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=============
Changes: 3.12
=============
.. rubric:: General:
- PetscRoundReal() has been removed, since the math routine round()
is not supported on all systems: perhaps use PetscCeilReal() or
PetscFloorReal()<\li>
- The legacy and CMake compile systems (make all-legacy and
all-cmake) are removed
- make gnumake is now make libs
- PetscArraycmp() should be used instead of PetscMemcmp(), it takes
a count argument instead of a byte argument
- PetscArraycpy() should be used instead of PetscMemcpy(), it takes
a count argument instead of a byte argument
- PetscArrayzero() should be used instead of PetscMemzero(), it
takes a count argument instead of a byte argument
- PetscArraymove() should be used instead of PetscMemmove(), it
takes a count argument instead of a byte argument
- The ./configure options -with-gnu-compilers and
-with-vendor-compilers are removed
- The ./configure option --with-avx512-kernels defaults to true now
so the manually optimized AVX-512 kernels are used by default
- The order ./configure tests compilers has changed so there may be
a different compiler selected if you do not provide them
- Added --with-64-bit-blas-indices that will switch to 64-bit
indices when using MKL libraries for BLAS/LAPACK and build
OpenBLAS with this support
- Changed PETSC_DEPRECATED() to PETSC_DEPRECATED_FUNCTION() and
PETSC_DEPRECATED_TYPEDEF() to match naming of
PETSC_DEPRECATED_ENUM() and PETSC_DEPRECATED_MACRO
- -help now causes the printing of the current value and the newly
set value for PetscOptionsInt(), etc
- PetscFunctionListPrintTypes() takes an additional final argument
after the current value, the set value
- PetscCalloc*() now calls the system calloc() routine instead of
malloc() plus memzero()
- -malloc is now marked as deprecated, use -malloc_debug instead
- -malloc_log and -malloc_log_threshold are now -malloc_view and
-malloc_view_threshold
- PetscMallocDebug() is now PetscMallocSetDebug()
- PetscMallocDumpLog() is now PetscMallocView(), see also
PetscMallocViewSet()
- PetscMallocSetDumpLogThreshold() and PetscMallocSetDumpLog() are
now PetscMallocViewSet()
- With -malloc_test or -malloc_debug allocated memory is initialized
with NaN to detect use of uninitialized numerical arrays
- PetscMallocSet() now takes three arguments instead of two
- Moved PetscCUBLASGetHandle() to a separate header file
petscublas.h
- Moved VecCUDA*-routines from petsccuda.h into petscvec.h. Removed
petsccuda.h
.. rubric:: Configure/Build:
- C++ dialect is now auto-detected (C++14 first and then C++11). One
can disable this check using --with-cxx-dialect=0, or force it to
only check for C++11 using --with-cxx-dialect=C++11
- New option --download-hpddm to enable PCHPDDM and KSPHPDDM
.. rubric:: IS:
.. rubric:: PetscDraw:
.. rubric:: PF:
.. rubric:: Vec:
- VecCUDAGet/RestoreArrayReadWrite() changed to
VecCUDAGet/RestoreArray()
- VecViennaCLGet/RestoreArrayReadWrite() changed to
VecViennaCLGet/RestoreArray()
- Added VecGet/RestoreArray/ReadInPlace() to get array of a vector
where it is without copying from GPU to CPU.
.. rubric:: PetscLayout:
- Added PetscLayoutCreateFromSizes()
- Added PetscLayoutCreateFromRanges()
- Calling PetscLayoutSetUp() twice with different sizes is now
forbidden
.. rubric:: PetscSection:
.. rubric:: VecScatter & PetscSF:
- The default VecScatter implementation is changed to PetscSF. In
other words, the default VecScatter shares PetscSF's MPI
communication code. One can use -vecscatter_type mpi1 to go back
to the old implementation.
- Added new InsertMode MAX_VALUES and MIN_VALUES support in
VecScatterBegin/End and VecGhostUpdateBegin/End.
- PetscSFComputeMultiRootOriginalNumbering: add output argument with
the number of multiroots for convenience
- Added an enum type PetscSFPattern for SF graph patterns. Valid
values include PETSCSF_PATTERN_ALLGATHER, PETSCSF_PATTERN_GATHER
and PETSCSF_PATTERN_ALLTOALL.
- Added PetscSFSetGraphWithPattern() to set SF graphs with
predefined patterns.
- Added PetscSFComposeInverse() to compose a new SF by putting the
inverse of an SF under the another SF.
- Added MPI-3.0 neighborhood collectives support. One can use
command line option -sf_type neighbor to let SF use MPI-3.0
neighborhood collectives for communication instead of the default
MPI_Send/Recv.
- PetscSF is now CUDA-aware. The rootdata, leafdata arguments passed
to SF routines can be either GPU pointers or CPU pointers. Use a
CUDA-aware MPI and option -use_gpu_aware_mpi to enable it.
- VecScatter is also CUDA-aware. You can do VecScatter on CUDA
vectors without copying them from GPU to CPU. Again, you need a
CUDA-aware MPI and option -use_gpu_aware_mpi.
- Removed PetscSFCreateFromZero. Instead, users should use
PetscSFCreate() to create an SF, and then set its graph with
PetscSFSetGraphWithPattern(..,PETSCSF_PATTERN_GATHER).
