Changes: 3.15 — PETSc 3.17.0 documentation

# Changes: 3.15

General:

- Add `PetscKokkosInitializeCheck()`, which initializes Kokkos if it is not yet initialized

- Add support for `-debug_terminal` Terminal to use Apple’s Terminal instead of xterm, allowing use of cut-paste

- Make Terminal the default device to display the debugger on Apple instead of xterm

- Add PetscHasExternalPackage() determining whether PETSc has been configured with the given external package such as “hdf5”

Configure/Build:

- On macOS, `MACOS_FIREWALL=1` or `MACOS_FIREWALL_REFRESH=1` can be passed to make to automatically add firewall rules preventing firewall popups during testing. See `make -f gmakefile.test help` for details

- `./configure --with-macos-firewall-rules` makes `MACOS_FIREWALL=1` the default

- Change `--download-petsc4py` to `--with-petsc4py` to have PETSc build and use petsc4py

- Add `--download-mmg` and `--download-parmmg`, 3D unstructured mesh adaptation package (interaction with DMPlex not available yet)

- Improve detection of Git repositories when a `--download-package` option is used

  - Support `ssh://*.git` and `https://*.git` URLs without the additional `git://` prefix

  - Local directories can be specified without the `git://` prefix as well

  - Any valid Git repository (including bare and with `--separate-git-dir`) is now correctly detected

- `--download-yaml` or `--with-yaml` are no longer required for YAML support (but can still be used to avoid compiling source included with PETSc)

Sys:

- Add `PETSCRANDOMCURAND` to support CURAND random number generator

- Add `PetscRandomGetValues()` and `PetscRandomGetValuesReal()` to retrieve an array of random numbers

- Add `PetscOptions` argument to `PetscOptionsInsertFileYAML()`

- Add `PetscCalloc()` to allocate zeroed memory

- Automatically detect YAML and JSON option files by extension or particular first line

- Update YAML options file processing to ignore keys starting with `$`, Add some special processing

- Add `PetscBagViewFromOptions()`

- Add `PetscLogEventDeactivatePush()`, `PetscLogEventDeactivatePop()`

- Add new option to `-log_view` to view nested event timing information as a flame graph

PetscViewer:

- `PetscViewerAndFormat` now allows a payload

- Change `PetscViewerFlowControlStepMaster()`, `PetscViewerFlowControlEndMaster()` to `PetscViewerFlowControlStepMain()`, `PetscViewerFlowControlEndMain()`

- HDF5: `FILE_MODE_APPEND` (= `FILE_MODE_UPDATE`) now creates a new file if it does not exist yet

- VU: `PetscViewerVUSetMode()` is now deprecated; please use standard `PetscViewerFileSetMode()` instead

PetscDraw:

AO:

IS:

VecScatter / PetscSF:

- `VecScatter` is now the same type as `PetscSF`, in other words, we have `typedef PetscSF VecScatter`

- Remove `VecScatter` types `VECSCATTER{SEQ,MPI1,MPI3,MPI3NODE,SF}`. One can use all `PetcSF` types as `VecScatter` types

- Rename `PetscLayoutsCreateSF()` to `PetscSFCreateFromLayouts()` and move its declaration from `petscis.h` to `petscsf.h`

- Deprecate `MPIU_REPLACE`; Use `MPI_REPLACE` instead

- Deprecate `PetscSFBcastAndOp` variants; Use `PetscSFBcast` instead

- Deprecate `PetscSFCreateEmbeddedSF`; Use `PetscSFCreateEmbeddedRootSF` instead

- Add experimental NVIDIA NVSHMEM support; For details on how to use it, contact petsc-maint@mcs.anl.gov

- Add `PetscSFCreateByMatchingIndices()` to create SF by matching root and leaf indices

PF:

Vec:

- Change `Vec{Get,Restore}Array{Read}Inplace` to `Vec{Get,Restore}Array{Read}AndMemType()` and add an extra argument to also return the memory type of the array

- Remove vector type `VECNODE`

- Add `VecConcatenate()` function for vertically concatenating an array of vectors into a single vector. Also returns an array of index sets to access the original components within the concatenated final vector

PetscSection:

PetscPartitioner:

Mat:

- Add `MatSetPreallocationCOO` and `MatSetValuesCOO` to preallocate and set values in a matrix using COO format. Currently efficiently implemented only for `MATCUSPARSE`

- Add the option `MAT_FORCE_DIAGONAL_ENTRIES` for `MatSetOption()`. It forces allocation of all diagonal entries

