Merge branch 'master' into stefano_zampini/feature-fetidp-ex69

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.

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Merge branch 'master' into knepley/feature-plex-boundary-values

* master: (487 commits)
Bib: More refs
Fixed errors in the manuals and ts_glee source code doc
fix bug to enable '-xxx_via [alg]

Merge branch 'master' into knepley/feature-plex-boundary-values

* master: (487 commits)
Bib: More refs
Fixed errors in the manuals and ts_glee source code doc
fix bug to enable '-xxx_via [alg]' to showup in '-help' Reported-by: Mark Adams <mfadams@lbl.gov>
Plex: Remove dead code
TS tutorials ex11: remove unused functions
TSAdapt: Set TSADAPTNONE as default adapt type
DMPlex: missed viewer change in synchronized output
Revert "Merge branch 'hzhang/ts-ex9busdmnetwork'"
TSAdapt: Update changes/dev.html
TSAdapt: Set default type for TSGLEE
TS tutorials ex11: make work with complex scalars
Bib: Added ref
TS ex18: Fix initializer
TS ex11: Fix M_PI
Plex ex1f90: FUCK FORTRAN
f2cblaslapack: remove duplicate xerbla.o and xerbla_array.o from lapack [they are already in blas]
TSAdapt: Refactor handling of default adapt type
TSAdapt: Update changes/dev.html
TSAdapt: Update manual
TSAdapt: Refactor interface and implementations
...

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Merge branch 'tisaac/feature-plex-tests-new'

This merge changes PetscSpace and PetscQuadrature to have a number of
components, so that vector-valued functionals can be defined for
non-Lagrange finit

Merge branch 'tisaac/feature-plex-tests-new'

This merge changes PetscSpace and PetscQuadrature to have a number of
components, so that vector-valued functionals can be defined for
non-Lagrange finite elements. Along the way, this branch also converts
the regression tests related to DMPlex that were in config/builder.py to
the new test harness, and makes lots of changes necessary for them to
be portable tests.

* tisaac/feature-plex-tests-new: (263 commits)
TS tutorials ex11: remove unused functions
DMPlex: missed viewer change in synchronized output
TS tutorials ex11: make work with complex scalars
TS ex18: Fix initializer
TS ex11: Fix M_PI
Plex ex1f90: FUCK FORTRAN
TS tutorials ex11: use a union when punning
silence compiler warnings
SNES tutorials ex56: set partitioner from options
Plex: once again, MPI_Barrier() can't be used to synch output
windows compile fixes balay@ps4 ~/petsc/src/ts/examples/tutorials $ make PETSC_DIR=$HOME/petsc ex11 /home/balay/petsc/bin/win32fe/win32fe cl -o ex11.o -c -MD -wd4996 -Z7 -I/home/balay/petsc/include -I/home/balay/petsc/arch-mswin-uni/include -I/home/balay/petsc/include/petsc/mpiuni `pwd`/ex11.c ex11.c C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(300): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(301): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(370): error C2229: struct '<unnamed-tag>' has an illegal zero-sized array C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(463): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(505): error C2229: struct '<unnamed-tag>' has an illegal zero-sized array C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(724): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(728): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1179): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1184): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1191): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1194): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1383): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1521): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1522): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1523): warning C4090: 'function': different 'const' qualifiers
PetscMath: check for math functions by function pointer resolvability
another windows fix for log2() C:\cygwin64\home\petsc\PETSC~1.CLO\include\petscmath.h(28): warning C4273: 'log2': inconsistent dll linkage C:\Program Files (x86)\Windows Kits\10\include\10.0.10240.0\ucrt\../ucrt/math.h(506): note: see previous definition of 'log2'
fix log2() compile error on windows /home/petsc/petsc.clone-4/include/petscmath.h:28:8: error: expected ‘)’ before ‘/’ token double log2(double); ^
SNES tutorials ex12: turn off complex for restart test
Add empty file to silence warnings
TS tutorials ex46: make output match floating point filter
TS tutorials ex18: remove unused flags
SNES tutorials ex69: use end of line anchor instead of word boundary
SNES tutorials ex69: portable word boundary regex
...

