Merge remote-tracking branch 'origin/maint'

Merge branch 'scott/test-small-fixes' into 'maint'

Few fixes for test harness

See merge request petsc/petsc!2807

Multiple fixes to test system

Allow setting duplicated loop variables in subtests
Fix stray line in gmakegentest.py and the problem with redundant variables in loop variables.
Also fixes some output

Multiple fixes to test system

Allow setting duplicated loop variables in subtests
Fix stray line in gmakegentest.py and the problem with redundant variables in loop variables.
Also fixes some output_file checks by moving them to getCmds
Reported by: Pierre Jolivet

Fixes default test labeling: Tests with no fields (default tests) were
getting not getting the '_1' added to the label the way other tests were.
Fixes Issue #625
Reported by: Vaclav Hapla

Add diff_args to list of accepted keywords: This passes arguments
petscdiff. Includes documentation for new option
Fixes Issue #616
Reported by: Stefano Zampini

Have build requires propogate to all tests
Requested by: Stefano Zampini

Unset env's in petscdiff to avoid Window's 32-bit problems with xargs.

Fixes for ksp/ksp/tutorials/ex11.c (deflation)
The other fixes exposed some problems with the way this test was
written so clean it up.

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Merge remote-tracking branch 'origin/maint'

Merge branch 'scott/test-diff-filter' into 'maint'

Move to new filter/filter_output method

See merge request petsc/petsc!2329

Move to new filter/filter_output method

Change to using filters as arguments to petscdiff. By moving the
manipulation of the input and output into petscdiff, this fixes problems
in using piped comm

Move to new filter/filter_output method

Change to using filters as arguments to petscdiff. By moving the
manipulation of the input and output into petscdiff, this fixes problems
in using piped commands (based on original, ancient test system), which
is problematic in capturing the right error codes. This also required
fixes for some tests: the "filter: Error: ..." is used to test stderr of
tests.

This fixes problems with REPLACE=1 as reported by @knepley and debugged by @sbalay.

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Merge branch 'scott/test-improve' into 'master'

Various improvements to test harness

See merge request petsc/petsc!2024

Various improvements

1. Test logging now separates tap output and just the error output.
What is streamed is now controlled with the -o flag to the shell
scripts which now has two options curr

Various improvements

1. Test logging now separates tap output and just the error output.
What is streamed is now controlled with the -o flag to the shell
scripts which now has two options currently: 'interactive' and
'err_only'. The V=0 flag and OUTPUT=1 flags to gmakefile.test
turn on the err_only option
The OUTPUT=1 is default for gitlab

2. gmakegentest.py has a (-c,--check-output) option which does nothing
but check if the output files specified by tests are in the output
directories, and return a non-zero error code if they are not there
check_output target is in outer makefile and add `make check_output` to
stage zero tests to prevent running stage 2 and 3 with missing output
files

3. report_tests.py was not giving the correct command to invoke just the
files that failed. This is because it was coded assuming a
particular naming scheme for the tests: an assumption that was both
incorrect, and led to an ill-posed problem for fixing: If a test
label has underscores, it was not easy to fix. The solution was to
change to telling users to globsearch. In fixing, globsearch had to
be generalized to allow for multiple patterns: e.g.,
make -f gmakefile test globsearch='dm_impls_plex_tutorials-ex5_* ts_tutorials-ex11_*'

4. Bug fix for subtests with loop variables
(Reported Jakub Kruzik <jakub.kruzik@vsb.cz> on 6/26/19)

5. This does a minor fix in this utility script which prints out datafiles.

Commit-type: testing-fix, feature

Out check_output rule to outer makefile

Commit-type: feature
Reported-by: gitlab-ci

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Merge branch 'master' into wence/feature-patch-all-at-once

Merge branch 'stefano_zampini/feature-gmakegen-pkgs' [PR #1344]

* stefano_zampini/feature-gmakegen-pkgs:
This PR improves support for generating makefiles and tests for a package different from PETSc

config/gmakegentest Use pkg_name in example template

Merged petsc/petsc into master

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merge branch 'master' into jpustay/feature-swarm-example

Merged petsc/petsc into master

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

* master: (393 commits)
Bib: Update reference
Mat: Doc fix
Bib: Updated ref
PetscDS: Doc fixes
PC+LU: Do not try to refactor an

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

* master: (393 commits)
Bib: Update reference
Mat: Doc fix
Bib: Updated ref
PetscDS: Doc fixes
PC+LU: Do not try to refactor an already factored matrix
Mat: Small fix for checking and docs
Mat: Added MatSetFactorType() - Needed it when making a shell matrix look factored
PetscDS: Added PetscDSUpdateBoundary() - Lets the user change the boundary condition
single precision produces different convergence history
p4est: has a dependency on zlib - so handle it correctly
Add -mat_mffd_complex to use the Lyness complex number trick to compute J_u * v instead of differencing.
Replace VecWAXPY by VecAXPY if needed
Revert "Replace VecWAXPY by VecAXPY if needed"
Replace VecWAXPY by VecAXPY if needed
MatHermitianTransposeGetMat and MatCreateVecs
ex19: Updated test filter to avoid false positives.
DM: Improved Global-To-Natural docs Suggested-by: Josh L <ysjosh.lo@gmail.com>
Do not build shared openblas when doing static build
Upgrade OpenBLAS to 0.3.3
test: add alt output file for changes in OSX-10.14 and Xcode-10.0 [perhaps related to ML]
...

