Merge branch 'master' into knepley/fix-configure-petsc-dep

* master: (210 commits)
error out on special cases where DMLocalToGlobal_DA won't work
remove unneed uses of local DM vectors and DMLoc

Merge branch 'master' into knepley/fix-configure-petsc-dep

* master: (210 commits)
error out on special cases where DMLocalToGlobal_DA won't work
remove unneed uses of local DM vectors and DMLocalToGlobalBegin/End in examples removed to prevent cut and paste repeats of their use
openmpi: update to version 1.8.3
added more movies and pubs
more movies
MatGetDiagonalBlock() can be called before matrix is assembled
added a couple more movies/images
PetscLogEventGetId() was missing public prototype
simply output from make streams benchmark test
c2html: fixup so that C2HTML make variable is set [similar to cmake.py]
chaco: current blas test does'nt work with Cray CC [which automatically links with blas] and linux - where -lm needs to be listed explicitly. Switch the test to check if we are using PETSc modifled chaco
builddist: always install c2html/sowing
argonne logo for users manual cover
Remove PETSC_HAVE_CUSP_SMOOTHED_AGGREGATION, use PETSC_HAVE_CUSP instead.
mpich: use older tarball with cygwin/gnu compilers
updated information about packages PETSc can use in users manual
Updated users manual to latest ANL Report format requirements
mpich: update to mpich-3.1.3.tar.gz - remove -download-mpich-mpe [mpich no longer packages mpe] - remove -download-mpich-shared. It was added as a split from --with-mpi-shared to --known-mpi-shared and --download-mpich-shared in 50237a55163f90ac7341b723c6422dfa1dbce792 removing this gives back the control of shared=0/1 to package.py - remove download_solaris as the new tarball works with both gcov and on solaris - remove MPICHInstall() [and use GNUPackage.Install()] as the new tarball fixes 'make clean' requiring sudo
added more images and PETSc pubs
Doc: More refs
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Merge branch 'barry/fix-dmlocaltoglobal_da'

remove unneed uses of local DM vectors and DMLocalToGlobalBegin/End in examples
removed to prevent cut and paste repeats of their use

Merge branch 'tisaac/feature-fe-geom-dim' into tisaac/plex-flexible-projection

Use the new PetscFECellGeom

Conflicts:
include/petscdmplex.h
include/petscfe.h
src/dm/impls/plex/plexfem.c

Merge branch 'tisaac/thplex'

This merge brings in related work in the following areas:
- Added a local constraint matrix to DM (see DMSetDefaultConstraints())
- Added point-to-anchor-point constrain

Merge branch 'tisaac/thplex'

This merge brings in related work in the following areas:
- Added a local constraint matrix to DM (see DMSetDefaultConstraints())
- Added point-to-anchor-point constraints in DMPlex (see
DMPlexSetAnchors()), which build on the DM constraints
- Added hierarchically-constrained points to DMPlex (see
DMPlexSetReferenceTree(), DMPlexSetTree()), which builds on the anchor
constraints
- Tests for these constraints in src/dm/impls/plex/examples/ex3.c (try
runex3_* examples in that directory)
- Added quadrature order (see PetscQuadratureGet/SetOrder()) (work by
Matt Knepley)
- Added default return values for DMGetCoordinateDim() (defaults to
DMGetDimension())

Conflicts:
include/petscdmplex.h
src/dm/dt/interface/dt.c
src/dm/impls/plex/examples/tests/ex3.c
src/dm/impls/plex/makefile
src/dm/impls/plex/plexfem.c

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DM: remove deprecated MatGetVecs()

Merge branch 'knepley/feature-fe-fv-hybrid'

* knepley/feature-fe-fv-hybrid: (43 commits)
PetscFE: Small fixes
Plex+SNES: Volumes are PetscReal
Plex+SNES: Missing declaration
TS ex11: Remove

Merge branch 'knepley/feature-fe-fv-hybrid'

