Merge branch 'denera/fix-tablevels-for-views' [PR #869]

* denera/fix-tablevels-for-views:
Instead of manual push-pop tab operations, views now inherit tablevels automatically.
This makes views consi

Merge branch 'denera/fix-tablevels-for-views' [PR #869]

* denera/fix-tablevels-for-views:
Instead of manual push-pop tab operations, views now inherit tablevels automatically.
This makes views consistent with default convergence monitors.

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Wrapping up for a pull request

All views changed to inherit tab levels from associated objects

Merge branch 'barry/cleanup-bjacobi'

get rid of unneeded PC_ApplyOnMproc, fix manual page for parallel blocks for PCBJACOBI

Commit-type: style-fix, documentation

Merge branch 'maint'

PC: added logical check on coordinates dimension in PCSetCoordinates()

Merge remote-tracking branch 'origin/maint' into stefano_zampini/fix-matis-dmda-l2g

PC: fix memory leak in PCComputeExplicitOperator

Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with

Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with updated 17.10 compilers
Fix for test dirs that are not tutorials/tests
fix use of double in PetscAbsReal() which produces compiler warnings with single precision build
elemental: remove info on conflict of -with-cxx-dialect=C++11 on osx - it works now.
Cleanup .bib files
Fix allfortranstubs rule to rm generated files from correct directory, not outdated location
ierr set but not checked
Remove initial refine so test runs faster and does not time out on some machines
Gail's copyedits for bibtex items
Docs: manual: add further description of 3 different current testing options
DM: check for ops->localtolocalbegin/end before calling
PetscSF: fix typo in tutorial ex1
Vec+HDF5: Fix output for complex - Need to check for empty group name
SNES: SNESDestroy() can be called with snes->dm == NULL
SNES: SNESDestroy() can be called with snes->dm == NULL
Vec+HDF5: Fix output for complex - Need to check for empty group name
Docs: Manual: Update tests section
gmakegentest: also exclude .#filenames created by emacs
DMPlex: Fix output of test ex1 after changes to Gmsh reader
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Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maint

Obtain changed (v3.5) handling of MatMPIBAIJSetPreallocationCSR to match
documentation.

Merge branch 'maint'

Merge remote-tracking branch 'origin/balay/fix-chkerrq-after-seterrq/maint' into maint

fix: redundant CHKERRQ() call after SETERRQ()

Craycc complained about a stray CHKERRQ after SETERRQ in plextree.c
Reported-by: Patrick Sanan <patrick.sanan@gmail.com>

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
ini

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
initialize ap as complained by the nightly tests
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
SNES ex12: Mix misnaming Nf --> Nc
update tests
add tests
add MatView_SeqXAIJ_ASCII_structonly(); enable A->structure_only in MatSetValuesBlocked_SeqBAIJ
typo
fill-in some references
Bib: Fixed ref
Plex: Added PLY to file support
Plex: Adding PLY support
PetscDS: Turn off Fortran bindings for Constants
Plex tests: Updated to new point function API
SNES ex56: Moved tests to new format
DM: Allow field projection functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tutorials/ex63.c

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

* master: (156 commits)
Doc: Added headers for documentation sections
Bib: Small corrections
doc: update example makefiles with del

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

* master: (156 commits)
Doc: Added headers for documentation sections
Bib: Small corrections
doc: update example makefiles with deleted sourcefile info
doc: fix manual build errors
doc: fix SOURCEH for some fortran includes that got moved
doc: fix broken manualpages - bug introduced by 1b266c9
MatMissingDiagonal() is actually not a collective operation
PetscFECreateDefault(): allow 0th order quadrature
fix gmakegentest.py to ignore *.xx files that are not source code but are in the files
increase table input size to (A->cmap->n + a->B->cmap->N) for MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ()
gtest: add TEST and RM clean output for Satish
gtest: set PATH for windows DLL tests, and enable -Dpetsc_EXPORTS only during (dll) build - and not for examples
gtest: use target-specific var to deduplicate FC rules for modules
gtest: for 'allgtest' and 'allgtest-tap' - use V=0 instead of 'grep -v CC' etc..
gtest: quiet absoft compiler commands [so they can be filtered].
remove incorrect requires from more test files, remove output from -fp_trap example in test because it cannot be machine independent
gtest: windows fixes. add filter to remove filename from compiler stdout. And fix filters to use petscdiff
Removed generated requires in the wrong place from test examples.
Fix test output for additional information printed about computed eigenvalues
gtest: fix ex5f.F to use 'format' so that the output from ifort matches the one from gfortran
...

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Have Chebyshev view eigenvalues computed via eigest before transformation

Fix Eisenstat PC so that it can generate eigenvalue estimates without noisy right hand side

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 '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-matshell-matgetdiagonalblock-fortran'

Removed the use of PetscObjectQueryFunction() with with MatGetDiagonalBlock()

that I missed when I first converted MatGetDiagonalBlock() from a query function
to a table function

Time: .3 hours
Re

Removed the use of PetscObjectQueryFunction() with with MatGetDiagonalBlock()

that I missed when I first converted MatGetDiagonalBlock() from a query function
to a table function

Time: .3 hours
Reported-by: nightly tests

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Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary c

Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary commitid] - and dirname in tarball
Plex: Moved ReconstructGradients_Internal() and ApplyLimiter_Internal() to Plex from SNES
CUDA: Added external declaration for cuBLAS handle.
docs: fix reference to KSP_Create in parent commit
Add information on PETSC_EXTERN and PETSC_INTERN to developers manual
Plex: Symbol is shared between DM and SNES, so must be EXTERN
Plex: Remove unused variables
Configure: Fix check for spaces in PETSC_DIR
Plex: Updated examples to new DMPlexCreateBoxMesh()
sick of failure due to incorrect master branch
SNES ex12: Fixed unstructured GMG test
SNES ex12: Added another unstructured GMG test
petsc4py: use the snapshot with the fix for dmplex change
Examples that require Fortran to compile but were listed in tests that did not require Fortran
Plex ex19: Added DMSetFromOptions()
Plex: Store a flag indicating whether the boundary should change during remeshing - Set using -dm_plex_remesh_bd - Changed Remesh_Internal() signature
Always coarsen boundaries.
Plex: Fixed option name
Plex: Protect unused variables
...

Conflicts:
src/dm/impls/plex/makefile
src/snes/utils/dmplexsnes.c

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