Conflicts:
src/vec/is/utils/vsectionis.c

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Merge branch 'jed/python3-futurize' [PR #1122]

Merge announces support for Python 3.4+ in changes/dev.html.

* jed/python3-futurize: (44 commits)
gmakegentest: avoid prefix matching in regex
dm

Merge branch 'jed/python3-futurize' [PR #1122]

Merge announces support for Python 3.4+ in changes/dev.html.

* jed/python3-futurize: (44 commits)
gmakegentest: avoid prefix matching in regex
dm tests ex23.c: fix test args: -one -two -three
gmakegentest: more fixes
gmakegentest: fix processing of arguments containing number followed by "-"
gmakegentest: always loop over nsize; Python-3 fixes
python3: add in a python-3.4 test
python: fix build on osx/opensolaris - where 'RANLIB=ranlib -c' i.e with a space..
python3: fix --download-ptscotch error
configure: glob() gets executed early - whereas we need to get file list later [after 'make all' or equivalent] so revert back to using shell to get file-list
python3: map() requires a list modifier for this usage.
python: replace ModuleNotFoundError a python3.6+ feature with ImportError
config: call setup to ensure that debugLevel is set
nightlies: switch linux-pkg-dbg-ftn-interfaces to python3
config: enable Python-3
config: urllib/urlparse updates for Python-3 compatibility
config fblaslapack: use isIBM instead of manual test
python: replace commands with subprocess
Fix LOCDIR paths
generateetags.py: switch from commands to subprocess; unicode fix
python: don't import commands when it isn't used
...

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gmakegentest: always loop over nsize; Python-3 fixes

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 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
...

Conflicts:
src/snes/examples/tutorials/ex13.c

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

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep us

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

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep usage on solaris [use egrep]
opensolaris: fix errors
Update timer reporting and minor reporting fix
Remove redundant if statement. Found by @jedbrown
Fixed problem with order of developer photos on website.
superlu_dist: use correct flag in example [PETSC_HAVE_SUPERLU -> PETSC_HAVE_SUPERLU_DIST]
Bib: PERMON ref
fix for osx
doc: more author fixes
doc: more author fixes
Italicized "orderings" in MPI process placement discussion.
Added Richard to the user manual author list.
Added Richard to the list of active developers on the website.
add string check for MS-MPI and IMPI timeout errors
opensolaris does not have multiple grep utils - but default one does not support -F. So use fgrep instead
Standardizing timeout checks
Report wall clock time of total tests
Use time instead of date %s
...

Conflicts:
include/petscpc.h
src/ksp/ksp/interface/itfunc.c

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Merge branch 'jed/gmakefile-paths' [PR #885]

* jed/gmakefile-paths:
makefile: add + to recursive recipes so that "make test" does not warn about -j
gmakefile: use absolute path for SL_LINKER_FUN

Merge branch 'jed/gmakefile-paths' [PR #885]

* jed/gmakefile-paths:
makefile: add + to recursive recipes so that "make test" does not warn about -j
gmakefile: use absolute path for SL_LINKER_FUNCTION
gmakefile: avoid replication of shared library recipe
makefile: use + in common recursive make invocations
gmakegentest: support localrunfiles naming individual files in subdirectories
gmake: remove src/ from build (PETSC_ARCH/obj) and test paths
gmake tests: enable testing prefix install without write access

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gmake tests: enable testing prefix install without write access

Standard configurations should work as before, except that test
executables are once again named using relative paths (as documented i

gmake tests: enable testing prefix install without write access

Standard configurations should work as before, except that test
executables are once again named using relative paths (as documented in
"make help-test"). For prefix installs, testing is performed as

export PETSC_DIR=/path/to/prefix PETSC_ARCH=
make TESTDIR=/tmp/petsc-tests -f $PETSC_DIR/share/petsc/examples/gmakefile.test test

where TESTDIR is some location that is writable.

A side-effect of this change is that the generated
$PETSC_ARCH/lib/petsc/conf/testfiles has moved to $TESTDIR/testfiles.

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Merge branch 'scott/test-harness-installfixes'