Changes: 3.3#
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 
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() 
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 
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). 
- 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 bjacobifor the original behavior.
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). 
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. 
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 
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(). 
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(). 
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. 
PetscViewer:
- A VTK binary viewer was added, see PETSCVIEWERVTK. 
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. 
Fortran:
- PETSC_NULL_TRUTH is now PETSC_NULL_BOOL 
- PetscOptionsGetEnum() now available from Fortran 
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. 
Build:
- If Python 2.7 is available, the config/builder2.py is now available for a complete build, including dependency tracking. 
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