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Merge branch 'master' of bitbucket.org:petsc/petsc

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

Merge branch 'knepley/feature-mantle-example' into stefano_zampini/feature-fetidp-ex69

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-plex-pragmatic-parallel

* knepley/feature-plex-tests-new: (105 commits)
SNES ex62: Make test 31 less sensitive
Plex: Remove ext

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-plex-pragmatic-parallel

* knepley/feature-plex-tests-new: (105 commits)
SNES ex62: Make test 31 less sensitive
Plex: Remove extra semicolons
Test: Reverted cherry pick
Plex: Damn Absoft, Trying to get under the 132 character line limit for Absoft
Testing: Cherry picked a fix
Plex: Trying to get under the 132 character line limit for Absoft
Plex: Fix small compiler warnings
Plex ex2f90: Removed comment line Absoft does not like
Plex: Turn off some tests for quad
Plex ex6: Fix printing for quad
Plex: Removed extra semicolon
SNES ex12: Moved restart test to subtests
Plex ex15: Switched to simple partitioning
SNES ex12: Switched to simple partitioning
SNES ex62: Updated output for small numerical diffs
SNES ex62: Switched to simple partitioning
Tests: Turned off some tests that do not very in single precision
all requires need to go on the same line in test definition otherwise they are skipped
TS ex47: Added test output
replace numProcs with standard size
...

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Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes

Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
superlu: libray is installed in PREFIX/lib64 - fix this to use PREFIX/lib
backport fixes cc105cc3 2b35c90a - required for 3bf428d - that was backported from master - 80c96bb
'echo -n' fails on opensolaris/osx - so avoid using it.
fix diffs in nightlybuilds due to options in ~/.petscrc
add Kelley03 to src/docs/tex/petsc.bib
build: determine moudles, mpi.h used during buildtime and print in 'info'
fix analyzer warnings
fix build failure on opensolaris - where -lm from flibs is removed due to -lm in cxxlibs. But then - only flib gets used for some configure tests [blaslapack, parms]
config: prefer __restrict over C99 restrict keyword
...

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Improve error reporting in parsing

Make python 2.6 compliant.

A bug in python 2.6's re module meant implementing a different parser

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-mantle-example

* knepley/feature-plex-tests-new: (103 commits)
Test: Reverted cherry pick
Plex: Damn Absoft, Trying to get unde

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-mantle-example

* knepley/feature-plex-tests-new: (103 commits)
Test: Reverted cherry pick
Plex: Damn Absoft, Trying to get under the 132 character line limit for Absoft
Testing: Cherry picked a fix
Plex: Trying to get under the 132 character line limit for Absoft
Plex: Fix small compiler warnings
Plex ex2f90: Removed comment line Absoft does not like
Plex: Turn off some tests for quad
Plex ex6: Fix printing for quad
Plex: Removed extra semicolon
SNES ex12: Moved restart test to subtests
Plex ex15: Switched to simple partitioning
SNES ex12: Switched to simple partitioning
SNES ex62: Updated output for small numerical diffs
SNES ex62: Switched to simple partitioning
Tests: Turned off some tests that do not very in single precision
all requires need to go on the same line in test definition otherwise they are skipped
TS ex47: Added test output
replace numProcs with standard size
Plex+Gmsh: Fix for complex
fix accidently changed code
...