- Remove `MAT_NEW_DIAGONALS` from `MatOption`

- Add `UNKNOW_NONZERO_PATTERN` as new value for `MatStructure`. It indicates that the relationship is unknown, when set the AIJ matrices check if the two matrices have identical patterns and if so use the faster code

- Add `MAT_FACTOR_QR`, `MatQRFactor()`, `MatQRFactorSymbolic()`, and `MatQRFactorNumeric()` for QR factorizations. Currently the only built-in implementation uses LAPACK on sequential dense matrices

- Change option `-mat_cusparse_transgen` to `-mat_form_explicit_transpose` to hint PETSc to form an explicit transpose for repeated operations like MatMultTranspose. Currently implemented only for `AIJCUSPARSE` and `AIJKOKKOS`

- Add a `MatOption` `MAT_FORM_EXPLICIT_TRANSPOSE`

PC:

- Add `PCGAMGSetRankReductionFactors()`, provide an array, `-pc_gamg_rank_reduction_factors factors`, tp specify factor by which to reduce active processors on coarse grids in `PCGAMG` that overrides default heuristics

- Change `PCCompositeAddPC()` to `PCCompositeAddPCType()`, now `PCCompositeAddPC()` adds a specific `PC` object

- Add a Compatible Relaxation (CR) viewer `PCMG` with `-pc_mg_adapt_cr`

- Experimental: Add support for assembling AIJ (CUSPARSE and KOKKOS) matrix on the Cuda device with `MatSetValuesDevice()`, `MatCUSPARSEGetDeviceMatWrite()`, and Kokkos with `MatKokkosGetDeviceMatWrite`

- Add `PCMGSetResidualTranspose()` to support transposed linear solve using `PCMG` and `PCGAMG`

KSP:

- Add `-all_ksp_monitor` which turns on monitoring for all KSP solvers regardless of their prefix. This is useful for monitoring solvers with inner solvers such as `PCMG`, `PCGAMG`, `PCFIELDSPLIT`.

- Add support for monitor `KSPPREONLY`. This is useful for monitoring solvers with inner solvers such as `PCMG`, `PCGAMG`, `PCFIELDSPLIT`.

- Add `KSPConvergedReasonViewSet()` to set an ADDITIONAL function that is to be used at the end of the linear solver to display the convergence reason of the linear solver

- Add `KSPConvergedReasonViewCancel()` to remove all user-added converged reason view functions

- Add `KSPGetConvergedReasonString()` to retrieve a human readable string for ksp converged reason

- Change `KSPReasonView()` to `KSPConvergenceReasonView()`

- Change `KSPReasonViewFromOptions()` to `KSPConvergedReasonViewFromOptions()`

- Add `KSPConvergedDefaultSetConvergedMaxits()` to declare convergence when the maximum number of iterations is reached

- Fix many `KSP` implementations to actually perform the number of iterations requested

- Chebyshev uses `MAT_SPD` to default to CG for the eigen estimate

- Add `KSPPIPECG2`, a pipelined solver that reduces the number of allreduces to one per two iterations and overlaps it with two PCs and SPMVs using non-blocking allreduce

- Add `KSPConvergedRateView()` and `KSPComputeConvergenceRate()` to check the convergence rate of a linear solve

- Add `KSPSetUseExplicitTranspose()` to explicitly transpose the system in `KSPSolveTranspose()`

- Add `KSPMonitorLGCreate()`, and remove `KSPMonitorLGResidualNorm*()` and `KSPMonitorLGTrueResidualNorm*()`

- Add `KSPMonitorError()`, used by `-ksp_monitor_error`

- Add arguments to `KSPMonitorSetFromOptions()` to allow line graphs to be configured

- Deprecate `KSP{Set|Get}MatSolveBlockSize()`, use `KSP{Set|Get}MatSolveBatchSize()` instead

- Reduce default `KSPView()` ASCII output to a single subdomain’s KSP/PC information for `PCASM`, resp. `PCBJacobi`. Use `-ksp_view ::ascii_info_detail` to output KSP/PC information for all subdomains

SNES:

- Add `SNESConvergedCorrectPressure()`, which can be selected using `-snes_convergence_test correct_pressure`

- Remove `SNESMonitorLGCreate()` and `SNESMonitorLGResidualNorm()` which are now handled by the default monitor

- Add `SNESConvergedReasonViewSet()` to set an ADDITIONAL function that is to be used at the end of the nonlinear solver to display the convergence reason of the nonlinear solver

- Add `SNESConvergedReasonViewCancel()` to remove all user-added converged reason view functions

