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<h1> Docs: Changes: 3.0.0</h1>
<p align="center"><font color="#ff0000" size="5"><a name="CHANGES">CHANGES</a>
in the PETSc 3.0.0</font></p>
<p><u><b>General:</b></u><br>
</p>
<ul>
<li>Changed the Matlab engine portion of the Matlab configure
code to require a separate flag --with-matlab-engine</li>
<li>Changed the Socket viewer to be the same as the binary
viewer except for its creation </li>
<li>Changed the Matlab Socket code to work the same as the
Matlab binary reader except for its creation</li>
<li>You can now replace the PetscVFPrintf() function pointer to
redirect all stdout/stderr output in Windows for example.</li>
<li>Removed MPICCommToFortran() and MPIFortranCommToC() since
MPI_Comm_c2f() and f2c() are now always available.</li>
<li>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.</li>
<li>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.</li>
</ul>
<br>
<u><b>Logging:</b></u>
<ul>
<li>The int stage used in the PetscLogStageXXX() routines is
now a PetscLogStage</li>
<li>PetscLogEventRegister() and PetscLogStageRegister() now
return the result in the final argument instead of the first</li>
<li>PetscLogClassRegister() is changed to PetscClassIdRegister()
and returns the classid in the final argument, not the first</li>
<li>PetscEvent is now PetscLogEvent</li>
</ul>
<p></p>
<u><b>config/configure.py: <br>
</b></u>
<ul>
<li>Changed location of base makefiles to conf from bmake/common</li>
<li>Changed location of generated base makefiles to
$PETSC_ARCH/conf instead of bmake/$PETSC_ARCH</li>
<li>Changed location of generated include files to
$PETSC_ARCH/include </li>
<li>Changed location of generated libraries (including from
external packages) to $PETSC_ARCH/lib</li>
<li>You will need to change include
${PETSC_DIR}/bmake/common/base to ${PETSC_DIR}/conf/base </li>
</ul>
<p><u><b>IS:</b></u></p>
<ul>
<li>ISPartitioningCount() now takes an additional argument, the
length of the count array (that is the number of partitions).</li>
</ul>
<p><u><b>Vec: </b></u></p>
<ul>
<li>Added logical argument to VecSetOption() to toggle option
in either way</li>
<li>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.</li>
</ul>
<p><u><b>VecScatter:<br>
</b></u></p>
<ul>
</ul>
<p><u><b>Mat:</b></u></p>
<ul>
<li>MatSetOption() now takes a final PetscTruth flag to toggle
the option. The redundant options like MAT_NO_SYMMETRIC are removed</li>
<li>The MatSetOption() options MAT_ROWS_SORTED,
MAT_COLUMNS_SORTED are no longer needed and are removed.</li>
<li>MatConvert() now uses the matrix prefix when using option
-matconvert_type.</li>
<li>The bdiag matrix formats have been removed</li>
<li>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).</li>
<li>MATPLAPACK is removed; instead so long as PETSc is
config/configure.py with --download-plapack the MATMPIDENSE matrix will
automatically use the parallel plapack solvers</li>
<li>The "parallel direct solver" matrix types like<br>
MATAIJSPOOLES are ALL gone. Now you use -pc_factor_mat_solver_package<br>
spooles etc or PCFactorSetMatSolverPackage() or if working directly with<br>
matrices, MatGetFactor(A,MATSPOOLES,...)</li>
<li>Removed MatFDColoringSetRecompute(), now use
MatFDSetFrequency(mat,-2) to have Jacobian computed at next Newton step
but never again.</li>
<li>Removed MatFDColoringSet/GetFrequency() and
-mat_fd_coloring_freq since you can now use SNESSetLagJacobian() or
-snes_lag_jacobian</li>
<li>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.</li>
<li>The first argument to MatXXXFactorSymbolic/Numeric() is now
the factored matrix</li>
<li>The fields
global_rows,global_columns,local_rows,local_columns have been removed
from the MatGetInfo() data. User MatGetSize(), MatGetLocalSize() to get
that data</li>
</ul>
<u><b>PC:</b></u>
<ul>
<li>PCHasApplyTranspose() was renamed to
PCApplyTransposeExists().</li>
<li>Added much faster matrix converter to use hypre
preconditioners for PETSc AIJ matrices</li>
<li>ILU preconditioner now defaults to use shift to prevent
zero pivot</li>
<li>ICC preconditioner now defaults to use Manteuffel shift to
force positive definiteness</li>
<li>Added -pc_factor_shift_in_blocks and
PCFactorSetShiftInBlocks() made default for ILU</li>
<li>PCApplyRichardson() now returns two additional arguments,
