Merge remote-tracking branch 'origin/maint'

Merged in haplav/fix-hdf5v-circular-dependencies (pull request #1643)

fix hdf5v circular dependencies

Approved-by: Matthew Knepley <knepley@gmail.com>
Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

Merged in haplav/fix-hdf5v-circular-dependencies (pull request #1643)

fix hdf5v circular dependencies

Approved-by: Matthew Knepley <knepley@gmail.com>
Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Jed Brown <jed@59a2.org>

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Move HDF5 array IO stuff from sys to vec.

- Fix issue 288.
- Moved PetscViewerHDF5Load,PetscViewerHDF5ReadSizes and their helpers from
src/sys/classes/viewer/impls/hdf5/hdf5v.c
into the new fi

Move HDF5 array IO stuff from sys to vec.

- Fix issue 288.
- Moved PetscViewerHDF5Load,PetscViewerHDF5ReadSizes and their helpers from
src/sys/classes/viewer/impls/hdf5/hdf5v.c
into the new file
src/vec/is/utils/hdf5io.c
- PetscViewerHDF5Load() header moved from viewerimpl.h to petscis.h
- PetscViewerHDF5ReadSizes() header moved from petscviewerhdf5.h to petscis.h

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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 '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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Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in m

Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in master (the introduction of MatFactorGetError()) therefor need
to merge in master and use the new construct before merging to next

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

fixed merge with master

Merge branch 'tisaac/dualspace-feature-symmetry'

In finite element assembly, to compute a residual or assemble a Jacobian
on an element, the dual space functionals of a reference finite element are

Merge branch 'tisaac/dualspace-feature-symmetry'

In finite element assembly, to compute a residual or assemble a Jacobian
on an element, the dual space functionals of a reference finite element are related
(i.e., pushed forward) to the functionals that make of the degrees of
freedom of the discretized system.

In doing so, we have to draw a correspondence between the boundary
points of the reference element (its edges and vertices) and the
boundary points of each cell in the mesh. Sometimes, this
correspondence is not perfect, because the orientations of the boundary
points of a cell may be different than the orientations of the boundary
points of the reference element. For example, an edge that runs
clockwise around the reference element may map onto an edge that runs
counter-clockwise around the real cell.

For some finite elements (such as the most common P1 Lagrange finite
elements) this doesn't matter. But for others---high-order elements,
H-div and H-curl conforming elements---a difference in orientation
affects the mapping between reference functionals and degrees of
freedom.

The simplest example is a high-order nodal Lagrange finite element in
2D: the degrees of freedom on an edge of the reference element are
numbered left-to-right, but if the orientation of the real edge is
reverse, then we must read/write degrees of freedom right-to-left.

Things get more complicated in 3D: a quadrilateral face between
hexahedra may have any of 8 different orientations (that make of the
dihedral symmetries), and each one corresponds to a different reordering
of the 2D grid of nodes supported on that quadrilateral.

Things also get more complicated for H-div elements. Functionals on the
interfaces between cells represent the flux from one cell to another,
and thus have direction. Reversing the orientation of an edge changes
the sign of the mapping between the reference functional and the degree
of freedom.

To assemble generic finite elements, we thus need to accommodate
transforms between reference functionals and degrees of freedom that
encompass (1) permutations, and (2) scalar multipliers.

This branch accomplishes this in two steps:

- We add PetscDualSpaceGetSymmetries() to the interface, to allow a dual
space to describe how symmetries of the mesh points affect
referent-to-real maps of functionals.

- We add PetscSectionSym, an object that encapsulates symmetries of the
degrees of freedom whose layout is described by a PetscSection.

When a section is created from a DM that has a finite element
discretization in its PetscDS, it will automatically construct the
appropriate PetscSectionSym when it creates a PetscSection to describe a
discretized function space.

If a PetsFE finite element discretization is not used, the user can
create a PetscSectionSym for their degrees of freedom for themselves.
We give an example of this for spectal elements in
src/dm/impls/plex/examples/tutoerials/ex6.c.

* tisaac/dualspace-feature-symmetry: (22 commits)
cast memzeros to void to avoid compiler complaints about const qualifiers
DMPlex: fix stray PetscScalar to PetscReal
DMPlex: fix stray PetscScalar to PetscReal
Plex tutorials ex6: use symmetries in SEM example
Plex tests ex3: added high order tests
Plex tests ex3: add matrix-free near null space test
DMPlex: fix PetscInt %D PetscPrintf character
DMPlexTree: use symmetries when computing constraint matrices
DMPlex: use symmetries in DMPlexGetIndicesPoint{Fields}_Internal() and DMPlexAnchorsModifyMat()
DMPlex: use PetscSectionGet/RestorePointSyms() in DMPlexVecGet/SetClosure()
DMPlex: added DMPlexGet/RestoreCompressedClosure()
DMPlex: added DMPlexGetPointDualSpaceFEM()
DMPlex: set PetscSectionSym in DMPlexCreateSectionInitial()
DMLabel: added PETSCSECTIONSYMLABEL
PetscSection: add PetscSectionSym
PetscDualSpace: added PetscDualSpaceGetSymmetries()
PetscDualSpace_Lagrange: setup recursively on dimension
PetscDualSpace_Lagrange: order functions now go after tuple used
PetscDualSpace_Lagrange: use lexicographic order for nodes
DMPlex: added DMPlexComputePointGeometry_Internal()
...

