Merge branch 'barry/minor-draw-improvements' into jed/chem

configure: do not suggest using builder.py to users

Merge branch 'master' into knepley/feature-dmda-section

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fi

Merge branch 'master' into knepley/feature-dmda-section

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fix for TSGetRHSMats_Private() in the creation of the Arhs and Brhs matrices
protect logging of objects (which uses global variables) with PETSC_USE_LOG
error handler API had been previously changed but this example was not updated to new API.
DMPlex: Fixed bug in coordinate permutation
PetscSection: Doc fix for permutation
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bugfix of MatCreateSeqAIJFromTriple() contributed by Nicolas Marsic <nicolas.marsic@montefiore.ulg.ac.be>
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
completed removing server code that was not removed in previous commit
removed PETSc webserver and configure package files that supported it
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
fix outdated PetscOptionsList
SNESQN: only monitor real part of dot product (fails with C++ complex)
Fix for multiple definitions in mat/color/interface/ custom fortran bindings
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/da/dageometry.c
src/dm/impls/plex/examples/tests/ex4.c
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexinterpolate.c

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Merge branch 'master' into knepley/feature-fem-dgspace

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key

Merge branch 'master' into knepley/feature-fem-dgspace

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
SNESQN: only monitor real part of dot product (fails with C++ complex)
Corrected the #include statement in the man pages for the PetscObjectComposedDataSet/Getwhatever routines.
DMPlex: Added doc for DMPlexGetHybridBounds()
winzip: detect if winzip is used to extract petsc.tar.gz and error out.
configure: remove self.archIndependent as its not being used. [it is used to create externalpackages/package/arch dir which is unused]
configure: fix packages using package-dir/PETSC_ARCH as out-of-source-build location Perhaps this should be changed to package-dir/build?
configure: remove dead code previously used to download BuildSystem
configure: check if compilerDefines [and compilerFixes] exist in framework before using them
configure: save/restore reconfigure.py when --with-clean is used
configure: add --with-clean option to delete buildfiles/externalpackages in PETSC_DIR/PETSC_ARCH and potential externalpackages in --with-external-package-dir/PETSC_ARCH
configure: With --with-externalpackages-dir=dir store/build packages in dir/PETSC_ARCH
Add MatSeqSBAIJSetPreallocationCSR()
configure: switch to using PETSC_DIR/PETSC_ARCH/externalpackages by updating package.py to use externalpackages.py as the externalPackagesDirProvider
configure: move dead code configureExternalPackagesDir() from petscdir.py to externalpackagesdir.py Also set PETSC_DIR/PETSC_ARCH/externalpackages as the externalpackagesdir
...

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Merge branch 'balay/move-externalpackages-dir'

Merge branch 'master' into barry/saws

Conflicts:
src/ksp/pc/impls/gamg/gamg.c
src/sys/classes/viewer/impls/ams/ams.c
src/sys/objects/pinit.c

configure: add --with-clean option to delete buildfiles/externalpackages in PETSC_DIR/PETSC_ARCH
and potential externalpackages in --with-external-package-dir/PETSC_ARCH

configure: switch to using PETSC_DIR/PETSC_ARCH/externalpackages by
updating package.py to use externalpackages.py as the externalPackagesDirProvider

configure: switch to setting defaultInstallDir [in package.py] directly from PETSc/Configure.py
[instead of guessing from petscdir.dir and arch.dir]

configure: update MPI.py with this change

Merge branch 'master' into knepley/feature-dmda-section

* master: (397 commits)
PetscSynchronizedFGets: fix deadlock at EOF
Compiler: Fix warnings from MPI impls which do not initialize outputs

