petsc-3.12.1 2019-10-22
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# Documentation: Changes: 3.11

## CHANGES in the PETSc 3.12 Version

#### 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:

- 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.

#### AO:

#### Sieve:

#### Fortran: