Documentation: Changes: 3.12

General:

• PetscRoundReal() has been removed, since the math routine round() is not supported on all systems: perhaps use PetscCeilReal() or PetscFloorReal()<\li>
• The legacy and cmake compile systems (make all-legacy and all-cmake) are removed
• make gnumake is now make libs
• PetscArraycmp() should be used instead of PetscMemcmp(), it takes a count argument instead of a byte argument
• PetscArraycpy() should be used instead of PetscMemcpy(), it takes a count argument instead of a byte argument
• PetscArrayzero() should be used instead of PetscMemzero(), it takes a count argument instead of a byte argument
• PetscArraymove() should be used instead of PetscMemmove(), it takes a count argument instead of a byte argument
• The ./configure options -with-gnu-compilers and -with-vendor-compilers are removed
• The ./configure option --with-avx512-kernels defaults to true now so the manually optimized AVX-512 kernels are used by default
• The order ./configure tests compilers has changed so there may be a different compiler selected if you do not provide them
• Added --with-64-bit-blas-indices that will switch to 64 bit indices when using MKL libraries for BLAS/LAPACK and build OpenBLAS with this support
• Changed PETSC_DEPRECATED() to PETSC_DEPRECATED_FUNCTION() and PETSC_DEPRECATED_TYPEDEF() to match naming of PETSC_DEPRECATED_ENUM() and PETSC_DEPRECATED_MACRO
• -help now causes the printing of the current value and the newly set value for PetscOptionsInt(), etc
• PetscFunctionListPrintTypes() takes an additional final argument after the current value, the set value
• PetscCalloc*() now calls the system calloc() routine instead of malloc() plus memzero()
• -malloc is now marked as deprecated, use -malloc_debug instead
• -malloc_log and -malloc_log_threshold are now -malloc_view and -malloc_view_threshold
• PetscMallocDebug() is now PetscMallocSetDebug()
• PetscMallocDumpLog() is now PetscMallocView(), see also PetscMallocViewSet()
• PetscMallocSetDumpLogThreshold() and PetscMallocSetDumpLog() are now PetscMallocViewSet()
• With -malloc_test or -malloc_debug allocated memory is initialized with NaN to detect use of uninitialized numerical arrays
• PetscMallocSet() now takes three arguments instead of two
• Moved PetscCUBLASGetHandle() to a separate header file petscublas.h
• Moved VecCUDA*-routines from petsccuda.h into petscvec.h. Removed petsccuda.h

Configure/Build:

• C++ dialect is now auto-detected (C++14 first and then C++11). One can disable this check using --with-cxx-dialect=0, or force it to only check for C++11 using --with-cxx-dialect=C++11
• New option --download-hpddm to enable PCHPDDM and KSPHPDDM

IS:

PetscDraw:

PF:

Vec:

• VecCUDAGet/RestoreArrayReadWrite() changed to VecCUDAGet/RestoreArray()
• VecViennaCLGet/RestoreArrayReadWrite() changed to VecViennaCLGet/RestoreArray()
• Added VecGet/RestoreArray/ReadInPlace() to get array of a vector where it is without copying from GPU to CPU.

PetscLayout:

• Added PetscLayoutCreateFromSizes()
• Added PetscLayoutCreateFromRanges()
• Calling PetscLayoutSetUp() twice with different sizes is now forbidden

PetscSection:

VecScatter & PetscSF:

• The default VecScatter implementation is changed to PetscSF. In other words, the default VecScatter shares PetscSF's MPI communication code. One can use -vecscatter_type mpi1 to go back to the old implementation.
• Added new InsertMode MAX_VALUES and MIN_VALUES support in VecScatterBegin/End and VecGhostUpdateBegin/End.
• PetscSFComputeMultiRootOriginalNumbering: add output argument with the number of multiroots for convenience
• Added an enum type PetscSFPattern for SF graph patterns. Valid values include PETSCSF_PATTERN_ALLGATHER, PETSCSF_PATTERN_GATHER and PETSCSF_PATTERN_ALLTOALL.
• Added PetscSFSetGraphWithPattern() to set SF graphs with predefined patterns.
• Added PetscSFComposeInverse() to compose a new SF by putting the inverse of an SF under the another SF.
• Added MPI-3.0 neighborhood collectives support. One can use command line option -sf_type neighbor to let SF use MPI-3.0 neighborhood collectives for communication instead of the default MPI_Send/Recv.
• PetscSF is now CUDA-aware. The rootdata, leafdata arguments passed to SF routines can be either GPU pointers or CPU pointers. Use a CUDA-aware MPI and option -use_gpu_aware_mpi to enable it.
• VecScatter is also CUDA-aware. You can do VecScatter on CUDA vectors without copying them from GPU to CPU. Again, you need a CUDA-aware MPI and option -use_gpu_aware_mpi.
• Removed PetscSFCreateFromZero. Instead, users should use PetscSFCreate() to create an SF, and then set its graph with PetscSFSetGraphWithPattern(..,PETSCSF_PATTERN_GATHER).
• Renamed PetscSFGetRanks() to PetscSFGetRootRanks().

