Merge branch 'barry/fix-dmcreatematrix-dmda'

Merge branch 'stefano_zampini/feature-pcbddc-saddlepoint'

Conflicts:
src/mat/impls/aij/mpi/mpiaij.c
src/mat/impls/is/matis.c

Modified ex23.c for the API change of the function CheckMat

Bug in computing matrix preallocation for DMDA with skinny domains and periodic boundary conditions

Time: 3 hours
Reported-by: Davide Monsorno <davide.monsorno@uclouvain.be>

Merge branch 'hzhang/opt-matgetsubmatrices-rebased-v2'

implement MatGetSubMatrices_MPIAIJ_single() to optimize MatGetSubMatrices_MPIAIJ() when ismax = 1

update src/mat/examples/tests/ex4.c for testing MatGetSubMatrices()

introduce ctable to remove nons

implement MatGetSubMatrices_MPIAIJ_single() to optimize MatGetSubMatrices_MPIAIJ() when ismax = 1

update src/mat/examples/tests/ex4.c for testing MatGetSubMatrices()

introduce ctable to remove nonscalable malloc C->rmap->N array for MatIncreaseOverlap_MPIAIJ_Once()

remove nonscalable d_p by using ctable

add MAT_SUBMAT_SINGLEIS to MatOption. Set this flag in PCSetUp_ASM() to
reduce MPI_AllReduce() in MatGetSubMatrices()

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Look for zero rows, not zero diagonals, in MatGalerkin.

Merge branch 'stefano_zampini/feature-mathypre'

Merge branch 'stefano_zampini/feature-getmat-mattranspose'

Implement MatGalerkin, a specialised routine for Galerkin construction
of coarse grid problems.

This simplifies some code in mg.c, and also extends Galerkin construction
to certain cases of non-nest

Implement MatGalerkin, a specialised routine for Galerkin construction
of coarse grid problems.

This simplifies some code in mg.c, and also extends Galerkin construction
to certain cases of non-nested geometric multigrid where the interpolation
matrix is not of full rank.

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Merge branch 'balay/update-cmake-elemental-v0.87-squashed'

elemental: remove wrapper interface to elemental - such as MatElementalHermitianGenDefEig().
One should call elemental directly for such functionality

Thanks-to: Hong Zhang <hzhang@mcs.anl.gov>

MatTranspose: added API to get the inner matrix object

MatHYPRE: added include/mathypre.h as Barry suggested

Added getter function for the ParCSR object

Merge branch 'jose/matlrc'

Added support for SetValues and Preallocation

MAT_FLUSH_ASSEMBLY is not currently supported
There's are some problems during the assembly of rectangular matrices, need to investigate

MatLRC: add an interface function to retrieve the constituents of the LRC matrix

MatLRC: add argument c to the constructor, now the matrix is A+U*C*V'

MatHYPRE: added support for MAT_INPLACE_MATRIX when converting from HYPRE to AIJ

Added man pages
Added support to create AIJ from a ParCSR

MatHYPRE: added MatHYPRECreateFromParCSR

MatHYPRE: create new matrix type

The conversion from AIJ to HYPRE has been taken from src/dm/impls/da/hypre/mhyp.c
HYPRE to AIJ is new

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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Added more information to MatStencil manual page, specifically the meaning of c.

Time: .1 hour
Reported-by: Victor Eijkhout <eijkhout@tacc.utexas.edu>

References to MatGetColumn() that doesn't exist

Reported-by: Victor Eijkhout <eijkhout@tacc.utexas.edu>

remove dead Adifor code

Time: .1 hours
Reported-by: Sebastien Gilles <sebastien.gilles@inria.fr>