PETSc

Documentation: Changes: 3.13

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General:

• Update make test to run the full test suite. Use make check to run the short test
• Remove last PetscBool argument from PetscBinaryWrite() and PetscBinarySynchronizedWrite()
• Change PetscLayoutFindOwner() and PetscLayoutFindOwnerIndex() to return a PetscMPIInt instead of a PetscInt
• Support for Compaq F90 is removed along with supporting flags PETSC_HAVE_FORTRAN_STDCALL, PETSC_BLASLAPACK_STDCALL, HAVE_FORTRAN_MIXED_STR_ARG
• Promote all example directories examples/tutorials/ and examples/tests/ to tutorials/ and tests/ respectively
• Make title argument of PetscOptionsBegin() obligatory

Configure/Build:

IS:

• Add ISSetInfo(): set local and global properties of an IS (whether the IS is sorted, unique, a permutation, an interval, or identity)
• Add ISGetInfo(): query local and global properties of an IS

PetscDraw:

PetscSF:

• Fix few bugs in PETSCSFWINDOW when using PETSCSF_WINDOW_SYNC_LOCK or PETSCSF_WINDOW_SYNC_ACTIVE synchronization types
• Add window reusage for PETSCSFWINDOW and support for different creation flavor types. See PetscSFWindowFlavorType man page for details
• Set default of -use_gpu_aware_mpi from false to true

PF:

Vec:

• VecPinToCPU() is deprecated in favor of VecBindToCPU()
• Add Vec{Set|Get}PinnedMemoryMin() and -vec_pinned_memory_min option. Note that VECCUDA now defaults to using pinned memory for host allocations

VecScatter:

PetscSection:

PetscPartitioner:

• PetscPartitionerPartition() does not longer gets a DM as input. Vertex weights can be specified through PetscSection
• Add support for target partition weights for PETSCPARTITIONERSIMPLE, PETSCPARTITIONERPARMETIS and PETSCPARTITIONERPTSCOTCH

Mat:

• Improve the performance of MatConvert_AIJ_BAIJ by preallocating the Mat before dispatching to MatConvert_Basic
• Change the behavior of MatConvert_AIJ_SBAIJ for block size greater than one, the block structure is now preserved (even for the diagonal entries)
• Fix various bugs related with matrix conversions from Hermitian SBAIJ matrices with complex numbers
• Add MatPropagateSymmetryOptions to propagate symmetry information from one matrix to another
• Fix a bug in MATSUPERLU_DIST interface when MATMPIAIJ with commsize 1 is used
• Add MATCHOLMOD support for block solves
• --download-suitesparse now uses the official SuiteSparse repository
• MatPinToCPU() is deprecated in favor of MatBindToCPU()
• Fix MatAXPY for MATSHELL
• MatAXPY(Y,0.0,X,DIFFERENT_NONZERO_PATTERN) no longer modifies the nonzero pattern of Y to include that of X
• Add support of selective 64-bit MUMPS, i.e., the regular/default build of MUMPS. One should still build PETSc --with-64-bit-indices to handle matrices with >2G nonzeros
• Add MatProductCreate(), MatProductCreateWithMat(), MatProductSetType(), MatProductSetAlgorithm(), MatProductSetFill(), MatProductSetFromOptions(), MatProductSymbolic(), MatProductNumeric(), MatProductReplaceMats(), MatProductClear()
• Deprecate MatMatMultSymbolic(), MatMatMultNumeric()
• Deprecate MatMatTransposeMultSymbolic(), MatMatTransposeMultNumeric()
• Deprecate MatPtAPSymbolic(), MatPtAPNumeric()
• Deprecate MatRARtSymbolic(), MatRARtNumeric()
• Fix a deadlock with MATELEMENTAL; if one configures PETSc with Elemental and has PETSC_COMM_WORLD != MPI_COMM_WORLD, it is now one's responsability to explicitly call PetscElementalInitializePackage()/PetscElementalFinalizePackage() outside of PetscInitialize()/PetscFinalize(). PetscElementalInitializePackage()/PetscElementalFinalizePackage() are collective on MPI_COMM_WORLD.

PC:

• Change the default behavior of PCASM and PCGASM to not automatically switch to PCASMType BASIC if the matrices are symmetric
• Change the default behavior of PCCHOLESKY to use nested dissection ordering for AIJ matrix

KSP:

• Add KSPHPDDMGetDeflationSpace and KSPHPDDMSetDeflationSpace for recycling Krylov methods in KSPHPDDM

SNES:

• Deprecate -snes_test_jacobian_display and -snes_test_jacobian_display_threshold. -snes_test_jacobian accepts an optional threshold parameter (since v3.10) and -snes_test_jacobian_view should be used in favor of -snes_test_jacobian_display

SNESLineSearch:

• Add SNESLineSearchGetType() in v3.13.1.

