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>

MatPreallocator: handle block size

MatPreallocator: support upper-triangular nonzeros

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
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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: (107 commits)
cast in GAMG_HASH so that it works for PetscInt32 near PETSC_INT_MAX without overflow to negative numbers
Add link for

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

* master: (107 commits)
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
Copy & paste the change on PetscSparseDensePlusDot
Fix a wrong macro
PetscInfo: Add missing errorchecking
Log: various fixes and cleanups
...

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

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Merged in dalcinl/hash (pull request #970)

Update hash table implementation

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

Update hash table implementation

* Upgrade khash.h to version 0.2.8
* Add common API for hash table iterators
* Add generic hash map and set APIs
* Add hash map and set for integer and pair of integ

Update hash table implementation

* Upgrade khash.h to version 0.2.8
* Add common API for hash table iterators
* Add generic hash map and set APIs
* Add hash map and set for integer and pair of integers

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Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warni

Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ may be used uninitialized in this function [-Wmaybe-uninitialized] ierr = DMInterpolationSetUp(interpolator, dm, pointsAllProcs);CHKERRQ(ierr);
migrate 'build requires: !mpiuni' to new format
migrate 'build requires: !complex' to new format
workarround 'division by zero' compiler warning on windows C:\cygwin64\home\petsc\PETSC~3.CLO\src\ts\examples\TUTORI~1\ex11.c(416): warning #39: division by zero if (uL->h < 0 || uR->h < 0) {for (i=0; i<1+dim; i++) flux[i] = 0./0.; return;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */
dos2unix to prevent warnings on opensolaris "/export/home/petsc/petsc.clone/src/ksp/ksp/examples/tests/ex53.c", line 6: warning: invalid white space character in directive
fix output file - corresponding to code changes in efd4aadf157bf1ba2d80c2be092fcf4247860003
disable test on windows
update log from opensolaris so that the diff is clean on linux aswell
update grep in sync with change in efd4aadf157bf1ba2d80c2be092fcf4247860003
Fixed code that did not correctly set current color for block insertion
Update output files that did not get fixed after previous merges
Change MPIUni to not immediately abort on operations it cannot perform, instead return error code
Add filter for example that can produce 1 different iteration count
Example add system calloc, bad formating of %d in print, commented out code
Always use (void) for functions that take no arguments, never ()
always need to caste PetscReal variables to (double) in print statements
updates to manual page for clarity
update help menu for MatRARt() -- MatRARt_mpiaij_mpiaij is supported now, but not efficient.
fix nightlybuild error with c1cbb1def3f8ddca04c3998b9c06618fd1ffef35 on arch-linux-IPL64 src/ksp/pc/examples/tests ex5_1
...

Conflicts:
include/petscdm.h
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/dm/impls/plex/plexhdf5.c

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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
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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 stefano_zampini/feature-fetidp-ex69

Merge branch 'master' into knepley/feature-plex-boundary-values

* master: (487 commits)
Bib: More refs
Fixed errors in the manuals and ts_glee source code doc
fix bug to enable '-xxx_via [alg]

Merge branch 'master' into knepley/feature-plex-boundary-values

* master: (487 commits)
Bib: More refs
Fixed errors in the manuals and ts_glee source code doc
fix bug to enable '-xxx_via [alg]' to showup in '-help' Reported-by: Mark Adams <mfadams@lbl.gov>
Plex: Remove dead code
TS tutorials ex11: remove unused functions
TSAdapt: Set TSADAPTNONE as default adapt type
DMPlex: missed viewer change in synchronized output
Revert "Merge branch 'hzhang/ts-ex9busdmnetwork'"
TSAdapt: Update changes/dev.html
TSAdapt: Set default type for TSGLEE
TS tutorials ex11: make work with complex scalars
Bib: Added ref
TS ex18: Fix initializer
TS ex11: Fix M_PI
Plex ex1f90: FUCK FORTRAN
f2cblaslapack: remove duplicate xerbla.o and xerbla_array.o from lapack [they are already in blas]
TSAdapt: Refactor handling of default adapt type
TSAdapt: Update changes/dev.html
TSAdapt: Update manual
TSAdapt: Refactor interface and implementations
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Merge branch 'master' into knepley/feature-plex-torus

* master: (174 commits)
Bib: Another ref
Increase patchlevel to 3.7.6
Explicitly listing the LTO library causes difficulties on MacOS so a

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

* master: (174 commits)
Bib: Another ref
Increase patchlevel to 3.7.6
Explicitly listing the LTO library causes difficulties on MacOS so avoid it
TSBDF: Update changes/dev.html
Added Fortran TaoType and TaoLineSearchType definitions
Add Fortran TaoType and TaoLineSearchType definitions
setblocksize for iscol_sub
TSBDF: Use standard TS API and options to control adaptivity
Bib: More refs and a correction
SNESTest: Bug-fix in SNESTest when threshold printing option is turned on.
fix warning and valgrind complains reported by the nightly tests
Section+Doc: Small doc fix
pflotran: switch to using the new upstream git repo
DMPlex: Error if attempt to partition a distributed graph with Chaco
fix complex build error
fix complex build
PetscError() did not properly copy over the specific error message when error type was PETSC_ERROR_INITIAL
TSAdapt: Refactor handling of the always_accept flag
Additional clarification for MatMeshToCellGraph() manual page
optimize MatCreateSubMatrix_MPIAIJ() by merging check of sameXXXDist() into one MPI_AllReduce
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Conflicts:
config/BuildSystem/config/packages/med.py

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Merge branch 'dalcinl/fix-bdf-adapt' into barry/update-petscfileretrieve

Merged in dalcinl/fix-khash-include (pull request #663)

Move hash.h to include/petsc/private/

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Jed Brown <jed@59a2.org>

Move hash.h to include/petsc/private/.

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 '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 stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/imp

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

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c

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Merge branch 'master' into barry/add-pcfieldsplit-logevent