Merge branch 'knepley/feature-error-logging' of bitbucket.org:petsc/petsc into knepley/feature-error-logging

Merge branch 'master' into knepley/feature-error-logging

* master: (324 commits)
DT: Reverting the tgamma change broke MPFR - I guess we need a nightly build with it in
Revert "tgamma: icc on wi

Merge branch 'master' into knepley/feature-error-logging

* master: (324 commits)
DT: Reverting the tgamma change broke MPFR - I guess we need a nightly build with it in
Revert "tgamma: icc on windows requires mathimf.h for tgamma."
setup routine no longer calls PetscCalloc5 if the arrays have already been allocated in a previous setup call
clarify SNESGetFunction()
Move MOAB docs to submansec so as not to clutter DM mansec
doc: remove matlab from doc generation dependency - i.e remove 'alldoc3' and use 'html' to generate corresponding '*.m.html' files.
Remove matlab pounders related cruft that is not required. Document the matlab code better and include an appropriate message in the help text.
Fixed typo.
Remove the inclusion of matlab in testing.
Finalizing comments and the work for the test problems.
Finished the testing and generation of plots. Some simple bug fixes addressed.
Set -Wl,-rpath for Mac OS Matlab mkl directory; don't pass -nojvm to matlab since it causes crashes on Barry's machine and is not needed
Added list of known problems with the code.
Added a comment on ignoring the return from Tao.
Finish with initial implementation of matlab interface to test TAO pounders.
Working through the matlab interface for pounders testing.
Fix typo in manual Reported-by: Jaroslaw Piwonski (CAU) <jpi@informatik.uni-kiel.de>
Fixed mkl_sparse_sypr() calls that were using an unsupported value in the matrix descriptor.
test harness: simplify code that checks for sequential-only tests
Fix the doc for call-backs drdyf drdpf
...

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Plex: DMPlexSNESComputeJacobianActionFEM() --> DMPlexSNESComputeJacobianAction()
- Expose cellIS and other args

Merge branch 'knepley/fix-plex-residual-loop'

* knepley/fix-plex-residual-loop:
Plex+SNES: Protect Destroy
Plex+SNES/TS: Moved zeroing of Jacobian out of DMPlexComputeJacobian_Internal() - Shoul

Merge branch 'knepley/fix-plex-residual-loop'

* knepley/fix-plex-residual-loop:
Plex+SNES: Protect Destroy
Plex+SNES/TS: Moved zeroing of Jacobian out of DMPlexComputeJacobian_Internal() - Should probably go in DMLocal versions, but now its in the top-level Plex FEM versions
SNES+Plex: Needed cell offset, not cell number
Sys: Added a check for gnome-terminal, which never uses -display - Added some docs
Plex: Made a public interface for ComputeBdResidualSingle()
Plex: The first argument to a pointfunc should be the coordinate dimension

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Plex+SNES: Protect Destroy

missing CHKERRQ()

Commit-type: bug-fix
Reported-by: clang static analyzer

Merge branch 'master' into knepley/feature-error-logging

* master: (221 commits)
dashboard: count and list example compile failures like:
fix fix-pr879-jczhang-optimize-vecscatter-multi-copy
a

Merge branch 'master' into knepley/feature-error-logging

* master: (221 commits)
dashboard: count and list example compile failures like:
fix fix-pr879-jczhang-optimize-vecscatter-multi-copy
add manual page cross links for SNESLineSearchSetPostCheck() and related routines
fix help manual of MatCreateSubmatrices() Reported-by: Tim Steinhoff <kandanovian@gmail.com>
Add manual pages for PetscRealPart() and PetscImaginaryPart()
fix compile error with missing MPI_C_DOBULE_COMPLEX
fix typo Reported-by: Febrian Setianto <febrian.setianto@gmail.com>
plex tutorial ex5: updated test requirements
DMPlexLoad_HDF5_Xdmf_Internal: fix for complex PetscScalar.
DMPlexLoad_HDF5_Xdmf_Internal: fix for 64-bit PetscInt.
DMPlexBuildFromCellList_Internal: use DMPlexInvertCell_Internal (with PetscInt* arg)
petscviewer.h: removed notice which is no longer relevant
DMPlexCreateFromFile: document option
check only if PETSC_USE_DEBUG
DMPlexBuildFromCellList_Internal optionally inverts cells.
ex5: new test 4 with -compare without repartitioning
ex5: new test 3 using -compare
ex5: HDF5 write+read moved to separate function
ex5: option -format processed in ProcessOptions()
ex5: added missing hdf5 requirement
...

Conflicts:
include/petsclog.h

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Plex+SNES: If no exact solutions are provided to Check, get them from DS

Plex: Fixed call

Added DMPlexComputeBdResidualSingle()

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead code.
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
...

