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 'dmay/dmswarm-remove-binary-readwrite'

DMSwarm:
* Removed relic binary load/write functionality associated with DataBucket.
* This functionality should be replaced with either HDF5 or using single binary file generated by streaming bytes

DMSwarm:
* Removed relic binary load/write functionality associated with DataBucket.
* This functionality should be replaced with either HDF5 or using single binary file generated by streaming bytes to rank 0 and using PetscBinaryWrite() (just like Vec does)
* Resolves issue report by Barry Smith "ISO IC90 does not support the ‘z’ gnu_scanf length modifier [-Wformat=]"

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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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DMSwarm: silence -Wmaybe-uninitialized

Merge branch 'barry/fix-ignore-returns'

DMSwarm (DataBucket):
* Imposed explicit void cast to shut up compiler warnings related to ignoring return value.

fread() returns a size_t so caste the PetscInt it is compared to

Reported-by: nightly tests

Added error checking to system routines such as fscanf() that return codes

This improves error checking and eliminates compiler warnings about ignored return codes

Time: 2 hours
Reported-by: nightl

Added error checking to system routines such as fscanf() that return codes

This improves error checking and eliminates compiler warnings about ignored return codes

Time: 2 hours
Reported-by: nightly tests

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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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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 'knepley/feature-realloc'

* knepley/feature-realloc:
SNES ex63: Updated for new GAMG settings
DMSwarm: Changed to PetscRealloc()
Sys: Added PetscRealloc() - Added PetscTrRealloc()

Merge branch 'knepley/feature-realloc'

* knepley/feature-realloc:
SNES ex63: Updated for new GAMG settings
DMSwarm: Changed to PetscRealloc()
Sys: Added PetscRealloc() - Added PetscTrRealloc() and PetscTrReallocDefault() - Added PetscReallocAlign()

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DMSwarm: Changed to PetscRealloc()

Merge branch 'knepley/feature-plex-particle-example'

* knepley/feature-plex-particle-example: (103 commits)
PetscTypes: * Added newly types into fortran definition
DMSwarmMigrate: printf fix for

Merge branch 'knepley/feature-plex-particle-example'

* knepley/feature-plex-particle-example: (103 commits)
PetscTypes: * Added newly types into fortran definition
DMSwarmMigrate: printf fix for __float128
fix c++ comments for c89
fix scanf warnings using PetscInt_FMT
Sys+DM: Fixing 64-bit format strings
Swarm: Fixed 64-bit integer problems
Swarm: Fixed PetscFree() usage
Swarm: Correct format in scanf
Plex: Small cleanup
Plex: Fixes to draw for complex
Plex: Fixed type for GetNeighbors
Swarm: Cleanup of Dave's code - Guy has a kid and think he doesn't have to play by the rules anymore
SNES ex63: Stokes example with Particles
Swarm: Fixed prototypes
Swarm: Added missing PetscFunctionBegin
Swarm: Fixed DMGetLocalVecTor_Swarm()
Swarm: Added DMSwarmCreate/DestroyLocalVectorFromField()
Swarm: Added missing prototype
Plex: Since we are using an SF, ranks that are not found default to 0, not -1 - You need to check the index for the negative value
Plex: Added a new point location type to remove entries which are not found - This was the default, but its not what DMSwarm wanted and its non-intuitive I agree
...

Conflicts:
src/dm/impls/plex/plexcreate.c
src/dm/interface/dm.c

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fix scanf warnings using PetscInt_FMT

Sys+DM: Fixing 64-bit format strings

Swarm: Fixed 64-bit integer problems

Swarm: Correct format in scanf

Swarm: Cleanup of Dave's code
- Guy has a kid and think he doesn't have to play by the rules anymore

Merge branch 'dmay/feature-dm-swarm' into knepley/feature-plex-particle-example

* dmay/feature-dm-swarm: (69 commits)
DMSwarm: * Check for size compatabaility between vectors created for DMSwarm f

Merge branch 'dmay/feature-dm-swarm' into knepley/feature-plex-particle-example

* dmay/feature-dm-swarm: (69 commits)
DMSwarm: * Check for size compatabaility between vectors created for DMSwarm fields * Bug fix for the field register function
DMSwarm DataBucket: * Added guards to ensure that internal arrays are never re-sized if any raw pointers are being currently being accessed
DMSwarm: * Added missing part of macro
DMSwarm: * Added documentation
DMSwarm example: * Added example with DMShell and user point location
DMSwarm Migrate: * Updated to use DMLOCATEPOINT_POINT_NOT_FOUND flag
DM definition: * Added special flag for marking points as being not found within an element during a call to DMLocatePoints
DMSwarm migrate: * Fixed bug with point removal
DMSwarm: * Removed print from data exchanger
DMSwarm: * Use common field names * Re-organized init/finalize fields with DMCreate/DMSetUp * Added methods, flags, checks when using DMSwarmType PIC
SwarmMigrate: * Use common field names
PetscDMSwarm: * Added common names * Corrected extern to PETSC_EXTERN * Added names for migrate
DMSwarm implementation: * Remove unused member
DM implementation: * Added new method locatepointssubdomin
DataBucket: * Print block size
DMSwarm example: * Removed comment
DMSwarm example: * Updated function names
DMSwarm test: * Added new test for variable block sizes
DMSwarm: * Fixed typo in vector name
DMSwarm: * Finishing support for block size != 1
...

Conflicts:
include/petsc/private/dmimpl.h

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DMSwarm DataBucket:
* Added guards to ensure that internal arrays are never re-sized if any raw pointers are being currently being accessed