petsc_testrun: use exit code even when no job control

Merge remote-tracking branch 'origin/knepley/fix-snes-ex69' into tisaac/feature-dmfield

* origin/knepley/fix-snes-ex69: (311 commits)
PetscFECreateDefault: fix custom Fortran interface to use MPI_

Merge remote-tracking branch 'origin/knepley/fix-snes-ex69' into tisaac/feature-dmfield

* origin/knepley/fix-snes-ex69: (311 commits)
PetscFECreateDefault: fix custom Fortran interface to use MPI_Comm
SNES ex69: Updated test output
SNES ex69: Removed all mantle stuff and change fields to constants - Also use dsymutil for executables
SNES ex69: Removed special partition
SNES ex69: Fixed null space creation - Null space locks its vectors
PetscFE: PetscFECreateDefault() now takes MPI_Comm instead of DM
cleanup very ugly PCGAMG manual page
minor clarifications for VecScatterCreate() manual page
gcov: PETSC_ARCH is required onlyfor -run_gcov - and not for -merge_gcov [where it doesn't exist]
make clearer in help statements what --with-external-packages-dir is for.
Website: Added news entry for PETSc User Meeting 2018 on main page.
CUDA: Further test output fixes for mat_tests-ex2
Turn off elemental test for parmetis running since this does not work on batch systems.
3.8 Changes: KSPCHEBYSHEV
CUDA: Fixed most test errors due to MatMultTranspose*
website: update urls
website: fix Jason's name to match pic. Also add Todd's pic
Dev manual: copyedit
DMPlexDistributeLabels: Propagate the output flag
cuda/cusp: update minimum supported versions of cuda to 7.5 and cusp to 0.5.0
...

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tests: fix for multiple 'localrunfiles'. i.e support:

localrunfiles: ex1options power/case9.m water/sample1.inp

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

Adding timing feature to test harness and report

This adds a simple timer in the test harness using
elapsed time based on `date %s`. Having O(0.1) second
errors O(10^3) tests can give O(10^2-3) sec

Adding timing feature to test harness and report

This adds a simple timer in the test harness using
elapsed time based on `date %s`. Having O(0.1) second
errors O(10^3) tests can give O(10^2-3) seconds errors
so for total timing, the numbers may be a bit suspect.

However, for figuring out what tests are taking the longest
time, the elapsed time is now written out the counts file,
and report_tests.py can show the top n times that
are the longest, along with the tests associated with it.
Documentation upgraded to show new feature.

Example:
```
gabrielle 154: config/report_tests.py -t 3
```

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Merge branch 'scott/ksp-ksp-tutorials'

Merge branch 'barry/ksp/tests-to-new-harness'

Merge branch 'barry/add-ftn-linfinity-conv-test' of bitbucket.org:petsc/petsc into barry/add-ftn-linfinity-conv-test

Fix odd test cases where stderr->stdout

We have observed behavior where tests fail, and the error code is
captured correctly, but stderr mysteriously went to stdout. This adds a
quick test to see i

Fix odd test cases where stderr->stdout

We have observed behavior where tests fail, and the error code is
captured correctly, but stderr mysteriously went to stdout. This adds a
quick test to see if that is the case, and if so, shows stdout.

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Forgot to put -f flag back in after testing

Clean out rundir of files to avoid append issues (e.g., sys/classes/view/examples/tests/runex4_4.sh)

Merge branch 'master' into scott/ksp-ksp-tutorials

Merge branch 'barry/all-new-test-harness-branches'

Remove testing of filters themselves.

We have cases where grep returns a non-zero error code even though
we do not care about it. Because we aren't testing sed/grep/...
themselves, don't worry about

Remove testing of filters themselves.

We have cases where grep returns a non-zero error code even though
we do not care about it. Because we aren't testing sed/grep/...
themselves, don't worry about capturing their error codes.

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Adding alt file replace functionality

Adding ALT=1 to the gmakefile.test arguments will enable passing the -M
to the shell harness which then passes it to petsc_diff which will then
replace the alt

Adding alt file replace functionality

Adding ALT=1 to the gmakefile.test arguments will enable passing the -M
to the shell harness which then passes it to petsc_diff which will then
replace the alt file. Should use with caution if multiple alt files are
present.

A bug was found while enabling this for alt files. I used a || operator
instead of a && operator.

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Merge branch 'barry/tao-to-new-test-harness' into barry/all-new-test-harness-branches

Merge branch 'barry/move-to-new-test-harness' into barry/all-new-test-harness-branches

Minor cleanup of command line

Converted another directory to new test harness

Added support for localrunfiles: keyword to be the name of a directory that is copied

Commit-type: testing-fix, feature

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (251 commits)
yaml: add a backup download URL
Fix documentation of MatSetRandom function
Ignore -malloc-hbw option if m

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (251 commits)
yaml: add a backup download URL
Fix documentation of MatSetRandom function
Ignore -malloc-hbw option if malloc is already set
Plex: Fixed array initialization
pgi: compile fix
knl: update test to use memkind and remove option that worked arround a bug with intel 17
Check the return value for memkind_posix_memalign
Change the default behavour for -malloc_hbw
Bib: More refs
test: remove runex13f90 as its now converted to new test suite
fix win32 crash. This test was previously run with '-n 4' - so restoring it
Fix petscsfgetgraph_ to work for all Fortran compilers by directly using array of PetscSFNodes
bugfix for MatDuplicate_MPIAIJ_PtAP Reported-by: Samuel Lanthaler <s.lanthaler@gmail.com>
strip out dead sundials usage code; change sundials test to only run 5 timesteps to prevent different number of steps on different systems.
Remove extra lines of output file
Example uses C99 constructs so must mark with requires: c99
fix const missmatch for DMDAVecRestoreArrayRead()
remove conflict between function name in example and new PETSc TS function
builds: attempt to do maint/master/next test builds in separate clones
ex62: it turned out that CHACO partioning is not deterministic. Use a prescribed partition instead
...

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

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Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with

Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with updated 17.10 compilers
Fix for test dirs that are not tutorials/tests
fix use of double in PetscAbsReal() which produces compiler warnings with single precision build
elemental: remove info on conflict of -with-cxx-dialect=C++11 on osx - it works now.
Cleanup .bib files
Fix allfortranstubs rule to rm generated files from correct directory, not outdated location
ierr set but not checked
Remove initial refine so test runs faster and does not time out on some machines
Gail's copyedits for bibtex items
Docs: manual: add further description of 3 different current testing options
DM: check for ops->localtolocalbegin/end before calling
PetscSF: fix typo in tutorial ex1
Vec+HDF5: Fix output for complex - Need to check for empty group name
SNES: SNESDestroy() can be called with snes->dm == NULL
SNES: SNESDestroy() can be called with snes->dm == NULL
Vec+HDF5: Fix output for complex - Need to check for empty group name
Docs: Manual: Update tests section
gmakegentest: also exclude .#filenames created by emacs
DMPlex: Fix output of test ex1 after changes to Gmsh reader
...

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

Refactoring to clean up coding and minor bug fixes.

Per discussion on last commit, this is refactored to simplify
the coding and hopefully make it less obtuse.

Also found some minor errors as devel

Refactoring to clean up coding and minor bug fixes.

Per discussion on last commit, this is refactored to simplify
the coding and hopefully make it less obtuse.

Also found some minor errors as development and testing occurred on some
of the install testing.

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Merge branch 'scott/test-harness-skipdiff'

tests: set TIMEOUT to 10min for nightlybuilds (and 20min for valgrind builds)
And revert default TIMEOUT to 1min for regular use i.e revert ec4485d6ebb8fd2c3c1e36c227d007bdd5acb860