Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes

Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
superlu: libray is installed in PREFIX/lib64 - fix this to use PREFIX/lib
backport fixes cc105cc3 2b35c90a - required for 3bf428d - that was backported from master - 80c96bb
'echo -n' fails on opensolaris/osx - so avoid using it.
fix diffs in nightlybuilds due to options in ~/.petscrc
add Kelley03 to src/docs/tex/petsc.bib
build: determine moudles, mpi.h used during buildtime and print in 'info'
fix analyzer warnings
fix build failure on opensolaris - where -lm from flibs is removed due to -lm in cxxlibs. But then - only flib gets used for some configure tests [blaslapack, parms]
config: prefer __restrict over C99 restrict keyword
...

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Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-mantle-example

* knepley/feature-plex-tests-new: (103 commits)
Test: Reverted cherry pick
Plex: Damn Absoft, Trying to get unde

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-mantle-example

* knepley/feature-plex-tests-new: (103 commits)
Test: Reverted cherry pick
Plex: Damn Absoft, Trying to get under the 132 character line limit for Absoft
Testing: Cherry picked a fix
Plex: Trying to get under the 132 character line limit for Absoft
Plex: Fix small compiler warnings
Plex ex2f90: Removed comment line Absoft does not like
Plex: Turn off some tests for quad
Plex ex6: Fix printing for quad
Plex: Removed extra semicolon
SNES ex12: Moved restart test to subtests
Plex ex15: Switched to simple partitioning
SNES ex12: Switched to simple partitioning
SNES ex62: Updated output for small numerical diffs
SNES ex62: Switched to simple partitioning
Tests: Turned off some tests that do not very in single precision
all requires need to go on the same line in test definition otherwise they are skipped
TS ex47: Added test output
replace numProcs with standard size
Plex+Gmsh: Fix for complex
fix accidently changed code
...

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Merge remote-tracking branch 'origin/knepley/feature-plex-tests-new' into tisaac/fix-pipeline-tests

* origin/knepley/feature-plex-tests-new: (101 commits)
Plex: Fix small compiler warnings
Plex

Merge remote-tracking branch 'origin/knepley/feature-plex-tests-new' into tisaac/fix-pipeline-tests

* origin/knepley/feature-plex-tests-new: (101 commits)
Plex: Fix small compiler warnings
Plex ex2f90: Removed comment line Absoft does not like
Plex: Turn off some tests for quad
Plex ex6: Fix printing for quad
Plex: Removed extra semicolon
SNES ex12: Moved restart test to subtests
Plex ex15: Switched to simple partitioning
SNES ex12: Switched to simple partitioning
SNES ex62: Updated output for small numerical diffs
SNES ex62: Switched to simple partitioning
Tests: Turned off some tests that do not very in single precision
all requires need to go on the same line in test definition otherwise they are skipped
TS ex47: Added test output
replace numProcs with standard size
Plex+Gmsh: Fix for complex
fix accidently changed code
another fix for Plex for complex numbers
fix for example that did not handle complex numbers correctly
mark example tests that do not work with complex, fix warning about use of possibly uninitialized values
Fix MPI type to match PetscReal
...

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Plex: helper function used in all cases now

MatAIJ KLU: remove redefinition of SuiteSparse_long

SuiteSparse_config.h has it's own logic for determining what SuiteSparse_long should be,
and provides a mechanism for overriding it, but that shou

MatAIJ KLU: remove redefinition of SuiteSparse_long

SuiteSparse_config.h has it's own logic for determining what SuiteSparse_long should be,
and provides a mechanism for overriding it, but that should be done at configure time,
not in a source file. Dictating causes compliance errors, even when
is the same size.