the number of iterations performed and the reason it finished.</li>
<ul>
</ul>
</ul>
<ul>
</ul>
<ul>
</ul>
<p><u><b>KSP:</b></u><br>
</p>
<ul>
</ul>
<ul>
<li> KSPSetConvergenceTest() now takes an optional final
argument, destroy() that will be called to destroy the context passed
in as the second to last argument</li>
<li>KSPDefaultConverged() now has a KSPDefaultConvergedCreate()
and KSPDefaultConvergedDestroy() that creates the default context to be
passed KSPSetConvergenceTest() and the destroy to be passed in.</li>
<li>Added KSPIBCGS a varient of Bi-CG-stab that has only 1
synchronization point rather than 3 in the usual.</li>
</ul>
<ul>
</ul>
<p><u><b>SNES:</b></u></p>
<ul>
<li>SNESSetRhs() and SNESSetSolution() were removed. Use
instead SNESSolve(snes, b, x) to pass right hand side (optional, can be
PETSC_NULL) and solution (required).</li>
<li>SNES now takes ownership of user-provided vector for right
hand side and solution passed to SNESSolve(), and until the next
SNESSolve() is called.</li>
<li>SNES now takes ownership of user-provided vector for
function evalutation passed to SNESSetFunction(), thus this vector can
be safely destroyed after this call.</li>
<li>SNESConverged_LS() and SNESConverged_LS() were removed. Use
SNESDefaultConverged() or SNESSkipConverged() as convergence test.</li>
<li>Option -snes_convergence_test was added, accepting values
default|short, for setting SNESDefaultConverged() or
SNESSkipConverged() as convergence test.</li>
<li>Option -snes_no_convergence_test was removed. Use instead
"-snes_convergence_test skip".</li>
<li>Do not use the error PETSC_ERR_ARG_DOMAIN within your
FormFunction() rather call SNESSetFunctionDomainError.</li>
<li>The line search functions now take an additional argument
xnorm.</li>
<li>SNESSetConvergenceTest() takes another optional argument
PetscErrorCode (*destroy)(void*) that will be called with SNESDestroy()
to destroy the context.</li>
<li>Added SNESSetLagPreconditioner(), -snes_lag_preconditioner,
SNESGetLagPreconditioner()</li>
<li>Added SNESSetLagJacobian(), -snes_lag_jacobian,
SNESGetLagJacobian()</li>
</ul>
<ul>
</ul>
<p><u><b>TS:</b></u></p>
<p><u><b>DA:</b></u></p>
<ul>
<li>Added DAGetNeighbors() </li>
<li>Added DAGetOwnershipRanges() </li>
</ul>
<ul>
</ul>
<p><u><b>DMMG:</b></u></p>
<ul>
<li>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.</li>
<li>Removed -dmmg_snes_monitor since now -snes_monitor and
-snes_monitor_short
will now do the proper indenting so this is no longer needed</li>
<li>Removed -dmmg_ksp_monitor since now -ksp_monitor[_short)
and -mg_levels_ksp_monitor[_short) etc will handle the proper indenting.</li>
<li>Removed -dmmg_jacobian_period since you can use
-snes_lag_jacobian</li>
</ul>
<u><b>PetscViewer: <br>
</b></u>
<ul>
<li>added PETSC_VIEWER_STDOUT_(comm) for Fortran</li>
<li>binary viewer now supports MPI IO for Vec loading and
storing, use -viewer_binary_mpiio or PetscViewerBinarySetMPIIO() to
enable it.</li>
<li>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</li>
</ul>
<ul>
</ul>
<p><u><b>SYS:</b></u></p>
<ul>
<li>PetscLogFlopsNoCheck() no longer exists; you can simply
call PetscLogFlops() it no longer has a return in it.<br>
</li>
</ul>
<p><u><b>AO:<br>
</b></u></p>
<p><u><b>Sieve:</b></u></p>
<p><u><b>Fortran:</b></u><br>
</p>
<li> If you previously used text like the following [perhaps in
data section of f90 modules]
<pre>#define PETSC_AVOID_DECLARATIONS<br>#include "finclude/petsc.h"<br>#include "finclude/petscvec.h"<br>#endif<br></pre>
you should replace it with
<pre>#include "finclude/petscdef.h"<br>#include "finclude/petscvecdef.h"<br></pre>
</li>
<li>PetscTruth is now logical*4 or logical(kind=4) an unsigned
int of 4 bytes. To get back PetscTruth as an integer*4 put a #define
PETSC_FORTRAN_PETSCTRUTH_INT 1 into $PETSC_ARCH/conf/petscconf.h </li>
<li>You can now use PETSc as Fortran 90 modules, see the manual
page for UsingFortran</li>
<li>You can now have PETSc build interface definitions for most
PETSc functions by config/configure.py with the additional option
--with-fortran_interfaces see the manual page for UsingFortran</li>
<p></p>
<ul>
</ul>
<p><u><b><a
href="http://www.mcs.anl.gov/petsc/petsc-as/miscellaneous/external.html">ExternalPackages</a>:</b></u></p>
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