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 filebase_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, whilers6000_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 callTSSetRHSJacobian
(...TSDefaultJacobianColor
,....) directly from Fortran  Changed
TSDefaultJacobianSlow()
toTSDefaultJacobian()
SNES (Nonlinear Solvers):

S
NESSetConvergenceHistory()
takes an additional argument; see the manual page for details. 
Changed the interface for matrixfree methods in SNES so that is more
flexible, in particular:

Changed
SNESDefaultMatrixFreeMatCreate()
toMatSNESFDMFCreate()
. 
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 matrixfree methods using the WalkerPernice
srategy, accessible via the option
snes_mf_type
wp

Changed

Changed the calling sequence of
SNESSetLineSearch()
so that it accepts an optional userdefined 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 GramSchmidt method with one optional step of iterative refinement as the default orthogonalization procedure, instead of the modified GramSchmidt 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 GaussSeidel 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()
andpc_eisenstat_diagonal_scaling
have been replaced withPCEisenstatNoDiagonalScaling()
andpc_eisenstat_no_diagonal_scaling
MAT (Matrices):
 Replaced
MatGetSubMatrixCall
() withMatReuse().

Changed the calling sequence of
MatILUFactor()
andMatILUFactorSymbolic()
to increase flexibility of adding new ILU options. 
Added an additional argument to
MatCopy()
;SAME_NONZERO_PATTERN
orDIFFERENT_NONZERO_PATTERN.

Added an additional argument to
MatDuplicate()
,MAT_COPY_VALUES
orMAT_DO_NOT_COPY_VALUES.

Changed the flag
MAT_NEW_NONZERO_LOCATION_ERROR
toMAT_NEW_NONZERO_LOCATION_ERR
; also changedMAT_NEW_ALLOCATION_ERROR
toMAT_NEW_ALLOCATION_ERR

Changed
MatOrder
xxx toMatOrdering
xxx; changedMatOrderingType
to char* from enum 
Changed
Mat
xxxReordering
xxx toMat
xxxOrdering
xxx changed command line optionmat_order
to mat_ordering_type;
changedMatColoringType
to char* from enum  Changed
Partitioning
xxx toMatPartitioning
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 extraPETSC_NULL
as a final argument.
VEC (Vectors):

After a call to
VecCreate()
you MUST either callVecSetType()
orVecSetFromOptions()
on the vector before using it for any purpose. TheVecCreate
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 aVecRestoreArray()
call; previous PETSc versions did not force compliance with this rule. 
The command line names for changing the vector type in
VecCreate(
) are nowvec_type mpi
orvec_type shared
rather thanvec_mpi
orvec_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()
andVecGhostRestoreLocalRepresentation()
, toVecGhostGetLocalForm()
andVecGhostRestoreLocalForm()
, respectively; the previous names had too many characters for some machines.
IS (Index Sets):
Draw (Graphics):
 Replaced
VIEWER_DRAWX_
.... withVIEWER_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 useVecView()
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()
toViewerASCIIOpen().
 Changed
ViewerDrawOpenX(
) toViewerDrawOpen().
 Changed
ViewerFileOpenBinary()
toViewerBinaryOpen().
 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:
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()
andAOApplicationToPetscIS()
, when passed a stride index set, now handle them correctly.
TS (Timestepping Solvers):
 Added
TSSetTypeFromOptions().
SNES (Nonlinear Solvers):

Added
snes_vecmonitor
andSNESMonitorVec()
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 optionksp_avoid_norms
. For the methods CG, Richardson, BiCGstab, 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 withKSPSetTolerances().
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
andKSPMonitorVec()
to allow graphically monitoring the solution's convergence.  Added
KSPSetTypeFromOptions().
PC (Preconditioners):

Added
PCLUSetReuseReordering()
andPCLUSetReuseFill()
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
andpc_lu_reuse_fill
. These two options only have an effect when theSLESSetOperators()
option ofDIFFERENT_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 routinePCILUSetAllowDiagonalFill()
; 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()
andMatSeqBAIJSetColumnIndices()
. 
If the option
MAT_IGNORE_OFF_PROC_ENTRIES
is used, then the routinesMatAssemblyBegin()
andMatAssemblyEnd()
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 theMatAssemblyEnd()
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()
andMatAssemblyXXX()
for parallel matrices a great deal. 
Added the option
matstash_initial_size
<stashsize> andmatstash_block_initial_size
<stashsize> and the routineMatSetStashInitialSize()
to allow further optimization of offprocessorMatSetValues().
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 withVecRegister()
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, theVecAssemblyBegin()
andVecAssemblyEnd()
routines will not cause any parallel communication or synchronization (previouslyVecAssemblyBegin()
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
andvecscatter_ssend
andvecscatter_sendfirst
; these may improve performance a great deal when using MPICH for MPI on ethernet or fast ethernet. 
Added
VecStrideNorm(), VecStrideScatter()
, andVecStrideGather().

Improved the performance of
VecSetValues()
andVecAssemblyXXX()
for parallel vectors. 
Added the option
vecstash_initial_size
<stashsize> andvecstash_block_initial_size
<stashsize> and the routineVecSetStashInitialSize()
to allow further optimization of offprocessorVecSetValues()
.
IS (Index Sets):
 Added
ISStrideToGeneral()
, which converts a stride type index set to a general type.
Draw (Graphics):
Viewers:

Added
ViewerASCIIPushTab()
,ViewerASCIIPopTab()
andViewerASCIIPrintf()
. These allow multilevel 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.