- Add `SNESGetConvergedReasonString()` to retrieve a human readable string for snes converged reason

- Add `SNESFASFullSetTotal()` to use total residual restriction and total solution interpolation in the initial cycle of full FAS multigrid

- Deprecate `-snes_nasm_sub_view`, use `-snes_view ::ascii_info_detail` instead

SNESLineSearch:

TS:

- Change to `--download-sundials2` to indicate the version of SUNDIALS PETSc downloads, which is very old and out-dated

- Add forward and adjoint sensitivity support for cases that involve parameterized mass matrices

- Add `TSGetNumEvents()` to retrieve the number of events

- Add `-ts_monitor_cancel`

- Now `-ts_view_solution` respects the TS prefix

- Add `TSSetMatStructure()` to indicate the relationship between the nonzero structures of the I Jacobian and the RHS Jacobian

- Automatically set the `MatStructure` flag of TS to `SAME_NONZERO_PATTERN` if the RHS matrix is obtained with a `MatDuplicate()` from the I Jacobian

TAO:

- Add `TaoSetRecycleFlag()` and `TaoGetRecycleFlag()` interfaces to enable some Tao algorithms to re-use iterate information from the previous `TaoSolve()` call

- Add new Augmented Lagrangian Multiplier Method (`TAOALMM`) for solving optimization problems with general nonlinear constraints

DM/DA:

- Remove unneeded `Vec` argument from `DMPatchZoom()`

- Change `DMDACreatePatchIS()` to collective operation and add an extra argument to indicate whether off processor values will be returned

- Add `DMComputeError()`, which uses `PetscDS` information for the exact solution

- Add `DMShellGetGLobalVector()`

- Add `DMInterpolateSolution()` for interpolating solutions between meshes in a potentially nonlinear way

- `DMInterpolationSetUp()` now can drop points outside the domain

DMSwarm:

- `DMSwarmViewXDMF()` can now use a full path for the filename

- Add `DMSwarmSetPointCoordinatesRandom()`

- Add `-dm_view_radius` to set size of drawn particles

DMPlex:

- Using `-petscpartitioner_simple_node_grid` and `-petscpartitioner_simple_process_grid`, the Simple partitioner can now make grid partitions

- Add `DMGet/SetFieldAvoidTensor()` to allow fields to exclude tensor cells in their definition

- Remove regular refinement and marking from `DMPlexCreateDoublet()`

- Add high order FEM interpolation to `DMInterpolationEvaluate()`

FE/FV:

- Add `PetscDualSpaceTransformHessian()`, `PetscDualSpacePushforwardHessian()`, and `PetscFEPushforwardHessian()`

- Now `PetscFEGetCellTabulation()` and `PetscFEGetFaceTabulation()` ask for the number of derivatives

- Add `PetscDualSpaceLagrangeGet/SetUseMoments()` and `PetscDualSpaceLagrangeGet/SetMomentOrder()` to allow a moment integral for P0

DMNetwork:

- Add `DMNetworkAddSubnetwork()` for network of subnetworks

- Add `DMNetworkAdd/GetSharedVertices()`, `DMNetworkIsSharedVertex()`

- Remove `DMNetworkSetEdgeList()`, `DMNetworkSet/GetComponentNumVariables()`, `DMNetworkSet/Add/GetNumVariables()`, `DMNetworkGetComponentKeyOffset()`, `DMNetworkGetVariableOffset()`, `DMNetworkGetVariableGlobalOffset()`

- Change the prototypes for `DMNetworkAdd/GetComponent()`

- Rename `DMNetworkSet/GetSizes()` to `DMNetworkSet/GetNumSubNetworks()`

- Rename `DMNetworkGetComponentVariableOffset()` to `DMNetworkGetLocalVecOffset()`, `DMNetworkGetComponentVariableGlobalOffset()` to `DMNetworkGetGlobalVecOffset()`

- Rename `DMNetworkGetSubnetworkInfo()` to `DMNetworkGetSubnetwork()`

DT:

- `PetscDSCopyBoundary()` now takes a list of fields for which boundary copying is done

- Add `PetscDSGet/SetJetDegree()`, and `-dm_ds_jet_degree` is needed to enable it under a DM

- Add `PetscWeakForm` class to manage function pointers for problem assembly

Fortran:

- Add configure option `--with-mpi-f90module-visibility` [default=``1``]. With `0`, `mpi.mod` will not be visible in use code (via `petscsys.mod`) - so `mpi_f08` can now be used

- Add `PetscDLAddr()` to get name for a symbol

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