PETSc

Documentation: Changes: 3.6

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General:

• User makefiles must be updated. You must change the lines
  • include ${PETSC_DIR}/conf/variables and
  • include ${PETSC_DIR}/conf/rules
  to
  • include ${PETSC_DIR}/lib/petsc/conf/variables and
  • include ${PETSC_DIR}/lib/petsc/conf/rules
• PetscOptionsBool() no longer sets the value of the boolean based on the value passed in
• Script for running MPIUni jobs is now bin/petsc-mpiexec.uni
• Removed all threadcomm support including --with-pthreadclasses and --with-openmpclasses configure arguments
• Updated MUMPS version to 5.0.0 - and updated metis to 5.1.0, parmetis to 4.0.3-p1 - in sync with MUMPS.
• Updated to hypre-2.10.0b, scotch_6.0.3, Elemental-0.85

Configure/Build:

• Add toplevel makefile targets clean and distclean. Target clean deletes petsc libraries built by makefile target all. Target distclean deletes all build files created by configure and [make all]. Target clean in example directories continues to work as before [deletes object files and executables]

IS:

PetscDraw:

• PetscDrawBoxedString() changed to PetscDrawStringBoxed() added PetscDrawBar object for drawing bar graphs added PetscDrawStringCentered()

PF:

Vec:

VecScatter:

PetscSection:

Mat:

• MatGetVecs() replaced with MatCreateVecs() because it actually does create the Vecs that need to be destroyed
• MatCreateMPIAIJConcatenateSeqAIJ and MatCreateMPIBAIJConcatenateSeqBAIJ replaced with MatCreateMPIMatConcatenateSeqMat
• MatGetRedundantMatrix() replaced with MatCreateRedundantMatrix()
• Added support for MUMPS sequential solver in Schur complement mode
• MatGetSubMatricesMPI() will extract parallel submatrices on subcommunicators of the supplied IS objects. Unsorted, but not repeated indices are okay.
• Removed MatMFFDAddNullSpace() just use MatSetNullSpace()

PC:

• Removed -pc_hypre_type euclid due to bit-rot
• Upgraded to SuiteSparse 4.4.1; Cholmod supports using GPUs (developer repository only feature) --with-cuda --download-suitesparse-gpu --with-64-bit-indices; -mat_cholmod_useGPU 1 or 0; 1 by default when configured for it
• Upgraded to Superlu_DIST 4.0; Superlu_DIST supports using GPUs (developer repository only feature) --with-cuda --with-openmp --download-superlu_dist-gpu (developer repository only feature) --with-64-bit-indices -mat_cholmod_useGPU 1 or 0; 1 by default when configured for it
• Added PCBDDCSetChangeOfBasisMat for user defined change of basis
• PCBDDC: added adaptive selection of constraints: it is available by command line options
• PCJacobiSetUseAbs() now takes a PetscBool argument allowing toggling the option
• PCJacobiSetUseRowMax() and PCJacobiSetUseRowSum() have been merged into PCJacobiSetType()
• PCFactorSetUseInplace() now takes a PetscBool argument. Added PCFactorGetUseInplace()
• PCFactorSetAllowDiagonalFill() now takes a PetscBool argument. Added PCFactorGetAllowDiagonalFill()
• PCEisenstatNoDiagonalScaling() changed to PCEisenstatSetNoDiagonalScaling() and takes a boolean
• Added Interface to AMS solver from HYPRE for Nedelec discretizations (-pc_hypre_type ams)
• Added Interface to ADS solver from HYPRE for Raviart-Thomas discretizations (-pc_hypre_type ads)
• Contributed MKL Pardiso interface providing PCCholesky support. Useable with: -pc_type cholesky -mat_type sbaij -pc_factor_mat_solver_package mkl_pardiso
• PCGASMSetTotalSubdomains() can now create multirank subdomains if their number is less than comm size.
• PCGAMGSetReuseProl() is changed to PCGAMGSetReuseInterpolation()

KSP:

• Removed KSPSetNullSpace() always use MatSetNullSpace() provided to the FIRST matrix argument to KSPSetOperators(), or SNESSetJacobian(), or TSSetIJacobian()
• Added MatSetTransposeNullSpace() to indicate the null space of the transpose operator
• Removed KSPSPECEST since its functionality is replaced by the esteig functionality within KSPChebyshev
• Unified KSPChebyshev routines that work with estimating eigenvalues with the prefix name KSPChebyshevEstEig... For example KSPChebyshevSetEstimateEigenvalues() is now KSPChebyshevEstEigSet() and KSPChebyshevSetEstimateEigenvaluesRandom() is now KSPChebyshevEstEigSetRandom() similarly -ksp_chebyshev_estimate_eigenvalues_random is -ksp_chebyshev_esteig_random. The previous for the (GMRES) KSP used to estimate the eigenvalues is now esteig_ not est_
• KSPGetVecs() replaced with KSPCreateVecs() because it actually does create the Vecs that need to be destroyed

SNES:

• Added KSPMonitorSNES() with command line option -ksp_monitor_snes and -ksp_monitor_snes_lg to monitor SNES residual norm at each linear iteration SNESMonitorVI() becomes SNESVIMonitor()
• Added SNESVIMonitorResidual() and -snes_vi_monitor_residual

SNESLineSearch:

TS:

• The postevent routine set with TSSetEventMonitor() now takes an additional PetscBool argument 'forwardsolve'. The forwardsolve flag is used to distinguish between a TS forward solve (forwardsolve = 1) and adjoint solve (forwardsolve = 0).
• Added TSAdjointSolve() for adjoint sensitivity analysis
• EquationType is introduced to distinguish between ODEs and DAEs. It needs to be set accordingly before solving the problem through TSSetEquationType(). It currently only affects arkimex methods.

DM/DA:

• DMCreateInjection() now returns a Mat, rather than a VecScatter
• The MatType argument is removed from DMCreateMatrix(), you can use DMSetMatType() to indicate the type you want used with a DM, defaults to MATAIJ
• You can now use DMDASetAOType() to indicate the type of AO you want used with a DMDA (defaults to AOBASIC)

DMPlex:

• Can now redistribute parallel meshes
• Can now increase the overlap of parallel meshes
• Added new mesh formats, Fluent CAS and Gmsh

PetscViewer:

• HDF5 viewer will save Vecs and DMDA Vecs with a dimension of 1 if the bs/dof of the vector is 1. To always include this dimension as a specific dimension in the HDF5 file even if if it is of size 1 use PetscViewerHDF5SetBaseDimension2() or -viewer_hdf5_base_dimension2 true

SYS:

• PetscOptionsHead() now takes a PetscOptions argument.
• PetscObjectAddOptionsHandler() now takes an event handler that includes a PetscOptions argument. PetscObjectProcessOptionsHandlers() requires this as input.

AO:

Fortran:

• Fortran include files are now in include/petsc/finclude instead of include/finclude. Thus replace uses of #include "finclude/xxx.h" with #include "petsc/finclude/xxx.h". Reason for change: to namespace the finclude directory with PETSc for --prefix installs of PETSc and for packaging systems