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

show more ...

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

Merged petsc/petsc into master

Merge branch 'knepley/feature-plex-hdf5-parallel-load'

* knepley/feature-plex-hdf5-parallel-load:
HDF5: Fixed Xdmf script
Plex+HDF5: Do not use vectors for periodic visualization
Plex+HDF5: Ig

Merge branch 'knepley/feature-plex-hdf5-parallel-load'

* knepley/feature-plex-hdf5-parallel-load:
HDF5: Fixed Xdmf script
Plex+HDF5: Do not use vectors for periodic visualization
Plex+HDF5: Ignore negative sequence numbers
DMPlex: Now Plex output is parallel - We now write visualization specific topology in /viz/topology - We output a point reordering, coneSizes, cones, and orientations - Now longer need to interpolate on load
DMPlex: Use the presence of faceGeometry in the DM to signal we are using FVM - This will become a PetscFVM object soon
DMPlex: Preserve the block size of the coordinate vector after distribution
Plex+HDF5: Moved all HDF5 to a separate file, and mapped 2D periodic mesh to the cylinder - Now visualization specific things are in /viz
HDF5: Made petsc_gen_xdmf.py executable
Viewer+Options: Added Fortran interface for PetscObjectViewFromOptions()
IS: Stupid mistake. Damn you compiler
DMPlex: Now parallel HDF5 label output does not fail - However, it is also now clear that we will have to write the full interpolation connectivity in order for these to be meaningful
DMPlex: Added DMPlexCreatePointNumbering() - Made DMPlexCreateNumbering_Private() more flexible
IS: Added ISSortRemoveDups()
DMPlex: Added DMPlexInvertCell_Internal() - Stupid type matching
HDF5: Added petsc_gen_xdmf.py which processes PETSc HDF5 output and produces an Xdmf file
DMPlex: Force a serial load in DMLoad_HDF5(), after which we call DMPlexDistribute() - Eventually we would load into a naive partition
IS+HDF5: Corrected code for new block size interface where it is never negative
Viewer+HDF5: Added PetscViewerHDF5ReadSizes() - This allows me to check the size of a Vec or IS to be loaded

show more ...

Plex+HDF5: Moved all HDF5 to a separate file, and mapped 2D periodic mesh to the cylinder
- Now visualization specific things are in /viz

Fixing merge conflicts in dmregall.

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

DMPlex: Reorganized the handling of point adjacency
- Replaced centerDim with useCone, useClosure, Added DMPlexGet/SetAdjacencyUseCone/Closure()
- Now partitioning and preallocation use the same adja

DMPlex: Reorganized the handling of point adjacency
- Replaced centerDim with useCone, useClosure, Added DMPlexGet/SetAdjacencyUseCone/Closure()
- Now partitioning and preallocation use the same adjacency routines
- Added DMPlexGetAdjacency() and the internal version which does not allocate
- Moved distribution and partitioning code into separate files
-

show more ...

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

Merged petsc/petsc into master

Merge branch 'master' into prbrune/snes-fascontinuation

Conflicts:
include/petscsnesfas.h

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

Merge branch 'knepley/fix-plex-closure-index'

* knepley/fix-plex-closure-index:
DMPlex: work around -Wmaybe-uninitialized
DMPlex: Small fix
PetscSection: Added PetscSectionGetField()
DMPlex:

Merge branch 'knepley/fix-plex-closure-index'

* knepley/fix-plex-closure-index:
DMPlex: work around -Wmaybe-uninitialized
DMPlex: Small fix
PetscSection: Added PetscSectionGetField()
DMPlex: Reorganization of closure operations - Rename DMPlexVecGetClosure_Static() —> DMPlexVecGetClosure_Depth1_Static() - Added special cases with/out fields - Removed the need for field offsets by interchanging loops over points and fields - Fixed bug where field offsets were not calculated if an array was passed in - Made all local functions static - Using SNES ex62 to verify changes, and DMPlex ex9 to time them
DMPlex: Fixed object check
DMPlex ex9: Now test VecClosure with index - Made functions static
DMPlex: Optimization for Get/SetClosure - Only need field offsets if there is more than one field
PetscSection: Change clIndices member to clPoints - Added some docs
SNES ex12: Use ViewFromOptions correctly
DMPlex: Use closure index in DMPlexVecSetClosure() and DMPlexMatSetClosure() - Moved depth 1 optimization to static function
DMPlex: Reorgnized closure index - Now index stores points and orientations instead of offsets, so it can be used for updates as well - Moved index creation to plexindices.c - Moved optimization for depth 1 mesh to a static function
DMPlex: Fixed two bugs with DMPlexCreateClosureIndex() - Must make index for entire DM chart - Need to update cloff when no fields are present

