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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PetscViewerASCIIRead(): fix __float128 read

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

* knepley/feature-plex-tests-new:
fix accidently changed code
another fix for Plex for complex numbers
fix for

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

* knepley/feature-plex-tests-new:
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
No Matt triangle is not by default installed on every machine in the world
Matt forgot to require triangle in many tests
fix incorrect requires, fix incorrect name for __float128
since hdf5 doesn't allow PETSc to be built with 16 or 128 bit floating point then say it
fix requires
removed unneeded change to test harness since already supports requires: double
bunch of fixes in plex tests and code for single precision
Many missing requires ctetgen
Certain test examples require ctetgen but it is not listed in test rules

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fix incorrect requires, fix incorrect name for __float128

bunch of fixes in plex tests and code for single precision

Reported-by: nightly tests

Merge branch 'barry/remove-funct'

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-t

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-to: Andreas Mang <andreas@ices.utexas.edu>

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Merge branch 'barry/fortran-update'

Updated and simplified Fortran interface

Reduced from 4 distinct approaches to using PETSc from Fortran to 1
No more .h90 files (Fortran 90 functionality is now always available)
Parameters and func

Updated and simplified Fortran interface

Reduced from 4 distinct approaches to using PETSc from Fortran to 1
No more .h90 files (Fortran 90 functionality is now always available)
Parameters and function prototypes are now provide through Fortran modules, not includes;
only #define are provided in the petscXXXdef.h files
PETSc objects can be declared as either type(tXXX) or XXX. For example type(tVec) or Vec
Moved now private Fortran include files out of public include directory since uses don't use them;
they are only used to generate the Fortran modules
Easier to support and test; we can now easily add more function prototypes
Also had to rework generation of manual pages to consistently use MANSEC and SUBMANSEC
since these variables also handle how the Fortran modules are generated.

Time: 57 hours

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Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_A

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_ATTRIBUTEALIGNED flag to makefile
PCSetUp_SVD() used incorrect matrix for matrix size in parallel, also need to skip LAPACK call if matrix size is zero
strumpack: update to latest version 1.0.4
Remove valgrind warning about MPI_Allreduce() with uninitialized data
sed for test output that has atol convergence with quad precision
updated ex1_nest tests
fixed incorrect key value
fix: bad merge a69d34a
test: move runex78 to TESTEXAMPLES_C_NOTSINGLE
build: fix warnings
sys: update test to produce same result - irrespective of debug/opt build - and presence of ~/.petscrc
sys: src/sys/examples/tests/ex30.c -> src/sys/examples/tests/ex32.c to avoid conflict in master
Sed output, since quad precision reduces below atol on these tests
remove automatically generated matrix names from test output files since can be different
Fixes for MatMPIXXXSetPreallocation(), they were not reentrant, since they kept the information used for matrix-vector products
GAMG: fix PCView_GAMG() format - and update output/ex56_0.out
superlu_dist: 64-bit-indices fix https://github.com/xiaoyeli/superlu_dist/issues/4
Add SNESSetDivergenceTolerance / -snes_divergence_tolerance.
fixed unit read in Plex
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Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/featu

Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/feature-pcbddc-saddlepoint
that prevents me to smoothly merge stefano_zampini/feature-convert-matnest-matis into next.

This will also facilitate merging stefano_zampini/feature-pcbddc-saddlepoint into master

Conflicts:
src/docs/website/documentation/changes/dev.html

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added manual pages for missing PETSCVIEWERXXX such as PETSCVIEWERBINARY

Thanks-to: apostol <apostol.faliagas@gmail.com>

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddc.c

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcfetidp.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c
src/mat/impls/is/matis.h

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Merge branch 'maint'

Merge remote-tracking branch 'origin/balay/fix-PetscInt-scanf/maint' into maint

Merge branch 'balay/fix-PetscInt-scanf/maint' into knepley/feature-plex-particle-example

This merge is done to be able to use 'PetscInt_FMT' in data_bucket.c

sys: int64_t shoud use PRId64 - and not '%ld'. Also add PetscInt64_FMT and PetscInt_FMT to better manage this

Sys+DM: Fixing 64-bit format strings

Merge branch 'tisaac/plex-fix-copy-coordinates' into tisaac/dm-boundary-in-ds

Fixes some regression tests so that I can verify the changes of this branch

* tisaac/plex-fix-copy-coordinates:
DMPle

Merge branch 'tisaac/plex-fix-copy-coordinates' into tisaac/dm-boundary-in-ds

Fixes some regression tests so that I can verify the changes of this branch

* tisaac/plex-fix-copy-coordinates:
DMPlex: don't copy coordinates to self
add X monitoring of residual norm and true residual norm to example since not currently tested
TSAdaptSetType() had no manual page
remove a couple of seemingly strange unneeded PetscReturnFunction(ierr)
manual page for PetscLogObjectMemory()
missing manual page for TaoConvergedReason
tree: workarround bug 'cannot handle multipe #requirespackage listing'.
add no-change test for KSPCR and KSPLCD
configure: improve -fPIC test for ubuntu 16.10
sys: print scanf/PetscInt with --with-clanguage=C++ --with-64-bit-indices=1 --with-scalar-type=complex --with-mpi=0
Fix PCTFS and add test code for symmetric and non-symmetric version
fix a bug due to Lisandro Dalcin's commit d61f013 TS: Run forward cost integral after event handling if step not rolled back
name space Event* and Class* utility functions with Petsc

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Merge remote-tracking branch 'origin/balay/fix-PetscInt-scanf/maint' into maint