Merge branch 'jed/tests-cxx-linker'

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

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

Merge branch 'jed/tests-cxx-linker' into barry/more-to-new-test-harness

testparse: add all test sources to testsrcs-${pkg}.${lang}

This enables building test executables regardless of whether they have a
/*TEST block.

test: Do not suppress the stack trace on error

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

show more ...

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
...

show more ...

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.

show more ...

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

Bug fix for empty tests (default)

Not sure why this was not caught earlier as the bug was
introduced awhile ago (changed return types for non-empty test).

Merge branch 'scott/test-harness-skipdiff'

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.

show more ...

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

show more ...

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.
...

show more ...

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

show more ...

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
...

show more ...

Merge remote-tracking branch 'origin/scott/test-datafiles-fix'

Merge branch 'knepley/test-process-arg' into knepley/feature-adapt-interface

* knepley/test-process-arg: (49 commits)
Test: Can now use make test NP=<num procs>
Testing: Fix error reporting
I

Merge branch 'knepley/test-process-arg' into knepley/feature-adapt-interface

* knepley/test-process-arg: (49 commits)
Test: Can now use make test NP=<num procs>
Testing: Fix error reporting
I didn't realize there was a hacky special case for dense B matrix
Fix example to support -snes_mf_operator
cleanup src/ksp/ksp/examples/tutorials/network/makefile
add missing input in the help menu of PetscOptionsView() Reported-by: Richard Katz <richard.katz@earth.ox.ac.uk>
Fix docs for MatMatMult() that C matrix can only be created by user for sequential case.
protect '-' in macros
fix compile error with --download-petsc4py
Plex: Removed useless CHKERRQ
Configure: Replace use of PETSc modules
Plex ex7: Damn, quad precision is named __float128
TSSetFromOptions: Give subtypes a chance to set the default adapt type
TS ex11.c: fix corrupt filename initialization
small fix
Plex ex1: Update output
DT: Fixed Fortran module - Add DT module to DM and Petsc modules - Fix makefile to generate DT F90 module - Fix PetscQuadratureGet/Restore/SetData() F90 defs
Plex ex19: Updated output
Plex ex7: Update output
p4est: Update to new API
...

show more ...

Testing: Fix error reporting

Merge branch 'scott/test-datafiles-fix' of https://bitbucket.org/petsc/petsc into scott/test-datafiles-fix

Move build requirements

Move build specification from /*T ... T*/ block to a *build:*
sub-block in the /*TEST ... TEST*/ section. This required updating
current test files that had build requiremen

Move build requirements

Move build specification from /*T ... T*/ block to a *build:*
sub-block in the /*TEST ... TEST*/ section. This required updating
current test files that had build requirements as well as the
documentation.

show more ...

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
ini

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
initialize ap as complained by the nightly tests
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
SNES ex12: Mix misnaming Nf --> Nc
update tests
add tests
add MatView_SeqXAIJ_ASCII_structonly(); enable A->structure_only in MatSetValuesBlocked_SeqBAIJ
typo
fill-in some references
Bib: Fixed ref
Plex: Added PLY to file support
Plex: Adding PLY support
PetscDS: Turn off Fortran bindings for Constants
Plex tests: Updated to new point function API
SNES ex56: Moved tests to new format
DM: Allow field projection functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tutorials/ex63.c

show more ...