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

Math: Add the golden ratio

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

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

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

Merged in dalcinl/fix-math (pull request #675)

Fix math calls to use the macros in petscmath.h

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

Fix math calls to use the macros in petscmath.h

PetscMath: check for math functions by function pointer resolvability

I had previously tried to solve the issue of hidden symbols in math
libraries being misused in c89. Trying to set a pointer to

PetscMath: check for math functions by function pointer resolvability

I had previously tried to solve the issue of hidden symbols in math
libraries being misused in c89. Trying to set a pointer to the
functio will fail if the symbol is hidden, so this is a better
solution. I have applied it to other c99 math functions (erf, tgamma)
as well.

Suggested-by: Jed Brown <jed@jedbrown.org>

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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\

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'

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fix log2() compile error on windows
/home/petsc/petsc.clone-4/include/petscmath.h:28:8: error: expected ‘)’ before ‘/’ token
double log2(double);
^

petscmath.h: redeclare log2() for c89 usage

Using gcc -std=c89 on linux, the log2 symbol is accessible but does the wrong thing
if the prototype isn't given. I don't get it, but it works.

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

* knepley/feature-plex-tests-new:
Plex ex12: Added logging stages
Plex ex1: Added logging stages
TS e

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

* knepley/feature-plex-tests-new:
Plex ex12: Added logging stages
Plex ex1: Added logging stages
TS ex18: Indicate broken tests
TS ex11: Indicate broken test
SNES ex62: Added SIMPLE tests
SNES ex12: Removed old tests
Plex: Fixing test descriptions
update to latest hypre tag on github
fix 'inf' vs 'Inf' diff wrt vec_vec_utils_tagger_tutorials-ex1_8,9,18,19
MatSetOption(mat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE) no longer applies to zero values set or added to the matrix diagonal, they are now not ignored and are included in the matrix nonzero structure. This is useful for Jacobians passed to TS.
replace use/mention of depreciated -log_summary in many places
add extchem.py which was written years ago but never put in the distribution (hence it is broken).
refix 96a2602 as it gives parsing erros with gmakegentest.py from scott/test-harness-altfiles
petsc4py: update to snapshot with MatGetSubMatrices -> MatCreateSubMatrices etc API changes
PetscCMPLX: assume type punning is safe

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Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-torus

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stages

Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-torus

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stages
update to latest hypre tag on github
fix 'inf' vs 'Inf' diff wrt vec_vec_utils_tagger_tutorials-ex1_8,9,18,19
MatSetOption(mat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE) no longer applies to zero values set or added to the matrix diagonal, they are now not ignored and are included in the matrix nonzero structure. This is useful for Jacobians passed to TS.
replace use/mention of depreciated -log_summary in many places
add extchem.py which was written years ago but never put in the distribution (hence it is broken).
petsc4py: update to snapshot with MatGetSubMatrices -> MatCreateSubMatrices etc API changes
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
PetscCMPLX: assume type punning is safe
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
...

Conflicts:
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/examples/tests/ex12.c

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

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stag

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

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stages
update to latest hypre tag on github
fix 'inf' vs 'Inf' diff wrt vec_vec_utils_tagger_tutorials-ex1_8,9,18,19
MatSetOption(mat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE) no longer applies to zero values set or added to the matrix diagonal, they are now not ignored and are included in the matrix nonzero structure. This is useful for Jacobians passed to TS.
replace use/mention of depreciated -log_summary in many places
add extchem.py which was written years ago but never put in the distribution (hence it is broken).
petsc4py: update to snapshot with MatGetSubMatrices -> MatCreateSubMatrices etc API changes
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
PetscCMPLX: assume type punning is safe
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
...

Conflicts:
src/dm/impls/plex/examples/tests/ex12.c

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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 'tisaac/fix-petsccmplx'

* tisaac/fix-petsccmplx:
PetscCMPLX: assume type punning is safe

PetscCMPLX: assume type punning is safe

Merge branch 'tisaac/feature-vec-tagger'

* tisaac/feature-vec-tagger: (31 commits)
VecTagger: documentation
TS tutorials ex11: use updated VecTagger interface
VecTagger: rename Intervals and B

Merge branch 'tisaac/feature-vec-tagger'

* tisaac/feature-vec-tagger: (31 commits)
VecTagger: documentation
TS tutorials ex11: use updated VecTagger interface
VecTagger: rename Intervals and Boxes, declare VecTaggerBox
PetscCMPLX: fix inline declaration
VecTagger: silence some compiler complaints
VecTagger: 64-bit indices fixes
TS tutorials ex11: use VecTagger
VecTagger: cxx fixes
VecTagger: complex fixes and tests
VecTagger: fix view of andor types
VecTagger: fixes for complex
VecTagger: Implementation of union and intersection taggers
VecTagger: cdf interval implementation
VecTagger: create regression tests based on ex1
VecTagger: complex/c++ fixes
VecTagger: added tutorial ex1
VecTagger: simple backend should check that interval is set at setup
VecTagger: relax strict block size restrictions
VecTagger: comment out unimplemented registrations
VecTagger: fix header function misnames
...

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PetscCMPLX: fix inline declaration

VecTagger: silence some compiler complaints

Sys: add PetscCMPLX() for complex declaration

If the imaginary part is +/-Inf, there isn't a good portable way to
construct a complex number in C99. The CMPLX macro, standardized in
C11, should hop

Sys: add PetscCMPLX() for complex declaration

If the imaginary part is +/-Inf, there isn't a good portable way to
construct a complex number in C99. The CMPLX macro, standardized in
C11, should hopefully become standard.

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Merge branch 'barry/half-precision'

Support for half-precision using __fp16.

Requires repository trunk of gcc and ARM systems
Configure with --with-precision=__fp16 --download-f2cblaslapack --with-fc=0 --with-cxx=0
Many standard PETSc

Support for half-precision using __fp16.

Requires repository trunk of gcc and ARM systems
Configure with --with-precision=__fp16 --download-f2cblaslapack --with-fc=0 --with-cxx=0
Many standard PETSc tests fail due to lack of precision

Funded-by: ECP
Project: fp16
Time: 24 hours

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Merge branch 'master' into psanan/pc-telescope-nearnullspace

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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