Merge branch 'master' into knepley/feature-dmda-section

* master: (397 commits)
PetscSynchronizedFGets: fix deadlock at EOF
Compiler: Fix warnings from MPI impls which do not initialize outputs
Increase patchlevel to 3.4.3
SNES: Now work vectors come from the DM
SNES ex62: Remove code generation
SNES: Move setup involving snes->vec_sol from SNESSetUp() to SNESolve()
Compiler: Fix warnings from MPI impls which do not initialize outputs
DMPlex ex7: Added missing test output
SNES ex52: Removed old Jacobian stuff, and fixed call to DMPlexProjectFunction() - Fixed calls for new element handling
SNES ex12: Added a performance profiling mode
DMPlex ex8: Fixed leak
PetscSection: Must reset the section when changing the number of fields
DMPlex ex7: Fixed test output - Corrected orientations in interpolation
DMPlex ex1: Fixed test output - Uniform refinement for quads changed
DMPlex: Fix overagressive checks
PC: Removed support graph PC
configure: both downloadonWindows and worksonWindows refer to MS compilers. Also fix isWindows() -> isWindows(CC).
MatXAIJSetPreallocation: use array[] notation to help out Fortran
__float128: when blas/lapack is not found instruct using f2cblaslapack
Configure: Package.downloadonWindows is supposed to mean that Windows compilers work. not Cygwin - Also changed doc for Package.worksonWindows, which does refer to Cygwin
...

Conflicts:
src/dm/impls/da/dalocal.c

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Merge branch 'knepley/fix-plex-examples' into knepley/feature-plex-refine-3d

* knepley/fix-plex-examples: (36 commits)
DMPlex ex7: Added missing test output
SNES ex52: Removed old Jacobian stuff

Merge branch 'knepley/fix-plex-examples' into knepley/feature-plex-refine-3d

* knepley/fix-plex-examples: (36 commits)
DMPlex ex7: Added missing test output
SNES ex52: Removed old Jacobian stuff, and fixed call to DMPlexProjectFunction() - Fixed calls for new element handling
SNES ex12: Added a performance profiling mode
DMPlex ex8: Fixed leak
PetscSection: Must reset the section when changing the number of fields
DMPlex ex7: Fixed test output - Corrected orientations in interpolation
DMPlex ex1: Fixed test output - Uniform refinement for quads changed
DMPlex: Fix overagressive checks
configure: both downloadonWindows and worksonWindows refer to MS compilers. Also fix isWindows() -> isWindows(CC).
MatXAIJSetPreallocation: use array[] notation to help out Fortran
__float128: when blas/lapack is not found instruct using f2cblaslapack
Configure: Package.downloadonWindows is supposed to mean that Windows compilers work. not Cygwin - Also changed doc for Package.worksonWindows, which does refer to Cygwin
SNES example: fix bad merge
config: only define DATAFILESPATH for non-null value
config: define lang-specific macros in petscconf.h, choose in petscsys.h
Mat: add MATOP_ values for missing functions
DMPlex: use VECSTANDARD for coordinates
PetscSF: Fixed PetscSFCreateEmbeddedSF() - We were using sf->nleaves for the leaf buffer, which is completely wrong. We have to use the largest thing in sf->mine[]
replaced ISCreateGeneral in CompositeDM with ISCreateStride. MatNest calls ISStrideGetInfo on these vectors, which was causing errors
DMPlex: Fix completely broken code in PetscSFCreateRemoteOffsets() - Non-broken example was in PetscSFDistributeSection()
...

Conflicts:
src/dm/impls/plex/plex.c

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Merge branch 'master' into prbrune/mat-matcolor

Conflicts:
src/snes/interface/snesj2.c

Merge branch 'master' into prbrune/removeunwrappedmathfunctions

Merge branch 'jed/fix-restrict-cxx' into maint

== PETSC_ARCH must be reconfigured ==

Fix C/C++ choice for PETSC_RESTRICT and PETSC_STATIC_INLINE.

* jed/fix-restrict-cxx:
config: define lang-spec

Merge branch 'jed/fix-restrict-cxx' into maint

== PETSC_ARCH must be reconfigured ==

Fix C/C++ choice for PETSC_RESTRICT and PETSC_STATIC_INLINE.

* jed/fix-restrict-cxx:
config: define lang-specific macros in petscconf.h, choose in petscsys.h

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Merge branch 'jed/attribute-deprecated-compat' into maint

Fixes error encountered when using Intel compiler and changing gcc on
PATH between configuring PETSc and building an application.

* jed/att

Merge branch 'jed/attribute-deprecated-compat' into maint

Fixes error encountered when using Intel compiler and changing gcc on
PATH between configuring PETSc and building an application.

* jed/attribute-deprecated-compat:
config: avoid string argument to __attribute((deprecated))

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Merge branch 'jed/avoid-getpwuid' into maint

The file path routines were broken because the current directory was
placed in front of the given path before checking for leading ~ or
~user. This is

Merge branch 'jed/avoid-getpwuid' into maint

The file path routines were broken because the current directory was
placed in front of the given path before checking for leading ~ or
~user. This is now fixed, along with the removal of getpwuid (a
liability on BG/Q and Cray). We still attempt to use getpwnam when
encountering ~user.

