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AMReX-Codes/amrex: AMReX 26.04

Authors: the AMReX Development Team; Almgren, Ann; Beckner, Vince; Blaschke, Johannes; Chan, Cy; Day, Marcus; Friesen, Brian; +12 Authors

AMReX-Codes/amrex: AMReX 26.04

Abstract

What's Changed Hypre: Remove unused code in HypreABecLap3 by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5099 PETSc: Fix potential memory leak by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5097 PETSc: Remove unused code by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5091 PETSc: Use PetscInt by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5090 FFT::Clear: Clear the map after the stored plans are destroyed by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5089 Doxygen PETSc by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5087 Doxygen Boundary by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5096 FFT: Use ParallelContext's communicator by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5088 Nosync broadly by @ax3l in https://github.com/AMReX-Codes/amrex/pull/4957 Hypre: Fix a typo in CMake by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5100 Add new test and fix dual grid restart bug by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5075 Use HYPRE capitalization consistently in Sphinx docs by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5071 STL: Assert it's not empty by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5109 EB: Validate lookup status in getLevel/getGeometry by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5107 OpenBCSolver: Make define safer by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5129 ReadAndBcastFile: Use the correct I/O process when sub-communicator is used. by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5131 ParallelDescriptor: Avoid the non-standard variable-length array by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5130 FabArrayCopyDescriptor: Add assertion by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5132 Rename the NonManagedVector to NonManagedDeviceVector by @ax3l in https://github.com/AMReX-Codes/amrex/pull/5124 Hypre: Remove unimplemented 1d functions to avoid confusion by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5103 FillPatchSingleLevel: Robustify assertion by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5121 AmrMesh: Validate input by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5119 Fujitsu MPI: Fix potential null-dereference by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5122 MultiMask: Fix initval for multiple components by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5118 StateDescriptor: Add assertion by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5125 StateDescriptor: Remove deprecated functions by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5126 BndryData: Robustify reuse check by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5116 SpMatrix: Add assertion in communication by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5128 Update Fortran BC type module by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5113 Marching Cubes: Fix GPU memcpy by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5110 EB: Assert there is no int overflow by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5111 AmrLevel::FillPatch: Fix assertion by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5127 Boundary: Fix forward declarations by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5114 COMM_PROFILING: Fix size bug by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5135 ParallelDescriptor: Assert team size is positive by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5134 LineDistFcnElement2d::single_seg_cpdist: Fix degenerate case by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5106 HypOptParse: Remove operator()(key, func) by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5105 Hypre: No need to call hypre if local row count is zero by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5104 VisMF: Avoid UB-prone assertions on potentially empty strings by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5133 FillPatcher: Robustify assertions by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5120 BndryRegister: Make sure assertion does not access out-of-bound memory by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5112 Mask: Fix writeOn/readFrom for multiple components by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5117 FileSystem::Remove: Fix return value by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5136 Workaround for deprecation warnings on Perlmutter by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5101 Move PETSc Initialize and Finalize to amrex::Initialize and Finalize by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5098 Fix caching mechanism for neighbor particle mask by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5080 Fix restart where you lose a level and NReaders > NProcs() by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5074 ParmParse: Add TOML-like features by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/4950 Parser: Improve documentation and fix minor issues with help from Claude by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5144 ParmParse: Refactor countval for TOML arrays by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5143 Fix a warning in Fortran module by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5142 Add Gpu::isStreamActive function by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5139 Add FillBoundaryAndSync(Vector) by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5138 Parser optimization by Claude by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5146 ParmParse: Improve documentation and comments by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5148 ParmParse: Support query/get a specific element from TOML array. by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5149 Fix bug in bisect by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5167 Fix assertion in bisect by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5169 Fix BaseFab::contains by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5171 HDF5: Fix missing GPU device-to-host_copy in writing plotfile by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5174 BLBackTrace: Fix null terminator by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5173 Fix typo in N_VConstrMask_MultiFab by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5175 SUNDIALS: Fix memory leak in N_VWL2Norm_MultiFab by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5177 SUNDIALS: Fix a memory leak in N_VDestroy_MultiFab by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5176 SUNDIALS: remove MemoryHelper's move operator= by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5178 ParmParse: Fix printing TOML array by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5180 ParmParse: accept true/false t/f for int keys by @charlesgwaldman in https://github.com/AMReX-Codes/amrex/pull/5150 Fix hidden direction support for multilevel composite solves by @desjardi in https://github.com/AMReX-Codes/amrex/pull/5141 Fix resource leaks in ParticleContainer::RestartHDF5 by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5185 Fix InitFromBinary for the case that NP % NReaders != 0 by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5184 Fix HDF5 handle leaks in early exits by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5187 Make sure number of neighbor particles is preserved on swap by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5186 ParmParse: Preserve quotes when printing strings by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5188 Managed Arena: Do not pre-allocate if managed memory is not supported. by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5183 Doxygen AmrCore by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5179 Parser: fix self assignment of locals by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5189 Doxygen Amr by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5190 Fix Dual Grid restart with HDF5 format by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5137 Fix tracer particle Timestamp to respect indices argument by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5194 Fix empty vector dereference in HDF5 particle IO by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5195 Add a comment to selectActualNeighbors by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5193 Avoid clang warnings with -Wshadow-field by @charlesgwaldman in https://github.com/AMReX-Codes/amrex/pull/5197 ParmParse::add: Improve TOML compatibility by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5196 Filter transform fix by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5192 Add comment that is safe to assume divisors are not zero in tracer mod by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5198 Clean up RedistributeCPU by @AlexanderSinn in https://github.com/AMReX-Codes/amrex/pull/4529 Add external GPU stream override support by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5199 Fix GCC warning in AllGatherBoxes by @AlexanderSinn in https://github.com/AMReX-Codes/amrex/pull/5203 Bump dorny/paths-filter from 3 to 4 by @dependabot[bot] in https://github.com/AMReX-Codes/amrex/pull/5202 Fix assertions in particle IO to include runtime int comps by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5205 Avoid undefined behavior in Random_int by having it always return 0 for n = 0. by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5206 Add AGENTS.md by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5208 Fix typo in Gitlab CI README by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5213 Fix some typos in the docs by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5212 Add section on using LLMs to CONTRIBUTING.md by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5211 Sphinx Documentation: Minor wording fixes by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5217 Fix typo in README.md by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5214 Geometry: Exceptions by @ax3l in https://github.com/AMReX-Codes/amrex/pull/5219 Geometry: Better assertion message by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5224 Avoid invalid in AMReX_MFInterp_3D_C.H by @dpgrote in https://github.com/AMReX-Codes/amrex/pull/5215 Implement pure-SoA HDF5 particle IO by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5204 FFT: Fix one-d mode in 2D & 3D builds by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5225 Typos in .gitlab/README.md by @eebasso in https://github.com/AMReX-Codes/amrex/pull/5234 ParReduce: Fix comments by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5238 FilFC: Fix a copy-paste typo by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5240 Fix facediv_int z indexing by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5239 CI: Use C++20 by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/4976 Fix particle dual-grid test by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5255 Bump Jimver/cuda-toolkit from 0.2.30 to 0.2.35 by @dependabot[bot] in https://github.com/AMReX-Codes/amrex/pull/5256 Remove emoji in README.md by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5259 Update CHANGES for 26.04 by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5264 New Contributors @desjardi made their first contribution in https://github.com/AMReX-Codes/amrex/pull/5141 Full Changelog: https://github.com/AMReX-Codes/amrex/compare/26.03...26.04

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