============
Changes: 3.3
============


.. rubric:: config/configure.py:

-  Building PETSc using CMake is enabled automatically if CMake is
   installed (enabling parallel builds and fast incremental builds),
   otherwise the plain make-based system is used.
-  Added --with-cuda-only flag to allow compiling CUDA files without
   requiring Thrust and Cusp

.. rubric:: Vec:

-  VecCreateSeqWithArray() and VecCreateMPIWithArray() now take a
   blocksize argument before the local length
-  VecSetBlockSize() cannot be called after VecCreateSeq() or
   VecCreateMPI() and must be called before VecSetUp() or
   VecSetFromOptions() or before either VecSetType() or VecSetSizes()

.. rubric:: Mat:

-  MatScaleSystem() and MatUnScaleSystem() are gone, they didn't do
   anything.
-  Renamed MatNullSpaceAttach() to MatSetNullSpace()
-  MatMult() no longer removes the nullspace set by MatSetNullSpace()
-  Renamed MatMatMultTranspose() for C=A^T*B to MatTransposeMatMult()
-  Added MatMatTransposeMult() for C=A*B^T
-  Added MatRARt() for C=R*A*R^T
-  Preallocation routines now automatically set
   MAT_NEW_NONZERO_ALLOCATION_ERR, if you intentionally preallocate
   less than necessary then use
   MatSetOption(mat,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE) to
   disable the error generation.
-  MatSetBlockSize() must be called before MatSetUp() or
   MatXXXXSetPreallocation() or block size defaults to 1
-  -mat_block_size is NOT processed by MatXXXXSetPreallocation() you
   MUST call MatSetFromOptions() before MatSetUp() to have it
   processed
-  You MUST now call MatXXXSetPreallocation() or MatSetUp() on any
   matrix you create directly (not using DMCreateMatrix()) before
   calling MatSetValues(), MatSetValuesBlocked() etc.
-  MatGetOwnershipRange() will not work without setting up the
   matrix.
-  MatSetUpPreallocation() and MatPreallocated() are removed, use
   MatSetUp()
-  MatPreallocateSymmetricInitialize() is removed, use
   MatPreallocateInitialize()
-  MatCreateMPIAIJ(), MatCreateMPIBAIJ(), MatCreateMPISBAIJ(),
   MatCreateMPIDense() are now MatCreateAIJ(), MatCreateBAIJ(),
   MatCreateSBAIJ(), MatCreateDense(). Note that on a single process
   they have always created the sequential version of the matrix so
   this naming is more accurate.
-  Renamed MatMerge_SeqsToMPI() to MatCreateMPIAIJSumSeqAIJ()
-  Renamed MatMerge() to MatCreateMPIAIJConcatenateSeqAIJ()
-  Added block size in call to MatCreateIS()
-  MatInvertBlockDiagonal() now returns a const pointer

.. rubric:: PC:

-  Remove PCASASetDM(), use PCSetDM() instead.

-  Add PCFieldSplitSetSchurFactType(), rename
   -pc_fieldsplit_schur_factorization_type to
   -pc_fieldsplit_schur_fact_type.

-  Added native algebraic multigrid method -pc_type gamg. Aggregation
   method is recommended: -pc_gamg_type agg and for elliptic
   operators smoothing is recommended: -pc_gamg_agg_nsmooths 1.

-  PCSetCoordinates(PC,PetscInt,PetscInt,PetscReal*) added second
   integer argument for number of local vertices.

-  Added PCISSetSubdomainScalingFactor(PC,PetscScalar).