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PetscSection: add PetscSectionSym

This object's is essentially a Petsc-idiom way of letting the user
specify implementations of

PetscSectionGetPointSyms()
PetscSectionRestorePointSyms()
PetscSectio

PetscSection: add PetscSectionSym

This object's is essentially a Petsc-idiom way of letting the user
specify implementations of

PetscSectionGetPointSyms()
PetscSectionRestorePointSyms()
PetscSectionGetFieldPointSyms()
PetscSectionRestoreFieldPointSyms()

Like PetscDualSpaceGetSymmetries(), the symmetries are descibed by R *
P, where R is a flip (or rotation with complex scalars). I had thought
about a more managed approach, like PetscSectionGet/SetValues, which
entirely hid the existence of symmetries to begin with, but:

- then you have to differentiate between different PetscDataTypes (e.g.,
for indices, just perform the permutation, not the flips/rotations),
and
- what about inserting an element matrix? When inserting an element
matrix, it makes the most sense to apply flips/rotations to the
element matrix, and the permutations to the indices where the matrix
is to be inserted with MatSetValues().

so in the end I decided to just provide a simple interface to pass the
symmetries to the users and let them figure out how they want to use
them.

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Merge branch 'master' into pr263/PierreBdR/ts-domain-error-in-stage/master

Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of

Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of git. I think it is not justified to ever have anything in next for more than a few weeks at most.
Either take it out of next if it is broken or put it in master if it is not broken. Hanging around in next but
not master for ever is not a good policy.

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Merge branch 'master' into knepley/solkx

* master: (6933 commits)
Bib: Added reference
Includegraph: Updated for compatibility with new folder layout.
Add SNESLineSearchReason to fortran inclu

Merge branch 'master' into knepley/solkx

* master: (6933 commits)
Bib: Added reference
Includegraph: Updated for compatibility with new folder layout.
Add SNESLineSearchReason to fortran includes Also truncate names to fit 32 char fortran limit
fix compile warnings /usr/home/balay/petsc.clone-2/src/vec/vec/interface/vector.c:1944: warning: division by zero in '1.0e+0 / 0.' /usr/home/balay/petsc.clone-2/src/ksp/ksp/interface/itfunc.c:508: warning: 'vec_rhs' may be used uninitialized in this function
updated output for new trust region initial size
initial size of the trust region is set as a percent of the norm of the initial guess, it should not be related to the initial norm of the function (which is kind of nuts).
The default bounds for SNESVISetVariableBounds() in the manual page were reversed from correct values
Bib: Added refs
Bib: Update MPICH webpage
Plex: Forgot to close file
removed nonexistent ex46f from makefile test rule
Revert "fixed bad merge into master"
fixed bad merge into master
fix memory leak in mkl_pardiso fix some formatting in mkl_pardiso code
mv runex111 from TESTEXAMPLES_C to TESTEXAMPLES_DATAFILESPATH
Mat+Doc: More Fortran docs
Plex ex3: Run tests with the correct number of field components
Bib: Added TetGen cite
parmetis: make sure 'ldd libparmetis.so' points to the correct libmetis.so that its linked with.
small fix as reported by the nightly test
...

Conflicts:
config/builder.py

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Merge branch 'master' into tisaac/dmforest

directory layout changed again: merging to switching branches back and forth
doesn't cause reconfigure to have a hard time

* master: (357 commits)
remov

Merge branch 'master' into tisaac/dmforest

directory layout changed again: merging to switching branches back and forth
doesn't cause reconfigure to have a hard time

* master: (357 commits)
removed nonexistent ex46f from makefile test rule
Revert "fixed bad merge into master"
fixed bad merge into master
fix memory leak in mkl_pardiso fix some formatting in mkl_pardiso code
mv runex111 from TESTEXAMPLES_C to TESTEXAMPLES_DATAFILESPATH
Mat+Doc: More Fortran docs
Bib: Added TetGen cite
parmetis: make sure 'ldd libparmetis.so' points to the correct libmetis.so that its linked with.
small fix as reported by the nightly test
add a test for MatPtAP()
small cleanup; add tests
cleanup MatPtAPSymbolic_MPIAIJ_MPIAIJ()
Fix nonzerostate tracking in all MATMPI types.
update location of test matrices in faq.html file
unused variable still declared
Fix for MatLoad_MPIDense() from sparsely stored matrix also fix for MatLoad_MPIDense_DenseInFile() when matrix has not had its local sizes preset by user
Preserve the B nonzerostate during disassembly.
TSEvent: Fix arch-mswin nightly errors due to declaring variables in the middle of a function.
Fix error in parallel loading of dense format matrix
removed KSPSetNullSpace() since mat already carries that information and having two locations for it is confusing, unnecessary and prone to error added MatSetTransposeNullSpace() for providing the null space of the transpose of the matrix and added support in KSPSolve() to remove this null space from the right handside of the linear system thus making the system consistent.
...