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Test: Reverted cherry pick

Merge branch 'scott/test-harness-forloopfix' into scott/test-harness-altfiles

Testing: Cherry picked a fix

Merge remote-tracking branch 'origin/knepley/feature-plex-tests-new' into tisaac/fix-pipeline-tests

* origin/knepley/feature-plex-tests-new: (101 commits)
Plex: Fix small compiler warnings
Plex

Merge remote-tracking branch 'origin/knepley/feature-plex-tests-new' into tisaac/fix-pipeline-tests

* origin/knepley/feature-plex-tests-new: (101 commits)
Plex: Fix small compiler warnings
Plex ex2f90: Removed comment line Absoft does not like
Plex: Turn off some tests for quad
Plex ex6: Fix printing for quad
Plex: Removed extra semicolon
SNES ex12: Moved restart test to subtests
Plex ex15: Switched to simple partitioning
SNES ex12: Switched to simple partitioning
SNES ex62: Updated output for small numerical diffs
SNES ex62: Switched to simple partitioning
Tests: Turned off some tests that do not very in single precision
all requires need to go on the same line in test definition otherwise they are skipped
TS ex47: Added test output
replace numProcs with standard size
Plex+Gmsh: Fix for complex
fix accidently changed code
another fix for Plex for complex numbers
fix for example that did not handle complex numbers correctly
mark example tests that do not work with complex, fix warning about use of possibly uninitialized values
Fix MPI type to match PetscReal
...

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Fix parsing when args contain a :

Update of for-loop and top-level specification

Per discussion on petsc-dev:
* {{ ... }shared output} and {{ ... }separate output} handles how
the test harness should deal with for loops and impa

Update of for-loop and top-level specification

Per discussion on petsc-dev:
* {{ ... }shared output} and {{ ... }separate output} handles how
the test harness should deal with for loops and impact on output
* Top level test: is changed to testset: when child testblocks are
present. This enables removing the "subtest" language and
simplifies things conceptually.

Documentation has been updated to reflect these new changes.

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Final fixes for ksp-ksp-tutorials-ex10 tests

These changes allow most of the ex10 tests to pass.

Adding additional debugging feature

Enable multiple test from single test block

To split the tests specified into the testblock,
the implementation is done at the testparse.py level
to enable easier debugging and implementation.
For l

Enable multiple test from single test block

To split the tests specified into the testblock,
the implementation is done at the testparse.py level
to enable easier debugging and implementation.
For loops and subtests are still specified at the
gmakegentest.py level. Improvements to parsing
for some error checking were implemented as well.

To test, the changes two examples have been converted:
src/dm/impls/plex/examples/tests/ex10.c
src/ksp/ksp/examples/tutorials/ex10.c

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Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-fe-dual-apply

* knepley/feature-plex-tests-new: (72 commits)
SNES ex69: Mantle tests are currently broken
SNES ex69: Added outp

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-fe-dual-apply

* knepley/feature-plex-tests-new: (72 commits)
SNES ex69: Mantle tests are currently broken
SNES ex69: Added output for mantle tests
Plex ex1: Parallel tests now use fixed partition
Plex ex3: Turn on tests for P3
Plex: Make in-box check more robust
Plex: Make in-cell check more robust to noise
fix more 'requires'
some fixes for arch-mswin-uni
TS ex18: Fixed declaration
more 'requires:' fixes
fix format error arch-next/lib/petsc/conf/testfiles:1112: *** empty variable name. Stop.
SNES ex69: Fixed requirements
SNES ex77: Fix for warning
SNES ex2: Fix for warning
TS ex18: Tests passing
Enable replace when file does not exist
TS ex18: Tests added
TS ex47: Tests added
TS ex46: Tests passing
TS ex45: Tests passing
...

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Improved comment handling in the test parsing.

Enable separation of args that can be overwritten

One of the features of the test system is overwriting args from the
command-line. With forloops this is tricky as we do not enable
those to be over

Enable separation of args that can be overwritten

One of the features of the test system is overwriting args from the
command-line. With forloops this is tricky as we do not enable
those to be overwritten. I had this working earlier, but I am now
following @tisaac superior structure of writing out the shell script
post-merge.

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Keep testparse.py dumb

Having testparse.py do a 1-to-1 mapping of the YAML to python
dictionary is easier for debugging.