- Renamed PetscSFGetRanks() to PetscSFGetRootRanks().
.. rubric:: Mat:
- MatShift(Mat,0); will no longer silently insure there are no
missing diagonal entries. (Previously it would put 0 into any
diagonal entry that was missing)
- Renamed MatComputeExplicitOperator() into MatComputeOperator() and
MatComputeExplicitOperatorTranspose() into
MatComputeOperatorTranspose(). Added extra argument to select the
desired matrix type
- MatLoad() now supports loading dense matrices from HDF5/MAT files.
- Added new Mat type, MATKAIJ, for matrices that can be expressed in
a particular Kronecker (tensor) product form.
- Added MatCompositeSetScalings() to set separate scaling factors
for component matrices.
- Added a Boolean option -mat_composite_merge_mvctx to merge Mvctx
of component matrices to optimize communication in MatMult() for
ADDITIVE matrices. Default is true.
- Added MATSEQDENSECUDA class to use GPUs for dense linear algebra.
.. rubric:: PC:
- Renamed PCComputeExplicitOperator() into PCComputeOperator().
Added extra argument to select the desired matrix type
- Added support for PCCHOLESKY with MATSOLVERMUMPS and SBAIJ
matrices with bs greater than 1
- Added support for PCLU with MATSOLVERMKL_PARDISO (resp.
MATSOLVERMKL_CPARDISO) and SEQBAIJ (resp. MPIBAIJ) matrices
- Added support for PCCHOLESKY with MATSOLVERMKL_PARDISO (resp.
MATSOLVERMKL_CPARDISO) and SEQSBAIJ (resp. MPISBAIJ) matrices
- Added new preconditioner PCHPDDM, cf.
src/ksp/ksp/examples/tutorials/ex71.c or
src/snes/examples/tutorials/ex56.c
.. rubric:: KSP:
- Renamed KSPComputeExplicitOperator() into KSPComputeOperator().
Added extra argument to select the desired matrix type
- KSPCGGLTRGetMinEig(KSP,PetscReal*) ->
KSPGLTRGetMinEig(KSP,PetscReal*)
- KSPCGGLTRGetLambda(KSP,PetscReal*) ->
KSPGLTRGetLambda(KSP,PetscReal*)
- KSPCGNASH, KSPCGSTCG, KSPCGGLTR -> KSPNASH, KSPSTCG, KSPGLTR
- Added new Krylov solver KSPHPDDM, cf.
src/ksp/ksp/examples/tutorials/ex75.c or
src/ksp/ksp/examples/tutorials/ex9.c
.. rubric:: SNES:
- Changed SNES_CONVERGED_TR_DELTA to SNES_DIVERGED_TR_DELTA with a
negative value to indicate diverged, unclear why it was ever
positive since tiny trust region would indicate trouble, not
converged
.. rubric:: SNES:
- -snes_mf no longer turns the preconditioner to none; to use it
generally you will also need -pc_type none
.. rubric:: SNESLineSearch:
.. rubric:: TS:
- Added tangent linear models for Runge-Kutta methods
- Added second-order adjoint solvers based on Runge-Kutta methods
and Theta methods
- Improved the usage of first-order adjoint solvers in an
optimization context. (The TS object can be reused in the
optimization loop)
- Changed the APIs for integrand evaluations and corresponding
derivative evaluations. TSSetCostIntegrand() is deprecated.
(Instead a quadrature TS is used to handle the callbacks)
- TSTrajectory creates a unique name for folders that store the
checkpoint data. Users can rerun adjoint codes without worrying
about the folder names, and run multiple codes under the same
directory.
- Added support for using finite-differencing (and coloring) to
approximate the Jacobians needed by the adjoint solvers.
-snes_fd_color can be used for both implicit and explicit methods.
.. rubric:: DM/DA:
- Add DMGetLocalSection() to be used in preference to
DMGetSection().
- Add DMSetLocalSection() to be used in preference to
DMSetSection().
- DMGetDefaultSF() replaced with DMGetSectionSF().
- DMSetDefaultSF() replaced with DMSetSectionSF().
- DMCreateDefaultSF() replaced with DMCreateSectionSF().
- DMAddLabel() now increments the reference count of the DMLabel.
- DMRemoveLabel() now destroys the DMLabel if the output argument is
NULL.
- Add DMRemoveLabelBySelf() which looks up the DMLabel by itself,
removes from DM and destroys.
.. rubric:: DMPlex:
- Rename DMPlexCreateSpectralClosurePermutation() to
DMPlexSetClosurePermutationTensor()
- Add DMPlexFindVertices() for vertex coordinates -> DAG point
lookup
- Add DMPlexGetOverlap() to get the partition overlap
.. rubric:: DMNetwork:
- Changed prototypes for DMNetworkSetSizes()
.. rubric:: PetscViewer:
- Removed PetscViewerHDF5{Get,Set}AIJNames() which are likely not
really needed
- PetscViewerHDF5SetCollective() and -viewer_hdf5_collective can be
used to switch between independent and collective transfer mode.
Defaults now to false (independent).
.. rubric:: SYS:
- Added PetscCheckDupsInt() to check if a PetscInt array has dups.
- Added an argument to PetscBinaryRead() and
PetscBinarySynchronizedRead() to return the number of items read.
.. rubric:: AO:
.. rubric:: Sieve:
.. rubric:: Fortran:
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