* jed/avoid-getpwuid:
Sys ex13: avoid non-portable realpath(1) in verification test
cleanup includes that are no longer needed. Also remove check for _fullpath() as the corresponding code is removed.
Sys: fix PetscGetFullPath expansion of ~ and ~user, ensure NULL termination
Sys: avoid getpwuid in file path routines
Sys: add failing test expanding ~/file-name and ~user/file-name

Conflicts:
config/PETSc/Configure.py

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Merge branch 'jed/avoid-getpwuid'

The file path routines were broken because the current directory was
placed in front of the given path before checking for leading ~ or
~user. This is now fixed, al

Merge branch 'jed/avoid-getpwuid'

The file path routines were broken because the current directory was
placed in front of the given path before checking for leading ~ or
~user. This is now fixed, along with the removal of getpwuid (a
liability on BG/Q and Cray). We still attempt to use getpwnam when
encountering ~user.

* jed/avoid-getpwuid:
Sys ex13: avoid non-portable realpath(1) in verification test
cleanup includes that are no longer needed. Also remove check for _fullpath() as the corresponding code is removed.
Sys: fix PetscGetFullPath expansion of ~ and ~user, ensure NULL termination
Sys: avoid getpwuid in file path routines
Sys: add failing test expanding ~/file-name and ~user/file-name

Conflicts:
config/PETSc/Configure.py

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Merge branch 'barry/dmvecmattypes' into shri/feature-dm-circuit

Conflicts:
src/dm/impls/makefile
src/dm/interface/dmregall.c

Merge branch 'jed/fix-restrict-cxx'

* jed/fix-restrict-cxx:
config: define lang-specific macros in petscconf.h, choose in petscsys.h

config: write CXX_FLAGS for building C++ even when clanguage=C

config: define lang-specific macros in petscconf.h, choose in petscsys.h

C and C++ compilers can use different spellings for concepts like
"restrict", "static inline", and "__func__". Previously, t

config: define lang-specific macros in petscconf.h, choose in petscsys.h

C and C++ compilers can use different spellings for concepts like
"restrict", "static inline", and "__func__". Previously, these were
defined for the "C language", meaning that they could fail if when
clanguage=C PETSc headers are included by a file that is being compiled
by the C++ compiler. This happens outside of PETSc, but also with
third-party packages like Elemental (matelem.cxx).

Karl Rupp proposed an implementation that puts the __cplusplus dispatch
into petscconf.h, but I prefer that petscconf.h contain no logic.

Reported-by: Geoffrey Irving <irving@naml.us>
Reported-by: Geoff Oxberry <goxberry@mit.edu>

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Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Ste

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Stefano
fixed bug that has appeared recently of false positive errors when there are zero local equations on coarse grids in gamg-agg.
MatSchurComplement: Must initialize KSP package
bib: fix inbook citation
Bib: Updated some refs
SNES: fix copy/paste in man page
fortran: fix KSPCONVERGEDDEFAULT and SNESCONVERGEDSKIP in fortran includes
Mat SBAIJ: avoid invalid memory read in MatSOR_SBAIJ
Revert "MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values"
PCGAMG: fix corruption for multiple solves when MatSetNearNullSpace is used
PCGAMG: remove distracting comment
KSP ex49: restrict near-null space for elasticity example with sym BC
MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values was provided ordered by row within the block rows instead of by block as it was originally designed to be. Also added more discussion to the manual pages on the expected order of the values
Fix accidental creation of the matrices in SNESNCG used for linear analogue LS.
PCGAMG: add man page for PCGAMGType
fortran: fix snesconvergedskip_() kspconvergedskip_() kspconvergeddefault*_()
rm //
Sys: new_ir changed from PetscInt to PetscObjectState - so fix mallocs to use the new type
SNES: Fixed package init in SNESLineSearchCreate()
...

Conflicts:
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex5.c
src/dm/impls/plex/plex.c
src/dm/interface/dm.c

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Merge branch 'balay/fix-fenv.h-check-on-cygwin64' into maint

Merge branch 'balay/fix-fenv.h-check-on-cygwin64'

cygwin64: _fe_dfl_env is missing in cygwin64/gcc - so update configure test to detect it.