Conflicts:
src/snes/examples/tutorials/ex13.c

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Merge branch 'master' into knepley/fix-plex-residual-loop
Warning: This merge includes real changes

* master: (188 commits)
Add JuMP citation
Copyedits and updates to developers manual
Add mor

Merge branch 'master' into knepley/fix-plex-residual-loop
Warning: This merge includes real changes

* master: (188 commits)
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
SNES ex62: Set name of solution vector - Update test output
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
move output file to the correct location. i.e fix 305862f9cd0dc399542ae11dd744508e4b6ad2e3
...

Conflicts:
src/snes/utils/dmplexsnes.c
src/ts/utils/dmplexts.c

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Merge remote-tracking branch 'origin/tisaac/feature-dmfield'

* origin/tisaac/feature-dmfield: (56 commits)
Plex: Updated test output for DMLabel change
DMLabel: make empty ISs strides
DMSwarm:

Merge remote-tracking branch 'origin/tisaac/feature-dmfield'

* origin/tisaac/feature-dmfield: (56 commits)
Plex: Updated test output for DMLabel change
DMLabel: make empty ISs strides
DMSwarm: silence static analyzer warning
PetscFECreateDefault: fix custom Fortran interface to use MPI_Comm
SNES ex69: Updated test output
SNES ex69: Removed all mantle stuff and change fields to constants - Also use dsymutil for executables
SNES ex69: Removed special partition
SNES ex69: Fixed null space creation - Null space locks its vectors
PetscFE: PetscFECreateDefault() now takes MPI_Comm instead of DM
DMField: default initialization of variable
PetscFE: fix integration for openCL
PetscFEGeomComplete(): correct normal vector in 2D.
DMField: c++/complex fixes
DMField: empty processor protections
DMField regression test fixes
DMLabel: try to keep stride IS as stride IS as much as possible
DMPlexRefine(): create depth before hybrid-bounded label
DMField: documentation of interface
DMField: implement shell
DMPlex: rename newly created label
...

Conflicts:
src/dm/dt/interface/dtfe.c
src/snes/examples/tutorials/ex69.c
src/snes/utils/dmplexsnes.c

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Merge remote-tracking branch 'origin/knepley/fix-fe-bd-integral'

* origin/knepley/fix-fe-bd-integral:
Plex+SNES: Fix BdResidual - Use DMPlexGetSubpoint() for aux closure, in case it is a boundary

Merge remote-tracking branch 'origin/knepley/fix-fe-bd-integral'

* origin/knepley/fix-fe-bd-integral:
Plex+SNES: Fix BdResidual - Use DMPlexGetSubpoint() for aux closure, in case it is a boundary mesh - Be careful about Plex conversion
FE: Fixed boundary integration - Allow auxiliary dm to be a different dimension, need dimAux and different tabulation
FE: Small confusion about topological vs coordinate dimension
PetscDS: The u_x array must have size dimEmbed because the derivatives are a function of the coordinate dim, not topological dim
Plex: Added DMPlexGetSubpoint() - This returns the point in a submesh corresponding to some point in the original mesh - This replaces custom code in projection

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Deprecate DMSet/GetDefaultSection() for DMSet/GetSection()

Revert manual page change per Matt's preference

Commit-type: style-fix
Thanks-to: Matthew Knepley

Plex+SNES/TS: Moved zeroing of Jacobian out of DMPlexComputeJacobian_Internal()
- Should probably go in DMLocal versions, but now its in the top-level Plex FEM versions

SNES+Plex: Needed cell offset, not cell number

Plex: Added DMPlexComputeJacobian_Patch_Internal()
- This should replace the old routine after more testing

Plex+SNES: In DMPlexComputeJacobian_Internal(), cleanup, removed debugging print, moved check for Shell matrix to the front

DM+SNES: Changed signature for internal check function

Plex+SNES: Fix BdResidual
- Use DMPlexGetSubpoint() for aux closure, in case it is a boundary mesh
- Be careful about Plex conversion

DMField: empty processor protections

DMLabel: try to keep stride IS as stride IS as much as possible

DMPlex: rename newly created label

DMPlexSNES: caching of new geometry constructs

The old paradigm cached one geometry object for all cells or all faces,
an approach that doesn't take into account that different quadratures
may requi

DMPlexSNES: caching of new geometry constructs

The old paradigm cached one geometry object for all cells or all faces,
an approach that doesn't take into account that different quadratures
may require different geometry objects. Now the geometry object
is composed with the index set over which the geometry ranges, and the composition
string include the object id of the quadrature. To take advantage of
this caching, we have to be careful not to reconstruct index sets on the
fly when they are known a priori. In particular, the hybrid bounds
have been encapsulated as a label, which makes them accessible as ISs.

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