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DMPlexRefine_CTetgen() mimics DMPlexRefine_Tetgen()

DMPlexGenerate_Tetgen(): mimic ctetgen so it can be used equivalently

DMPlexGenerate: use Tetgen if it's available

Merge remote-tracking branch 'origin/knepley/feature-fe-dual-apply' into tisaac/feature-fe-dual-apply

* origin/knepley/feature-fe-dual-apply: (75 commits)
Plex: Screwed up last fix
Plex: Fix ove

Merge remote-tracking branch 'origin/knepley/feature-fe-dual-apply' into tisaac/feature-fe-dual-apply

* origin/knepley/feature-fe-dual-apply: (75 commits)
Plex: Screwed up last fix
Plex: Fix overeager protection of function
PetscFE: Fixed declaration
Travis-CI: Attempt to solve issues with gfortran
Travis-CI: Use newer macOS image
clarify damping and other issues related to SNESLINESEARCHBASIC
change example in new harness to use simple partitioner so gets consistent output on all systems
remove unused function from test file
cleanup formatting in example, plus myrank not rank
all requires need to go on the same line in test definition otherwise they are skipped
missing - makes the manual page formatting wrong
The developer manual clearly states that MPI_Comm_size() returns size it doesn't return numProcs or other nonsense. Pretty soon you'll start using mype instead of rank?
fix typo and cut and paste error in docs
bugfix for !HYPRE
fix warning for ';;'
may switch to scalable only when B->cmap->N > 100000
MatLRC: store in the context the parallel matrices rather than the sequential ones
Bib: Add ref
set default algorithm based on B->cmap->N for MatMatMult_MPIAIJ_MPIAIJ()
Error in VecScatterView_MPI() had the meaning of from and to backwards
...

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Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-fe-dual-apply

* knepley/feature-plex-tests-new: (73 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to s

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-fe-dual-apply

* knepley/feature-plex-tests-new: (73 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to solve issues with gfortran
Travis-CI: Use newer macOS image
clarify damping and other issues related to SNESLINESEARCHBASIC
change example in new harness to use simple partitioner so gets consistent output on all systems
remove unused function from test file
cleanup formatting in example, plus myrank not rank
all requires need to go on the same line in test definition otherwise they are skipped
missing - makes the manual page formatting wrong
The developer manual clearly states that MPI_Comm_size() returns size it doesn't return numProcs or other nonsense. Pretty soon you'll start using mype instead of rank?
fix typo and cut and paste error in docs
bugfix for !HYPRE
fix warning for ';;'
may switch to scalable only when B->cmap->N > 100000
MatLRC: store in the context the parallel matrices rather than the sequential ones
Bib: Add ref
set default algorithm based on B->cmap->N for MatMatMult_MPIAIJ_MPIAIJ()
Error in VecScatterView_MPI() had the meaning of from and to backwards
fix build warning as reported by the nightly tests
Update alquimia.py to use Glenn's branch that updates alquimia for pflotran xsdk
...

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Merge branch 'master' into knepley/feature-plex-tests-new

* master: (94 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to solve issues with gfortran
Travis-CI: Use newe

Merge branch 'master' into knepley/feature-plex-tests-new

* master: (94 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to solve issues with gfortran
Travis-CI: Use newer macOS image
clarify damping and other issues related to SNESLINESEARCHBASIC
change example in new harness to use simple partitioner so gets consistent output on all systems
remove unused function from test file
cleanup formatting in example, plus myrank not rank
missing - makes the manual page formatting wrong
The developer manual clearly states that MPI_Comm_size() returns size it doesn't return numProcs or other nonsense. Pretty soon you'll start using mype instead of rank?
fix typo and cut and paste error in docs
bugfix for !HYPRE
fix warning for ';;'
may switch to scalable only when B->cmap->N > 100000
MatLRC: store in the context the parallel matrices rather than the sequential ones
Bib: Add ref
set default algorithm based on B->cmap->N for MatMatMult_MPIAIJ_MPIAIJ()
Error in VecScatterView_MPI() had the meaning of from and to backwards
fix build warning as reported by the nightly tests
Update alquimia.py to use Glenn's branch that updates alquimia for pflotran xsdk
fix divide by zero exposed by 8534686b5096cd4c91a8f3895408b386c0628431 - and produced by petsc4py testsuite
...

