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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Merge branch 'maint'

Merge branch 'rmills/fix-aijmkl-sypr/maint' into maint

Fixed mkl_sparse_sypr() calls that were using an unsupported value in the matrix descriptor.

Commit-type: bug-fix
Reported-by: Maria Zhukova <maria.zhukova@intel.com>

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

Removed use of #ifdef/#ifndef in favor of #if defined()/#if !defined().

Commit-type: style-fix

Old sparse BLAS interfaces are now not referenced by MKL versions that deprecate them.

The old interfaces were deprecated in MKL version 18, update 2.
The inspector-executor routines can still be "t

Old sparse BLAS interfaces are now not referenced by MKL versions that deprecate them.

The old interfaces were deprecated in MKL version 18, update 2.
The inspector-executor routines can still be "turned off" by the user, but
in version 18, update 2 and onwards, the new inspector-executor interface is
used, with mkl_sparse_optimize() not called if the user does not want the
inspector-executor functionality.

show more ...

Merge remote-tracking branch 'origin/rmills/fix-aijmkl-deprecated-calls'

Old sparse BLAS interfaces are now not referenced by MKL versions that deprecate them.

The old interfaces were deprecated in MKL version 18, update 2.
The inspector-executor routines can still be "t

Old sparse BLAS interfaces are now not referenced by MKL versions that deprecate them.

The old interfaces were deprecated in MKL version 18, update 2.
The inspector-executor routines can still be "turned off" by the user, but
in version 18, update 2 and onwards, the new inspector-executor interface is
used, with mkl_sparse_optimize() not called if the user does not want the
inspector-executor functionality.

show more ...

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 branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep us

Merge branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep usage on solaris [use egrep]
opensolaris: fix errors
Update timer reporting and minor reporting fix
Remove redundant if statement. Found by @jedbrown
Fixed problem with order of developer photos on website.
superlu_dist: use correct flag in example [PETSC_HAVE_SUPERLU -> PETSC_HAVE_SUPERLU_DIST]
Bib: PERMON ref
fix for osx
doc: more author fixes
doc: more author fixes
Italicized "orderings" in MPI process placement discussion.
Added Richard to the user manual author list.
Added Richard to the list of active developers on the website.
add string check for MS-MPI and IMPI timeout errors
opensolaris does not have multiple grep utils - but default one does not support -F. So use fgrep instead
Standardizing timeout checks
Report wall clock time of total tests
Use time instead of date %s
...

Conflicts:
include/petscpc.h
src/ksp/ksp/interface/itfunc.c

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Merge remote-tracking branch 'origin/rmills/doc-update-matcreateseqaijmkl-man-page'

Updated manual page for MatCreateSeqAIJMKL().

Merge remote-tracking branch 'origin/rmills/feature-aijmkl-add-matptap-symmetric'

Improved MKL error checking in MatSeqAIJMKL_create_from_mkl_handle().

Removed functions such as MatScale_SeqAIJMKL(); no longer needed because we track ObjectState.

Fixed bugs preventing proper tracking of object state.

Added MatPtAP() implementations that use MKL routines optimized for symmetric matrices.

Also fixed bugs affecting MatMatMultNumeric() and MatPtAPNumeric().

Merge branch 'rmills/feature-aijmkl-add-matmatmultnumeric'

Updated a comment.

Added support for MatMatMultNumeric() for AIJMKL matrices.

Note that this requires MKL version 18, update 2 or later.

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

Merge branch 'rmills/fix-aijmkl-use-petscobjectstate'

Merge branch 'master' into scott/ksp-ksp-tutorials