optimize matgetsubmatrices_mpiaij to use only one MPI_AllReduce

add id to Mat_Sub; works for the case of initial_matrix, not for reuse yet

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 'hzhang/opt-matgetsubmatrices-rebased-v2'

rm all while (row >= C->rmap->range[proc+1]) proc++;

use r2pmap to replace while-loop for finding proc for each row

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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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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remove dead Adifor code

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

Merge branch 'barry/add-matfdcoloring-ghosted-example'

Hoist management of DM usage for MatFDColoringApply() for IS_COLORING_LOCAL up to dm

This is because the DM calls cannot be made in the Mat library when not using --with-single-library

Time: 1.6 ho

Hoist management of DM usage for MatFDColoringApply() for IS_COLORING_LOCAL up to dm

This is because the DM calls cannot be made in the Mat library when not using --with-single-library

Time: 1.6 hours
Reported-by: nightly tests

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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 'maint'

Merge branch 'stefano_zampini/fix-matgetrowij' into maint

Fix bugs in MatGetRowIJ_SeqBAIJ and MatGetRowIJ_SeqSBAIJ

MatGetRowIJ_SeqBAIJ had a bug for blockcompressed case and shift ==1
MatGetRowIJ_SeqSBAIJ was almost completely broken: the code is now a dup

Fix bugs in MatGetRowIJ_SeqBAIJ and MatGetRowIJ_SeqSBAIJ

MatGetRowIJ_SeqBAIJ had a bug for blockcompressed case and shift ==1
MatGetRowIJ_SeqSBAIJ was almost completely broken: the code is now a duplicate of MatGetRowIJ_SeqBAIJ
Added an extra PetscBool parameter to MatToSymmetricIJ_SeqAIJ to select whether to symmetrize the lower triangular or the upper triangular part (default is lower triangular, as before); this is needed by MatGetRowIJ_SeqBAIJ to work properly

Added ex26.c to test MatGetRowIJ for SEQAIJ,SEQBAIJ and SEQSBAIJ

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

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax error with error message
SNES ex5: Correct Jacobian handling on patches
SNES ex5: Stupid complex fixes
DMP4est: fix transfer of labels to parents
petsc4py: update to latest snapshot. Fixes da example breakage in petsc4py test suite
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logging in interpolator creation
Plex: Correct use of tabs in ASCII viewer
DM: Shorten long event name
Plex ex12: Create boundary label automatically at all levels of mesh hierarchy
Plex ex12: Change PetscViewerSetFormat --> PetscViewerPushFormat - Fix order of SetMode and SetFilename
Plex ex12: Change all functions to static
Since DMDA with periodic boundary conditions does support P0 interpolation remove checks that error out under those conditions
ascem-io.py and amanzi.py need to handle self.hdf5.include being None correctly
fix MPI Uni to recycle communicators so it won't run out like with the petsc4py tests also fix check for location of python shared library on mac to check all cases each time
Switch back to Sherry's version since she accepted by pull request
PetscDraw: Update help messages for -draw_save* options
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Conflicts:
src/dm/impls/plex/plexfem.c

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Merged petsc/petsc into master

Merge branch 'barry/fix-private-functions'

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

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/imp

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

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c

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More decreasing visibility of symbols from outside libraries
Also fix a few bugs related to having multiple PETSc libraries

Merge branch 'master' into barry/add-pcfieldsplit-logevent