PETSc

Documentation: Changes: 2.3.0

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General:

• The equivalent of building BOPT=g, BOPT=O versions for PETSC_ARCH=linux-gnu is now: config/configure.py [options] -PETSC_ARCH=linux-gnu config/configure.py [options] --with-debugging=0 -PETSC_ARCH=linux-gnu-opt
• Python bindings added to PETSc. To use, configure with: --with-python=1 ---with-shared=1 To build, use: 'make python' after building PETSc libraries. Example in src/snes/examples/tutorials/ex1.py
• Options database keys -trmalloc[_xxx] are changed to -malloc[_xxx]
• -get_resident_set_size and -trinfo are changed to -memory_info
• PetscTrValid() -> PetscMallocValidate(), PetscTrDebug() -> PetscMallocDebug()
• -trdebug -> -malloc_debug
• PetscGetResidentSetSize() -> PetscMemoryGetCurrentUsage(), added PetscMemoryGetMaximumUsage() and PetscMemorySetGetMaximumUsage()
• PetscTrSpace() -> PetscMallocGetCurrentUsage() and PetscMallocGetMaximumUsage()
• added PetscOptionsEnum() and PetscOptionsGetEnum()
• added PetscBag object for managing user created structs including initializing them and serializing them.
• removed PetscSetCommWorld(). Now you can directly assign to PETSC_COMM_WORLD before PetscInitialize().

Vec:

• Faster generation of VecScatter for many processes when indices are mostly sorted
• Changed BLAS-type interfaces to PETSc-style:
  • VecShift
  • VecScale
  • VecSet
  • VecSetRandom
  • VecAXPY
  • VecAXPBY
  • VecAYPX
  • VecMAXPY
  • VecWAXPY
• Changed order of arguments in pointwise routines:
  • VecPointwiseMult
  • VecPointwiseMax
  • VecPointwiseMin
  • VecPointwiseMaxAbs
  • VecPointwiseDivide

Mat:

• Changed MatConvert to require a reuse parameter to denote inplace converstion
• Added Cholesky and ICC support to SeqBAIJ
• Added the argument MatFactorInfo to MatLUFactorNumeric() and MatCholeskyFactorNumeric()
• Faster MatSetValues()
• Faster parallel-matrix vector products
• Changed MatCreate() to take only a communicator
• Added MatSetSize() to specify matrix sizes
• Changed BLAS-type interfaces to PETSc-style:
  • MatAXPY
  • MatAYPX
  • MatScale
  • MatShift
• Change MatZeroRows() and MatZeroRowsLocal() to use arrays, and added IS versions

PC:

• Added PCILUReorderForNonzeroDiagonal() and PCLUReorderForNonzeroDiagonal()
• Replace PCLUSetDamping(), PCILUSetDamping(), PCCholeskySetDamping() and PCICCSetDamping() by PCFactorSetShiftNonzero(). Change the option database keys -pc_lu_damping, -pc_ilu_damping, -pc_cholesky_damping and -pc_icc_damping to -pc_factor_shift_nonzero
• Replace PCLUSetShift(), PCILUSetShift(), PCCholeskySetShift() and PCICCSetShift() by PCFactorSetShiftPd(). Change the option database keys -pc_lu_shift, -pc_ilu_shift, -pc_cholesky_shift and -pc_icc_shift to -pc_factor_shfit_positive_definite
• PCMG: will automatically using the outer pmat operator to define the finest level operator if not user supplied
• PCMG: added MGUseGalerkin(), -pc_mg_galerkin option to have coarser grid matrices computed from the finest grid matrix
• PCMG: now does referencing counting on set vectors and restriction/interpolation matrices so user need not keep reference to free later
• PCMG: if user does not provide restriction the interpolation is used and vis versa
• PCMG: if user does not provide Vecs for each level, will automatically provide them
• All routines that began with MG now begin with PCMG
• Added PCShellSet/GetContext() and removed the context passed into PCSetApply() and PCSetApplyRichardson()

KSP:

• -ksp_cg_Hermitian and -ksp_cg_symmetric have been changed to -ksp_cg_type Hermitian or symmetric
• Changed options for -ksp_gmres_cgs_refinement_type from never or ifneeded or always to REFINE_NEVER or REFINE_IFNEEDED or REFINE_ALWAYS

config/configure.py:

SNES:

• Changed the name and calling sequence for SNESSetLineSearchCheck() to SNESLineSearchSetPostCheck() and added a SNESLineSearchSetPreCheck()
• Changed the names of all SNESxxxxLineSearchyyyy() to SNESLineSearchxxxxyyyy() per PETSc naming standard.
• Now allow a constant vector to be specified in SNESSolve()
• Removed the Vec argument from SNESSetUp()
• Corrected the order of function and context arguments in:
  • SNESGetFunction()
  • SNESGetJacobian()

TS:

DA:

• Added DAVecGet/RestoreArrayDOF() allowing indexing in the dimension of degrees of freedom at each point on the lattice.
• Faster DAGlobalToLocal() etc for dof > 1.

DMMG:

• Consolidated DMMG functionality into the new header file "petscdmmg.h".

SYS:

• PetscSetCommWorld() removed. [one can directly do PETSC_COMM_WORLD = comm - before PetscInitialize()]

Fortran:

ExternalPackages:

• ML support added.