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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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?

Using consistent names for va

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?

Using consistent names for variables makes code simpler to maintain

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Doc+Plex: Document DMPlexCreateOverlapMigrationSF()
- Make functions static

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-plex-replicate'

* knepley/feature-plex-replicate:
Plex: Now DMPlexGetRedundantDM() has more sensible behavior on 1 proc

Plex: Now DMPlexGetRedundantDM() has more sensible behavior on 1 proc

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 'pr575/knepley/fix-labels-coordinatedm/master'

* pr575/knepley/fix-labels-coordinatedm/master:
Plex: swap DMPlexDistributeCoordinates() and DMPlexDistributeLabels()

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_A

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_ATTRIBUTEALIGNED flag to makefile
PCSetUp_SVD() used incorrect matrix for matrix size in parallel, also need to skip LAPACK call if matrix size is zero
strumpack: update to latest version 1.0.4
Remove valgrind warning about MPI_Allreduce() with uninitialized data
sed for test output that has atol convergence with quad precision
updated ex1_nest tests
fixed incorrect key value
fix: bad merge a69d34a
test: move runex78 to TESTEXAMPLES_C_NOTSINGLE
build: fix warnings
sys: update test to produce same result - irrespective of debug/opt build - and presence of ~/.petscrc
sys: src/sys/examples/tests/ex30.c -> src/sys/examples/tests/ex32.c to avoid conflict in master
Sed output, since quad precision reduces below atol on these tests
remove automatically generated matrix names from test output files since can be different
Fixes for MatMPIXXXSetPreallocation(), they were not reentrant, since they kept the information used for matrix-vector products
GAMG: fix PCView_GAMG() format - and update output/ex56_0.out
superlu_dist: 64-bit-indices fix https://github.com/xiaoyeli/superlu_dist/issues/4
Add SNESSetDivergenceTolerance / -snes_divergence_tolerance.
fixed unit read in Plex
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Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/featu

Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/feature-pcbddc-saddlepoint
that prevents me to smoothly merge stefano_zampini/feature-convert-matnest-matis into next.

This will also facilitate merging stefano_zampini/feature-pcbddc-saddlepoint into master

Conflicts:
src/docs/website/documentation/changes/dev.html

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Plex: swap DMPlexDistributeCoordinates() and DMPlexDistributeLabels()

Now the coordinate DM inherits the correct distributed labels via DMClone() in the first call to DMGetCoordinateDM().

Merge branch 'balay/clang-Wcomma'

clang: more -Wcomma fixes [use (void)() notation]

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

fixed merge with master

Merge branch 'barry/fix-xml-logging'

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 remote-tracking branch 'origin/maint'

Merged in dalcinl/fix-plex-coord-local (pull request #512)

DMPlex: Local coordinate vectors

DMPlex: local coordinate vector should be a sequential vector