petsc-3.7.3 2016-07-24
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# Documentation: Changes: 2.0.24

## CHANGES in PETSc 2.0.24 (see new features)

#### General:

- Changed PETSC_ARCH on Windows platforms from nt to win32, and from nt_gnu to win32_gnu.
- Moved all the compiler/optimization information for each PETSC_ARCH from the various `base.g`, `base.O_c++` etc. files all into the single file `base_variables`. Now configuration for your system should require only editing the files ${PETSC_ARCH}/base and ${PETSC_ARCH}/`base.site`
- The PETSC_ARCH `rs6000` is now intended for IBM rs6000 workstations running MPICH or LAM, while `rs6000_sp` is for IBM SPs.
- Removed the gvec directory from the distribution. If you are using this please let us and know and we can provide it or provide alternative code to do what you need.
- Routines with the suffix "`withcoloring`" have been changed to the suffix "`color`" to get around the 31 character limit in names.
- The source code directory structure has changed slightly: pc and ksp are now subdirectories of sles, and ao and da are subdirectories of a new directory called dm (data management).
- The PETSc libraries are now: -lpetscts -lpetscsnes -lpetscsles -lpetscdm -lpetscmat -lpetscvec -lpetsc. Each library is now only dependent on libraries to the right of it in the list above. For example, if you are only using the linear solvers, you only need to list "-lpetscsles -lpetscdm -lpetscmat -lpetscvec -lpetsc" and if you are only using the vectors you only need to list "-lpetscvec -lpetsc".
- For users who previously could not use the PETSc makefiles because the PETSc rules for making .o files conflicted with the user's rules, we have introduce a new file that may be included by the user, `${PETSC_DIR}/bmake/${PETSC_ARCH}/base_variables`, which defines all the useful PETSc makefile variables, but not the rules. This should make it easier for people who previously had trouble using the PETSc makefiles. We highly recommend using the PETSc makefiles when possible because they are immediately portable across all systems that support PETSc.

#### AO (Application Orderings):

#### TS (Timestepping Solvers):

- Removed `TSSetRHSJacobianDefault`() - you can now call `TSSetRHSJacobian`(... `TSDefaultJacobianColor`,....) directly from Fortran
- Changed `TSDefaultJacobianSlow()` to `TSDefaultJacobian()`

#### SNES (Nonlinear Solvers):

- S`NESSetConvergenceHistory()` takes an additional argument; see the manual page for details.
- Changed the interface for matrix-free methods in SNES so that is more flexible, in particular:
  - Changed`SNESDefaultMatrixFreeMatCreate()` to `MatSNESFDMFCreate()`.
  - Added routines
    - MatSNESFDMFSetHHistory(Mat,Scalar *,int);
    - MatSNESFDMFResetHHistory(Mat,Scalar *,int);
    - MatSNESFDMFSetParameters(Mat,double,double);
    - MatSNESFDMFGetH(Mat,Scalar *);
    - MatSNESFDMFKSPMonitor(KSP,int,double,void *); and the corresponding option `-snes_mf_ksp_monitor`
  - Added support for an alternative way to compute the differencing parameter in matrix-free methods using the Walker-Pernice srategy, accessible via the option `-snes_mf_type` wp
- Changed the calling sequence of `SNESSetLineSearch()` so that it accepts an optional user-defined context variable. Likewise, changed the calling sequences of the various line search routines, e.g., `SNESCubicLineSearch(), SNESQuadraticLineSearch()`, etc.

#### SLES (Linear Solvers):

- See PC and KSP

#### KSP (Krylov Subspace Methods):

- Changed the calling sequence of `KSPComputeEigenvalues(KSP,int,double*,double*,int *neig);` to return as the final value the number of eigenvalues computed; see the manual page for more details.
- Changed GMRES to use the Gram-Schmidt method with one optional step of iterative refinement as the default orthogonalization procedure, instead of the modified Gram-Schmidt method. This change was urged by Rich Lehoucq. It could cause very minor differences in convergence rates for codes run before and after this change.
- The option `-ksp_bsmonitor` is not longer needed; use -`ksp_truemonitor` for the same affect.
- Added an additional argument to `KSPSetResidualHistory()`; see the manual page for details. This change was suggested by Maria Murillo.

#### PC (Preconditioners):

- Removed support for block Gauss-Seidel from the distribution; `-pc_type bgs` is no longer supported.
- The Eisenstat preconditioner (SSOR variant) now uses diagonal scaling by default, and the options `PCEisenstatUseDiagonalScaling()` and `-pc_eisenstat_diagonal_scaling` have been replaced with `PCEisenstatNoDiagonalScaling()` and `-pc_eisenstat_no_diagonal_scaling`

