PETSc
General:

Changed the Matlab engine portion of the Matlab configure code to
require a separate flag withmatlabengine

Changed the Socket viewer to be the same as the binary viewer except
for its creation

Changed the Matlab Socket code to work the same as the Matlab binary
reader except for its creation

You can now replace the PetscVFPrintf() function pointer to redirect
all stdout/stderr output in Windows for example.

Removed MPICCommToFortran() and MPIFortranCommToC() since
MPI_Comm_c2f() and f2c() are now always available.

PetscOptionsInsertFile() now takes a MPI_Comm as the first argument
and a final flag argument indicating if the file MUST be
located. It is also changed to be more scalable, only the 0th process
opens it and broadcasts the input to the other processes.

Added PetscObjectIncrementTabLevel() to allow proper indenting of
monitor output for imbedded solvers for multigrid levels, for block
Jacobi, for SNES inside TS and KSP inside SNES etc.
Logging:
 The int stage used in the PetscLogStageXXX() routines is now a PetscLogStage

PetscLogEventRegister() and PetscLogStageRegister() now return the
result in the final argument instead of the first

PetscLogClassRegister() is changed to PetscClassIdRegister() and
returns the classid in the final argument, not the first
 PetscEvent is now PetscLogEvent
config/configure.py:
 Changed location of base makefiles to conf from bmake/common

Changed location of generated base makefiles to $PETSC_ARCH/conf
instead of bmake/$PETSC_ARCH
 Changed location of generated include files to $PETSC_ARCH/include
 Changed location of generated libraries (including from external packages) to $PETSC_ARCH/lib
 You will need to change include ${PETSC_DIR}/bmake/common/base to ${PETSC_DIR}/conf/base
IS:

ISPartitioningCount() now takes an additional argument, the length of
the count array (that is the number of partitions).
Vec:
 Added logical argument to VecSetOption() to toggle option in either way

The PetscMap inside the Vec object is now allocated and reference
counted and shared between vectors and matrices, this will decrease
memory usage on systems with a large size.
VecScatter:
Mat:

MatSetOption() now takes a final PetscTruth flag to toggle the
option. The redundant options like MAT_NO_SYMMETRIC are removed

The MatSetOption() options MAT_ROWS_SORTED, MAT_COLUMNS_SORTED are no
longer needed and are removed.
 MatConvert() now uses the matrix prefix when using option matconvert_type.
 The bdiag matrix formats have been removed

MatTranspose() now takes a new second argument MatReuse; also to do
an inplace transpose use MAT_REUSE_MATRIX and pass the address of the
first argument as the third argument (you can no longer pass 0).

MATPLAPACK is removed; instead so long as PETSc is
config/configure.py with downloadplapack the MATMPIDENSE matrix
will automatically use the parallel plapack solvers

The "parallel direct solver" matrix types like
MATAIJSPOOLES are
ALL gone. Now you use pc_factor_mat_solver_package
spooles etc
or PCFactorSetMatSolverPackage() or if working directly with
matrices, MatGetFactor(A,MATSPOOLES,...)

Removed MatFDColoringSetRecompute(), now use
MatFDSetFrequency(mat,2) to have Jacobian computed at next Newton
step but never again.

Removed MatFDColoringSet/GetFrequency() and mat_fd_coloring_freq
since you can now use SNESSetLagJacobian() or snes_lag_jacobian

The PetscMap inside the Mat object is now allocated and reference
counted and shared between vectors and matrices, this will decrease
memory usage on systems with a large size.

The first argument to MatXXXFactorSymbolic/Numeric() is now the
factored matrix

The fields global_rows,global_columns,local_rows,local_columns have
been removed from the MatGetInfo() data. User MatGetSize(),
MatGetLocalSize() to get that data
PC:
 PCHasApplyTranspose() was renamed to PCApplyTransposeExists().
 Added much faster matrix converter to use hypre preconditioners for PETSc AIJ matrices
 ILU preconditioner now defaults to use shift to prevent zero pivot
 ICC preconditioner now defaults to use Manteuffel shift to force positive definiteness
 Added pc_factor_shift_in_blocks and PCFactorSetShiftInBlocks() made default for ILU

PCApplyRichardson() now returns two additional arguments, the number
of iterations performed and the reason it finished.
KSP:

KSPSetConvergenceTest() now takes an optional final argument,
destroy() that will be called to destroy the context passed in as the
second to last argument

KSPDefaultConverged() now has a KSPDefaultConvergedCreate() and
KSPDefaultConvergedDestroy() that creates the default context to be
passed KSPSetConvergenceTest() and the destroy to be passed in.

Added KSPIBCGS a varient of BiCGstab that has only
1 synchronization point rather than 3 in the usual.
SNES:

SNESSetRhs() and SNESSetSolution() were removed. Use instead
SNESSolve(snes, b, x) to pass right hand side (optional, can be
PETSC_NULL) and solution (required).

SNES now takes ownership of userprovided vector for right hand side
and solution passed to SNESSolve(), and until the next SNESSolve() is
called.

SNES now takes ownership of userprovided vector for function
evalutation passed to SNESSetFunction(), thus this vector can be
safely destroyed after this call.

SNESConverged_LS() and SNESConverged_LS() were removed. Use
SNESDefaultConverged() or SNESSkipConverged() as convergence
test.

Option snes_convergence_test was added, accepting values
defaultshort, for setting SNESDefaultConverged() or
SNESSkipConverged() as convergence test.

Option snes_no_convergence_test was removed. Use instead
"snes_convergence_test skip".

Do not use the error PETSC_ERR_ARG_DOMAIN within your FormFunction()
rather call SNESSetFunctionDomainError.
 The line search functions now take an additional argument xnorm.

SNESSetConvergenceTest() takes another optional argument
PetscErrorCode (*destroy)(void*) that will be called with
SNESDestroy() to destroy the context.

Added SNESSetLagPreconditioner(), snes_lag_preconditioner, SNESGetLagPreconditioner()
 Added SNESSetLagJacobian(), snes_lag_jacobian, SNESGetLagJacobian()
TS:
DA:
 Added DAGetNeighbors()
 Added DAGetOwnershipRanges()
DMMG:

Added DMMGSetFromOptions(), this can only be used in conjunction with
DMMGSetSNES(). You should call this sometime after DMMGSetSNES() is
called, otherwise the SNES/KSPSetFromOptions() does not get
called.

Removed dmmg_snes_monitor since now snes_monitor and
snes_monitor_short will now do the proper indenting so this is no
longer needed

Removed dmmg_ksp_monitor since now ksp_monitor[_short) and
mg_levels_ksp_monitor[_short) etc will handle the proper
indenting.

Removed dmmg_jacobian_period since you can use
snes_lag_jacobian
PetscViewer:
 added PETSC_VIEWER_STDOUT_(comm) for Fortran

binary viewer now supports MPI IO for Vec loading and storing, use
viewer_binary_mpiio or PetscViewerBinarySetMPIIO() to enable
it.

Reworked the Matlab objects sreader and freader to be called
PetscOpenSocket and PetscOpenFile, now PetscBinaryWrite and
PetscBinaryRead can be used on the same socket connection to send
matrix/vectors in both directions. See
src/ksp/ksp/examples/tutorials/ex41.c and ex41.m
SYS:

PetscLogFlopsNoCheck() no longer exists; you can simply call
PetscLogFlops() it no longer has a return in it.