Improving report_tests

Adding some improved reporting of how to rerun the test system based on
Satish's suggestions.

Merge remote-tracking branch 'origin/scott/test-harness-improve2'

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Fix allfortranstubs rule to rm generated files from correct directory, not outdated location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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Fix for test dirs that are not tutorials/tests

Fixed couple of bugs in testparse. Cleanup

While testing the changes from the last commit more thouroughly, I found
a bug that pops up intermittently. While debugging that, I cleaned
various thing

Fixed couple of bugs in testparse. Cleanup

While testing the changes from the last commit more thouroughly, I found
a bug that pops up intermittently. While debugging that, I cleaned
various things up.

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Dependency fixes.

The actual extra dependencies from the `depend:` keyword
were not being written out explicitly to testfiles. This
now does so.

The new rules for compiling test executables then

Dependency fixes.

The actual extra dependencies from the `depend:` keyword
were not being written out explicitly to testfiles. This
now does so.

The new rules for compiling test executables then requires that all of
the dependencies be added to the link line which changed the rule from
using `$< $(PETSC_LIB)` to a `$^`.

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gmakegentest: also exclude .#filenames created by emacs

test: if 'nsize' is not specified in 'testset' - use nsize=1

Fixes ksp_ksp_tutorials-ex10_mumps_lu-c

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

Skip emacs files in processing.

Two improvements: dependencies, label mult tests

1. Adding dependencies

2. Improve labeling of multiple tests within testset

When there are multiple tests in a testset, they
were cur

Two improvements: dependencies, label mult tests

1. Adding dependencies

2. Improve labeling of multiple tests within testset

When there are multiple tests in a testset, they
were currently using the same label (unless the tests
were defined by a loop). This adds a simple -[ascii]
character to the end of each label in the test (*-a, *-b, etc.)

Also, this uncovered a bug introduce when the feature of having
nsize on the commandline was added. For::
testset:
test:
nsize=2
test:
nsize=3

There will now be hardcoded nsizes written out before the test is run.
For this case, this would not allow nsize to be overwritten, but trying
to add logic to overwrite this specific case would add too much
complexity.

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Bug fixes based on previous reports to PR

Various bug fixes to improve the robustnesses:
- Giving full path of testsrcs dependency enables invoking it from outside
of its source directory (removes

Bug fixes based on previous reports to PR

Various bug fixes to improve the robustnesses:
- Giving full path of testsrcs dependency enables invoking it from outside
of its source directory (removes reported infinite loop)
- Adding a dependency to the TESTDIR/.DIR uses Jed's previously
defined sentinel file rules fixes some inconsistent behavior
*and* enables fullpath TESTDIR specification (as in Satish's report)
- Install.py was accidently adding an extraneous 'all' target
- gmakegentest.py was using inInstallDir inconsistently in a few places

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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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Enable tests to run from install directories.

Previous incarnations of the test harness did not run from installation
(prefix) directories. To enable this feature, the make part of the test
harness

Enable tests to run from install directories.

Previous incarnations of the test harness did not run from installation
(prefix) directories. To enable this feature, the make part of the test
harness was separated from the build gmakefile to create
gmakefile.examples. Install.py then installs the harness, and fixes up
the gmakefile.examples to make it work robustly in the installation dir.
The install paths are:
```
<prefix_dir>/share/petsc/examples/gmakefile.example
<prefix_dir>/share/petsc/examples/config/*
```

Example usage:
```
cd <prefix_dir>
make -f share/petsc/examples/gmakefile.example
```
will run tests in ```<prefix_dir>/tests```.

Another example:
```
cd <prefix_dir>/share/petsc/examples/
make -f gmakefile.example TESTDIR=$PWD/mytests
```
will run tests in ```<prefix_dir>/share/petsc/examples/mytests```.

For developers, other than ```gmakefile``` -> ```gmakefile.examples```,
it should remain the same.

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Merge branch 'scott/test-harness-skipdiff'

Merge remote-tracking branch 'origin/barry/feature-simple-spectral'

