Merge branch 'master' into barry/saws-options

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bdd

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddcprivate.c

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Merge remote-tracking branch 'origin/master' into feature-dmmoab

Merged petsc/petsc into master

Merge branch 'master' into prbrune/docs-snesmanualupdate

* master:
Doc: fix spelling errors in users manual
superlu_dist determines namemangled based on blas/lapack mangling, NOT fortran manglin

Merge branch 'master' into prbrune/docs-snesmanualupdate

* master:
Doc: fix spelling errors in users manual
superlu_dist determines namemangled based on blas/lapack mangling, NOT fortran mangling
SNESNASM: Explicitly set the NASM type to PC_ASM_BASIC in ASPIN.
SNESNASM: Add missing SNESNASMSet/GetType()
changed prototypes for args for KSPComputeEigenvalues[Explicitly] to arrays and improved manual pages to clarify that arrays are provided by users
update src/mat/examples/tests/ex72.c for reading symmetric matrix in MatrixMarket to petsc binary file
allocate one more space for row data for ml matrix then one might think is correct. This resolves a problem in a user code and won't break anything since it is just space allocated (possibly due to bug in ml).
Revert "metis/parmetis: update to metis-5.1.0/parmetis-4.0.3" There were a couple of reports of breakage of mumps with this update http://lists.mcs.anl.gov/pipermail/petsc-dev/2013-September/012853.html Subject: [petsc-maint] Issue with Metis in PETSC-DEV?
unitialized values outside array size, found by valgrind this example is still funky since it does not seem to handle array sizes properly everywhere
make sure example does not send uninitialized data through MPI to confuse valgrind
make sure no initialized data is sent via MPI to confuse valgrind
create rule for testexamples_SSL to prevent warning in make alltests
variable of wrong type and not even used
cleanup the function prototype representation for pre and post linesearch checking functions and improve documentation minor cleanup of documentation of several basic SNES functions
removed definition of DMADDA and documented removal

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changed prototypes for args for KSPComputeEigenvalues[Explicitly] to arrays and improved manual pages to clarify that arrays are provided by users

Merged petsc/petsc into master

Merge branch 'master' into shri/ts-events

Conflicts:
src/ts/interface/ts.c

Merge branch 'master' into shri/feature-dm-circuit

Conflicts:
src/dm/impls/makefile

Merge branch 'master' into prbrune/matcoloring-greedy

Merge branch 'master' into barry/nonlinearsolvertable

Conflicts:
include/petscsnes.h

Merge branch 'master' into knepley/feature-plex-fas

* master: (863 commits)
Revert "mpich: use latest mpich tarball with gcov but use '--enable-coverage' mpich configure option."
MatCreateTransp

Merge branch 'master' into knepley/feature-plex-fas

* master: (863 commits)
Revert "mpich: use latest mpich tarball with gcov but use '--enable-coverage' mpich configure option."
MatCreateTranspose: fix for lazy block size
mpich: use latest mpich tarball with gcov but use '--enable-coverage' mpich configure option.
configure: add FC_DEFINE_FLAG to petscvariables
added a citation for pounders, Stefan finally came through
update to latest netcdf fixes bug that did not allow building on recent Mac OS X
DMPlex: Fixes for CGNS - Fixed loop bounds since CGNS uses closed intervals - Bug with mixed cell types - Typo with coordinates
final updates from nightly tests
fix for countcfunction
removed outdated docs and comments on MatStructure usage removed SAME_PRECONDITIONER since no longer used removed unneed use of MatStructure in Schur complement matrix
removed MatStructure arguments from Tao
fixes for Sundials and fun3d cannot use MPIU_SUM for integer arrays
inplace ILU factorization must update state of inplace matrix to prevent infinite recursion of updating PC
fixes for BDDC by the way not having BDDC always in the testing is going to lead to trouble
the compute Jacobian functions for SNES and TS now do not take a MatStructure flag
KSPSetOperators() no longer has the MatStructure argument. The Mat objects now track that information themselves. Use KPS/PCSetReusePreconditioner() to prevent the recomputation of the preconditioner if the operator changed in the way that SAME_PRECONDITIONER did with KSPSetOperators()
tracks when Mat's have a change in nonzero structure this information can be used by PC to determine how preconditioners must be rebuilt currently only does an error check if the user said same nonzero pattern but actually changed the pattern
completed cleanup of removal of matrix pointers to compute jacobian routines
makefile: Added 'make includegraph' to create an inclusion dependency graph.
Contrib: Updated include-graph.sh script to ignore *.hh files
...

Conflicts:
src/dm/dt/interface/dt.c

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Merging master with feature-dmmoab. Only conflict was with SOURCECXX specification under impls/moab/makefile.

