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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fix duplicate definitions warned by -Wredundant-decls

Also a bugfix? BLASdotu_ -> dotu

Reported-by: Till Martens <till.martens@dlr.de>

Merge branch 'tisaac/fix-pipeline-tests' into tisaac/feature-fe-dual-apply

* tisaac/fix-pipeline-tests:
mpiuni: disable tests that don't work with mpiuni
Various tests complex scalar fixes
Ple

Merge branch 'tisaac/fix-pipeline-tests' into tisaac/feature-fe-dual-apply

* tisaac/fix-pipeline-tests:
mpiuni: disable tests that don't work with mpiuni
Various tests complex scalar fixes
Plex tests ex10: 64bit indices fix
Plex tests ex4: fix for c++ bools
PetscHash: correct test for 64 bit indices use
proper manual pages for PetscObjectXXXOptionsPrefix()

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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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mpiuni: disable tests that don't work with mpiuni

Some tests use only one processor but use parts of the mpi interface not covered by mpiuni

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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DMPlex: get non fv non-conforming tests working

Doc+Plex: Fix function name

Doc+Plex: Added function docs

Plex+HDF5: Make functions internal

more __FUNCT__ fixes

Merge branch 'master' into knepley/fix-plex-examples-cleanup

* master: (24 commits)
Bib: Added ref
shorten a url
remove the outdated paragraph on Eclipse instructions
Docs: manual - copyedit

Merge branch 'master' into knepley/fix-plex-examples-cleanup

* master: (24 commits)
Bib: Added ref
shorten a url
remove the outdated paragraph on Eclipse instructions
Docs: manual - copyedit for @caidao22 's update
I missed a n -> ierr changed needed in one of the error macros
Fix Fortran SETERRQ() to new calling sequence when compiled with no error checking
minor modifications for the added text
add Eclipse instructions to manual
PCHYPRE: add block nodal interpolations from command line customization
Plex: Now DMPlexGetRedundantDM() has more sensible behavior on 1 proc
SNES tutorial ex5s: fix typo ("parallism")
DMDA: fix typo in error messages ("parallism")
Plex: Drawing Vecs now works for multiple fields and components
SNES ex69: Started mantle test
SNES ex69: Fixed test
SNES ex69: Started a composite viscostiy test
SNES ex69: Updated BC specification
SNES ex69: Must use -pc_use_amat with FieldSplit
Plex+Draw: Improve viewer - Nice title - Allow override of min/max scale - Allow P0 and P1 (just quick and dirty)
Plex+VTK: Set boundary values with the time specified by the OutputSequence number
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Merge branch 'knepley/feature-snes-stokes-test'

* knepley/feature-snes-stokes-test:
Plex: Drawing Vecs now works for multiple fields and components
SNES ex69: Started mantle test
SNES ex69: Fi

Merge branch 'knepley/feature-snes-stokes-test'

* knepley/feature-snes-stokes-test:
Plex: Drawing Vecs now works for multiple fields and components
SNES ex69: Started mantle test
SNES ex69: Fixed test
SNES ex69: Started a composite viscostiy test
SNES ex69: Updated BC specification
SNES ex69: Must use -pc_use_amat with FieldSplit
Plex+Draw: Improve viewer - Nice title - Allow override of min/max scale - Allow P0 and P1 (just quick and dirty)
Plex+VTK: Set boundary values with the time specified by the OutputSequence number
Plex: Now only local vectors are used with the Draw viewer - Set boundary values with the time specified by the OutputSequence number
Plex: Fixed raw array access in DMPlexVecGetClosure()
Doc+SNES: I think the option should also be with the monitor function
TS ex47: Advection with Plex - I want to see if I can use MG

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Plex: Drawing Vecs now works for multiple fields and components

Merge branch 'knepley/feature-plex-ex-advection' into knepley/feature-snes-stokes-test

* knepley/feature-plex-ex-advection:
Plex+Draw: Improve viewer - Nice title - Allow override of min/max sca

Merge branch 'knepley/feature-plex-ex-advection' into knepley/feature-snes-stokes-test

* knepley/feature-plex-ex-advection:
Plex+Draw: Improve viewer - Nice title - Allow override of min/max scale - Allow P0 and P1 (just quick and dirty)
Plex+VTK: Set boundary values with the time specified by the OutputSequence number
Plex: Now only local vectors are used with the Draw viewer - Set boundary values with the time specified by the OutputSequence number
Plex: Fixed raw array access in DMPlexVecGetClosure()
Doc+SNES: I think the option should also be with the monitor function
TS ex47: Advection with Plex - I want to see if I can use MG

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

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Merge branch 'barry/remove-funct'

Plex+Draw: Improve viewer
- Nice title
- Allow override of min/max scale
- Allow P0 and P1 (just quick and dirty)

Plex+VTK: Set boundary values with the time specified by the OutputSequence number

Plex: Now only local vectors are used with the Draw viewer
- Set boundary values with the time specified by the OutputSequence number

Plex: Fixed raw array access in DMPlexVecGetClosure()

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 'knepley/fix-plex-mat-dm'

* knepley/fix-plex-mat-dm:
Plex: Attach DM to Mat

Plex: Attach DM to Mat