Merge remote-tracking branch 'origin/maint'

Merge branch 'hongzh/fix-valgrind-sell' into 'maint'

Fix valgrind error in MatDiagonalScale_SeqSELL()

See merge request petsc/petsc!2242

Fix valgrind error in MatDiagonalScale_SeqSELL()

Address issue 446 on gitlab

Merge remote-tracking branch 'origin/maint'

Merge branch 'barry/2019-10-15/bug-gamg-complexity/maint' into 'maint'

Bug fix: computing MG complexity had integer overflow. Would only occur for very large problems

See merge request petsc/petsc!

Merge branch 'barry/2019-10-15/bug-gamg-complexity/maint' into 'maint'

Bug fix: computing MG complexity had integer overflow. Would only occur for very large problems

See merge request petsc/petsc!2179

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Bug fix: computing MG complexity had integer overflow. Would only occur for very large problems

Also fixed code that computes parallel matrix storage information to communicate with PetscLogDouble i

Bug fix: computing MG complexity had integer overflow. Would only occur for very large problems

Also fixed code that computes parallel matrix storage information to communicate with PetscLogDouble instead of PetscReal.

Commit-type: bug-fix
Reported-by: Mark Lohry <mlohry@gmail.com>

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Merge branch 'barry/2019-07-30/add-use-petscintcast-corrected' [PR #1924]

* barry/2019-07-30/add-use-petscintcast-corrected:
Add PetscIntCast() to check for integer overflow

Add PetscIntCast() to check for integer overflow

Used in MatSeqXAIJSetPreallocation() to determine if the number of nonzeros in the matrix
(and hence the ai[] column indices and lengths of a

Add PetscIntCast() to check for integer overflow

Used in MatSeqXAIJSetPreallocation() to determine if the number of nonzeros in the matrix
(and hence the ai[] column indices and lengths of aj[] columns indices and a[] numerical values) fit
in PetscInt.

Commit-type: error-checking
Reported-by: Karl Lin <karl.linkui@gmail.com>

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Merged in barry/optimize-aij-da (pull request #1762)

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

1) PetscCalloc*() now uses system calloc()
2) Merged some Pets

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

1) PetscCalloc*() now uses system calloc()
2) Merged some PetscMalloc*()
3) Eliminated unneeded PetscCalloc*()
4) Removed some memory allocations and copies in MatFDColoringSetUp(), added local variables for better compiler optimization
5) Added MatSetValues_SeqAIJ_SortedFull(), added MatSetOption(MAT_SORTED_FULL)
6) Optimized DMCreateMatrix_DA_*AIJ for nonperiodic case to automatically have sorted columns (faster MatSetValues() times)
7) Eliminated call to PetscMemzero() in PetscFree()

Commit-type: style-fix, feature

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Merge remote-tracking branch 'origin/barry/add-petscarrayxxx-ops' [PR #1771]

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*()

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*() with PetscArraymove()

Commit-type: style-fix, feature

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Merge remote-tracking branch 'origin/maint'

Merged in rmills/fix-doc-paradigm-spelling/maint (pull request #1765)

Fixed misspelling of "paradigm" throughout manual pages.

Fixed misspelling of "paradigm" throughout manual pages.

Merged in barry/update-collective-on (pull request #1744)

Update the use of Collective on in the manual pages to reflect the new style

Update the use of Collective on in the manual pages to reflect the new style

Commit-type: style-fix, documentation
Thanks-to: Patrick Sanan <patrick.sanan@gmail.com>

Merge from master

Merged petsc/petsc into master

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (345 commits)
Update dev notes for the coming release
Increase patchlevel to 3.9.4
doc fixes
Added some AIJSELL tests t

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (345 commits)
Update dev notes for the coming release
Increase patchlevel to 3.9.4
doc fixes
Added some AIJSELL tests that mirror the SELL tests.
Bib: More refs
Removed use of hardwired -1 to represent PETSC_NULL_XXX object, since the null value is now 0.
fix memleaks flagged by valgrind
ex62: disable long running test and workaround differences in iteration counts on various builds.
Add FAQ we can point to when users get error messages such as: "PETSc was configured with one OpenMPI mpi.h version but now appears to be compiling using a different OpenMPI mpi.h version"
swith test from mpich to openmpi as mpich ch3:sock is unuserable per PetscShmCommGet()
DM: Forgot to move include statement
fix nightlybuild issues - disable hypre [for openmp] and fix uninitialized variables
tests: enable openmp and hwloc with one of the mumps tests
Default BoomerAMG smoothers
Configure: Revert changes from debb90c, so that we are back to the original Libmesh
Configure: Reverted change for Libmesh from 83cd5d7
Split vecimpl.h into vecimpl.h and vecscatterimpl.h
SNES ex62: Turned off some tests for other precisions and shortened output of sensitive tests
Use mmap to allocate the shared pthread barrier if available
Add configure test for functional mmap
...

