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

Fix for when >1 petscdiff option is specified

See merge request petsc/petsc!2428

Fix for when >1 petscdiff option is specified

Reported by: Stefano Zampini <stefano.zampini@gmail.com>

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 'maint'

Merge branch 'scott/cat_stdout' into 'maint'

Increase verbosity after 'not ok'

See merge request petsc/petsc!2289

Increase err verbosity

In commit 984117c42c7 a fix was put in to handle cases when stderr
goes to stdout; however, it seems that sometimes we have cases where
mpi_abort messages go to stdout but the

Increase err verbosity

In commit 984117c42c7 a fix was put in to handle cases when stderr
goes to stdout; however, it seems that sometimes we have cases where
mpi_abort messages go to stdout but the petsc trace goes to stdout.
Here, we cat both stdout and stderr with stdout first. This might be
too verbose, but worth gaining experience.

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Merge branch 'maint'

Merge branch 'scott/fix_test_reporting' into 'maint'

Fix reporting

See merge request petsc/petsc!2211

Fix reporting

The function get_test_data was not parsing the count files correctly --
fixes problems seen in the CI reporting.

Valgrind runs were losing the error code. Need Yet Another Flag To
Va

Fix reporting

The function get_test_data was not parsing the count files correctly --
fixes problems seen in the CI reporting.

Valgrind runs were losing the error code. Need Yet Another Flag To
Valgrind in order for the harness to work correctly.

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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 this one.

Merge branch 'jed/gitlab-ci'

tests: create check-test-errors allgtests-tap [which ignores timeout errors] for gitlab-ci.

Also pass PETSC_ARCH/PETSC_DIR to gmakefile for allgtest, allgtest-tap, cleantest

fix allgtests-tap - as

tests: create check-test-errors allgtests-tap [which ignores timeout errors] for gitlab-ci.

Also pass PETSC_ARCH/PETSC_DIR to gmakefile for allgtest, allgtest-tap, cleantest

fix allgtests-tap - as it was not stopping on error

do not flag failure on test timeout

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Merge branch 'jczhang/fix-test-harness-empty-ouput-after-grep' [PR #1864]

* jczhang/fix-test-harness-empty-ouput-after-grep:
Accept empty output file after filter.
In the old logic, if a user meant

Merge branch 'jczhang/fix-test-harness-empty-ouput-after-grep' [PR #1864]

* jczhang/fix-test-harness-empty-ouput-after-grep:
Accept empty output file after filter.
In the old logic, if a user meant to have an empty output file after grep -v (for example, use it to get rid of timing info), the grep command's return value is 0 (since no line is selected) and the empty file move command won't be executed, leading to diff errors.

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Accept empty ouput file after filter

In the old logic, if a user meant to screen out all output by grep -v, the grep command's
return value is 0 and the file move command won't be executed, causing

Accept empty ouput file after filter

In the old logic, if a user meant to screen out all output by grep -v, the grep command's
return value is 0 and the file move command won't be executed, causing diff errors.

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Merge from master

Merged petsc/petsc into master

Merge branch 'master' into knepley/fix-superdm-is

* master: (455 commits)
bib: spell out some names for format consistency with related refs
bib: two 2018 pubs now appeared
cleaning up analyze

Merge branch 'master' into knepley/fix-superdm-is

* master: (455 commits)
bib: spell out some names for format consistency with related refs
bib: two 2018 pubs now appeared
cleaning up analyzer warnings
compile fixes (workarround PGI bug?):
undoing the branch's changes to leastsquares outputs
more fixes for complex builds
compile error fix for complex builds
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix Pardiso code to only compile pardiso_init64 when needed, otherwise can generate warnings/errors
jenkins: run 'cleantest' before 'allgtest-tap' - an attempt to fix errors of type:
cuda: protect cuda includes
fix cuda warnings.
fix complex compile error
Revert "Improved polymorphism of interfaces for MatSetValuesBlocked()"
Bib: Updated ref
Doc: More function documentation
petscvec: move PetscSFCreateFromZero from vscat to vec sources
Fixed an uninitialized variable and got rid of an unused one.
memleak fixed and output files updated
fixing build errors on some archs
Mat: obey options prefix of Mat in MatNullSpaceTest
...

Conflicts:
include/petsc/private/dmpleximpl.h
src/dm/interface/dmi.c

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

* master: (281 commits)
compile fixes (workarround PGI bug?):
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix

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

* master: (281 commits)
compile fixes (workarround PGI bug?):
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix Pardiso code to only compile pardiso_init64 when needed, otherwise can generate warnings/errors
jenkins: run 'cleantest' before 'allgtest-tap' - an attempt to fix errors of type:
cuda: protect cuda includes
fix cuda warnings.
fix complex compile error
Revert "Improved polymorphism of interfaces for MatSetValuesBlocked()"
Bib: Updated ref
Doc: More function documentation
petscvec: move PetscSFCreateFromZero from vscat to vec sources
Mat: obey options prefix of Mat in MatNullSpaceTest
Plex+SNES: Must pass user context through
vscat: move ftn-custom to correct location remove custom vecscatterdestroy_()
vscat: move interface routines to correct location
vscat: delete dead code
fix compile error
FE: Correct coordinates in IntegrateBd
Bib: Added refs
SNES ex17: 3D tests must require a 3D grid generator
Plex+TS: We cannot run the check with the same vector that is the TS solution
...

Conflicts:
include/petsc/private/dmpleximpl.h
src/docs/website/documentation/changes/dev.html
src/snes/examples/tutorials/ex13.c
src/snes/utils/dmplexsnes.c

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

* master: (249 commits)
Bib: Added refs
Netcdf should always build netcdf-4 (needed for example by exodusii.
trivial fixes of incor

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

* master: (249 commits)
Bib: Added refs
Netcdf should always build netcdf-4 (needed for example by exodusii.
trivial fixes of incorrect formatting in SNES linesearch routines
ISSetBlockSize_General: removed blockwise contiguity check.
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out
config prefix: avoid ad-hoc path substitutions
config/install: no need to rename paths for installBinDir
rules: fix path in (evidently unimportant) uncrustify target
config pkgconfig: use ${prefix} in PETSc.pc and do not modify in install
fix gcov obj path
Improved polymorphism of interfaces for MatSetValuesBlocked()
-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
...

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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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