DMDA: Make closure operations also return the size

Merge branch 'master' into barry/xcode

DMDA: Fix compiler warnings

DMDA: Add transitive closure
- Only working in 2D

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fix outdated PetscOptionsList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 '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

Merge branch 'jed/doc-restore-zeros-pointer'

* jed/doc-restore-zeros-pointer:
DMPlex: fix my mistake using NULL in place of (int) 0
doc: restore functions in PETSc zero their arguments

Conflict

Merge branch 'jed/doc-restore-zeros-pointer'

* jed/doc-restore-zeros-pointer:
DMPlex: fix my mistake using NULL in place of (int) 0
doc: restore functions in PETSc zero their arguments

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

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DMDA: Fixed 2D geometry
- Should reuse DMPlex routines

DMDA: Fix bug in 2D closure operation for cells

DMDA: Make closure operations also return the size

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 '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 'knepley/fix-fem-0d'

* knepley/fix-fem-0d:
PetscDualSpace: Updated to new PetscQuadrature names
PetscDualSpace: Add 0d corner case
PetscQuadrature: Add a 0d corner case
PetscFE:

Merge branch 'knepley/fix-fem-0d'

* knepley/fix-fem-0d:
PetscDualSpace: Updated to new PetscQuadrature names
PetscDualSpace: Add 0d corner case
PetscQuadrature: Add a 0d corner case
PetscFE: Fixed quadrature names for OpenCL
PetscSpace: Added a DG space - Defined on a set of quadrature points - Need tests
PetscQuadrature: Revamped - Removed basis tabulation - Shortened names - Added PetscQuadratureView()

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doc: restore functions in PETSc zero their arguments

This is done to prevent accidental misuse. In general, one can pass
NULL for the pointer argument to keep the pointer around for longer, but
use

doc: restore functions in PETSc zero their arguments

This is done to prevent accidental misuse. In general, one can pass
NULL for the pointer argument to keep the pointer around for longer, but
use of arrays after restoration is invalid.

Suggested-by: Wolfgang Bangerth <bangerth@math.tamu.edu>

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Merge branch 'knepley/feature-fem-dgspace' into knepley/fix-fem-0d

* knepley/feature-fem-dgspace:
PetscFE: Fixed quadrature names for OpenCL
PetscSpace: Added a DG space - Defined on a set of qu

Merge branch 'knepley/feature-fem-dgspace' into knepley/fix-fem-0d

* knepley/feature-fem-dgspace:
PetscFE: Fixed quadrature names for OpenCL
PetscSpace: Added a DG space - Defined on a set of quadrature points - Need tests
PetscQuadrature: Revamped - Removed basis tabulation - Shortened names - Added PetscQuadratureView()

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Merge branch 'master' into barry/wirth-fusion-materials

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

PetscQuadrature: Revamped
- Removed basis tabulation
- Shortened names
- Added PetscQuadratureView()

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
s

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
src/snes/impls/composite/snescomposite.c
src/snes/impls/gs/snesgs.c
src/snes/impls/nasm/nasm.c
src/snes/impls/ngmres/snesngmres.c

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

* master: (71 commits)
Sys: revert packed PetscMalloc to PetscMallocN in PetscCommBuildTwoSided_Allreduce
SNESMonitorCancel: enable fort

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

* master: (71 commits)
Sys: revert packed PetscMalloc to PetscMallocN in PetscCommBuildTwoSided_Allreduce
SNESMonitorCancel: enable fortran interface
PetscSection: Added docs for Fortran binding for VecSetValuesSection()
Vec: Removed old F90 binding for PetscSection
bgq: fix deadlock on bgq due to inconsistant values returned by getpwuid(getuid()) on runs with 256nodes [or 4096 cores]. This fix removes the reliance on PetscGetHomeDirectory() returning 'same' value across nodes. [using the fact that PetscOptionsInsertFile() uses HOMEDIR from node-0 only]
DMPlex: change order of assignment to appease -Wmaybe-initialized (gcc-4.8.1)
DMPlex: Fix 64-bit int problem in VTK
Mat: Fix for PetscSparseDenseMaxDot() for complex
Vec: Correct VecUniqueEntries() for 64-bit indices
MatSeqAIJGetArrayF90: add man pages and fix typo in MatDense version
SF docs: add link to summary page and fix title
Doc: Fixed DM code in manual
metis/parmetis: update to metis-5.1.0/parmetis-4.0.3 Also update the test output as the partitioning appears to have changed.
DMPlex: remove unused variables
blaslapack: update f,f2c tarballs to 3.4.2 version
DMPlex ex5: Added test for 2 face cohesive submesh - Fixed old tests for cohesive cell orientation
DMPlex: Put in depth label optimization
DMPlex: Fix flipping of fault normal
DMPlex: We label cells with only vertices on the fault, but they have no cone replacement
DMPlex: Fix translation to cohesive edges in 3D - They are labeled by the vertices they connect
...