Conflicts:
src/dm/impls/plex/makefile
src/dm/impls/plex/plex.c

show more ...

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

Conflicts:
include/makefile

Merge branch 'master' into knepley/feature-mat-zerorowscols-baij

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

Conflicts:
src/ts/examples/tutorials/advection-dif

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

show more ...

Merged petsc/petsc into master

DMPlex: Reorgnized closure index
- Now index stores points and orientations instead of offsets, so it can be used for updates as well
- Moved index creation to plexindices.c
- Moved optimization for

DMPlex: Reorgnized closure index
- Now index stores points and orientations instead of offsets, so it can be used for updates as well
- Moved index creation to plexindices.c
- Moved optimization for depth 1 mesh to a static function

show more ...

Merge branch 'master' into knepley/feature-dmda-section

* master: (319 commits)
SNESGS: Fix for uninitialized variable warning in gssecant.c
DMPlex: Fix for orientation in Gmsh files - Fixed tes

Merge branch 'master' into knepley/feature-dmda-section

* master: (319 commits)
SNESGS: Fix for uninitialized variable warning in gssecant.c
DMPlex: Fix for orientation in Gmsh files - Fixed test output
do not use C99 struct initialization code in PETSc
Nightly Summary: Added time taken to each of the tests in the dashboard.
ASCII printing of floating point numbers must cast to (double) to support quad precision
configure: check fortranDatatypes only when fortran is enabled [this fixes configure crash with --with-fc=0]
don't use non-portable and also dependent on floating point precision system level math constants
picky compilers
fix a couple compiler warnings/errors (depending on compiler) for Matlab engine code
DMPlex: More fixup from bad rebase, moved to DMGet/SetCoordinateSection()
DM: Added DMGet/SetCoordinateSection()
Fuckup: Fix for merge that is still untangling bad rebase from Oct. 17th 2013 - Fixed const in declarations - Fixed merge from PetscFE - Fixed 2 mallocs
replace all echo in test/tutorial makefiles with printf since echo behaves differently on different systems
DMDA: Missing header - Damn rebase
DMPlex ex3: Added 2D Q_1 and 3D P_2 tests
DMDA: Added DMDAProjectFunction() and DMDAComputeL2Diff()
DMDA: Fixed 2D geometry - Should reuse DMPlex routines
DMDA: Fix bug in 2D closure operation for cells
DMDA: Make closure operations also return the size
DMDA: Changed DMDACreateSection() to emulate DMPlexCreateSection()
...

Conflicts:
config/builder.py
include/petscdmda.h
src/dm/dt/interface/dtfe.c
src/dm/impls/da/dageometry.c
src/dm/impls/da/dalocal.c
src/dm/impls/plex/plexgeometry.c

show more ...

Merge branch 'knepley/feature-plex-gmsh'

* knepley/feature-plex-gmsh:
DMPlex: Fix for orientation in Gmsh files - Fixed test output
DMPlex GMSH: fix MPIU_INT
DMPlex: Slience bogus compiler war

Merge branch 'knepley/feature-plex-gmsh'

* knepley/feature-plex-gmsh:
DMPlex: Fix for orientation in Gmsh files - Fixed test output
DMPlex GMSH: fix MPIU_INT
DMPlex: Slience bogus compiler warning
DMPlex Gmsh: Fixed integer size problem
DMPlex Gmsh: Fixed interface for coordinates
DMPlex ex1: Added test for Gmsh
DMPlex: Added Gmsh input

show more ...