for HDF5 Read/Write attributes to speed up compile times
• [PR 990] Partial refactor of HDF5 I/O code for readability/extendability
• [PR 982] add some gut check testing for parthenon-VIBE

Incompatibilities (i.e. breaking changes)

• [PR 987] Change the API for what was IterativeTasks
• [PR 974] Change GetParentPointer to always return T*
• [PR 996] Remove dynamic allocations from swarm particle creation

New Contributors

• @mari2895 made their first contribution in #998

Full Changelog: v23.11...v24.03

Regression test gold standard v21

Update gold files for advection_outflow to include derived var produced by UserMeshWorkBeforeOutput

Release 23.11

Release 23.11

Date: 2023-11-16

Added (new features/APIs/variables/...)

• [PR 962] Add support for in-situ histograms/profiles
• [PR 911] Add infrastructure for geometric multi-grid
• [PR 971] Add UserWorkBeforeLoop
• [PR 907] PEP1: Allow subclassing StateDescriptor
• [PR 932] Add GetOrAddFlag to metadata
• [PR 931] Allow SparsePacks with subsets of blocks
• [PR 921] Add more flexible ways of adding and using MeshData/MeshBlockData objects to DataCollections
• [PR 900] Add Morton numbers and expand functionality of LogicalLocation
• [PR 902] Add ability to output NaNs for de-allocated sparse fields
• [PR 887] Add ability to dump more types of params and read them from restarts
• [PR 884] Add constant derivative BC and expose GenericBC
• [PR 892] Cost-based load balancing and memory diagnostics
• [PR 889] Add PreCommFillDerived
• [PR 872] Boundary communication for non-cell centered fields
• [PR 877] Add flat sparse packs
• [PR 868] Add block-local face, edge, and nodal fields and allow for packing

Changed (changing behavior/API/variables/...)

• [PR 977] Change to CalVer from SemVer
• [PR 975] Construct staged integrators via arbitrary name
• [PR 976] Move UserWorkBeforeLoop to be after first output
• [PR 965] Allow leading whitespace in input parameters
• [PR 926] Internal refinement op registration
• [PR 897] Deflate compression filter is not called any more if compression is soft disabled
• [PR 896] Update Kokkos integration to support installed version. Use serial (flat MPI) host parallelization by default (instead of OpenMP)
• [PR 894] Demand that sparse pool order sparse ids
• [PR 888] Bump Kokkos submodule to 4.0.1
• [PR 885] Expose PackDescriptor and use uids in SparsePacks

Fixed (not changing behavior/API/variables/...)

• [PR 955] Only permit rank0 to mkdir when -d flag specified
• [PR 952] Fix format string in sparse advection example
• [PR 947] Add missing ForceRemeshComm dependencies
• [PR 928] Fix boundary comms during refinement next to refined blocks
• [PR 937] Fix multiple line continuations
• [PR 933] Remove extraneous debug check
• [PR 917] Update Iterative Tasking Infrastructure
• [PR 890] Fix bugs in sparse communication and prolongation

Infrastructure (changes irrelevant to downstream codes)

• [PR 967] Change INLINE to FORCEINLINE on par_for_inner overloads
• [PR 938] Restructure buffer packing/unpacking kernel hierarchical parallelism
• [PR 944] Move sparse pack identifier creation to descriptor
• [PR 904] Move to prolongation/restriction in one for AMR and communicate non-cell centered fields
• [PR 918] Refactor RegionSize
• [PR 901] Implement shared element ownership model

Removed (removing behavior/API/varaibles/...)

• [PR 930 Remove ParthenonManager::ParthenonInit as it is error-prone and the split functions are the recommended usage.

Regression test gold standard v20

Upgolded to account for fixed behavior when outputting string parameters.

Regression test gold standard v19

Revert true sparse gold file to version from v16 after fixing bugs that were introduced into the gold file in v17.

Regression test gold standard v18

Update params to output additional information, such as kokkos views and std::vectors stored in params objects.

Regression test gold standard v17

Update the final data for the sparse_true test after changing the order of deallocation in the sparse advection test. This introduces changes at the level of the sparse threshold in the results.

Release 0.8.0

Release 0.8.0

Date: 2023-05-26

Added (new features/APIs/variables/...)