TS:

TAO:

• TAOPDIPM: A new solver in TAO for general NLP problems

DM/DA:

• DMCopyLabels(): add two additional input flags
• DMPlexDistribute(): fix a bug associated with vertex partition weights and overlapped meshes
• DMPlexDistribute(): vertex partition weights are now computed by summing all the local section dofs in the transitive closure of each cell
• Add PetscTabulation to hold function tabulation data
• Add DMEnclosureType to describe relations between meshes
• Add DMGetEnclosureRelation() and DMGetEnclosurePoint() to discover relations between meshes
• Add DMPolytopeType to describe different cell constructions

DMPlex:

• DMPlexInterpolate() now works correctly for distributed DMPlex
• The idea of hybrid and ghost cells has been removed from Plex in favor of cell type
• Plex can now classify points by cell type, stored in a DMLabel. This is useful for operations that require more than topological data, such as mesh interpolation, geometric calculations, and is also used an index to avoid repeated topological queries
• Add DMPlexSetCellType() and DMPlexCreateReferenceCellByType()
• Distribution sorts strata by cell type.
• Plex can now allow any number of cell types in a single mesh. Interpolation, refinement, and extraction of submeshes mixed meshes work smoothly. Both oriented and tensor-product prisms can be used in the same mesh
• Cell refiners have been abstracted. Currently there are two (regular refinement, and conversion to hexes). The plan is to add more, such as local extrusion and conversion to simplices
• Remove SimplexToTensor in favor of DM_REFINER_TO_BOX
• DMForest now responds to DMPlexGetOverlap() and propagates its overlap to the underlying Plex
• Add DMPlexGetSimplexOrBoxCells() to replace DMPlexGetInteriorCellStratum()
• Add DMPolytopTypeGetDim(), DMPolyTopeTypeGetConeSize(), DMPolytopeTypeGetNumVertices()
• Add DMLabelSetStratumBounds()
• Add DMPlexOrientCell() which orients a single cell
• Add DMPlexCompareOrientations() which compares the cone point order of a single cell with the given reference cone
• Add DMPlexIsInterpolated() which finds out whether the plex is interpolated
• Add DMPlexIsInterpolatedCollective() which finds out whether the plex is interpolated on all ranks
• Add DMPlexIsDistributed() which finds out whether the plex is distributed

DMNetwork:

• Add DMNetworkSetComponentNumVariables(), DMNetworkGetComponentVariableOffset(), and DMNetworkGetComponentVariableGlobalOffset() to set number of variables for a component, and retrieve its local/global offsets.

DT:

• All tabulated data is now stored in PetscTabulation structures. This changes interfaces in PetscDS, PetscFE, and PetscFV
• Rename DefaultTabulation to CellTabulation everywhere
• PetscDTGaussJacobiQuadrature() is now truly Gauss-Jacobi quadrature. The quadrature for the simplex (without weight function) is now called PetscDTStroudConicalQuadrature()
• Add PetscDTJacobiEval(), PetscDTGaussLobattoJacobiQuadrature()
• Add PetscDTIndexToBary() and PetscDTBaryToIndex() for barycentric lattice calculations
• Add PetscDTNodeType to enumerate methods of defining interpolation nodes
• PetscDualSpace now has PetscDualSpaceSetFormDegree() and PetscDualSpaceGetFormDegree() for governing functional pushforward/pullback behavior
• PETSCDUALSPACELAGRANGE now has PetscDualSpaceGetTrimmed() and PetscDualSpaceSetTrimmed() for creating degrees of freedom for trimmed polynomial spaces
• PETSCDUALSPACELAGRANGE now has PetscDualSpaceGetNodeType() and PetscDualSpaceSetNodType() for controlling the placement of interpolation nodes
• PETSCDUALSPACEBDM is no longer a standalone type of PetscDualSpace: it is now a constructor alias for PETSCDUALSPACELAGRANGE

PetscViewer:

• Remove last PetscBool argument from PetscViewerBinaryWrite()
• Add "fieldnum" argument to PetscViewerVTKAddField() to indicate only one field of the vector should be viewed

SYS:

• Rename PetscSignalSegvCheckPointer() to PetscSignalSegvCheckPointerOrMpi()
• Extend -info option controlling PetscInfo(). It now takes takes optional arguments -info [filename][:[~]list,of,classnames[:[~]self]]. See PetscInfo() manpage
• Add new API to control PetscInfo() programatically:
  • Add PetscInfoEnabled() - Indicate whether a given PETSc class is allowed in PetscInfo()
  • Add PetscInfoSetFile() - Set output destination of PetscInfo()
  • Add PetscInfoGetFile() - Get output destination of PetscInfo()
  • Add PetscInfoSetClasses() - Sets the classes which PetscInfo() is filtered for/against
  • Add PetscInfoGetClass() - Indicates whether the provided classname is marked as a filter in PetscInfo() as set by PetscInfoSetClasses()
  • Add PetscInfoProcessClass() - Activates or deactivates a class based on the filtering status of PetscInfo()
  • Add PetscInfoGetInfo() - Returns the current state of several indicator flags for PetscInfo()
  • Add PetscInfoSetFilterCommSelf() - Sets PetscInfoCommFlag enum to control communicator size filtering for PetscInfo()
  • Add PetscInfoDestroy() - Destroys and resets internal PetscInfo() filter options
  • Change PetscInfoAllow() to only activate/deactivate PetscInfo(), file setting is now handled separately by PetscInfoSetFile()
• Add PetscSubcommGetParent() - Gets the communicator that was used to create the PetscSubcomm
• Add PetscSubcommGetContiguousParent() - Gets a communicator that that is a duplicate of the parent but has the ranks reordered by the order they are in the children
• Add PetscSubcommGetChild() - Gets the communicator created by the PetscSubcomm
• Change the default option of -build_twosided from ibarrier to allreduce for communicators with no more than 1024 ranks

AO:

Sieve:

Fortran: