PETSc
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 matrixfree 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 matrixfree methods using the WalkerPernice
srategy, accessible via the option
snes_mf_type
wp

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):
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()
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
xxxReordering
xxx to
Mat
xxxOrdering
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:
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, 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 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 offprocessor
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 offprocessor 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 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.