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

Regression test gold standard v16

Required update to reflect new component label logic

Regression test gold standard v15

Update regression tests after fixing prolongation stages bug.

Regression test gold standard v14

Required update for parthenon HDF5 output format 3

Version 0.7.0

Release 0.7.0

Date: 2022-08-04

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

• [PR 702] Allow for ParArrayGeneric to accept enums
• [PR 694] Add C++11 implementation of concepts lite
• [PR 692] Add SparsePack machinery
• [PR 690] Use power9 partition for Darwin CI
• [PR 689] Add Mesh::ProblemGenerator (allows reductions during init)
• [PR 667] Add parallel scan
• [PR 654] Add option for returning FlatIdx when requested variable doesn't exist
• [PR 653] Allow for multi-D particle variables
• [PR 622] Extend reduction framework to support more general data types. Now uses PR 623.
• [PR 619] Sort particles by cell
• [PR 605] Add output triggering by signaling.
• [PR 602] Added tuning functionality for HDF5 output
• [PR 586] Implement true sparse capability with automatic allocation and deallocation of sparse

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

• [PR 682] Add prolongate-in-one
• [PR 685] Add *pmb to MeshBlockUserWorkBeforeOutput. Remove unused MeshBlockUserWorkInLoop.
• [PR 676] Remove broken swarm user boundary check
• [PR 662] Remove SetPrecise
• [PR 673] Remove smallest meshblock case from advection_performance
• [PR 655] Enable user boundary conditions for particles
• [PR 623] Enable Params to optionally return non-const pointers
• [PR 604] Allow modification of SimTime in PreStepUserWorkInLoop
• [PR 617] Unify the coordinates API for MeshBlockPack and VariablePack

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

• [PR 688] Restore component labels for multicomponent non-vector field
• [PR 679] Handle case of multidim var labeling for output
• [PR 680] Fix hanging compilation for sort unit test
• [PR 678] Fix FlatIdx packing for size-1 dimensions
• [PR 677] Fix restart without SparseInfo object
• [PR 670] Fix typo in parse_value for non-hdf5 builds
• [PR 656] Extend CC bvars to 5-, 6-D ParArrays
• [PR 629] Fix HIP backend (config and tests) and extend build coverage
• [PR 652] Fix issue with hsize_t and size_t in utils parser
• [PR 649] Ensure LoadBalancing send buffers are filled and allow async recv LB
• [PR 618] Fix bug in variable pack performance test
• [PR 616] Restore sparse base names in PackIndexMap
• [PR 609] Fix bug where .final is not written if signal raised while writing regular output
• [PR 595] Fix build options so that non-MPI builds cannot be paired with an MPI HDF5 lib

Infrastructure (changes irrelevant to downstream codes)

• [PR 703] Fixed mpi/serial logic in extended CI tests
• [PR 700] Moved CI testing from GitLab mirror to GitHub Actions
• [PR 698] Remove matplotlib from required python libraries and make desired instead
• [PR 686] Remove coverage CI stage and add key features to README
• [PR 681] Refactor ParArrayNDGeneric to work with arbitrary rank Kokkos::views and hold state.
• [PR 669] Bump clang-format version (and checks) to >=11.0
• [PR 661] Replaced ids in MPI tags with separate MPI_Comms for each variable/swarm
• [PR 651] Bump Catch2 version due to GCC11.2 incompatibility
• [PR 646] Add machine configuration file for Stony Brook's Ookami A64FX and OLCF's Spock AMD systems.

Regression test gold standard v13

Required update for sparse advection test and updated advection example metadata

Version 0.6.1

Release 0.6.1

Date: 09/22/2021

Note, there's no tag/changelog for release 0.6.0 as the original version contained a typo in one of the regression tests that is now fixes with this "bugfix" release.

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

• [PR 563] Physical boundary options for particles
• [PR 582] Adding global reductions and basic functionality needed for solvers.
• [PR 556] Introduce iterative tasks and regionally dependent tasks
• [PR 578] Add some profiling regions to tasks in particles example
• [PR 577] Update invalid indices to allow for no-op loops
• [PR 564] Add EstimateTimestep to particles example task list
• [PR 557] Re-enable InitMeshBlockUserData so data can be set per-remeshing
• [PR 509] Add elapsed_main, elapsed_cycle, and elapsed_LBandAMR functions to Driver as static functions to enable access to timing information in output and restart files.
• [PR 479] Add Update function to Params to update the value of an existing key.
• [PR 482] Add support for package enrolled history outputs.
• [PR 511] Improvements/speed ups in phdf_diff, phdf_diff, analytic_compare.py
• [PR 497] Add tracer particles example.
• [PR 404] Add capability to communicate particles across meshblocks/MPI processes

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

• [PR 558] Boundary bugfix(es) incl. regression tests and exposing FluxDiv_ interface
• [PR 583] Fix file numbering logic for writing outputs after restarting a simulation.
• [PR 581] Change return status of ArgParse so that complete is returned when passing in the help flag.
• [PR 580] Hid variable/meshblock pack keys from public API, added unit tests for MeshBlockData.
• [PR 535] Modify various interfaces connected with
  variables, StateDescriptor, variable packing to support proper sparse variables. Replace
  SparseVariable with SparsePool. Remove MeshBlockDataIterator and make
  MeshBlockData::GetVariablesBy[Name|Flag] public instead. Remove public MeshBlockData::Add
  interface and add MeshBlockData::Initialize instead.
• [PR 553] Avoid use of variable named restrict
• [PR 476] Update min. CMake version to 3.16 (matching Kokkos) and add option to compile with C++17 (PARTHENON_ENABLE_CPP17 - default: off)
• [PR 532] Remove obsolete Properties_t, they have been replaced by Packages_t
• [PR 508] Modify RestrictCellCenteredVariables to support a restriction over meshblock packs.
• [PR 524] Enforce Metadata flags constraints and add new Metadata::WithFluxes flag. Note: Metadata::Independent will be set automatically unless Metadata::Derived is set
• [PR 517] Remove optional dims argument from MeshBlockData::Add and use the shape from the Metadata instead
• [PR 492] Modify advection example to have an arbitrary number of dense variables and to disable fill derived for profiling.
• [PR 486] Unify HDF5 output and restart file writing, add HDF5 compression support, add support for sparse fields in HDF5 output/restart files, add and rename some metadata in HDF5 files.
• [PR 522] Corrected ordering of OutputDatasetNames to match ComponentNames

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

• [PR 588] Switch from nbmax to nneighbors in particles
• [PR 572] Fix meshblockpack issue coming from variatic template shadowing
• [PR 569] Fix path to nvcc_wrapper in README example
• [PR 551] Hotfix to make particles compile without MPI again
• [PR 552] Fix missing include for fstream
• [PR 537] Fix inconsistent treatment of coarse buffers.
• [PR 539] Fix restart indexing/hdf5 bugs
• [PR 487] Add default tiling matching i index range to MDRange loop pattern.
• [PR 531] Work around in parthenon_hdf5.cpp for GCC 7.3.0

Infrastructure (changes irrelevant to downstream codes)

• [PR 575] Make file comparison more verbose, don't check File metadata
• [PR 502] Use subviews of a single view for fluxes
• [PR 505] Can also use buffer-pack-in-one function also in Mesh::Initialize (and thus during load balancing/mesh refinement). Breaks sparse variables with FillGhost. Enable with PARTHENON_ENABLE_INIT_PACKING=ON (default OFF).
• [PR 493] Use subviews of a single view for comm buffers
• [PR 500] Update docker file and CI environment (for Cuda 11.3 and latest nsys)
• [PR 490] Adjust block size in OverlappingSpace instance tests to remain within Cuda/HIP limits
• [PR 488] Update GitLab Dockerfile to use HDF5 version 1.10.7
• [PR 510] Fix calling noexistant logger in python performance regression app
• [PR 527] Fix problem with CI when rebase is used.
• [PR 518] Added MPI performance regression tests to CI performance app
• [PR 530] Fixed issue with CI plotting the oldest 5 commit metrics for each test, also cleaned up legend formatting.
• [PR 536] Updated to latest Kokkos release.
• [PR 520] Add black python formatter to github actions
• [PR 519] Add checksum to bash uploader script to verify file is trusted
• [PR 549] Add deep-code badge.
• [PR 554] Small fix to documentation related to python parthenon tools README
• [PR 555 Added documentation for darwin CI and scripts
• [PR 560] Rename png_files_to_upload to more generic figure_files_to_upload
• [PR 561] Adding documentation to help with adding new performance regression tests.

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

• [PR 498] Cleanup unused user hooks and variables
• [PR 481] Cleanup unused/untested/not fully ported code (mostly OpenMP and reconstruction)

Regression test gold standard v12

Updating the gold for the Poisson test.