* knepley/feature-fe-fv-hybrid: (43 commits)
PetscFE: Small fixes
Plex+SNES: Volumes are PetscReal
Plex+SNES: Missing declaration
TS ex11: Remove unused var
Plex+SNES+TS: Complete reorganization of residual evaluation - Now both FE and FV examples use the same method, but there are a bunch of switches which should be eliminated - There is a confusion about IFunction and RHS, but I think they can both be in one function - Added DMPlexSNESGetGeometryFVM() and DMPlexSNESGetGradientFVM() - Added DMPlexGet/RestoreCellFields() and DMPlexGet/RestoreFaceFields() and DMPlexGet/RestoreFaceGeometry() - I think that FV geometry caching needs to be redone - Added DMPlexReconstructGradients_Internal() - Added DMPlexComputeBdResidual_Internal() which does not work for FV - Replaced DMPlexComputeResidualFEM_Internal() with DMPlexComputeResidual_Internal()
Plex: Added DMPlexInsertBoundaryValues() - Unified FE and FV boundary values
Plex: DMPlexProjectFunctionLableLocal() gets discretizations from the DM now
Plex: Added DMPlexComputeGradientFVM()
PetscDS: Fix up some functions to work for both FV and FE
PetscFV: Change PetscFVIntegrateRHSFunction() to get info from PetscDS
TS ex11: There is only one field in our current paradigm - We would need to split Riemann solvers for multiple fields right now
Plex+TS: Remove use of computeGradients in favor of check for dmGrad
TS ex11: Updated interface calls
Plex+TS: Change DMPlexTSGetGradientDM() to automatically construct the gradient info, DMPlexTSSetRHSFunctionLocal() can now be replaced by the DMTS version - Remove unnecessary declarations
Plex+SNES: Add missing declaration
Plex+FE: Removed all use of PetscCellGeometry, Changed FE integration to use PetscFECellGeom
DMSNES+Plex: Added DMPlexSNESGetGeometryFEM() to cache geometry
PetscDualSpace: Remove use of PetscCellGeometry in PetscDualSpaceApply() - Fixed up calls to it for projection into spaces
DMDA: Remove use of PetscCellGeometry in DMDAProjectFunctionLocal()
Plex: Added DMPlexComputeGeometryFEM() and PetscFECellGeom structure
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DM+Plex: change the collective status of default constraints, anchors, and reference tree

The default constraints, anchors, and reference tree are changed to have
PETSC_COMM_SELF communicators.

The

DM+Plex: change the collective status of default constraints, anchors, and reference tree

The default constraints, anchors, and reference tree are changed to have
PETSC_COMM_SELF communicators.

The reasoning is that we would like tree constraints to cause only
minimal changes to the solution workflow demonstrated in
snes/examples/tutorials/ex12.c. We would like to insert only the
following code:

/* ... (construct/choose a reference tree) */
DMPlexSetReferenceTree(dm,refTree);
/* ... (construct the tree structure) */
DMPlexSetTree(dm,...);

This means that the presence of some type of constraints may not be
detected until DMPlexMatSetClosure(), within a cell loop. If that
happens, the following call graph occurs:

DMPlexMatSetClosure(dm,...) calls
DMGetDefaultConstraints(dm,...) calls
*DMCreateDefaultConstraints_Plex(dm,...) calls
DMPlexGetAnchors(dm,...) calls
*DMPlexCreateAnchors_Tree(dm,...)
DMPlexComputeAnchorMatrix_Tree_FromReference(dm,...) calls
DMGetDefaultConstraints(refTree,...) calls
*DMCreateDefaultConstraints_Plex(refTree,...) calls
DMPlexGetAnchors(refTree,...) calls
*DMPlexCreateAnchors_Tree(refTree,...)

The objects created in this cascade have to be local.

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Plex: complete rename of constraints to anchors, make matrix construction automatic.

Now all the user has to do is set the reference tree, set the tree, and
the constraint matrix is automatically co

Plex: complete rename of constraints to anchors, make matrix construction automatic.

Now all the user has to do is set the reference tree, set the tree, and
the constraint matrix is automatically constructed in the call to
DMGetDefaultConstraints()

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DM: allow DMGetDefaultConstraints() to take NULL arguments.

I anticipate usage where only one of the arguments, e.g. the matrix, is
given, as a way to check for the presence of constraints.

DM: put constraint hooks into DMGlobalToLocalEnd() and DMLocalToGlobalBegin().