Mat:

• MatShift(Mat,0); will no longer silently insure there are no missing diagonal entries. (Previously it would put 0 into any diagonal entry that was missing)
• Renamed MatComputeExplicitOperator() into MatComputeOperator() and MatComputeExplicitOperatorTranpose() into MatComputeOperatorTranspose(). Added extra argument to select the desired matrix type
• MatLoad() now supports loading dense matrices from HDF5/MAT files.
• Added new Mat type, MATKAIJ, for matrices that can be expressed in a particular Kronecker (tensor) product form.
• Added MatCompositeSetScalings() to set separate scaling factors for component matrices.
• Added a Boolean option -mat_composite_merge_mvctx to merge Mvctx of component matrices to optimize communication in MatMult() for ADDITIVE matrices. Default is true.
• Added MATSEQDENSECUDA class to use GPUs for dense linear algebra.

PC:

• Renamed PCComputeExplicitOperator() into PCComputeOperator(). Added extra argument to select the desired matrix type
• Added support for PCCHOLESKY with MATSOLVERMUMPS and SBAIJ matrices with bs greater than 1
• Added support for PCLU with MATSOLVERMKL_PARDISO (resp. MATSOLVERMKL_CPARDISO) and SEQBAIJ (resp. MPIBAIJ) matrices
• Added support for PCCHOLESKY with MATSOLVERMKL_PARDISO (resp. MATSOLVERMKL_CPARDISO) and SEQSBAIJ (resp. MPISBAIJ) matrices
• Added new preconditioner PCHPDDM, cf. src/ksp/ksp/examples/tutorials/ex71.c or src/snes/examples/tutorials/ex56.c

KSP:

• Renamed KSPComputeExplicitOperator() into KSPComputeOperator(). Added extra argument to select the desired matrix type
• KSPCGGLTRGetMinEig(KSP,PetscReal*) -> KSPGLTRGetMinEig(KSP,PetscReal*)
• KSPCGGLTRGetLambda(KSP,PetscReal*) -> KSPGLTRGetLambda(KSP,PetscReal*)
• KSPCGNASH, KSPCGSTCG, KSPCGGLTR -> KSPNASH, KSPSTCG, KSPGLTR
• Added new Krylov solver KSPHPDDM, cf. src/ksp/ksp/examples/tutorials/ex75.c or src/ksp/ksp/examples/tutorials/ex9.c

SNES:

• Changed SNES_CONVERGED_TR_DELTA to SNES_DIVERGED_TR_DELTA with a negative value to indicate diverged, unclear why it was ever positive since tiny trust region would indicate trouble, not converged

SNES:

• -snes_mf no longer turns the preconditioner to none; to use it generally you will also need -pc_type none

SNESLineSearch:

TS:

• Added tangent linear models for Runge-Kutta methods
• Added second-order adjoint solvers based on Runge-Kutta methods and Theta methods
• Improved the usage of first-order adjoint solvers in an optimization context. (The TS object can be reused in the optimization loop)
• Changed the APIs for integrand evaluations and corresponding derivative evaluations. TSSetCostIntegrand() is deprecated. (Instead a quadrature TS is used to handle the callbacks)
• TSTrajectory creates a unique name for folders that store the checkpoint data. Users can rerun adjoint codes without worrying about the folder names, and run multiple codes under the same directory.
• Added support for using finite-differencing (and coloring) to approximate the Jacobians needed by the adjoint solvers. -snes_fd_color can be used for both implicit and explicit methods.

DM/DA:

• Add DMGetLocalSection() to be used in preference to DMGetSection().
• Add DMSetLocalSection() to be used in preference to DMSetSection().
• DMGetDefaultSF() replaced with DMGetSectionSF().
• DMSetDefaultSF() replaced with DMSetSectionSF().
• DMCreateDefaultSF() replaced with DMCreateSectionSF().
• DMAddLabel() now increments the reference count of the DMLabel.
• DMRemoveLabel() now destroys the DMLabel if the output argument is NULL.
• Add DMRemoveLabelBySelf() which looks up the DMLabel by itself, removes from DM and destroys.

DMPlex:

• Rename DMPlexCreateSpectralClosurePermutation() to DMPlexSetClosurePermutationTensor()
• Add DMPlexFindVertices() for vertex coordinates -> DAG point lookup
• Add DMPlexGetOverlap() to get the partition overlap

DMNetwork:

• Changed prototypes for DMNetworkSetSizes()

PetscViewer:

• Removed PetscViewerHDF5{Get,Set}AIJNames() which are likely not really needed
• PetscViewerHDF5SetCollective() and -viewer_hdf5_collective can be used to switch between independent and collective transfer mode. Defaults now to false (independent).

SYS:

• Added PetscCheckDupsInt() to check if a PetscInt array has dups.
• Added an argument to PetscBinaryRead() and PetscBinarySynchronizedRead() to return the number of items read.

AO:

Sieve:

Fortran: