Regression test gold standard v26

Update gold fikes to include a flux variable in output hdf5 test.

Regression test gold standard v25

Updates the output_hdf5 test to include a Metadata::None variable.

v24.08

Release 24.08

Date: 2024-08-30

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

• [PR 1151] Add time offset c to LowStorageIntegrator
• [PR 1147] Add par_reduce_inner functions
• [PR 1159] Add additional timestep controllers in parthenon/time.
• [PR 1148] Add GetPackDimension to StateDescriptor for calculating pack sizes before Mesh initialization
• [PR 1143] Add tensor indices to VariableState, add radiation constant to constants, add TypeLists, allow for arbitrary containers for solvers
• [PR 1140] Allow for relative convergence tolerance in BiCGSTAB solver.
• [PR 1047] General three- and four-valent 2D forests w/ arbitrary orientations.
• [PR 1130] Enable parthenon::par_reduce for MD loops with Kokkos 1D Range
• [PR 1119] Formalize MeshData partitioning.
• [PR 1128] Add cycle and nbtotal to hst
• [PR 1099] Functionality for outputting task graphs in GraphViz format.
• [PR 1091] Add vector wave equation example.
• [PR 991] Add fine fields.
• [PR 1106] Add CMake options for turning on ASAN and HWASAN
• [PR 1100] Custom refinement ops propagated to fluxes
• [PR 1090] SMR with swarms
• [PR 1079] Address XDMF/Visit Issues
• [PR 1084] Properly free swarm boundary MPI requests
• [PR 1020] Add bi- and trilinear interpolation routines
• [PR 1081] Add GetSize and GetIndex to sparse pack
• [PR 1026] Particle BCs without relocatable device code
• [PR 1037] Add SwarmPacks
• [PR 1068] Add ability to dump sparse pack contents as a string
• [PR 1062] UserWorkBeforeRestartOutput
• [PR 1043] Unify flux correction with boundary communication, make fluxes variables, allow fluxes for non-cell fields
• [PR 1060] Add the ability to request new MeshData/MeshBlockData objects by selecting variables by UID.
• [PR 1039] Add ability to output custom coordinate positions for Visit/Paraview
• [PR 1019] Enable output for non-cell-centered variables

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

• [PR 1153] Allow base grid with fewer blocks than ranks before initial AMR
• [PR 1105] Refactor parameter input for linear solvers
• [PR 1078] Add reduction fallback in 1D. Add IndexRange overload for 1D par loops
• [PR 1024] Add .outN. to history output filenames
• [PR 1004] Allow parameter modification from an input file for restarts

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

• [PR 1145] Fix remaining swarm D->H->D copies
• [PR 1150] Reduce memory consumption for buffer pool
• [PR 1146] Fix an issue outputting >4GB single variables per rank
• [PR 1152] Fix memory leak in task graph outputs related to abi::__cxa_demangle
• [PR 1146] Fix an issue outputting >4GB single variables per rank
• [PR 1144] Fix some restarts w/non-CC fields
• [PR 1132] Fix regional dependencies for iterative task lists and make solvers work for arbirtrary MeshData partitioning
• [PR 1139] only add --expt-relaxed-constexpr for COMPILE_LANGUAGE:CXX
• [PR 1131] Make deallocation of fine and sparse fields work
• [PR 1127] Add WithFluxes to IsRefined check
• [PR 1111] Fix undefined behavior due to bitshift of negative number in LogicalLocation
• [PR 1092] Updates to DataCollection and MeshData to remove requirement of predefining MeshBlockData
• [PR 1113] Prevent division by zero
• [PR 1112] Remove shared_ptr cycle in forest::Tree
• [PR 1104] Fix reading restarts due to hidden ghost var
• [PR 1098] Move to symmetrized logical coordinates and fix SMR bug
• [PR 1095] Add missing include guards in hdf5 restart
• [PR 1093] Fix forest size for symmetry dimensions
• [PR 1089] Fix loading restart files without derefinement counter
• [PR 1079] Address XDMF/Visit Issues
• [PR 1088] Correctly fill fluxes for non-cell variables in SparsePacks
• [PR 1083] Correctly fill VariableFluxPack for edge fluxes in 2D
• [PR 1087] Make sure InnerLoopPatternTVR is resolved on device properly when it is the default loop pattern
• [PR 1071] Fix bug in static mesh refinement related to redefinition of Mesh::root_level
• [PR 1073] Fix bug in AMR and sparse restarts
• [PR 1070] Correctly exclude flux vars from searches by default
• [PR 1049] Catch task failures from threads
• [PR 1058] Vector history not being output if no scalar history present
• [PR 1057] Fix history output after restarts
• [PR 1053] Set the correct root level on restart
• [PR 1024] Add features to history output
• [PR 1031] Fix bug in non-cell centered AMR

Infrastructure (changes irrelevant to downstream codes)

• [PR 1117] Enable CI pipelines on AMD GPUs with ROCM/HIP
• [PR 1114] Enable sanitizers for extended CI host build
• [PR 1123] Default initialize ProResInfo.dir
• [PR 1121] Default initialize BndInfo.dir
• [PR 1116] Fix NumPy 2.0 test script breakage
• [PR 1055] Refactor mesh constructors
• [PR 1066] Re-introduce default loop patterns and exec spaces
• [PR 1064] Forbid erroneous edge case when adding MeshData on a partition
• [PR 1035] Fix multigrid infrastructure to work with forest
• [PR 1048] Tiny fixes to custom coords logic
• [PR 1028] Internal reorganization of LogicalLocation files
• [PR 1009] Move from a single octree to a forest of octrees

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

• [PR 1108] Remove NaN payload tags infrastructure

Incompatibilities (i.e. breaking changes)

• [[PR 1135]](http...

Regression test gold standard v24

Update the boundary exchange gold standard file.

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.