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
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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 'master' into scott/test-harness-forloopfix

Merge branch 'hzhang/opt-matgetsubmatrices-mpibaij'

bugfix for MatCreateRedundantMatrix(), MatCreateMPIMatConcatenateSeqMat()

Merge branch 'master' into knepley/feature-plex-tests-new

* master: (37 commits)
fortran: include petscversion.h
test: c++ pipeline build fix for d2a797cfef64a79a330b420f01b2d605a8acc690
Extra

Merge branch 'master' into knepley/feature-plex-tests-new

* master: (37 commits)
fortran: include petscversion.h
test: c++ pipeline build fix for d2a797cfef64a79a330b420f01b2d605a8acc690
Extract the submatrices
Convert C Null pointer to Fortran in Fortran stub before passing back to user
PC Galekin and KSP should properly propagate calls to SetFromOptions to subsolvers
Converted Fortran PetscSF to Fortran type, added PETSC_NULL_SF
clarification in documentation
Update of petscdiff and associated harness hooks
Fixup more F90 interface definitions for users
More space-in-dirname enabling quotes
Enable paths with spaces
add cast; bugfix for 64bit
Typo -- initialized TESTFLAGS to -v by mistake
Adding new options to test framework
gtest: add valgrind support [when PETSC_ARCH has 'valgrind' in the name]
bugfix for unsorted ISCols
optimize matgetsubmatrices_mpiaij to use only one MPI_AllReduce
small cleanup MatGetSubMatrices_MPIAIJ_Local()
rm allcolumns from the input of MatGetSubmatrices_mpiaij_local()
add a test to ex4.c for reuse
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Fixup more F90 interface definitions for users

Time: .15 hours
Reported-by: Manuel Valera <mvalera@mail.sdsu.edu>

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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Merge branch 'barry/add-MatSeqSBAIJGetArray'

Add MatSeqSBAIJGetArray() and MatSeqSBAIJRestoreArray()

Interestingly the private functions for SABIJ where already in the source code
Time: .15 hours
Reported-by: Eric Chamberland <Eric.Chamberland

Add MatSeqSBAIJGetArray() and MatSeqSBAIJRestoreArray()

Interestingly the private functions for SABIJ where already in the source code
Time: .15 hours
Reported-by: Eric Chamberland <Eric.Chamberland@giref.ulaval.ca>

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Merge branch 'barry/remove-funct'

Merge branch 'barry/fix-matreuse'

Add more error checks for use of MatReuse; change MatTranspose() to use MatReuse as used by other functions

Time: 2.5 hours
Reported-by: Stefano Zampini <stefano.zampini@gmail.com>, Eric Chamberlan

Add more error checks for use of MatReuse; change MatTranspose() to use MatReuse as used by other functions

Time: 2.5 hours
Reported-by: Stefano Zampini <stefano.zampini@gmail.com>, Eric Chamberland <Eric.Chamberland@giref.ulaval.ca>

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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 'stefano_zampini/allow-late-matsetblocksizes'

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

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

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 'barry/fix-matmpixxxsetpreallocation-reentrant'

Fixes for MatMPIXXXSetPreallocation(), they were not reentrant, since they kept the information used for matrix-vector products

from the previous load as well as the incorrectly sized aij->B matrix.

Fixes for MatMPIXXXSetPreallocation(), they were not reentrant, since they kept the information used for matrix-vector products

from the previous load as well as the incorrectly sized aij->B matrix.
Time: 1.75 hours
Reported-by: Satish Balay <balay@mcs.anl.gov>

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MatSeqSBAIJ: set preallocated flag after the calls to MatSetBlockSize and PetscLayout stuff

This is to mimic how it is done in SeqBAIJ

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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Mat: MatSetBlockSizes as a MATOP.

it allows to change the block sizes at a later stage.
For the block formats, the default op raise an error if the user tries to change them

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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