MATNEST: implement MatDiagonalSet

Merge branch 'barry/add-matshell-matgetdiagonalblock-fortran'

Removed the use of PetscObjectQueryFunction() with with MatGetDiagonalBlock()

that I missed when I first converted MatGetDiagonalBlock() from a query function
to a table function

Time: .3 hours
Re

Removed the use of PetscObjectQueryFunction() with with MatGetDiagonalBlock()

that I missed when I first converted MatGetDiagonalBlock() from a query function
to a table function

Time: .3 hours
Reported-by: nightly tests

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add support for MatShellSetOperation(Mat,MATOP_GET_DIAGONAL_BLOCK, for Fortran

This required changing the handling of MatGetDiagonalBlock() from a query function based
method to a regular method in

add support for MatShellSetOperation(Mat,MATOP_GET_DIAGONAL_BLOCK, for Fortran

This required changing the handling of MatGetDiagonalBlock() from a query function based
method to a regular method in the function table

Time: .75 hours
Reported-by: Steven Dargaville <dargaville.steven@gmail.com>
Thanks-to: Dave May <dave.mayhem23@gmail.com>

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Merge branch 'tisaac/sys-fix-realloc' into tisaac/petscfe-matching-quadrature-order

* tisaac/sys-fix-realloc: (71 commits)
Sys: fix PetscTrReallocDefault() and PetscReallocAlign()
clearify when

Merge branch 'tisaac/sys-fix-realloc' into tisaac/petscfe-matching-quadrature-order

* tisaac/sys-fix-realloc: (71 commits)
Sys: fix PetscTrReallocDefault() and PetscReallocAlign()
clearify when MatMkl_CPardisoSetCntl() can be used in the manual pages
Fixed manual page for -snes_anderson_beta
Update zfftf.c
remove Hermitian information from output since it is only produced in complex case and thus produces different test output
fixes for 64 bit integers in test example, fix uninitialized variable in test example
tests: move runex49 to TESTEXAMPLES_C_NOTSINGLE
add a PCView_SVD to show parameters
-petscpartitioner_type simple was not being picked up by options thus generating test error
missing CHKERRQ(ierr) on PetscPrintf() statements in newly added test example
PetscViewerVTK: Move DM reference increment into the VTK viewer and out of the DM implementation, as suggested by Jed Brown
missing crosslinks between manual pages
Updated 3.7 release notes to clearly indicate how to update usage of KSP/SNES/TS/SetMonitor(xxx,XXXMonitorDefault,NULL,NULL);
Fix for commit b6480e041dd2293a65f96222772d68cdb4ed6306 that broke this example
Example of factorization of a singular matrix may actually work due to round off
removed unused variables
matshell: clean up and add some new MATOPs to Fortran.
Remove unneeded checks for use of the compressed row for diagonal block of matrices in GAMG
ptscotch: update to version 6.0.4
ptscotch: fix buggy pthread detection code on Mac/Linux
...

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

Update to patch commit 04545d6dccef0bc76f6a1a6548f816a384daa3de to make it work with master

Now the patch respects the data encapsulation of _p_Mat and does not access into it directly.

Time: .1 ho

Update to patch commit 04545d6dccef0bc76f6a1a6548f816a384daa3de to make it work with master

Now the patch respects the data encapsulation of _p_Mat and does not access into it directly.

Time: .1 hours

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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

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Merge branch 'master' into psanan/pc-telescope-nearnullspace

Merge branch 'master' into mark/snes-ex56

* master: (93 commits)
Web: Added a tutorial
typo
rename X -> U
sowing: update to version that creates manpage URLs for 'enum' types/values
Increa

Merge branch 'master' into mark/snes-ex56

* master: (93 commits)
Web: Added a tutorial
typo
rename X -> U
sowing: update to version that creates manpage URLs for 'enum' types/values
Increase patchlevel to 3.7.3
move runex3_3 to NOTSINGLE [ partial backport 9ed0bd76d5c329eb91401ebabfbd851446214e20 ]
DMPlex: local coordinate vector should be a sequential vector
DM: Name coordinate vectors in subdomain and restrict hooks
tests: disable a couple of TS examples from single precision tests
reduce TS ex12_2 output
fix PetscFormatRealArray() to cast PetscReal in print statement to double so works for __float128 precision
Vec: enable Fortran interfaces for VecGetLocalVectorRead and VecRestoreLocalVectorRead
Bib: Added refs
PCShell: man page fixes
update handling of latex in example code to use https
fix typo in isltog comment
test: Avoid conversion of object <-> function pointer type [-Wpedantic]
fortran: enable interface for VecGetLocalVector(), VecRestoreLocalVector()
update citation for cmz2016
PCBDDC: silent compilation warnings from nightlybuilds
...

