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Parthenon AMR infrastructure

regression-gold-v23

2 weeks ago

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-gold-v22

1 month ago

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

v24.03

2 months ago

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

Full Changelog: https://github.com/parthenon-hpc-lab/parthenon/compare/v23.11...v24.03

regression-gold-v21

3 months ago

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

v23.11

6 months ago

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-gold-v20

7 months ago

Upgolded to account for fixed behavior when outputting string parameters.

regression-gold-v19

11 months ago

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

regression-gold-v18

11 months ago

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

regression-gold-v17

11 months ago

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.

v0.8.0

1 year ago

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<T> 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