removed warnings ("Elemental matrix (explicit ordering)") for elemental during Petscviewer output.

Merge branch 'stefanozampini/update-suitesparse' into 'master'

Update SuiteSparse to use github releases + fixes to SBAIJ hermitian complex case

See merge request petsc/petsc!2305

MATSBAIJ: Fix Hermitian MatMult for Seq and MPI code paths

we can reuse the same MatMult operation with no impact for non-complex builds
Remove improper check for the hermitian complex case from Mat

MATSBAIJ: Fix Hermitian MatMult for Seq and MPI code paths

we can reuse the same MatMult operation with no impact for non-complex builds
Remove improper check for the hermitian complex case from MatGetFactor and move it where it actually belongs
Fix conversion routines from SBAIJ when the hermitian flag is set

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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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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/maint'

Merged in stefano_zampini/fix-matcopy-sbaij (pull request #1571)

Fix SBAIJ

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

MATELEMENTAL: add support for MAT_REUSE_MATRIX in MatConvert_ routines

Merge branch 'maint'

Merged in hzhang/add-elemental-matsize-errorflg/maint (pull request #1526)

add error flg when Elemental matrix rows/columns are not equally distributed.

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

elemental: add error flg when matrix rows/columns are not equally distributed.

Reported-by: "Nair, Nirmal Jayaprasad" <njn2@illinois.edu>

Merge branch 'master' into knepley/feature-plex-functionals

* master: (984 commits)
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out

Merge branch 'master' into knepley/feature-plex-functionals

* master: (984 commits)
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out
fix gcov obj path
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Dev manual: remove duplicate entry
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
Tao: Added alternative output for chwirut2 test.
TS ex45,ex46: Removed overly refined tests for faster nightly tests.
KSP ex72: Fixed needlessly long-running PCTFS tests.
SNES ex56: Reduced test size to speed up nightly test suite.
KSPSolve_LSQR: don't compute unused norm of rhs
SNES ex13: Reduced problem sizes for nightly tests.
PetscOptionsDeprecated(): fix for NULL prefix
PetscOptionsDeprecated(): add option to print additional info
SNES ex12: Reduced sizes for BDDC tests.
...

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Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
config

Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
Tao: Added alternative output for chwirut2 test.
TS ex45,ex46: Removed overly refined tests for faster nightly tests.
KSP ex72: Fixed needlessly long-running PCTFS tests.
SNES ex56: Reduced test size to speed up nightly test suite.
KSPSolve_LSQR: don't compute unused norm of rhs
SNES ex13: Reduced problem sizes for nightly tests.
PetscOptionsDeprecated(): fix for NULL prefix
PetscOptionsDeprecated(): add option to print additional info
SNES ex12: Reduced sizes for BDDC tests.
PetscFileRetrieve(): Suppress output to STDERR when downloading a file.
MatMatMult: Fixed unused variable pN.
DMDestroy: Guard call to dm->ops->destroy * Similar guards are in place in many other methods (IS,Vec,Mat) and permit the DM to be destroyed even if DMSetType() was never called.
...

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Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComp

Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex type is missing from fortran
initialize variables so that static analyzer doesn't mistakenly think they are used uninitialized.
Move access of prefix until it is actually used
Remove DMDASplitComm2d(), used in one example that was not tested
Functions that do not return PetscErrorCode should not use PetscFunctionBegin/End paradgm
remove unneeded reassignment of same value
Missing CHKERRQ(); Mostly in Tao code
Remove clang static analyser warning about passing NULL variable to strncat()
missing newline in -ts_monitor_extreme
minor fixes for integer counters
Configure: Deal with '__func__' in C89 builds with newer Clang and GCC.
Jenkinsfile: Increased timeout for tests to 5 minutes.
3.9 changes: further clarify removal of -pc_factor_mat_solver_package
Options deprecations: add "PETSc" to inline warning
removing unused variable
MatShift support added to MATSUBMAT. Mimics MATSHELL functionality. Needed for matrix-free Hessians in TAO Newton-Line-Search methods.
Add -ts_monitor_extreme
Dev manual: add note on deprecating options database keys
...

Conflicts:
src/dm/impls/plex/examples/tests/ex4.c

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

* master: (353 commits)
Configure: Pragmatic now requires Cxx11
fix compile warning
mpiuni: build somempifort.o after mpiuni.mod

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

* master: (353 commits)
Configure: Pragmatic now requires Cxx11
fix compile warning
mpiuni: build somempifort.o after mpiuni.mod
Remove use of common block from MPIUNI code
use was in wrong location
Fortran line extends past 72 char
Moved the rest of the PETSc common block variables over to petscsys module
tests: fix breakage due to cd93b0e13c6da70ee1e038f55989cf888bc1d1c5
Need to use petscsys to get PETSC_COMM_SELF defined in example
Mat ex23 and ex40: fix errors reported from nightly tests
Put declaration on too lines because otherwise it generates an error for truncated line
Move PETSC_COMM_WORLD and PETSC_COMM_SELF from common blocks to petscsys module
tests: fix requires - and create out files for seqaijmkl tests
KSP ex72: nested dissection is likely to be different between machines
cmake: downgrade to version 3.9 - as newer versions require cxx11 compiler [which is not universal]. However stick with version 3.11 on opensolaris
Mat ex23: fix memory leaks
Bib: Some new refs
KSP examples: add missing casts to double in printf
updated GAMG KSP tests
PetscRound() should be PetscRoundReal() in __fp16
...