-  .. rubric:: PCGASM:

   -  Remove PCGASMSetLocalSubdomains(), use PCGASMSetSubdomains();
      **note:** the first argument is now the list of "inner"
      subdomains (without overlap), unlike before and for PCASM
   -  PCGASMSetTotalSubdomains(PC,PetscInt,PetscBool); added third
      argument to indicate whether local subdomains should be
      constructed.
   -  Removed PCGASMCreateSubdomains(), use
      PCGASMCreateLocalSubdomains(Mat,PetscInt,PetscInt,IS*[],IS*[]);
      second PetscInt argument is requested overlap
   -  PCGASMCreateSubdomains2D(PC,PetscInt,PetscInt,PetscInt,PetscInt,PetscInt,PetscInt,PetscInt*,IS[]*,IS[]*):
      the 9-th and 10-th argument have been swapped: the 9-th outputs
      the inner subdomains, the 10-th outputs the outer subdomains.

-  PCMG multigrid defaults changed to use a Chebyshev smoother with
   block Jacobi Gauss-Seidel relaxation. This is a linear
   preconditioner so it can be used with normal Krylov methods rather
   than only flexible methods, as well as having fewer
   synchronization pointst. Use
   ``-mg_levels_ksp_type gmres -mg_levels_ksp_max_it 1 -mg_levels_pc_type bjacobi``
   for the original behavior.

.. rubric:: KSP:

-  KSPSetOperators() will automatically set the null space present on
   the input matrix
-  Renamed KSPCHEBYCHEV to KSPCHEBYSHEV
-  Added Hybrid CHEBYCHEV (-ksp_chebyshev_hybrid)
-  Added pipelined GMRES (KSPPGMRES) which performs one non-blocking
   reduction per iteration instead of two blocking reductions.
-  Added flexible BiCGStab (KSPFBCGS) which tolerates a nonlinear
   preconditioner (like KSPFGMRES).
-  Added improved flexible BiCGStab (KSPIFBCGS) which tolerates a
   nonlinear preconditioner and performs one reduction every other
   iteration (like KSPIBCGS).

.. rubric:: SNES:

-  Added SNESGetSNESLineSearch
-  Changed default max_its and max_funcs for non-newton SNES solvers
   to 10000 and 30000 respectively
-  Changed options and command-line arguments for SNESFAS to be in
   line with PCMG
-  Added quasi-Newton (SNESQN), Nonlinear GMRES (SNESNGMRES),
   nonlinear conjugate gradients (SNESNCG), and multi-stage methods
   (SNESMS, used as a smoother for nonlinear multigrid).
-  Support for Full Approximation Scheme nonlinear multigrid
   (SNESFAS) moved from DMMG to SNES and made composable with the
   methods above.
-  SNES line search type should be set by name with
   SNESLineSearchSetType rather than with SNESLineSearchSet, see
   below.

.. rubric:: SNESLineSearch:

-  SNESLineSearch object added
-  The default SNESLineSearch of a SNES may be gotten with
   SNESGetSNESLineSearch(SNES snes, SNESLineSearch \*linesearch)
-  The linesearch type may be set with SNESLineSearchSetType() or
   -snes_linesearch_type
-  The line search (and pre and post checks) is applied using
   SNESLineSearchApply()
-  Pre/Post-check methods may be set with
   SNESLineSearchSetPre/PostCheck()
-  The previous steplength may be accessed through
   SNESLineSearchSetLambda()
-  The damping parameter may be set through
   SNESLineSearchSetDamping() or -snes_linesearch_damping
-  Success of the line search is determined using
   SNESLineSearchGetSuccess()
-  Custom linesearches may be built through
   SNESLINESEARCHSHELL,("shell") or by registering a new linesearch
   type with SNESLineSearchRegisterDynamic()
-  SNESLINESEARCHBT,("bt") replaces SNES_LS_CUBIC and
   SNES_LS_QUADRATIC, and order may be set with
   SNESLineSearchSetOrder() or -snes_linesearch_order
-  SNESLINESEARCHBASIC,("basic") replaces SNES_LS_BASIC and
   SNES_LS_BASICNONORMS. Norms may be turned off with
   SNESLineSearchSetComputeNorms() or -snes_linesearch_norms 0
-  SNESLineSearchSetTolerances() replaces SNESLSSetParams(), with the
   former alpha parameter set with SNESLineSearchBTSetAlpha() or
   -snes_linesearch_alpha
-  Added Line Search type SNESLINESEARCHL2,("l2") as the default for
   NRICHARDSON
-  SNESLINESEARCHCP,("cp") added as the default line search method
   for SNESNCG and SNESQN

