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AMReX-Codes/amrex: AMReX 26.05

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

AMReX-Codes/amrex: AMReX 26.05

Abstract

What's Changed Fix DistributionMapping::SFC_Threshold by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5250 DistributionMapping: Fix comments by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5249 ParallelAdd: Buffer unpacking should respect the deterministic flag by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5247 FabArray::copyTo(FAB): Fix a memory leak by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5246 SumBoundary: Add assertion on number of destination ghost cells by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5245 FABio_8bit reader: Fix overflow by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5244 SUNDIALS: Use ParallelContext's communicator by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5237 SUNDIALS: Fix N_VInvTest_MultiFab by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5236 Robustify AMREX_ASSUME by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5254 AMREX_ENUM: Allow non-decimal base by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5251 AmrMesh: Recompute roundoff domain for fine Geometry objects by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5248 Doxygen LinearSolvers by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5233 Doxygen HDF5 by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5231 Doxygen SUNDIALS by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5230 Doxygen Parser by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5229 Add version of ParticleTile using runtime-only 2D array by @AlexanderSinn in https://github.com/AMReX-Codes/amrex/pull/4404 Add unset capability for ParmParse by @baperry2 in https://github.com/AMReX-Codes/amrex/pull/5263 Update to new rocsparse by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5207 GNU Make: Update ifx options by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5242 Add CI checking release numbers in CHANGES.md by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5271 Remove un-needed streamSynchronize from unpackRemotes by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5260 Fix HIP CI on HPSF GitLab by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5273 Fix PolymorphicArenaWrapper Use-After-Free by @ax3l in https://github.com/AMReX-Codes/amrex/pull/5270 Tests: Narrowing Warning in Advection by @ax3l in https://github.com/AMReX-Codes/amrex/pull/5275 Reduce memory usage in ReduceToPlaneMF2Patchy by @BenWibking in https://github.com/AMReX-Codes/amrex/pull/5258 avoid duplicate find_package(Conduit) by @charlesgwaldman in https://github.com/AMReX-Codes/amrex/pull/5281 Create symbolic link during install by @nischild in https://github.com/AMReX-Codes/amrex/pull/5277 TrackedVector by @ax3l in https://github.com/AMReX-Codes/amrex/pull/5253 Fix out-of-bounds access in amrex::bisect by @AlexanderSinn in https://github.com/AMReX-Codes/amrex/pull/5284 CMake: Smoke Test w/ Prefix & Stage by @ax3l in https://github.com/AMReX-Codes/amrex/pull/5283 Fix Wrong noexcept Placements by @ax3l in https://github.com/AMReX-Codes/amrex/pull/5222 Add an implementation of ParticleCopyPlan::doHandShake that uses one-sided communication from MPI-3 by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5227 AmrMesh: Fix max_grid_size and blocking_factor checks by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5286 Fix type in BndryDataT::setValue by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5285 PhysBCFunct: Fix box index type by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5298 Gpu::Buffer: Add comments about GPU launch region by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5297 EB: Fix index bug in eb_interp_centroid2facecent_y by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5296 StateData::restart: Need to initialize DistribuionMapping and Factory by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5295 AsyncArray: Add a warning by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5294 Robustify AmrLevel::get_data in case old_time == new_time by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5293 Amr::Finalize: Clear state_small_plot_vars by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5292 Amr::regrid used wrong n_cycle index for new levels by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5291 EdgeFluxRegister: Fix comments by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5290 Fix bug in InterpCrseFineBndryEMfield by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5289 MFInterp quadratic slope: Fix index bugs by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5287 Doxygen EB by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5210 Fix comments for PreBuildDirectorHierarchy by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5299 SUNDIALS: Fix bug in N_VConstrMask_MultiFab by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5302 SUNDIALS: Fix bug in N_VMaxNorm_MultiFab by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5301 FillPatchNLevels: Fix component bugs by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5288 PlotFileData: Add refRatioVect by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5300 Comments: Add warnings on MPI collectives by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5303 Update AGENTS.md by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5304 Refactor AmrMesh::MakeNewGrids by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5269 EB: Fix typo in assertion by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5306 Guard flag-dependent tests in CTest setup by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5305 RealBox: Robustify operator>> by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5309 Gpu::Buffer: Remove some noexcept's to allow for exceptions by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5307 Remove deprecated GNU Make option: GPU_ERROR_CHECK by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5315 Fix Hypre bug in 2D by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5314 Hypre 3D: Fix index bug by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5313 Add comments to prefetch functions by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5311 Hypre 1D bug: Forgot to initialized diag_inv. by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5312 Fix bug in AMREX_GPU_LAUNCH_DEVICE_LAMBDA_RANGE_3 by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5316 SYCL: Fix potential resource leak in the large kernel path by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5317 Linear Solver Tests: Loosen convergence tolerance for single precision by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5319 AmrMesh::checkInput: No need to check blocking factor for single level by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5320 Fix noexcept warnings by Coverity by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5321 Robustify IntVect and RealVect read by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5310 Fix CPU implementation of Reduce::MinMax(n, ptr) by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5322 Fix bug in Tests/ParmParse by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5324 Align Arena allocations to 256 bytes by @AlexanderSinn in https://github.com/AMReX-Codes/amrex/pull/5278 RK: Add comments clarifying what callback should do by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5327 Tests: Fix AMREX_HOME in some tests' gnu make file by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5325 Add assertion to MultiFab and iMultiFab Copy by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5332 RK2: pass time+dt as stage 2 time to the RHS function by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5326 MFIter Tiling: Set a default tile size in MFItInfo::SetTiling(bool) by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5334 SmallMatrix: Omega by @ax3l in https://github.com/AMReX-Codes/amrex/pull/5330 EdgeFluxRegister: add plus() member function by @BenWibking in https://github.com/AMReX-Codes/amrex/pull/5329 Fix comments by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5341 Fix typo in amrex_avgdown_edges by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5340 Edge cases for boundary normal vector in coarsen_from_fine by @eebasso in https://github.com/AMReX-Codes/amrex/pull/5352 Add option to fill ghost cells in average_cellcenter_to_face by @BenDavisonPetch in https://github.com/AMReX-Codes/amrex/pull/5345 Remove noexcept from Vector's operator[] to allow for exception by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5356 Remove amrex::IsStdVector by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5355 Parser: Disallow setConstant and registerVariables after being compiled. by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5359 Parser: Strip CR (\r) by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5357 Parser: Add check for empty expression by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5358 Fix in 2D set_eb_data that gave incorrect vcent and vfrac for anisotropic cells (dx =/= dy) by @eebasso in https://github.com/AMReX-Codes/amrex/pull/5353 Table::copy: add assertion by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5350 Table: Fix missing template parameter by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5349 Scan: Handle empty range by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5348 Reimplement IsConvertible with std::conjunctionstd::is_convertible by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5360 TagParallelFor: Return early in case the number of warps is 0 by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5351 FaceDivFree interpolater: Fix component by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5361 C++20 is now the minimum required version by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5265 Merge RedistributeCPU and RedistributeGPU into one implementation by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5268 Curl Curl: Add support for variable alpha by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5276 ParticleContainer: take plotfile filters by const reference by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5374 Clang-Tidy: readability-container-contains by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5366 Support neighbor particle tiling on the GPU by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5373 Long in numParticlesOutOfRange by @ax3l in https://github.com/AMReX-Codes/amrex/pull/5379 Print: str() -> view() by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5377 Clang-Tidy: modernize-use-starts-ends-with by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5367 Add CUDA 12.2 CI test by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5381 Fix eb_add_divergence_from_flow for anisotropic cells by @eebasso in https://github.com/AMReX-Codes/amrex/pull/5385 Call HYPRE_DeviceInitialize after HYPRE_Init if using GPUs by @jrood-nrel in https://github.com/AMReX-Codes/amrex/pull/5336 Align capacity to 256 bytes in ParticleTileRT by @AlexanderSinn in https://github.com/AMReX-Codes/amrex/pull/5335 Add in-class AMREX enum registration macro AMREX_ENUM_IN_CLASS by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5387 Avoid stream string copies with view() by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5388 HIP: Add amrex:: to robustify the AMREX_LAUNCH_KERNEL macro by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5328 Fix MLABecLaplacian::setBCoeffs(int,Vector) by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5382 Support pure SoA for Neighbor particles by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5376 Fix OMP issue in BoxArray by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5403 Use std::atomic instead omp flush by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5406 Fix for race condition when using getConstParticleTileData in threaded region. by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5404 Update CHANGES.md for 26.05 by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5416 New Contributors @nischild made their first contribution in https://github.com/AMReX-Codes/amrex/pull/5277 @BenDavisonPetch made their first contribution in https://github.com/AMReX-Codes/amrex/pull/5345 Full Changelog: https://github.com/AMReX-Codes/amrex/compare/26.04...26.05

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