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Merge branch 'master' into knepley/feature-composable-callbacks

* master: (151 commits)
PetscMalloc: Fix handling of zero-sized allocations
add note to DMGetLocal/GlobalVector() about intended s

Merge branch 'master' into knepley/feature-composable-callbacks

* master: (151 commits)
PetscMalloc: Fix handling of zero-sized allocations
add note to DMGetLocal/GlobalVector() about intended short-time usage of the vectors.
sf: use patched openmpi tarball that has a potential fix for sf example hang
SNES problems that set VI bounds must use a VI solver since the other solvers ignore the bounds
pounders viewer did not cast PetscReal to double in printf nor use %D instead of %d
fix ts ex20adj
fix ts theta
fixed another variable declaration in the middle of a code block
example main() had PetscInt return type and argument that should be int
DMDAVTKWriteAll_VTS: Fix handling of higher-dimension coordinates
fixed example that declared variables in the middle of a function
C programs do not return PetscInt nor do they take an argument that is PetscInt, fixed example that did
You cannot declare variables in the middle of functions in PETSc.
add ierr checking to PetscOptionsBegin/End() in example
configure: add error check if user specifies PETSC_ARCH=-dbg [i.e starts with a '-']
scale norm of vector difference by norm of vector to insure it is small enough to consider the two vectors equal
missing PetscViewerDestroy() added
MatNestGetISs: use custom fortranstub to handle PETSC_NULL_OBJECT
update location of open-mx website on FAQ page
If the user sets bounds and calls a solver that does not support them, throw an error.
...

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Merge branch 'pr192/Fande-Kong/scalable-matincreaseoverlap/master' of https://bitbucket.org/petsc/petsc

Merged petsc/petsc into master

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/mat/impls/aij/mpi/mumps/mumps.c
s

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/mat/impls/aij/mpi/mumps/mumps.c
src/mat/impls/is/matis.h

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Merged master into semihozmen/ksp-fcg-eigen-comp-support

Merge branch 'master' into pr192/Fande-Kong/scalable-matincreaseoverlap/master

Needed to merge master to update to new calling sequence PetscCommBuildTwoSided

Merged petsc/petsc into master

Merge branch 'barry/fix-directory-layout'

updated PETSc directory layout to match standard packaging strategies

include/petsc finclude,private,mpiuni
lib/petsc conf
bin/petsc*

Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
thi

Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
this branch. Matt's and my fixes in DMPlex will also be relevant.

* master: (1557 commits)
MatLoad_MPIDense() always allocated array space even if it was previously provided
Clarified lumping options for PCFieldSplitSchurPreType SELFP.
fixed up PetscInfo in GAMG
TSErrorWeightedNorm[2|Infinity]: API changes
MatLoad_SeqDense() always allocated new space for the data even if the user already provided it
Fixed DMCompositeGetAccessArray() to support readonly vectors
Fix obviously-wrong aspects of documentation on SNESVINEWTONRSLS and SNESVINEWTONSSLS.
fixed example to compile - demonstrates a bug
var name 'len' was F90 key word
For user provided Jacobian functions they should always assembly into the second matrix, the one from which the preconditioner is built because the first may be used as matrix-free with -snes_mf_operator
Suggest --with-64-bit-indices if users mistakenly use --with-64bit-indices
Fix configure logging of integer size.
missing underscore in #define of vecgetarrayread translation of fortran stub for VECGETARRAYREAD
updated test output files to reflect differences introduced previously in PCView output
-ksp_type preonly does not support -ksp_monitor_short so remove from test line to prevent extranious warning output
missing CHKERRQ; and ugly double declaration of ierr
Plex ex3: For want of a semicolon, the kingdom was lost
MatSetValuesMPISBAIJ will now print correct global indices when error generated due to new nonzero location
completed basic use of MatSetValuesBlocked_SeqBAIJ_Inlined() by MatSetValuesBlocked_MPIBAIJ() to allow proper global indices being printed when error generated by new nonzero locations.
Added inline version of MatSetValuesBlocked_SeqBAIJ() to be used by MatSetValuesBlocked_MPIBAIJ() to print error message for nonzero block with global indices
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Merge branch 'master' into shri/ts-is-for-differential-variables

Conflicts:
include/petsc-private/tsimpl.h
src/ts/impls/eimex/eimex.c
src/ts/interface/ts.c