Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes

Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
superlu: libray is installed in PREFIX/lib64 - fix this to use PREFIX/lib
backport fixes cc105cc3 2b35c90a - required for 3bf428d - that was backported from master - 80c96bb
'echo -n' fails on opensolaris/osx - so avoid using it.
fix diffs in nightlybuilds due to options in ~/.petscrc
add Kelley03 to src/docs/tex/petsc.bib
build: determine moudles, mpi.h used during buildtime and print in 'info'
fix analyzer warnings
fix build failure on opensolaris - where -lm from flibs is removed due to -lm in cxxlibs. But then - only flib gets used for some configure tests [blaslapack, parms]
config: prefer __restrict over C99 restrict keyword
...

show more ...

Merge branch 'barry/remove-funct'

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-t

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-to: Andreas Mang <andreas@ices.utexas.edu>

show more ...

Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in m

Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in master (the introduction of MatFactorGetError()) therefor need
to merge in master and use the new construct before merging to next

show more ...

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

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

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcfetidp.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c
src/mat/impls/is/matis.h

show more ...

Merge branch 'tisaac/dmp4est-fix-overlap'

This branch makes a lot of fixes that fix PetscFV and DMP4est for
parallel. At the root of the issues were discrepencies related to the
overlapping cells t

Merge branch 'tisaac/dmp4est-fix-overlap'

This branch makes a lot of fixes that fix PetscFV and DMP4est for
parallel. At the root of the issues were discrepencies related to the
overlapping cells that are currently required for finite volume
calculations.

* tisaac/dmp4est-fix-overlap: (23 commits)
TS tutorial ex11: make p4est example parallel
TS tutorial ex11: globalize maxspeed before cfl computation
DMPlexTransferVecTree_Inject(): sum child to parent contributions
DMP4est: do not cause error if overlap > 1 in serial run
TS tutorial ex11: fix memory leaks
DMPlexTSComputeRHSFunctionFVM: ADD_VALUES from locF to F instead of INSERT_VALUES
DMPlexComputeResidual_Internal: global/local function mismatch
DMPlexShiftLabels_Internal: not-a-ghost is indicated by -1, not 0
DMPlexComputeResidual_Internal(): do not add contributions of ghost cells
DMPlexTree: do proper vector assembly
DMPlexReconstructGradients_Internal(): clarify ternary operator terms
DMPlexConstructGhostCells_Internal(): correct error message communicator
DMPforestGetTransferSF_Point: only compute covers for owned quads
TS tutorial ex11: only read gradients from local vectors
DMPlex: fix point migration / hybrid point interaction
DMPlex: fix PetscPartitionerPartition() to deal with overlap
DMPlexComputeInterpolatorTree: fix loop variables from recent change
DMP4est: search _both_ directions of tree for match
DMP4est: update regression tests for parallel
DMP4est: remove unused cell sf loop
...

show more ...

DMPlexReconstructGradients_Internal(): clarify ternary operator terms

Merge branch 'tisaac/ts-ex11-amr'

We now have an example (ts/examples/tutorials/ex11.c) where we can
use either DMPlex or DMP4est to handle adaptivity when time stepping.
We have tried to minimize t

Merge branch 'tisaac/ts-ex11-amr'

We now have an example (ts/examples/tutorials/ex11.c) where we can
use either DMPlex or DMP4est to handle adaptivity when time stepping.
We have tried to minimize the amount of code that is specialized to the
different DMs, and in the future more work can be done to improve this
interface.

* tisaac/ts-ex11-amr: (62 commits)
DMP4est: type fix
Plex: Fixes for analyzer
DMP4est: update snes ex12 regressions
DMPlex: fix parent/child interpolation with numFields > 0
DMP4est: also compute anyChange for uniformly refined/coarsened meshes
TS ex11: fix command line for AMR without computed gradients
TS ex11: remove gradient reconstruction from adaptivity requirements
DMPlexTree: some compilers want this var initialized
Plex: Changed Get/RestoreFaceFields() and Get/RestoreFaceGeometry() to return the number of active faces - This fixes a long-standing bad access in FV, although the values were never actually used.
DMPlexTS: removed unused variables
DMPlex/DMP4est: small fixes for next warnings and errors
SNES ex36 and ex52: These do not work anymore
DMPforestGetTransferSF_Point(): try to match parents
PetscViewerHDF5: destroy old file data if setting new filename
DMPlex + FV: remove leaky references in projection functions
Plex: Fixed incredibly stupid bug in Jacobian computation
PetscViewer HDF5: added get name method
DMPlexTree: do not skip out of child matrix loops early
PetscFV: correct field offsets when limiting gradients
DMP4estTree: ignore negative values when getting/setting vector values for transfer
...

show more ...

PetscFV: correct field offsets when limiting gradients

PetscFV: correct field offsets when calculating gradients

The offsets were originally calculated with respect to the closure of the discretization on a cell, but we only
want offsets that are with r

PetscFV: correct field offsets when calculating gradients

The offsets were originally calculated with respect to the closure of the discretization on a cell, but we only
want offsets that are with respect to the cell-centered variables, which is what the DMPlexPointLocalFieldRead()
funciton provides.

show more ...

Plex+FV: Integrated changes for FV support with multiple fields

DMPlex: move FV methods out of DMPlexSNES and into their own file