#### MAT (Matrices):

- Replaced`MatGetSubMatrixCall`() with `MatReuse().`
- Changed the calling sequence of `MatILUFactor()` and `MatILUFactorSymbolic()` to increase flexibility of adding new ILU options.
- Added an additional argument to `MatCopy()`; `SAME_NONZERO_PATTERN` or `DIFFERENT_NONZERO_PATTERN.`
- Added an additional argument to `MatDuplicate()`, `MAT_COPY_VALUES` or `MAT_DO_NOT_COPY_VALUES.`
- Changed the flag `MAT_NEW_NONZERO_LOCATION_ERROR` to `MAT_NEW_NONZERO_LOCATION_ERR`; also changed `MAT_NEW_ALLOCATION_ERROR` to `MAT_NEW_ALLOCATION_ERR`
- Changed `MatOrder`xxx to `MatOrdering`xxx; changed `MatOrderingType` to char* from enum
- Changed `Mat`xxx`Reordering`xxx to `Mat`xxx`Ordering`xxx changed command line option `-mat_order` to -`mat_ordering_type;` changed `MatColoringType` to char* from enum
- Changed `Partitioning`xxx to `MatPartitioning`xxx

#### DA (Distributed Arrays):

- `DAGetInfo()` has a new final argument, the stencil type. See the manual change your current code to work, you only need add an extra `PETSC_NULL` as a final argument.

#### VEC (Vectors):

- After a call to `VecCreate()` you MUST either call `VecSetType()` or `VecSetFromOptions()` on the vector before using it for any purpose. The `VecCreate`xxx() routines (e.g., `VecCreateSeq(), VecCreateMPI()`) do not need to have calls to VecSetType() or VecSetFromOptions() after them.
- All `VecGetArray()` calls MUST now be matched with a `VecRestoreArray()` call; previous PETSc versions did not force compliance with this rule.
- The command line names for changing the vector type in `VecCreate(`) are now `-vec_type mpi` or `-vec_type shared` rather than `-vec_mpi` or `-vec_shared`
- Changed the `VecType` variable type from an enum type to a string.
- Changed the calling sequence for `VecGetType()`; see the manual page for details.
- Changed `VecGhostGetLocalRepresentation()` and `VecGhostRestoreLocalRepresentation()`, to `VecGhostGetLocalForm()` and `VecGhostRestoreLocalForm()`, respectively; the previous names had too many characters for some machines.

#### IS (Index Sets):

#### Draw (Graphics):

- Replaced`VIEWER_DRAWX_`.... with `VIEWER_DRAW_`....
- The arguments of `ViewerDrawGetDraw`() have been changed; see the manual page for details.
- `DrawTensorContour()` has changed; its final argument is now an array can now use `VecView()` to create the contour plot.

#### Viewers:

- Changed the names associated with the Matlab viewer to Socket viewer; this reflects our plan to support additional graphics engines with PETSc.
- Changed `ViewerFileOpenASCII()` to `ViewerASCIIOpen().`
- Changed `ViewerDrawOpenX(`) to `ViewerDrawOpen().`
- Changed `ViewerFileOpenBinary()` to `ViewerBinaryOpen().`
- Changed `ViewerType` from an enum to a char *.

#### System:

- Changed the calling sequence of `PetscGetHomeDirectory(char dir[],int maxlen)`.
- Changed the calling sequence of `PetscFixFilename(const char filein[],char fileout[]).`
- Changed the calling sequence of `PetscGetDate().`

#### Error Handling:

#### Event Logging:

#### Fortran Interface:

## New features in PETSc 2.0.24 (see changes above)

#### General:

- Add the routine `OptionsGetAll().`
- Added support for Sun Solaris running on Intel processors; PETSC_ARCH solaris_x86.
- Added option -`optionsleft_off` so BOPT=g version of code will not print warnings about unused options.
- The environment variable PETSC_ARCH is now required to use the NT distribution.
- Added the routine `OptionsGetLogical().`
- We now include PETSC_ARCH of solaris_gnu, rs6000_gnu for those systems when using the gnu compilers.
- Thanks to the generosity of the FreeBSD organization, we are now supporting freebsd again.
- Added optional filename to `-log_info` <filename> option. PETSc will open a separate file, called filename.rank for each processor and print the output there.
- Added `PetscTypeCompare()`; see the manual page.

#### AO (Application Orderings):

- `AOPetscToApplicationIS()` and `AOApplicationToPetscIS()`, when passed a stride index set, now handle them correctly.

#### TS (Timestepping Solvers):

- Added `TSSetTypeFromOptions().`

#### SNES (Nonlinear Solvers):

- Added `-snes_vecmonitor` and `SNESMonitorVec()` to allow graphically monitoring the solution.
- Added `SNESSetTypeFromOptions().`
- Added the routine `SNESSetLineSearchCheck()`, which sets a routine to check the validity of new iterates computed by line search routines; see the manual page for details.