I put this directly into the functions instead of into the linked list
of hooks. My reasoning is that if constraints a

DM: put constraint hooks into DMGlobalToLocalEnd() and DMLocalToGlobalBegin().

I put this directly into the functions instead of into the linked list
of hooks. My reasoning is that if constraints are present, they should
be considered atomic with the PetscSFBcast()/PetscSFReduce(), and that
allowing other user-defined hooks to come between the communication and
the constraint hooks could result in the user trying to access or set
constrained values before they are defined.

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DM: initialize and destroy dm constraints.

DM: added DMGetDefaultConstraints()/DMSetDefaultConstraints().

I originally put the constraint matrix in DMPlex, but the constraint
matrix implies a choice of default section, whereas the same DMPle

DM: added DMGetDefaultConstraints()/DMSetDefaultConstraints().

I originally put the constraint matrix in DMPlex, but the constraint
matrix implies a choice of default section, whereas the same DMPlex
should be able to be referenced by multiple DMs with different sections.
This commit starts the process of moving the section-dependent
components into the DM implementation.

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DM: set default embedding dimension

dm: added LocalToGlobalHook

Merge branch 'jed/fix-checkpointer-char' into maint

* jed/fix-checkpointer-char:
Sys: PetscCheckPointer PETSC_CHAR checks char*, not char**
Sys: PetscCheckPointer for PETSC_CHAR checks char*, no

Merge branch 'jed/fix-checkpointer-char' into maint

* jed/fix-checkpointer-char:
Sys: PetscCheckPointer PETSC_CHAR checks char*, not char**
Sys: PetscCheckPointer for PETSC_CHAR checks char*, not char**

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DM: Fixed memory leak

Merge branch 'knepley/fix-dm-composition'

* knepley/fix-dm-composition:
DM: Removed code to uncompose nullspace/pmat - This was to prevent reference cycles, which happen with MatNullSpace using DM

Merge branch 'knepley/fix-dm-composition'

* knepley/fix-dm-composition:
DM: Removed code to uncompose nullspace/pmat - This was to prevent reference cycles, which happen with MatNullSpace using DM Vecs, but its fragile - My current solution is to strip out DM from Vecs in a MatNullSpace, but that sucks too. Need a better solution

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Merge branch 'knepley/feature-dm-dimension-handling'

* knepley/feature-dm-dimension-handling:
DM: Fixed DMDASetDim() in examples
Plex: Fix for isoparametric geometry
Plex: Complex fix
TS ex1

Merge branch 'knepley/feature-dm-dimension-handling'

* knepley/feature-dm-dimension-handling:
DM: Fixed DMDASetDim() in examples
Plex: Fix for isoparametric geometry
Plex: Complex fix
TS ex11: Fixed calls to DMSetCoordinateSection()
DM: FIxed DMClone() to copy dimension
Plex+DA: Now cell geometry routine can take a PetscFE in order to evaluate at quadrature points - We evaluate isoparametrically at the quadrature points - Changed DMDAComputeCellGeometry() --> DMDAComputeCellGeometryFEM() - Changed DMPlexComputeCellGeometry() --> DMPlexComputeCellGeometryFEM() - Added DMPlexComputeCellGeometryAffineFEM()
DM: Added a embedding dimension, different from the topological dimension - This can now be set in DMSetCoordinateSection(), or it can be automatically determined
Plex: Fix output for ex4
DM: Added DMGetDimPoints() - This replicates DMPlex/DAGetDepthStratum(), but uses the dimension which people have said is more intuitive
DM: Move dimension up into DM - Both DA and Plex had this and I think it makes sense

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

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Merge branch 'jed/fix-checkpointer-char'

* jed/fix-checkpointer-char:
Sys: PetscCheckPointer PETSC_CHAR checks char*, not char**
Sys: PetscCheckPointer for PETSC_CHAR checks char*, not char**

Sys: PetscCheckPointer PETSC_CHAR checks char*, not char**

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

DM: FIxed DMClone() to copy dimension

DM: Added a embedding dimension, different from the topological dimension
- This can now be set in DMSetCoordinateSection(), or it can be automatically determined

DM: Added DMGetDimPoints()
- This replicates DMPlex/DAGetDepthStratum(), but uses the dimension which people have said is more intuitive