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 'scott/test-harness-forloopfix' into scott/test-harness-altfiles

Merge remote-tracking branch 'origin/scott/test-harness-valgrind-v2'

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

* master: (94 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to solve issues with gfortran
Travis-CI: Use newe

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

* master: (94 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to solve issues with gfortran
Travis-CI: Use newer macOS image
clarify damping and other issues related to SNESLINESEARCHBASIC
change example in new harness to use simple partitioner so gets consistent output on all systems
remove unused function from test file
cleanup formatting in example, plus myrank not rank
missing - makes the manual page formatting wrong
The developer manual clearly states that MPI_Comm_size() returns size it doesn't return numProcs or other nonsense. Pretty soon you'll start using mype instead of rank?
fix typo and cut and paste error in docs
bugfix for !HYPRE
fix warning for ';;'
may switch to scalable only when B->cmap->N > 100000
MatLRC: store in the context the parallel matrices rather than the sequential ones
Bib: Add ref
set default algorithm based on B->cmap->N for MatMatMult_MPIAIJ_MPIAIJ()
Error in VecScatterView_MPI() had the meaning of from and to backwards
fix build warning as reported by the nightly tests
Update alquimia.py to use Glenn's branch that updates alquimia for pflotran xsdk
fix divide by zero exposed by 8534686b5096cd4c91a8f3895408b386c0628431 - and produced by petsc4py testsuite
...

Conflicts:
src/dm/impls/plex/examples/tests/ex13.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tests/ex2.c
src/snes/examples/tests/output/ex2_3.out
src/snes/examples/tests/output/ex2_4.out
src/snes/examples/tests/output/ex2_5.out

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Merge remote-tracking branch 'remotes/origin/scott/test-harness-valgrind-v2' into scott/test-harness-forloopfix

Improvements to overriding diff and mpiexec

Using this syntax:
mpiexec=${PETSCMPIEXEC:-"@MPIEXEC@"}
diffexec=${PETSCDIFF:-"${petsc_dir}/bin/petscdiff"}
in the shell scripts.

We can override the

Improvements to overriding diff and mpiexec

Using this syntax:
mpiexec=${PETSCMPIEXEC:-"@MPIEXEC@"}
diffexec=${PETSCDIFF:-"${petsc_dir}/bin/petscdiff"}
in the shell scripts.

We can override them from make [with command line make variable] or shell [with env variable] as:
make PETSCMPIEXEC=mpiexec allgtest
PETSCMPIEXE=mpiexec runex1.sh

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Added LABEL_SUFFIX functionality

Label_suffix is to enable the command tests and diff tests to be labeled
during loops which makes it easier for debugging.
This includes a few bug fixes and cleanup

Added LABEL_SUFFIX functionality

Label_suffix is to enable the command tests and diff tests to be labeled
during loops which makes it easier for debugging.
This includes a few bug fixes and cleanup as development progresses.

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Merge branch 'tisaac/feature-gentest-varsubst' into scott/test-harness-forloopfix

Multiple fixes enabling better for loop capability

Enabling args override in the shell script broke the
for loop functionality. By separating variables that
are in for loops and those that are not,

Multiple fixes enabling better for loop capability

Enabling args override in the shell script broke the
for loop functionality. By separating variables that
are in for loops and those that are not, arg override
are allowed even when for loops are present.

Because some for loops cause different outputs and
some produce the same output, we automate the two
extemes.

Also comments are now pulled out of the test specification
and placed at the top of the script.

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Merge branch 'master' of bitbucket.org:petsc/petsc

gtest: fix incorrect quotes for PATH [as @PETSC_LIB_DIR@ appears to add in the necessary quotes]

Fixes the following error on windows

# > /petsc.clone/arch-mswin-uni/tests/src/sys/examples/tests/ex

gtest: fix incorrect quotes for PATH [as @PETSC_LIB_DIR@ appears to add in the necessary quotes]

Fixes the following error on windows

# > /petsc.clone/arch-mswin-uni/tests/src/sys/examples/tests/ex31.exe: error while loading shared libraries: api-ms-win-crt-heap-l1-1-0.dll: cannot open shared object file: No such file or directory

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

* master: (37 commits)
fortran: include petscversion.h
test: c++ pipeline build fix for d2a797cfef64a79a330b420f01b2d605a8acc690
Extra

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

* master: (37 commits)
fortran: include petscversion.h
test: c++ pipeline build fix for d2a797cfef64a79a330b420f01b2d605a8acc690
Extract the submatrices
Convert C Null pointer to Fortran in Fortran stub before passing back to user
PC Galekin and KSP should properly propagate calls to SetFromOptions to subsolvers
Converted Fortran PetscSF to Fortran type, added PETSC_NULL_SF
clarification in documentation
Update of petscdiff and associated harness hooks
Fixup more F90 interface definitions for users
More space-in-dirname enabling quotes
Enable paths with spaces
add cast; bugfix for 64bit
Typo -- initialized TESTFLAGS to -v by mistake
Adding new options to test framework
gtest: add valgrind support [when PETSC_ARCH has 'valgrind' in the name]
bugfix for unsorted ISCols
optimize matgetsubmatrices_mpiaij to use only one MPI_AllReduce
small cleanup MatGetSubMatrices_MPIAIJ_Local()
rm allcolumns from the input of MatGetSubmatrices_mpiaij_local()
add a test to ex4.c for reuse
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gmakegentest.py: implement key substitution and change for loop behavior

gmakegentest.py: give subtests their own working arguments

Merge branch 'master' of bitbucket.org:petsc/petsc

Merge remote-tracking branch 'origin/scott/test-harness-options'

More space-in-dirname enabling quotes

Enable paths with spaces

Adding new options to test framework

o make -f gmakefile test OPTIONS='foo'
Passes '-a foo' to script which then overrides the default args
o make -f gmakefile test EXTRA_OPTIONS='bar'
Passes '-

Adding new options to test framework

o make -f gmakefile test OPTIONS='foo'
Passes '-a foo' to script which then overrides the default args
o make -f gmakefile test EXTRA_OPTIONS='bar'
Passes '-e bar' to script which then adds to the arguments
o make -f gmakefile test TESTFLAGS='-a foo -e bar' is equivalent to above
o make -f gmakefile test REPLACE=1
Passes -u to petscdiff which now *updates* the output file by mv'ing redirect file to output file
o make -f gmakefile test NO_RM=1
Turns of the RM of the executables which is useful for running
the scripts by hand if working in a specific directory

Some of the arguments were in petsc_harness.sh but not actually
working. In getting them updated, some cruft was removed as well.

Based petsc-dev discussions.

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Merge remote-tracking branch 'origin/balay/testharness-wPETSC_DIR'

gtest: add wPETSC_DIR for datafile access in test-scripts

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 'scott/testharness-update1'

gtest: set PATH for windows DLL tests, and enable -Dpetsc_EXPORTS only during (dll) build - and not for examples

Merge branch 'scott/testharness-update1' of bitbucket.org:petsc/petsc into scott/testharness-update1