PETSc

Documentation: Changes: 2.0.15

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Highlights of new features in version 2.0.15, added since the last public release of PETSc (2.0.Beta.13). See details in the sections below.

• Added support for shared version of PETSc libraries for several machines to enable faster linking and smaller executables
• Added new parallel block row matrix format, improved efficiency for block diagonal formats
• Added a suite of routines to help manage the mappings between an application-defined ordering of variables and the ordering used by PETSc for matrices and vectors
• Expanded users manual information for performance tuning and profiling
• The option -log_summary now summarize of message-passing activity as well as flop rates.
• Running the test suite now requires much less disk space.
• Example programs are in the process of being reorganized into tutorials and tests (see, e.g., petsc/src/sles/examples/tutorials for tutorial-style examples for the linear solvers).
• The HTML version of the PETSc man pages now provides indices (organized by both concepts and routine names) to tutorial examples.

General

• Added support for shared libraries for the machines PETSC_ARCH = [sun4,solaris,alpha,IRIX,IRIX64,linux] to enable faster linking and smaller executables. To compile the shared libraries, install PETSc as usual and then execute the command make BOPT=g shared from the PETSc home directory (or use whatever BOPT you like). You can remove the shared libraries with the command make BOPT=g deleteshared Note: Shared libraries can also be used with PETSC_ARCH=freebsd and PETSC_ARCH=hpux if some minor modifications are made. For detailed instructions, see the files ${PETSC_DIR}/bmake/${PETSC_ARCH}/base. Please write to us at [email protected] if you encounter any problems when using the shared libraries.
• Users must now ALWAYS set the environmental variable PETSC_DIR to indicate the PETSc home directory. Previously, PETSC_DIR was set within the various makefiles within the PETSc installation. However, since this causes problems for shared libraries on some machines, the environmental variable PETSC_DIR is now used instead.
• Added global variables for use in debuggers:
  • PetscGlobalRank - processor's rank in MPI_COMM_WORLD
  • PetscGlobalSize - number of processors in MPI_COMM_WORLD
• For complex numbers versions (e.g., BOPT=g_complex): Added a global variable defining the imaginary number "i": PETSC_i

TS (Time Stepping Module)

• Changed TS_PSEUDO_POSITION_INDEPENDENT_TIMESTEP -> TS_PSEUDO_POSIND -
• Changed TSPseudoSetPositionIndependentTimeStep() -> TSPseudoSetPosIndTimeStep(). Even Barry couldn't stand names that long :-)

SNES (Nonlinear Solvers):

• The user can now set parameters used in matrix-free approximations of Jacobian-vector products, with the options -snes_mf_err <err> : square root of relative error in computing function -snes_mf_umin <umin>: minimum iterate parameter or by calling the routine SNESSetMatrixFreeParameters().
• Added the option -snes_mf_operator, which allows the user to apply the default matrix-free Jacobian but retain the user-provided Jacobian preconditioner matrix.
• Added the routine SNESGetTolerances() to extract the various parameters used for convergence testing.
• Initialized iteration counter to 0 for successive calls to SNES solvers.
• Changed the names for SNES runtime options associated with particular solvers to the forms -snes_eq_ls_<parameter_name> - nonlinear equations, line search method -snes_eq_tr_<parameter_name> - nonlinear equations, trust region method -snes_um_ls_<parameter_name>- unconstrained minimization, line search method -snes_um_tr_<parameter_name> - unconstrained minimization, trust region method Run program with -help for a detailed list of options.

SLES (Linear Solvers): See PC and KSP

• Changed the default linear solvers from GMRES(30) with Jacobi preconditioning to uniprocessor: GMRES(30) with ILU(0) preconditioning multiprocessor: GMRES(30) with block Jacobi preconditioning, where there is 1 block per processor, and each block is solved with ILU(0) See the users manual for additional options for the block Jacobi method. You can still employ the old default at runtime with the option -pc_type jacobi

KSP (Krylov subspace methods):

• Added routines KSPComputeEigenvalues(), KSPComputeEigenvaluesExplicitly() and runtime options -ksp_compute_eigenvalues, -ksp_plot_eigenvalues, -ksp_compute_eigenvalues_explictly and -ksp_plot_eigenvalues_explicitly for users interested in examining the eigenvalues of the preconditioned operator to better understand the convergence of a chosen iterative method.
• Changed KSPSetCalculateExtremeSingularValues() -> KSPSetComputeExtremeSingularValues() - Changed KSPSetCalculateResidual() -> KSPSetComputeResidual()

PC (Preconditioners):

• Added the routine PCSetModifySubMatrices(), which allows the user to set an optional routine for modifying the entries of the submatrices that arise in certain subdomain-based preconditioners (ASM, block Jacobi, block Gauss-Seidel).

MAT (Matrices):

• Eliminated routine MatGetSubmatrix(); now use MatGetSubMatrices() even when extracting just 1 submatrix.
• Added routine MatDestroyMatrices()
• Fixed bug in MatGetSubMatrices() for successive calls for matrices having different nonzero structure.
• Added routine MatGetBlockSize(). - Changed routine MatGetInfo() so that it returns more information. See man page for details.
• Changed usage of MatGetReordering() and MatRegisterOrdering(); see man pages.
• Changed the prefix used for matrix operation names within MatShellSetOperation() and MatHasOperation(): MAT_<operation> -> MATOP_<operation> For example, MAT_MULT -> MATOP_MULT.

DA (Distributed Arrays):

VEC (Vectors):

IS (Index Sets):

• Changed ISCreateSeq() to ISCreateGeneral()
• Changed ISCreateStrideSeq() to ISCreateStride()
• Added routine ISCreateBlock() to create a blocked index set. See the man page for details and related routines.

Draw (Graphics):

• Added -draw_x_private_colormap option that causes PETSc to allocate a separate colormap for PETSc graphics windows. This prevents bad contour plots due to Netscape altering the default color map.
• You can now zoom in and out of contour plots using the option -draw_pause -1 and left and center mouse buttons.
• The option -draw_contour_grid will display the underlying grid on a contour plot.

VIEWERS:

• Added routine ViewerGetFormat().
• Added options -viewer_matlab_machine and -viewer_matlab_port
• - Changed ASCII_FORMAT_xxx to VIEWER_FORMAT_ASCII_xxx and ASCII_FORMAT_INFO_DETAILED to VIEWER_FORMAT_ASCII_INFO_LONG
• Changed BINARY_FORMAT_xxx to VIEWER_FORMAT_BINARY_xxx
• PETSc now provides basic support for VRML viewers. Currently, one can draw surface contours of vector fields with the routine DFVecDrawTensorSurfaceContour(). Note that the VRML utilities will be expanded and the interface will change in the near future.

SYSTEM:

EVENT LOGGING:

FORTRAN INTERFACE:

• Changed PETSC_NULL_CHAR to PETSC_NULL_CHARACTER - Replaced PETSC_DEFAULT with
• You no longer need MPE to build PETSc.
• Included petsc/include/options.h within petsc/include/petsc.h -
• Changed distributed array name from RA to DA. Also changed DAGlobalToLocal() to DAGlobalToLocalBegin() followed by DAGlobalToLocalEnd().
• Changed usage of KSPBuildSolution() slightly to avoid copying when not needed.
• Remove first argument (rflag) from ALL options database commands, i.e., OptionsGetInt(0,0,"-m",&m) => OptionsGetInt(0,"-m",&m), etc.
• Changed the way memory tracing is done. When compiling with BOPT=g it is the default, but you may turn it off with -notrmalloc. When compiling with BOPT=O it is by default off, but one may turn it on with -trmalloc or -trdump.