xref: /petsc/doc/changes/312.md (revision b11d9968bc79904c690b122f9399be46447eb113)

# Changes: 3.12

```{rubric} 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

```{rubric} 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

```{rubric} IS:
```

```{rubric} PetscDraw:
```

```{rubric} PF:
```

```{rubric} 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.

```{rubric} PetscLayout:
```

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

```{rubric} PetscSection:
```

```{rubric} 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().

```{rubric} 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
  MatComputeExplicitOperatorTranspose() 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.

```{rubric} 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

```{rubric} 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

```{rubric} 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

```{rubric} SNES:
```

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

```{rubric} SNESLineSearch:
```

```{rubric} 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.

```{rubric} 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.

```{rubric} DMPlex:
```

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

```{rubric} DMNetwork:
```

- Changed prototypes for DMNetworkSetSizes()

```{rubric} 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).

```{rubric} 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.

```{rubric} AO:
```

```{rubric} Sieve:
```

```{rubric} Fortran:
```