New features: time limit and logging

Enabling a time limit is now enabled. The default is set in
```config/petsc_harness.sh``` (at 60 seconds) but may be
overwritten at the shell level with the ```

New features: time limit and logging

Enabling a time limit is now enabled. The default is set in
```config/petsc_harness.sh``` (at 60 seconds) but may be
overwritten at the shell level with the ```-t intfoo``` flag,
and at the makefile with the ```TIMEOUT=intfoo``` option.
Individual tests can be extended with the
```timeoutfactor: intfoo``` in the test block.

Although the pipestatus variable in bash can get the
equivalent of ```$?``` for piped processes, such a thing does
not exist for ```$!```. To overcome this, a new script
```config/watchtime.sh``` is used for enforcing the timeout.
Because the timeout requires separating the filter from
execution of the job, pipestatus is no longer used and the
filter step is done separately. The implementation in
```petsc_harness.sh``` is explained by these. Also,
interrupting the tests with ```CTRL-C``` means you
will see a kill status appear at the terminal as this dies.

Logging is also enabled. Previous attempts at doing this
purely at the ```gmakefile``` level were unsatisfactory
because of pipe buffering issues. Moving the
```| tee -a ${testlogfile}``` command to
```petsc_harness.sh```
level gives acceptable performance. The logfile is:
```${PETSC_ARCH}/tests/examples-${PETSC_ARCH}.log``` and
```grep -v ^ok ${PETSC_ARCH}/tests/examples-${PETSC_ARCH}.log```
is very useful.

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Enable skip of diff tests when primary cmd fails

If the primary command fails, then the running the
diff test adds a lot of unneeded verbosity. This
fixes that by checking the error code and SKIPpi

Enable skip of diff tests when primary cmd fails

If the primary command fails, then the running the
diff test adds a lot of unneeded verbosity. This
fixes that by checking the error code and SKIPping
the diff test if the command fails.

As part of this, the capturing of error output and
status was changed to be more accurate:
see config/petsc_harness.sh for details.
Currently sys-tests-ex{1,2,3} are failing because
they are meant to capture the error codes.

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Simple examples of the spectral method in one dimension using stored matrices

linear steady state heat equation
"data assimulation" with time-dependent heat equation
The "data assimulation" code was

Simple examples of the spectral method in one dimension using stored matrices

linear steady state heat equation
"data assimulation" with time-dependent heat equation
The "data assimulation" code was written by Oana Marin

Commit-type: feature, example
Funded-by: ECP, IMEX
Time: 70 hours
Thanks-to: Oana Marin <oanam@mcs.anl.gov>
Development Tools: Vim, Emacs, Eclipse

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Merge branch 'master' into knepley/fix-fe-default

* master: (297 commits)
Bib: Added refs and fixed one
Doc: Fixed formatting problems for MatCreateAIJ() manual page.
Add to PCSOR manual page

Merge branch 'master' into knepley/fix-fe-default

* master: (297 commits)
Bib: Added refs and fixed one
Doc: Fixed formatting problems for MatCreateAIJ() manual page.
Add to PCSOR manual page information about convergence testing when using KSPRICHARDSON
SNES ex5: Restore old output since this breaks an example I have
Noted that some Cray XC systems will use 'aprun' instead of 'srun'. Thanks to Herr Doktor Hong Zhang for this suggestion.
Added example configure script for Cray XC40 with KNL processors (e.g., NERSC Cori).
Fix possible sprintf -Wformat-overflow
PetscMalloc2-7: fix -Wint-in-bool-context for GCC 7
SNES ex5: make boundary condition handling consistent for symmetry
SNES ex5: use L2 norm and *_monitor_short for output
SNES ex5: the L^2 norm scales with the l^2 norm over sqrt(N)
SNES ex5: refactor MMS capability to avoid extreme code duplication
Documentation fix: typo in PetscLogStageRegister manual page.
nodes -> vertices
rename DMNetworkGetComponentTypeOffset -> DMNetworkGetComponentKeyOffset
rename DMNetworkGetConnectedNodes() -> DMNetworkGetConnectedVertices()
Jacobians for adjoints for explicit methods and constant Jacobians never got initialized
fix complex build error
fix build failure with fortran interface
fix compile error with cdc753b64c658d532d7813e942002e67025667a6
...

Conflicts:
src/snes/examples/tutorials/ex13.c
src/snes/examples/tutorials/ex62.c
src/snes/examples/tutorials/ex69.c

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Merge remote-tracking branch 'origin/scott/test-harness-f90freeform'

Merge branch 'master' into knepley/feature-rigid-bodies

* master: (204 commits)
windows fixes
revert this change as a relavent fix is already in origin/knepley/fix-ex-types
regenerate output l

Merge branch 'master' into knepley/feature-rigid-bodies

* master: (204 commits)
windows fixes
revert this change as a relavent fix is already in origin/knepley/fix-ex-types
regenerate output log for snes_tutorials-ex62_fetidp_3d_tet that got corrupted in 188e10d6f1cffa866ec0197053a0e55fa4e7da41
fix opensolaris build error with --with-log=0 Undefined first referenced symbol in file PetscLogEventGetPerfInfo arch-opensolaris-misc/tests/src/dm/impls/plex/examples/tests/ex9.o
fix warnings on windows C:\cygwin64\home\petsc\PETSC~1.CLO\src\tao\examples\TUTORI~1\ex1.c(217): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)'
disable example with absoft (due to fixed/free form limit)
c89 fixes
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
Plex ex19: Remove unneeded code
Plex: Fix projection when we have a dmAux which is a domain boundary - If we are projecting on a lower dimension thing (effectiveHeight > 0), then we need to get the space and dual space on this subcell - The tabulation needs to be in the right dimension for both dm and dmAux
PetscFE: Added height subspaces to PetscFE - Added PetscFEGetHeightSubspace() - Added array in struct
PetscDualSpace: Small cleanup of parameter name
PetscSpace: Added height subspaces for PetscSpace - Added PetscSapceGetHeightSubspace() and member function - Added subspaces array
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ may be used uninitialized in this function [-Wmaybe-uninitialized] ierr = DMInterpolationSetUp(interpolator, dm, pointsAllProcs);CHKERRQ(ierr);
migrate 'build requires: !mpiuni' to new format
migrate 'build requires: !complex' to new format
workarround 'division by zero' compiler warning on windows C:\cygwin64\home\petsc\PETSC~3.CLO\src\ts\examples\TUTORI~1\ex11.c(416): warning #39: division by zero if (uL->h < 0 || uR->h < 0) {for (i=0; i<1+dim; i++) flux[i] = 0./0.; return;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */
dos2unix to prevent warnings on opensolaris "/export/home/petsc/petsc.clone/src/ksp/ksp/examples/tests/ex53.c", line 6: warning: invalid white space character in directive
fix some minor style issues
Extend AMS/ADS to support high-order element.
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Make PETSC_USING_F90FREEFORM default for f90 files

Fortran examples with .F90 require Fortran compilers that support infinite line
length. The absoft compiler only supports 132 hence it should not r

Make PETSC_USING_F90FREEFORM default for f90 files

Fortran examples with .F90 require Fortran compilers that support infinite line
length. The absoft compiler only supports 132 hence it should not run on
examples that have .F90. PETSc configure sets USING_F90FREEFORM only if infinite
line length supported.

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Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warni

Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ may be used uninitialized in this function [-Wmaybe-uninitialized] ierr = DMInterpolationSetUp(interpolator, dm, pointsAllProcs);CHKERRQ(ierr);
migrate 'build requires: !mpiuni' to new format
migrate 'build requires: !complex' to new format
workarround 'division by zero' compiler warning on windows C:\cygwin64\home\petsc\PETSC~3.CLO\src\ts\examples\TUTORI~1\ex11.c(416): warning #39: division by zero if (uL->h < 0 || uR->h < 0) {for (i=0; i<1+dim; i++) flux[i] = 0./0.; return;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */
dos2unix to prevent warnings on opensolaris "/export/home/petsc/petsc.clone/src/ksp/ksp/examples/tests/ex53.c", line 6: warning: invalid white space character in directive
fix output file - corresponding to code changes in efd4aadf157bf1ba2d80c2be092fcf4247860003
disable test on windows
update log from opensolaris so that the diff is clean on linux aswell
update grep in sync with change in efd4aadf157bf1ba2d80c2be092fcf4247860003
Fixed code that did not correctly set current color for block insertion
Update output files that did not get fixed after previous merges
Change MPIUni to not immediately abort on operations it cannot perform, instead return error code
Add filter for example that can produce 1 different iteration count
Example add system calloc, bad formating of %d in print, commented out code
Always use (void) for functions that take no arguments, never ()
always need to caste PetscReal variables to (double) in print statements
updates to manual page for clarity
update help menu for MatRARt() -- MatRARt_mpiaij_mpiaij is supported now, but not efficient.
fix nightlybuild error with c1cbb1def3f8ddca04c3998b9c06618fd1ffef35 on arch-linux-IPL64 src/ksp/pc/examples/tests ex5_1
...

Conflicts:
include/petscdm.h
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/dm/impls/plex/plexhdf5.c

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Merge branch 'master' into knepley/feature-dm-bc-components

* master: (320 commits)
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ m

Merge branch 'master' into knepley/feature-dm-bc-components

* master: (320 commits)
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ may be used uninitialized in this function [-Wmaybe-uninitialized] ierr = DMInterpolationSetUp(interpolator, dm, pointsAllProcs);CHKERRQ(ierr);
migrate 'build requires: !mpiuni' to new format
migrate 'build requires: !complex' to new format
workarround 'division by zero' compiler warning on windows C:\cygwin64\home\petsc\PETSC~3.CLO\src\ts\examples\TUTORI~1\ex11.c(416): warning #39: division by zero if (uL->h < 0 || uR->h < 0) {for (i=0; i<1+dim; i++) flux[i] = 0./0.; return;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */
dos2unix to prevent warnings on opensolaris "/export/home/petsc/petsc.clone/src/ksp/ksp/examples/tests/ex53.c", line 6: warning: invalid white space character in directive
fix output file - corresponding to code changes in efd4aadf157bf1ba2d80c2be092fcf4247860003
disable test on windows
update log from opensolaris so that the diff is clean on linux aswell
update grep in sync with change in efd4aadf157bf1ba2d80c2be092fcf4247860003
Fixed code that did not correctly set current color for block insertion
Update output files that did not get fixed after previous merges
Change MPIUni to not immediately abort on operations it cannot perform, instead return error code
Add filter for example that can produce 1 different iteration count
Example add system calloc, bad formating of %d in print, commented out code
Always use (void) for functions that take no arguments, never ()
always need to caste PetscReal variables to (double) in print statements
updates to manual page for clarity
update help menu for MatRARt() -- MatRARt_mpiaij_mpiaij is supported now, but not efficient.
fix nightlybuild error with c1cbb1def3f8ddca04c3998b9c06618fd1ffef35 on arch-linux-IPL64 src/ksp/pc/examples/tests ex5_1
output has changed with e6d0a238963c2a97dd04845ea512b529992c7cdb so update the output file
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