DMField: Fix Quadrature memory management
- Small doc fix

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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DT: Reverting the tgamma change broke MPFR
- I guess we need a nightly build with it in

Merge branch 'maint'

Merge remote-tracking branch 'origin/balay/revert-icc-tgamma-mathimf/maint' into maint

Revert "tgamma: icc on windows requires mathimf.h for tgamma."

This reverts commit a6fc04d992a3bc61f7f4f19e6cefc00749f3729d.

This change was hakey - and 2becd9dc3b70afefe001e0823eab9229dd4f1aab now

Revert "tgamma: icc on windows requires mathimf.h for tgamma."

This reverts commit a6fc04d992a3bc61f7f4f19e6cefc00749f3729d.

This change was hakey - and 2becd9dc3b70afefe001e0823eab9229dd4f1aab now has a better check for tgamma() [so mathimf.h shouldn't be needed]

Reported-by: He Zhong <he.chron@gmail.com>

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Merge remote-tracking branch 'origin/rmills/fix-dm-replace-ifdefs'

Change #if(n)def to #if (!)defined in all DM code.

Commit-type: style-fix

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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Merge branch 'psanan/manpages-notes-newlines' [PR #932]

* psanan/manpages-notes-newlines:
A large number of man pages are improperly formatted because of the lack of a newline after "Notes:", "Fortr

Merge branch 'psanan/manpages-notes-newlines' [PR #932]

* psanan/manpages-notes-newlines:
A large number of man pages are improperly formatted because of the lack of a newline after "Notes:", "Fortran Notes:", or "Developer Notes:".
This batch adds those newlines, with 4 spaces of indentation afterwards.
The uniform indentation arguably makes the man pages a little less readable in the source itself,
but overall this hopefully has a large positive impact on the readability of the HTML pages.

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Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \(

Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \( -name "*.c" -or -name "*.h" -or -name "*.cxx" \) | xargs gsed -i 's/Notes\s*:\s*\(\w.*\)/Notes:\n \1/'

This adds a newline and 4 spaces whenever "Notes:" is followed by any "word" character, in any .c, .h, or .cxx file in src/ or include/

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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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DMField: evaluate FV implementation for DS

PetscSpace: added PetscSpace Subspace, used for trace spaces

This was previously a property of just polynomial spaces, but PetscSpaceEvaluate() seems to
codify the fact that a PetscSpace has a domai

PetscSpace: added PetscSpace Subspace, used for trace spaces

This was previously a property of just polynomial spaces, but PetscSpaceEvaluate() seems to
codify the fact that a PetscSpace has a domain (NumVariables) and a range (NumComponents), so
I'm promoting this property to all spaces

PetscSpace: added PetscSpaceGet/SetNumVariables()

squash me

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Merge branch 'barry/add-fortran-custom-interfaces'

DT+Doc: Small fix

a few more Fortran interfaces

Commit-type: feature

add a collection of Fortran interfaces and additional docs

For some reason this cause failures in many examples, need to debug

Commit-type: testing-fix,style-fix,documentation, example

Merge branch 'barry/add-ftn-linfinity-conv-test' of bitbucket.org:petsc/petsc into barry/add-ftn-linfinity-conv-test

Merge branch 'jose/lapack-ungqr'

petscblaslapack.h: rename LAPACKungqr_ to LAPACKorgqr_

The intention is to be consistent with other subroutines like
LAPACKsyev_ where the 'real' name is used for both the 'real' subroutine
(_syev)

petscblaslapack.h: rename LAPACKungqr_ to LAPACKorgqr_

The intention is to be consistent with other subroutines like
LAPACKsyev_ where the 'real' name is used for both the 'real' subroutine
(_syev) and the 'complex' subroutine (_heev) depending on scalar-type

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Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maint

Obtain changed (v3.5) handling of MatMPIBAIJSetPreallocationCSR to match
documentation.