Conflicts:
src/dm/impls/plex/examples/tests/ex13.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tests/ex2.c
src/snes/examples/tests/output/ex2_3.out
src/snes/examples/tests/output/ex2_4.out
src/snes/examples/tests/output/ex2_5.out

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Merge branch 'knepley/fix-plex-docs'

* knepley/fix-plex-docs:
Plex: Fix the fix
fix -Wmaybe-uninitialized
Doc+Plex: Add PetscUnit to Fortran
Doc+Plex: Fix function name
Plex: Fix declarati

Merge branch 'knepley/fix-plex-docs'

* knepley/fix-plex-docs:
Plex: Fix the fix
fix -Wmaybe-uninitialized
Doc+Plex: Add PetscUnit to Fortran
Doc+Plex: Fix function name
Plex: Fix declaration
Doc+Plex: Added function docs
Doc+Plex: More function docs - Make functions static - Move internal declarations
Doc+Plex: More function docs
Doc+Plex: Document DMPlexGetOrientedFace() and DMPlexSetSubpointMap() - Make functions static
Doc+Plex: Document DMPlexCreateOverlapMigrationSF() - Make functions static
Plex: Make functions static - Move internal declarations to private header
Plex: Make functions internal
Plex+HDF5: Make functions internal
Plex: Make functions static
Plex: Make functions static
Doc+Plex: Document DMPlexCreateNeighborCSR() - Make functions static
Doc+Plex: Document DMPlexPreallocateOperator() - Make functions static
Plex: Make function static
Plex+VTK: Make functions static
Plex+VTK: Make DMPlexVTKGetCellType() internal

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

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Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-fe-dual-apply

* knepley/feature-plex-tests-new:
fix accidently changed code
another fix for Plex for complex numbers
fix for

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-fe-dual-apply

* knepley/feature-plex-tests-new:
fix accidently changed code
another fix for Plex for complex numbers
fix for example that did not handle complex numbers correctly
mark example tests that do not work with complex, fix warning about use of possibly uninitialized values
Fix MPI type to match PetscReal
No Matt triangle is not by default installed on every machine in the world
Matt forgot to require triangle in many tests
fix incorrect requires, fix incorrect name for __float128
since hdf5 doesn't allow PETSc to be built with 16 or 128 bit floating point then say it
fix requires
removed unneeded change to test harness since already supports requires: double
bunch of fixes in plex tests and code for single precision
Many missing requires ctetgen
Certain test examples require ctetgen but it is not listed in test rules

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bunch of fixes in plex tests and code for single precision

Reported-by: nightly tests

Plex: Make functions static
- Move internal declarations to private header

Merge branch 'barry/remove-funct'

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-t

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-to: Andreas Mang <andreas@ices.utexas.edu>

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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 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 'tisaac/dm-feature-adapt-label'

Adds an optional interface for adapting a DM by a specified label. Good
support in DMP4est; DMPlex will at least refine (I need to see if
Triangle/Tetge

Merge branch 'tisaac/dm-feature-adapt-label'

Adds an optional interface for adapting a DM by a specified label. Good
support in DMP4est; DMPlex will at least refine (I need to see if
Triangle/Tetgen support point-deletion coarsening); no DMDA
implementation, but I might put in one that at least detects uniform
coarsening/refinement.

* tisaac/dm-feature-adapt-label:
Plex tests ex20: add names to output meshes
DMPlex tests ex20: fix bad dev/null'd output in makefile test
DMPlex: gotta root out that c99 before it corrupts our kids
DMPlex test ex20: added triangle and ctetgen regression tests for DMLabelAdapt()
DMRefine_Plex_Label(): move DMPlexRestoreTransitiveClosure() after loop
DMPlex: added test ex20 for DMAdaptLabel()
DMPlex: put ifdef guards around static function only used when packages present.
DMFOREST: fix initialization
DMPlex: fix __FUNC__ of recent change
DMAdaptFlag: added DM_ADAPT_DETERMINE
DMPlex: added DMAdaptLabel implementation for DMPlex
DMAdaptLabel: change second argument to actual label
DM: added DMAdaptLabel() interface

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DMPlex: gotta root out that c99 before it corrupts our kids

DMRefine_Plex_Label(): move DMPlexRestoreTransitiveClosure() after loop

DMPlex: put ifdef guards around static function only used when packages present.

DMPlex: fix __FUNC__ of recent change