Conflicts:
include/petscdmplex.h

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Merge branch 'knepley/plex-speed-tests'

* knepley/plex-speed-tests:
DMPlex: Remove unused variables
DMPlex: Fixed bug in special case for DMPlexVecGetClosure() - Need to set outgoing size if arr

Merge branch 'knepley/plex-speed-tests'

* knepley/plex-speed-tests:
DMPlex: Remove unused variables
DMPlex: Fixed bug in special case for DMPlexVecGetClosure() - Need to set outgoing size if array is passed in
DMPlex: Added special case for DMPlexVecSetClosure() - Could add more modes
DMPlex: Optimizations for DMPlexVecGetClosure() - Removed branch (seems to have little effect) - Removed calculation of size when array is provided (profiled for 20% effect)
DMPlex: Forgot one init for DMPlexVecGetClosure()
DMPlex: Must initialize argument to DMPlexVecGetClosure()
DMPlex ex9: Added ability to reuse array in VecGetClosure()
DMPlex: Allow DMPlexVecGetClosure() to take an input array
DMPlex: Fix bug in specialization of DMPlexVecGetClosure()
DMPlex: Bug fix for special case in DMPlexVecGetClosure()
DMPlex: Added optimization for depth 1 DMPlexVecGetClosure()
DMPlex ex9: Does not fail by default - Will turn back on failure once we calculate variance
SNES ex12: Cleaning up in preparation for speed testing
DMPlex: Added ex9 to test performance, put in depth 1 special case for TransitiveClosure

Conflicts:
config/builder.py
src/dm/impls/plex/plexgeometry.c
src/snes/examples/tutorials/output/ex12_5.out

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Merge branch 'knepley/plex-speed-tests' into knepley/feature-dt-fem

* knepley/plex-speed-tests:
DMPlex: Remove unused variables
DMPlex: Fixed bug in special case for DMPlexVecGetClosure() - Need

Merge branch 'knepley/plex-speed-tests' into knepley/feature-dt-fem

* knepley/plex-speed-tests:
DMPlex: Remove unused variables
DMPlex: Fixed bug in special case for DMPlexVecGetClosure() - Need to set outgoing size if array is passed in
DMPlex: Added special case for DMPlexVecSetClosure() - Could add more modes
DMPlex: Optimizations for DMPlexVecGetClosure() - Removed branch (seems to have little effect) - Removed calculation of size when array is provided (profiled for 20% effect)
DMPlex: Forgot one init for DMPlexVecGetClosure()
DMPlex: Must initialize argument to DMPlexVecGetClosure()
DMPlex ex9: Added ability to reuse array in VecGetClosure()
DMPlex: Allow DMPlexVecGetClosure() to take an input array
DMPlex: Fix bug in specialization of DMPlexVecGetClosure()
DMPlex: Bug fix for special case in DMPlexVecGetClosure()
DMPlex: Added optimization for depth 1 DMPlexVecGetClosure()
DMPlex ex9: Does not fail by default - Will turn back on failure once we calculate variance
SNES ex12: Cleaning up in preparation for speed testing
DMPlex: Added ex9 to test performance, put in depth 1 special case for TransitiveClosure

Conflicts:
config/builder.py
src/snes/examples/tutorials/ex52.c
src/snes/examples/tutorials/output/ex12_10.out
src/snes/examples/tutorials/output/ex12_11.out
src/snes/examples/tutorials/output/ex12_5.out
src/snes/examples/tutorials/output/ex12_6.out
src/snes/examples/tutorials/output/ex12_8.out
src/snes/examples/tutorials/output/ex12_9.out

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DMPlex: Must initialize argument to DMPlexVecGetClosure()

Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

daimpl.h was never fixed? Well it is now

Hg-commit: a4f3f6d7e4f165ac5276405a089a596a28adc0b3