Merge branch 'barry/rm-matstructure-mat-pointer'

Conflicts:
include/petsctao.h

removed outdated docs and comments on MatStructure usage
removed SAME_PRECONDITIONER since no longer used
removed unneed use of MatStructure in Schur complement matrix

KSPSetOperators() no longer has the MatStructure argument. The Mat objects now track that information themselves. Use KPS/PCSetReusePreconditioner() to prevent the recomputation of the preconditioner

KSPSetOperators() no longer has the MatStructure argument. The Mat objects now track that information themselves. Use KPS/PCSetReusePreconditioner() to prevent the recomputation of the preconditioner if the operator changed in the way that SAME_PRECONDITIONER did with KSPSetOperators()

SNES/TS still need to be cleaned up to better utilize the new interfaces

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Merged petsc/petsc into master

Merge branch 'master' into prbrune/snes-fascontinuation

Conflicts:
include/petscsnesfas.h

Merge branch 'barry/update-some-manualpages'

update some /*MC manual pages, correcting errors and occassionally adding more information

Merge branch 'master' into barry/ts-rhsjacobian-only

Merge branch 'shri/update-SuiteSparse' into shri/external-package-KLU

Conflicts:
conf/test
config/examples/arch-linux-pkgs-dbg-ftn-interfaces.py
config/examples/arch-linux-pkgs-opt.py

Merge branch 'master' into balay/tao-to-petsc

Conflicts:
src/dm/examples/tests/ex42.c
src/dm/examples/tutorials/ex65dm.c
src/ksp/ksp/examples/tutorials/ex42.c
src/snes/examples/tutorials/cahn-hi

Merge branch 'master' into balay/tao-to-petsc

Conflicts:
src/dm/examples/tests/ex42.c
src/dm/examples/tutorials/ex65dm.c
src/ksp/ksp/examples/tutorials/ex42.c
src/snes/examples/tutorials/cahn-hilliard-schemes/ex1.c
src/snes/examples/tutorials/ex54.c
src/snes/examples/tutorials/ex55.c
src/snes/examples/tutorials/ex60.c
src/snes/examples/tutorials/ex61.c
src/snes/examples/tutorials/ex63.c
src/snes/examples/tutorials/ex633d_db.c
src/snes/examples/tutorials/ex64.c
src/snes/examples/tutorials/ex65.c
src/snes/examples/tutorials/ex653d.c
src/ts/examples/tutorials/ex23.c

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Merge remote-tracking branch 'origin/karpeev/ksp-matschurcomplement'

* origin/karpeev/ksp-matschurcomplement:
Fixed memory leak in MatSchurComplement.
MatSchurComplementXXXSubMatrices renamed fo

Merge remote-tracking branch 'origin/karpeev/ksp-matschurcomplement'

* origin/karpeev/ksp-matschurcomplement:
Fixed memory leak in MatSchurComplement.
MatSchurComplementXXXSubMatrices renamed for consistency.
PCFieldSplit: enable extraction of MatSchurComplement to configure it.
MatSchurComplement can use different approximations to inv(A00) when forming Sp.
PCFieldSplit: Schur can use lumping with MatSchurComplement.
MatSchurComplement: Allow lumping of A00 when forming Sp.
PCFieldSplit implements SELFP preconditioning for Schur using MatSchurComplementGetPmat to assemble Sp.
MatCreateSchurComplementPmat() now public.
MatSchurComplement now uses MatDiagonalScale to form Sp. Factored out Sp constructor for consistency and reuse.
More consistent matrix naming in arguments and docs to MatSchurComplement-related routines.
MatSchurComplement can now assemble Sp on demand.

Conflicts:
include/petscksp.h
include/petscpc.h
src/ksp/pc/impls/fieldsplit/fieldsplit.c

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Merge branch 'knepley/feature-schurm-explicit-op'

* knepley/feature-schurm-explicit-op:
KSP: Fix for name change in another branch
KSP: It looks like someone forgot this declaration
Mat: Impro

Merge branch 'knepley/feature-schurm-explicit-op'

* knepley/feature-schurm-explicit-op:
KSP: Fix for name change in another branch
KSP: It looks like someone forgot this declaration
Mat: Improve conversion of MATDENSE to MATAIJ - Previously, we were creating a fully dense AIJ matrix
Section: Small doc fix
PC: Allow FieldSplit to explicitly compute S for preconditioning - Yes I know it is generally slow
KSP: Added MatSchurComplementComputeExplicitOperator - This could be optimized to compute a sparse S for preconditioning (Saad has some papers here)

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