#### SLES (Linear Solvers):

- See PC and KSP
- Added `SLESSetTypesFromOptions().`

#### KSP (Krylov Subspace Methods):

- Added the function `KSPSetAvoidNorms()` and corresponding option `-ksp_avoid_norms`. For the methods CG, Richardson, Bi-CG-stab, CR, and CGS, this eliminates the computation of the residual norm at each iteration (which is an expensive, collective operation). Then the convergence criterion depends only on the maximum number of iterations the users sets with `KSPSetTolerances().` This is useful when using the Krylov method as a smoother with a fixed number of iterations (say, e.g., 3 iterations).
- Added the KSP type of `KSPBICG` (contributed by Victor Eijkhout) and added support to some of the preconditioners to apply the preconditioner transpose (required by KSPBICG).
- Added `-ksp_vecmonitor` and `KSPMonitorVec()` to allow graphically monitoring the solution's convergence.
- Added `KSPSetTypeFromOptions().`

#### PC (Preconditioners):

- Added `PCLUSetReuseReordering()` and `PCLUSetReuseFill()` so that SLES can reuse the reordering and fill information for a new factorization of a matrix with slightly different nonzero structure than the previous factorization. The corresponding command line options are -`pc_lu_reuse_reordering` and `-pc_lu_reuse_fill`. These two options only have an effect when the `SLESSetOperators()` option of `DIFFERENT_NONZERO_PATTERN` is used; otherwise the ordering and fill information is always reused.
- Added `PCGetVector()`, not expected to be used by application programmers.
- Added the option `-pc_ilu_diagonal_fill` and the corresponding routine `PCILUSetAllowDiagonalFill()`; see the manual page for details; helps ILU(k) on matrices with missing diagonal entries. Suggested by David Hysom.
- Added `PCSetTypeFromOptions().`

#### MAT (Matrices):

- Added `MatSeqAIJSetColumnIndices()` and `MatSeqBAIJSetColumnIndices()`.
- If the option `MAT_IGNORE_OFF_PROC_ENTRIES` is used, then the routines `MatAssemblyBegin()` and `MatAssemblyEnd()` will not cause any parallel communication or synchronization.
- If the option `MAT_NEW_NONZERO_LOCATIONS` is used, one less collective call will be made in the `MatAssemblyEnd()` routines for MPIAIJ and MPIBAIJ.
- Fixed bugs in `MatReorderForNonzeroDiagonal()` and made it more robust.
- Fixed bugs in factorization for AIJ matrices with variable size inodes.
- Indices that are negative passed into `MatSetValues...()` are now ignored (rather than generating an error). This allows easily keeping homogeneous Dirichlet boundary nodes out of the vectors and matrices for unstructured grid problems; just indicate those node numbers with negative numbers.
- Added additional optimized code for BAIJ matrices with block sizes 2, 3, 5, 6, and 7.
- Improved the performance of `MatSetValues()` and `MatAssemblyXXX()` for parallel matrices a great deal.
- Added the option `-matstash_initial_size` <stashsize> and `-matstash_block_initial_size` <stashsize> and the routine `MatSetStashInitialSize()` to allow further optimization of off-processor`MatSetValues().`

#### DA (Distributed Arrays):

- Added graphics support to DA vectors in 1d and 2d, with contour plotters for 2d.

#### VEC (Vectors):

- Extended `VecCreate()` by allowing registration of new vector types with `VecRegister()` see the manual page for details.
- Indices that are negative passed into `VecSetValues...()` are now ignored (rather than generating an error). This allows easily keeping homogeneous Dirichlet boundary nodes out of the vectors and matrices for unstructured grid problems; just indicate those node numbers with negative numbers.
- Added `VecDotBegin()`, `VecDotEnd()`, `VecNormBegin()`, `VecNormEnd()`, which reduce communication overhead in parallel; see the manual pages for details (suggested by Victor Eijkhout).
- If the option `VEC_IGNORE_OFF_PROC_ENTRIES` is used, the `VecAssemblyBegin()` and `VecAssemblyEnd()` routines will not cause any parallel communication or synchronization (previously `VecAssemblyBegin()` still used a barrier).
- Added `VIEWER_FORMAT_ASCII_INDEX` which causes the index for each vector entry to be printed with the vector values.
- Added three new vector scatter options; `-vecscatter_merge` and `-vecscatter_ssend` and `-vecscatter_sendfirst`; these may improve performance a great deal when using MPICH for MPI on ethernet or fast ethernet.
- Added `VecStrideNorm(), VecStrideScatter()`, and `VecStrideGather().`
- Improved the performance of `VecSetValues()` and `VecAssemblyXXX()` for parallel vectors.
- Added the option `-vecstash_initial_size` <stashsize> and `-vecstash_block_initial_size` <stashsize> and the routine `VecSetStashInitialSize()` to allow further optimization of off-processor `VecSetValues()`.

#### IS (Index Sets):

- Added `ISStrideToGeneral()`, which converts a stride type index set to a general type.

#### Draw (Graphics):

#### Viewers:

- Added `ViewerASCIIPushTab()`, `ViewerASCIIPopTab()` and `ViewerASCIIPrintf()`. These allow multi-level display of solver information (tabing the text further for each inner solver). Thanks to Victor Eijkhout and Matt Knepley for pushing this.

#### System:

#### Error Handling:

#### Event Logging:

#### Fortran Interface:

- Added Fortran 90 interface support for HP Convex and Solaris.machine.