Conflicts:
include/petscconvest.h
src/snes/examples/tutorials/ex13.c
src/snes/interface/snes.c
src/snes/utils/convest.c

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Merge branch 'master' into knepley/fix-superdm-is

* master: (123 commits)
Fix a few more Fortran objects to have their NULL value match the C NULL value
remove dead code
Add variable point blo

Merge branch 'master' into knepley/fix-superdm-is

* master: (123 commits)
Fix a few more Fortran objects to have their NULL value match the C NULL value
remove dead code
Add variable point block Jacobi for MPIAIJ matrix.
should not pass user contexts through CHKFORTRANNULLOBJECT in Fortran stubs
fix mpiuni test
Remove CHKFORTRANNULLOBJECTDEREFERENCE since it is no longer needed with Fortran null equal to C null
PETSCFEOPENCL: declare PetscFEGetTabulation_Basic as external
PETSCFEOPENCL: declare PetscFESetUp_Basic as external
Change Fortran null pointer to match C null pointer
one more fix
jenkins: run 'cleantest' after examples are run - to recover diskspace
logical order bug in diagbrdn update fixed, tests updated again
replace new -petscspace_order instances with -petscspace_degree
PETSCSPACETENSOR: clear up naming confusion of subspaces
regression.py: remove configure code related to old test suite - now that SLEPc no longer needs it
PetscSpaceSetup_Poly(): make idempotent
Plex ex3: update tests
Lift changes to defunct dtfe.c from [PR #1074]
PetscSpace_Tensor: clarification of vector-valued
PetscSpace_Tensor: allow height subspaces, fixes tabulation initialization
...

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Merge branch 'master' into knepley/feature-pc-patch

* master: (131 commits)
fix mpiuni test
PETSCFEOPENCL: declare PetscFEGetTabulation_Basic as external
PETSCFEOPENCL: declare PetscFESetUp_Ba

Merge branch 'master' into knepley/feature-pc-patch

* master: (131 commits)
fix mpiuni test
PETSCFEOPENCL: declare PetscFEGetTabulation_Basic as external
PETSCFEOPENCL: declare PetscFESetUp_Basic as external
one more fix
jenkins: run 'cleantest' after examples are run - to recover diskspace
logical order bug in diagbrdn update fixed, tests updated again
replace new -petscspace_order instances with -petscspace_degree
PETSCSPACETENSOR: clear up naming confusion of subspaces
regression.py: remove configure code related to old test suite - now that SLEPc no longer needs it
PetscSpaceSetup_Poly(): make idempotent
Plex ex3: update tests
Lift changes to defunct dtfe.c from [PR #1074]
PetscSpace_Tensor: clarification of vector-valued
PetscSpace_Tensor: allow height subspaces, fixes tabulation initialization
PetscSpace: add a dimension member
PetscSpaceSetDegree(): now take maxDegree argument
-petscspacepoly_tensor -> -petscspace_type tensor
PetscSpaceEvaluate_Polynomial(): fix temp array dependencies
PETSCSPACETENSOR: A generic tensor product of spaces.
PetscSpace: -petscspace_order -> -petscspace_degree
...

Conflicts:
src/dm/dt/interface/dtfe.c
src/snes/examples/tutorials/ex13.c
src/snes/examples/tutorials/ex17.c
src/snes/examples/tutorials/ex62.c
src/snes/examples/tutorials/output/ex62_bddc_quad.out
src/snes/examples/tutorials/output/ex62_fetidp_2d_quad.out
src/snes/examples/tutorials/output/ex62_fetidp_2d_tri.out
src/snes/examples/tutorials/output/ex62_fetidp_3d_hex.out
src/snes/examples/tutorials/output/ex62_fetidp_3d_tet.out

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Merged petsc/petsc into master

Merge branch 'rmills/fix-matseqsellsetpreallocation-typo' [PR #1102]

* rmills/fix-matseqsellsetpreallocation-typo:
Fixed two spelling errors in the MatSeqSELLSetPreallocation manual page.

Fixed typos in MatSeqSELLSetPreallocation manual page.

Reported-by: Richard Tran Mills <rmills@rmills.org>