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

Merge remote-tracking branch 'origin/knepley/feature-plex-tests-new' into tisaac/fix-pipeline-tests

* origin/knepley/feature-plex-tests-new: (101 commits)
Plex: Fix small compiler warnings
Plex

Merge remote-tracking branch 'origin/knepley/feature-plex-tests-new' into tisaac/fix-pipeline-tests

* origin/knepley/feature-plex-tests-new: (101 commits)
Plex: Fix small compiler warnings
Plex ex2f90: Removed comment line Absoft does not like
Plex: Turn off some tests for quad
Plex ex6: Fix printing for quad
Plex: Removed extra semicolon
SNES ex12: Moved restart test to subtests
Plex ex15: Switched to simple partitioning
SNES ex12: Switched to simple partitioning
SNES ex62: Updated output for small numerical diffs
SNES ex62: Switched to simple partitioning
Tests: Turned off some tests that do not very in single precision
all requires need to go on the same line in test definition otherwise they are skipped
TS ex47: Added test output
replace numProcs with standard size
Plex+Gmsh: Fix for complex
fix accidently changed code
another fix for Plex for complex numbers
fix for example that did not handle complex numbers correctly
mark example tests that do not work with complex, fix warning about use of possibly uninitialized values
Fix MPI type to match PetscReal
...

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Merge remote-tracking branch 'origin/test-harness-replacefix'

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

Update of for-loop and top-level specification

Per discussion on petsc-dev:
* {{ ... }shared output} and {{ ... }separate output} handles how
the test harness should deal with for loops and impa

Update of for-loop and top-level specification

Per discussion on petsc-dev:
* {{ ... }shared output} and {{ ... }separate output} handles how
the test harness should deal with for loops and impact on output
* Top level test: is changed to testset: when child testblocks are
present. This enables removing the "subtest" language and
simplifies things conceptually.

Documentation has been updated to reflect these new changes.

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

Because valgrind should be done routinely, the shell script now
have a -V option to add it, and setting VALGRIND=1 at the makefile
level will pass that flag to all tests.

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-fe-dual-apply

* knepley/feature-plex-tests-new: (72 commits)
SNES ex69: Mantle tests are currently broken
SNES ex69: Added outp

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-fe-dual-apply

* knepley/feature-plex-tests-new: (72 commits)
SNES ex69: Mantle tests are currently broken
SNES ex69: Added output for mantle tests
Plex ex1: Parallel tests now use fixed partition
Plex ex3: Turn on tests for P3
Plex: Make in-box check more robust
Plex: Make in-cell check more robust to noise
fix more 'requires'
some fixes for arch-mswin-uni
TS ex18: Fixed declaration
more 'requires:' fixes
fix format error arch-next/lib/petsc/conf/testfiles:1112: *** empty variable name. Stop.
SNES ex69: Fixed requirements
SNES ex77: Fix for warning
SNES ex2: Fix for warning
TS ex18: Tests passing
Enable replace when file does not exist
TS ex18: Tests added
TS ex47: Tests added
TS ex46: Tests passing
TS ex45: Tests passing
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Merge branch 'test-harness-replacefix' into scott/test-harness-forloopfix

Merge remote-tracking branch 'origin/test-harness-replacefix' into knepley/feature-plex-tests-new

* origin/test-harness-replacefix:
Enable replace when file does not exist
Regenerate test harnes

Merge remote-tracking branch 'origin/test-harness-replacefix' into knepley/feature-plex-tests-new

* origin/test-harness-replacefix:
Enable replace when file does not exist
Regenerate test harness if sources change
bugfix for MatGetSubmatrices_MPIAIJ() Reported-by: Matthew Knepley

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Enable replace when file does not exist

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

Merge branch 'balay/testharness-wPETSC_DIR'

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

Update of petscdiff and associated harness hooks

Changes to petscdiff:
o Changes -u flag to -m flag to avoid conflicts with diff
o Adds a -j flag which does an simple diff
o Adds a -J flag which

Update of petscdiff and associated harness hooks

Changes to petscdiff:
o Changes -u flag to -m flag to avoid conflicts with diff
o Adds a -j flag which does an simple diff
o Adds a -J flag which then uses diff with specified arguments

petsc_harness.sh and gmakefile were then updated to use the -m
flag with REPLACE=1 to gmakefile, and use the -j flag with
DIFF_NUMBERS=1 to gmakefile.

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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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gtest: add valgrind support [when PETSC_ARCH has 'valgrind' in the name]

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: filter TAP output instead of suppressing at the origin

To produce the output Barry likes -- without ok and SKIP lines, use

make allgtest

For TAP-compliant output, use either

make allgt

gtest: filter TAP output instead of suppressing at the origin

To produce the output Barry likes -- without ok and SKIP lines, use

make allgtest

For TAP-compliant output, use either

make allgtest-tap

or

make -f gmakefile test

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When filtering test output need to send stderr also to stdout since some Fortran compilers send abort messages to stderr

Need full path of testcompile.log; do not print ok or skip cases it just makes the logs unreadable

Time: .25 hours

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

gtest: use LC_ALL=C for tests and fix one output file