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

* master: (108 commits)
Bib: Added ref
Bib: Updated reference
Bib: Updated reference
Work around problems with Apple Xcode 8.3 and h

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

* master: (108 commits)
Bib: Added ref
Bib: Updated reference
Bib: Updated reference
Work around problems with Apple Xcode 8.3 and handling of rpath argument with gfortran
help menu update for MatCreateSubMatrices() Reported-by: Brad Aagaard <baagaard@usgs.gov>
fix flops for PCApply_PBJacobi_1 and PCApply_PBJacobi_7 Reported-by: Pierre Jolivet <pierre.jolivet@enseeiht.fr>
TSRK: Fix FSAL optimization to not skip update and check or stages.
Travis-CI: Workaround too long TMPDIR in macOS with Open MPI
test: Fix type mismatch in KSP test.
test: Fix warnings from gfortran -Wconversion (OS X, Homebrew build)
MPIUNI: Silence GCC -Wconversion warnings
Fortran: Add error checking for incorrect PETSC_NULL_XXX argument when expecting function
fix test output per changes in 517c9301b2e9239931bfd644803fd6bb859387ea
MUMPS: update to version 5.1.1 with opensolaris compile fixes
TSRK: Mention 5BS in the changelog.
TSRK: Mention the new 5BS scheme in the manual.
fix 'unused variable' warning
Remove unused code
added hbw_realloc
fixed undefined ptr
...

Conflicts:
config/BuildSystem/config/packages/med.py

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XXXDestroy() already checks if the pointer is NULL so no reason to check the pointer before calling the destroy

Commit-type: style-fix
Funded-by: ECP
Project: ECP/Tao

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 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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Merge branch 'tmunson/tao-bqpip-fix-code-and-documentation'

Updates to pounders code for subproblem solvers and consistency
between tao defaults and solver defaults.

Time: way too much

Updates to pounders code for subproblem solvers and consistency
between tao defaults and solver defaults.

Time: way too much

Merge branch 'tmunson/kspcg-fix-trust-region-functions'

Update bound constrained solvers for updated calling sequence

Time: 10 minutes

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 stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/mat/impls/aij/seq/mkl_pardiso/mkl_pardiso.c

Merge branch 'master' into barral/feature-dmplex-adapt

Merge branch 'jose/maint/tabs-print-class' into maint

Merge branch 'master' into knepley/feature-parallel-mesh-load

* master: (59 commits)
Increase patchlevel to 3.7.1
Fix manual page for MatGetTransposeNullSpace()
remove unneeded use of PetscCon

Merge branch 'master' into knepley/feature-parallel-mesh-load

* master: (59 commits)
Increase patchlevel to 3.7.1
Fix manual page for MatGetTransposeNullSpace()
remove unneeded use of PetscContainer to hold iscoloring in SNESComputeNGSDefaultSecant()
added SNESView for ngs, added options database to ngs manual page, removed dead routine
gcov: enable in mpiuni test
incorrect capitalization of an even name
force same number of iterations for output of ml example
changed output for ml example to not be machine dependent
DMP4est: access data after setup
SNESLineSearch_Apply was labeled with PETSC_EXTERN in one place but when declared this was not visible hence library build failed under Microsoft.
Example had print statements of complex numbers
Fix more errors in agmres for 64 bit integers
builds: fix nampespase conflict with 'analyzer-buid' and checkBuilds.py
gcov: add more packages to test
add a couple of KSP that were not represented in testing
gcov: enable more externalpackages for this test
fixes for agmres for 64 bit indices, fix for findvisibleprivatefunctions to be portable for Mac and Linux
get GAMG to get null space (more)
fix c++ compile errors
Add test example for kacmarz preconditioner since gcov indicated there was NONE
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Merge branch 'master' of bitbucket.org:petsc/petsc into mark/gamg-nullspacefix

Merge branch 'barry/make-functions-static'

Updated script for detecting visible symbols

Removed unneeded visibility of some symbols
Fixed some namespacing
Removed the use of unneeded implementation includes in the TAO code

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

completed removing "variable set but not used" based on output
from clang static analyzer

Time: . 1 hours

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

Merge branch 'master' into barry/add-pcreset-hypre-for-master

Needed to move PCDestroy_HYPRE() added to master to PCReset_HYPRE() since that was introduced
as a bug fix for maint