• [PR 830] Add particle output
• [PR 840] Generalized integrators infrastructure in a backwards compatible way
• [PR 810] Add suport for Ascent in-situ visualization
• [PR 831] Add set-based MetadataFlag logic
• [PR 803] Add skeleton for sphinx docs
• [PR 774] Add second order refinement criteria
• [PR 699] Add independent sparse thresholds and sparse control fields. Sparse bug fixes.
• [PR 780] Add Burgers' benchmark, GetVector interface for ParameterInput
• [PR 732] Add Metadata::ForceRemeshComm flag
• [PR 755] Add archive_parameters option to output all parameters to text file at start
• [PR 729] Optional modifications to output format
• [PR 717] Add ghost zone plotting capability to phdf.py and movie2d.py
• [PR 712] Allow to add params from cmdline

Changed (changing behavior/API/variables/...)

• [PR 870] Update component label logic in output to include basename
• [PR 853] Add multiple features and improve the performance of the movie2d.py tool
• [PR 775] Reorganize some of the bvals and prolongation/restriction machinery
• [PR 753] Cleanup uniform Cartesian variable names
• [PR 769] Thread custom prolongation-restriction functions through infrastructure and to userspace
• [PR 781] Output variables with same shape as in parthenon
• [PR 758] Bump required C++ standard to C++17
• [PR 710] Remove data transpose in hdf5 and restart outputs
• [PR 713] Remove Coordinates stub in favor of Coordinates_t
• [PR 711] Rename flux correction routines.
• [PR 663] Change bvals_in_one to use sparse boundary buffers and add flux_correction in one.

Fixed (not changing behavior/API/variables/...)

• [PR 876] Fix restarting from files which record ghost zones
• [PR 878] Catch2 target guard in CMake
• [PR 873] Prevent HDF5 from throwing a fit when a swarm has no particles
• [PR 866] Add missing guard for HDF5 on restart
• [PR 861] Fix filesystem include for experimental namespace
• [PR 859] fix off-by-one indexing error in Ascent ghost mask
• [PR 841] De-allocate MPI communicators when freeing Reduction objects
• [PR 851] Fix xdmf hyperslab definition for vectors
• [PR 843] Add guard rails to prolongation/restriction infrastructure
• [PR 832] Fix movie2d script after it broke due to change in HDF5 format
• [PR 820] Fix XDMF spec to conform to standard and handle scalar and vector variables
• [PR 795] Fix length-1 vectors in output format version >= 3
• [PR 824] Remove unsupported exception handling from device methods in UniformCartesian
• [PR 818] Fix boundary prolongation only occurring in base stage
• [PR 805] Add Crusher/Frontier machine file and bump Kokkos to 3.7.01
• [PR 797] Fix boundary flux correction boundary logic
• [PR 800] Fix rare and intermitted race condition to set allocation status
• [PR 777] Fix double-output of last file in rare cases
• [PR 740] Faster PHDF file load times in phdf.py
• [PR 751] Delete useless file in advection example
• [PR 765] Fix incorrect BC labeling in swarm
• [PR 759] Add metadata so Visit treats outputs as time series
• [PR 743] Add missing HDF5 type on MacOS
• [PR 739] Fix phdf.py for flattened vectors
• [PR 724] Fix failing CI on Darwin due to differing OutputFormatVersion attribute in hdf5 gold files.
• [PR 725] Fix improperly exited kokkos profiling region
• [PR 719] Fix type mismatch in swarm boundaries when host pinned memory enabled
• [PR 716] Remove unneeded assert from ParArrayND

Infrastructure (changes irrelevant to downstream codes)

• [PR 838] Move packing logic to from strings to unique IDs
• [PR 848] Implement recursive mkdir using std::filesystem in src/utils/change_rundir.cpp
• [PR 837] Migrate docs to Sphinx
• [PR 791] Set KOKKOS_DISABLE_WARNINGS=TRUE
• [PR 777] New action: check PR dependencies & warn until requirements merged
• [PR 772] Trigger short CI only for PRs and remove old SpaceInstances test
• [PR 757] Move to flux correction in-one and unify with bvals
• [PR 768] Update CI image and move to new CI machine (short and extended tests)
• [PR 766] Remove IAS performance regression test
• [PR 735] Clean up HDF5 output
• [PR 708] Bump minimum version of Kokkos to 3.6

Removed (removing behavior/API/varaibles/...)

• [PR 829] Remove dead output code
• [PR 738] Remove old incomplete face-centered variables