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

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Merge branch 'jose/veccuda-tests'

Conflicts:
config/PETSc/Regression.py

* jose/veccuda-tests:
This is an attempt to modify configure to run regression tests with VECCUDA.
The tests for CUSP ar

Merge branch 'jose/veccuda-tests'

Conflicts:
config/PETSc/Regression.py

* jose/veccuda-tests:
This is an attempt to modify configure to run regression tests with VECCUDA.
The tests for CUSP are left unchanged.
The new tests include CUSPARSE and work with real and complex scalars.
See PR #490 for discussion.

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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

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Merge branch 'maint'

Fortran stub for MatCreateRedundantMatrix() was not being automatically created

Reported-by: Constantin Nguyen Van <constantin.nguyen.van@openmailbox.org>

Miscellaneous changes in AIJCUSPARSE code

- Some operations need synchronization of data from CPU to GPU, e.g. MatScale
- Add assembly operation, so that lvec is set to type CUDA
- In MatSeqAIJCUSPA

Miscellaneous changes in AIJCUSPARSE code

- Some operations need synchronization of data from CPU to GPU, e.g. MatScale
- Add assembly operation, so that lvec is set to type CUDA
- In MatSeqAIJCUSPARSECopyToGPU do not recompute indices every time
- Operations MatMultAdd* need to get the array with ReadWrite
- In MatScale, do not change coherence flag if alpha=1.0
- VecDuplicate_MPICUDA must make sure that the GPU array exists
- Fix null pointer in VecScatterCUDAIndicesCreate_PtoP

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Merge branch 'knepley/fix-vec-visibility' into knepley/feature-dm-point-location-failure

* knepley/fix-vec-visibility:
Vec: DuplicateVecs_Default and DestroyVecs_Default should be available to the

Merge branch 'knepley/fix-vec-visibility' into knepley/feature-dm-point-location-failure

* knepley/fix-vec-visibility:
Vec: DuplicateVecs_Default and DestroyVecs_Default should be available to the user - This is needed is IBAMR
Fix error in MPI-uni when creating additional MPI communicators did not properly mark them as active
OSX: fix .dmg create script to set PETSC_DIR Also fix paths to work on case sensitive file systems.
Configure: Fix pickling error This is still a problem since it reveals that something is not cleaning up correctly. Configure needs a global rewrite badly
Configure: Silence warning on test compile
Configure: Bump MPFR version
remove multiple the the constructs
cd src/benchmarks/steams should be: cd src/benchmarks/streams
missing seealso for NASM

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Merge branch 'maint'

remove multiple the the constructs

Reported-by: Faraz Hussain <faraz_hussain@yahoo.com>

Merge branch 'maint'

fix bug for MatGetFactor()
Reported-by Jose E. Roman <jroman@dsic.upv.es>

Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary c

Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary commitid] - and dirname in tarball
Plex: Moved ReconstructGradients_Internal() and ApplyLimiter_Internal() to Plex from SNES
CUDA: Added external declaration for cuBLAS handle.
docs: fix reference to KSP_Create in parent commit
Add information on PETSC_EXTERN and PETSC_INTERN to developers manual
Plex: Symbol is shared between DM and SNES, so must be EXTERN
Plex: Remove unused variables
Configure: Fix check for spaces in PETSC_DIR
Plex: Updated examples to new DMPlexCreateBoxMesh()
sick of failure due to incorrect master branch
SNES ex12: Fixed unstructured GMG test
SNES ex12: Added another unstructured GMG test
petsc4py: use the snapshot with the fix for dmplex change
Examples that require Fortran to compile but were listed in tests that did not require Fortran
Plex ex19: Added DMSetFromOptions()
Plex: Store a flag indicating whether the boundary should change during remeshing - Set using -dm_plex_remesh_bd - Changed Remesh_Internal() signature
Always coarsen boundaries.
Plex: Fixed option name
Plex: Protect unused variables
...

Conflicts:
src/dm/impls/plex/makefile
src/snes/utils/dmplexsnes.c

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

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/mat/impls/aij/seq/mkl_pardiso/mkl_pardiso.c

Merge branch 'master' into barral/feature-dmplex-adapt

Merge branch 'barry/housekeeping-1'

removed a bunch of unneeded inclusions of xxximpl.h which exposed private data where it did not have to be exposed

also made more systematic the inclusion of the base xxximpl.h in the derived yyyimp

removed a bunch of unneeded inclusions of xxximpl.h which exposed private data where it did not have to be exposed

also made more systematic the inclusion of the base xxximpl.h in the derived yyyimpl.h
so the inclusion is done in the include file rather than in each source code that includes it

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