.. rubric:: TS:

-  -ts_max_time changed to -ts_final_time
-  TSDefaultComputeJacobian() and TSDefaultComputeJacobianColor()
   have been removed. Configure TS to use coloring with
   SNESSetJacobian().
-  Added TSROSW for Rosenbrock-W methods.
-  Added a common, extensible system for adaptive controllers, see
   TSGetAdapt().

.. rubric:: DM/DA:

-  Added DMCreateDecomposition(DM,PetscInt,char*[]*,IS[]*,DM[]*) for
   use with PCFIELDSPLIT,PCASM,PCGASM
-  Added DMCreateDecompositionDM(DM,const char*,DM*) to create a
   version of the DM encapsulating a named decomposition; use with
   DMCreateDecomposition()
-  Added DMRedundant for managing globally coupled degrees of
   freedom.
-  Removed DMCompositeAddArray(), use DMRedundantCreate() and
   DMCompositeAddDM().
-  Renamed DMGetMatrix(), DMGetInterpolation(), DMGetInjection(), and
   DMGetColoring() to DMCreateMatrix(), etc for semantic consistency.
-  The communicator argument to DMRefine() and DMCoarsen() can be
   MPI_COMM_NULL, but not PETSC_NULL, because the latter may not be
   the correct type.
-  Added DMCoarsenHookAdd() and DMRefineHookAdd() for shepherding
   persistent resolution-dependent data between levels.
-  Added DMGetNamedGlobalVector() for storing persistent
   resolution-dependent data.
-  DMDASNESSetFunctionLocal() and DMDASNESSetJacobianLocal() can be
   used for convenient local evaluation; these routines will
   eventually replace DMDASetLocalFunction() and
   DMDASetLocalJacobian().

.. rubric:: DMMG:

-  DMMG is now completely removed from PETSc. Equivalent (and better)
   functionality can now be obtained by calling SNESSetDM() or
   KSPSetDM(). Make sure to avoid resolution-dependent data in the
   user context. Use SNESGetDM() or KSPGetDM() in the function
   evaluation context to obtain the grid. DMGetNamedGlobalVector(),
   DMCoarsenHookAdd(), and DMRefineHookAdd() can be used to manage
   persistent resolution-dependent data.

.. rubric:: PetscViewer:

-  A VTK binary viewer was added, see PETSCVIEWERVTK.

.. rubric:: SYS:

-  PetscBagLoad() now requires you previously created and registered
   all the records in the PETSc bag, allows loading on systems with
   different struct layout/endianness.
-  PetscSF added as a type-generic graph communication mechanism. The
   current implementation requires MPI-2 one-sided and the interface
   is currently optional.

.. rubric:: Fortran:

-  PETSC_NULL_TRUTH is now PETSC_NULL_BOOL
-  PetscOptionsGetEnum() now available from Fortran

.. rubric:: ExternalPackages:

-  The Hypre interface was updated to 2.8.0b and now supports 64-bit
   integers.
-  SuperLU_DIST interface updated to 3.1.
-  SuperLU interface updated to 4.3.
-  Sundials interface updated to 2.5.0.
-  FFTW interface updated to 3.3.2.
-  ParMetis updated to 4.0.2 and split from Metis 5.0.2 which is now
   separate.

.. rubric:: Build:

-  If Python 2.7 is available, the config/builder2.py is now
   available for a complete build, including dependency tracking.

.. rubric:: Examples:

-  SNES ex62 illustrates the use of DMComplex to solve the Stokes
   equation on an unstructured mesh. The Python tests show how to use
   block preconditioning strategies from the command line.
-  SNES ex52 illustrates the use of CUDA for FEM integration