Conflicts:
include/petsclog.h
src/sys/logging/plog.c
src/sys/logging/utils/eventlog.c

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Merge branch 'master' into knepley/fix-plex-project-tests

* master: (477 commits)
Added correct report number for PETSc Developers Guide
Update PETSc Developers Guide title and final pages to ne

Merge branch 'master' into knepley/fix-plex-project-tests

* master: (477 commits)
Added correct report number for PETSc Developers Guide
Update PETSc Developers Guide title and final pages to new ANL style
Hash: Quick documentation fix
PetscBinaryViewerRead -> PetscViewerBinaryRead
cast in GAMG_HASH so that it works for PetscInt32 near PETSC_INT_MAX without overflow to negative numbers
Add link for DrMemory which may serve as an alternative to valgrind on Windows
Finish Gail's copyedits for developers manual.
openmpi: fix namespace conflict [with static build on ppc64le]
two pages of Gail's edits to developers guide
Another chapter of Gail's copyedits for the developers guide
Gail's copyedits on two more chapters of the developers guide
Fix more %d to %D in GAMG code. Fix code style in GAMG code
DMPlexVTK: vertices is int! need to use %d instead of %D
TS ex18: update outputs (reported by nightly tests)
Use %D in error messages for GAMG hash; fix style issues with GAMG hash
config: Update petsc4py git commit
Fix bad plain extern declaration.
Add Gail's copyedits for the initial portion of the developers guide
Add missing common block to subroutine
fix mpiuni tests with xl compilers
...

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

* master: (562 commits)
fix clang-analyzer warning
Developers manual never use system randomizers in PETSc and example source code.
missing

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

* master: (562 commits)
fix clang-analyzer warning
Developers manual never use system randomizers in PETSc and example source code.
missing CHKERRQ()
DT: Reverting the tgamma change broke MPFR - I guess we need a nightly build with it in
Add a test for ex21
Fix error in ex21
Add missing fortran interface that handles null objects
DMComposite: add missing guards
MatPreallocate: fix overpreallocation of local rows
style fixes
MatView_MPI_DA: do not print twice the class prefix
MatSetOperation: stash the original MatView_XXX in the viewnative function pointer
DMCreateInterpolation_DA gracefully error instead of catching FPE signals
MatIncreaseOverlap: preserve communicator of index sets
MatMPIAIJ: fix indentation and missing CHKERRQ
ISBuildTwoSided: remove tabs and fix style
Fix documentation
PetscViewerDraw: fix unininitialized warning from valgrind
MatConvert_SeqAIJ_SeqBAIJ: remove error for non square matrices and add MAT_REUSE_MATRIX case
Mat: MAT_INPLACE_MATRIX can be used for transposition with rectangular matrices
...

Conflicts:
src/dm/dt/interface/dtfe.c
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexfem.c
src/snes/examples/tutorials/ex13.c
src/snes/examples/tutorials/ex62.c
src/snes/examples/tutorials/makefile
src/snes/examples/tutorials/output/ex62_18.out
src/snes/examples/tutorials/output/ex62_19.out
src/snes/examples/tutorials/output/ex62_20.out
src/snes/examples/tutorials/output/ex62_20_parmetis.out
src/snes/examples/tutorials/output/ex62_21.out
src/snes/examples/tutorials/output/ex62_22.out
src/snes/examples/tutorials/output/ex62_23.out
src/snes/examples/tutorials/output/ex62_24.out
src/snes/examples/tutorials/output/ex62_25.out
src/snes/examples/tutorials/output/ex62_26.out
src/snes/examples/tutorials/output/ex62_27.out
src/snes/examples/tutorials/output/ex62_28.out
src/snes/examples/tutorials/output/ex62_29.out
src/snes/examples/tutorials/output/ex62_2d_p3_1.out
src/snes/examples/tutorials/output/ex62_30.out
src/snes/examples/tutorials/output/ex62_31.out
src/snes/examples/tutorials/output/ex62_32.out
src/snes/examples/tutorials/output/ex62_33.out
src/snes/examples/tutorials/output/ex62_34.out
src/snes/examples/tutorials/output/ex62_35.out
src/snes/examples/tutorials/output/ex62_36.out
src/snes/examples/tutorials/output/ex62_pc_simple.out
src/snes/examples/tutorials/output/ex62_pc_simplec.out
src/snes/examples/tutorials/output/ex62_quad_q2p1_full.out
src/snes/examples/tutorials/output/ex62_quad_q2q1_full.out
src/snes/utils/dmplexsnes.c

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Merge branch 'maint'

Merge branch 'stefano_zampini/cherrypick/maint' into maint

Mat: MAT_INPLACE_MATRIX can be used for transposition with rectangular matrices

Added a couple of tests

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead code.
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
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Conflicts:
src/snes/examples/tutorials/ex13.c

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Merge branch 'barry/fix-matsolvertype'