rename MatGetSubMat -> MatCreateSubMat

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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update how CPR can be implemented in PCFIELDSPLIT manual page

Extract the submatrices

Extract the submatrices from the preconditioning matrix instead of the Jacobian matrix.
The reason for this is that the MatMults for the submatrices (at line 1004, 2035 and 1

Extract the submatrices

Extract the submatrices from the preconditioning matrix instead of the Jacobian matrix.
The reason for this is that the MatMults for the submatrices (at line 1004, 2035 and 1054 of fieldsplit.c)
involves function evaluations (which is not cheap) when we are using the matrix-free method for inexact Newton.
I have some tests in MOOSE, and this change halves the compute time.

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

* master: (53 commits)
Docs: update manual author list with P. Sanan
Docs: manual - Eclipse Users edit
Docs: manual - rearrange Oth

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

* master: (53 commits)
Docs: update manual author list with P. Sanan
Docs: manual - Eclipse Users edit
Docs: manual - rearrange Other PETSc features sections so that XXX Users section are grouped together at the end
Docs: manual - remove newline in Numbers section title
Docs: manual - update Visual Studio section name
Docs: manual - Qt creator section copyedit (content still would benefit from an update from M. Mirzadeh)
Docs: manual - remove stub headings in TS using fully implicit methods section
Docs: manual - update PetscLogEvent signature and example (copied from man page)
Docs: manual - update Makefile chapter
Docs: remove PetscLogEventMPEActivate and PetscLogEventMPEDeactivate references from man pages and FAQ
Docs: manual - remove reference to specific MPE event deactivation
Docs: manual - XCode section copyedit
Docs: manual - SAWs section name fix
Docs: manual - format debugger names
Docs: manual - add short mentions of TikZ and Movie capabilities
Docs: manual - Graphics section copyedit
Docs: manual - add subsection on viewing from options
Docs: manual - Viewers section copyedit
Docs: manual SAWs section - format and copyedit
Docs: Manual - update and consolidate library overview graphics
...

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Always print full information about solver in view; never say if lumped was set

The reason we have viewers is so people can see what was set!

Merge branch 'master' of bitbucket.org:petsc/petsc

PC+Doc: Clarify CPR documentation in FieldSplit

Merge branch 'barry/remove-funct'

Merge branch 'barry/vecscattercreatetozero-fortran-null'

Add support for null argument from Fortran for VecScatterCreateToZero() VecScatterCreateToAll()

Also update a few uses of NULL_OBJECT to the appropriate PETSC_NULL_XXX

Time: .1 hours
Reported-by: T

Add support for null argument from Fortran for VecScatterCreateToZero() VecScatterCreateToAll()

Also update a few uses of NULL_OBJECT to the appropriate PETSC_NULL_XXX

Time: .1 hours
Reported-by: Tim Steinhoff <kandanovian@gmail.com>

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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 'barry/Sander/fix-pcreset-fieldsplit'

PCReset_FieldSplit() did not work correctly. Do a simple reset that cleans out the old data structures

The drawback to this is that the options are lost to the inner KSP objects; but that is better

PCReset_FieldSplit() did not work correctly. Do a simple reset that cleans out the old data structures

The drawback to this is that the options are lost to the inner KSP objects; but that is better than
buggy code. Eventually we should try to preserve the inner KSP, while removing all the matrices, vectors, and IS
Patch was provided by reporter.

Time: .5 hours
Reported-by: Sander Arens <Sander.Arens@ugent.be>

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

This is needed to deal with some changes in MatNullSpace from commit 9d2471e

incorrect argument name in manual page

Reported-by: Peter J. Puchyr <pjpuchyr@gmail.com>

phrasing in manual page results in false link and is incomplete.

Reported-by: Dave May <dave.mayhem23@gmail.com>

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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Merge branch 'barry/add-errorcheck-pcfieldsplitgetsubksp'

When the Schur complement form of PCFIELDSPLIT is called PCSetUp() needs to be called before PCFieldSplitGetSubKSP()

Add very useful error message to this case
Time: .1 hour
Reported-by: David Nolte

When the Schur complement form of PCFIELDSPLIT is called PCSetUp() needs to be called before PCFieldSplitGetSubKSP()

Add very useful error message to this case
Time: .1 hour
Reported-by: David Nolte
Thanks-to: Arthur Soprano, Lisandro Dalcin

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added test example for ex42.c

Improved manual page
Changed MatSchurComplementComputeExplicitOperator() to actually compute
the Schur complement and not ignore the 1,1 block of the matrix

Time: .1 h

added test example for ex42.c

Improved manual page
Changed MatSchurComplementComputeExplicitOperator() to actually compute
the Schur complement and not ignore the 1,1 block of the matrix

Time: .1 hours
Reported-by: Hoang Giang Bui <hgbk2008@gmail.com>

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Merged in Fande-Kong/fieldSplit_submatrix (pull request #549)

Extract the submatrices in the fieldsplit preconditioner

Extract the submatrices

Extract the submatrices from the preconditioning matrix instead of the Jacobian matrix.
The reason for this is that the MatMults for the submatrices (at line 1004, 2035 and 1

Extract the submatrices

Extract the submatrices from the preconditioning matrix instead of the Jacobian matrix.
The reason for this is that the MatMults for the submatrices (at line 1004, 2035 and 1054 of fieldsplit.c)
involves function evaluations (which is not cheap) when we are using the matrix-free method for inexact Newton.
I have some tests in MOOSE, and this change halves the compute time.

show more ...

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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