Plex: Move DM migration into subroutine that deals with point numberings

DMPlexMigrate can optionally back out any previous local numbering or
assume a zero-to-all-ranks pattern to derive the new lo

Plex: Move DM migration into subroutine that deals with point numberings

DMPlexMigrate can optionally back out any previous local numbering or
assume a zero-to-all-ranks pattern to derive the new local numbering.

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Plex: Bug fix in DMPlexDistribute; only kill the migration SF once

Plex: Enable n-level overlap in DMPlexDistribute

Adds a utility function DMPlexPartitionLabelAdjacency, which adds a full
level of adjacency to the partitioning label.

Plex: Switch initial distribution to using partition labels

After creating a cell partition we now convert this into a label and
reuse the same utility routines to add the closure and transform the

Plex: Switch initial distribution to using partition labels

After creating a cell partition we now convert this into a label and
reuse the same utility routines to add the closure and transform the
label into a migration SF.

Note: Obsoletes PetscSFConvertPartition and DMPlexCreatePartitionClosure

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Merge branch 'knepley/fix-plex-examples-refinement'

* knepley/fix-plex-examples-refinement:
Plex ex12: Add test output
Plex: Restore Fortran binding for DMPlexDistribute()
SNES ex12: Fix SetFr

Merge branch 'knepley/fix-plex-examples-refinement'

* knepley/fix-plex-examples-refinement:
Plex ex12: Add test output
Plex: Restore Fortran binding for DMPlexDistribute()
SNES ex12: Fix SetFromOptions usage
SNES ex12: Fix refinement usage

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Plex: Add DMPlexPartitionLabelClosure

Adds the closure of all points to the partition label.

Plex: Add DMPlexPartitionLabelInvert utility routine

Given a label describing a send pattern, this routine creates the
according receive pattern from which we can build the SF.

Plex: Add DMPlexPartitionLabelCreateSF utitlity routine

This routine creates an SF from a DMlabel assigning ranks
to remote root numbers.

Plex: Restore Fortran binding for DMPlexDistribute()

Merge branch 'master' into knepley/fix-plex-examples-refinement

* master: (62 commits)
Plex+Label: Fix logic for label distribution - It is restrictive now, but doing it right would mean a ton of

Merge branch 'master' into knepley/fix-plex-examples-refinement

* master: (62 commits)
Plex+Label: Fix logic for label distribution - It is restrictive now, but doing it right would mean a ton of infrastructure I think
Plex ex12: Fix output after label distribution fix
Plex: Only call SetFromOptions() after Distribute, since we cannot avoid it
TS ex11: Since DMPlexDistribute() calls SetFromOptions(), do not call it again, and cleaned up tests
Plex+FV: If using FVM adjacency, do not create ghost cells for faces in the overlap, or set BC on them
Plex: If using FVM adjacency, we must include the closure in the overlap
Plex+Label: All processes with a valid label should participate in label distribution - Formerly it was just proc 0
Plex: Add check that parallel renumbering fully covers the cone points
Plex: For one level adjacency, include the point itself since this makes sense when looking in parallel from the overlap
Plex: Cannot Malloc2() the arrays passed to PetscSFSetGraph()
Plex: Preallocation fixes for indegree > 1 - Again this should be rewritten
SNES ex62: Changes to output for fixes with quads
Plex+Label: Set default output flag to PETSC_TRUE
Plex ex1: Fixed LaTeX output
Plex ex12: Fixed overlap test
Plex: Fixed incorrect usage of PetscSFGatherBegin/End() in preallocation - This should be rewritten using new style
PetscSF: Incorrect check for computed degrees
Builder: Fix bad search and replace
Configure: Fix for Barry's change to organization - I do not know what happened here
Builder: Fix for Barry's change
...

Conflicts:
src/snes/examples/tutorials/ex12.c

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Merge branch 'mlange/feature-parallel-distribute'

* mlange/feature-parallel-distribute: (33 commits)
Plex+Label: Fix logic for label distribution - It is restrictive now, but doing it right would

Merge branch 'mlange/feature-parallel-distribute'

* mlange/feature-parallel-distribute: (33 commits)
Plex+Label: Fix logic for label distribution - It is restrictive now, but doing it right would mean a ton of infrastructure I think
Plex ex12: Fix output after label distribution fix
Plex: Only call SetFromOptions() after Distribute, since we cannot avoid it
TS ex11: Since DMPlexDistribute() calls SetFromOptions(), do not call it again, and cleaned up tests
Plex+FV: If using FVM adjacency, do not create ghost cells for faces in the overlap, or set BC on them
Plex: If using FVM adjacency, we must include the closure in the overlap
Plex+Label: All processes with a valid label should participate in label distribution - Formerly it was just proc 0
Plex: Add check that parallel renumbering fully covers the cone points
Plex: For one level adjacency, include the point itself since this makes sense when looking in parallel from the overlap
Plex: Cannot Malloc2() the arrays passed to PetscSFSetGraph()
Plex: Preallocation fixes for indegree > 1 - Again this should be rewritten
SNES ex62: Changes to output for fixes with quads
Plex ex1: Fixed LaTeX output
Plex ex12: Fixed overlap test
Plex: Fixed incorrect usage of PetscSFGatherBegin/End() in preallocation - This should be rewritten using new style
PetscSF: Incorrect check for computed degrees
Builder: Fix for Barry's change
PetscSF: Fixes for sparse leaves - When sf->mine exists, the leaves can be numbered non-sequentially. This causes allocation based upon sf->nleaves to underallocate. Replacing sf->nleaves with the maximum leaf number is sufficient in this case.
Plex: Fix leaks
Configure: How did this break?
...

Conflicts:
config/builder.py

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Merge branch 'knepley/feature-plex-partitioner-shell'

* knepley/feature-plex-partitioner-shell:
Plex: Cleanup of examples to use new interfaces
Plex: Added DMPlexCreateFromFile() - Dispatches to

Merge branch 'knepley/feature-plex-partitioner-shell'

* knepley/feature-plex-partitioner-shell:
Plex: Cleanup of examples to use new interfaces
Plex: Added DMPlexCreateFromFile() - Dispatches to the right constructor based on extension
Plex ex1: Added test partitioner
Plex: Added DMPlexGetPartitioner() and PetscPartitionerShellSetPartition()
PetscSection: Added PetscSectionCopy()
Plex ex1: Cleaned up mesh creation - Now use -dm_refine for uniform refinement
Plex: Remove superfluous argument from DMPlexDisitrbute()
Plex: Fixed Fortran stub
PetscFV: Lots of small naming fixes
Partitioner+Plex: Added PetscPartitioner class - Plex holds a PetscPartitioner - Changed args so that PetscSections are modified, not created (also of DMPlexEnlargePartition) - Now partition routine takes a number of partitions instead of assuming commSize - Added a shell partitioner intended to be used for regression testing

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

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Merge branch 'knepley/feature-plex-label-output'

* knepley/feature-plex-label-output:
Plex+Label: Set default output flag to PETSC_TRUE
Plex+Label: Added output flag for labels - Meant storing l

Merge branch 'knepley/feature-plex-label-output'

* knepley/feature-plex-label-output:
Plex+Label: Set default output flag to PETSC_TRUE
Plex+Label: Added output flag for labels - Meant storing labels in a struct inside Plex - Added DMPlexGetLabelByNum() - Added DMPlexGet/SetLabelOutput() - Got rid of most of the mucking with the internal label storage

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Merge branch 'knepley/feature-parallel-partition'

* knepley/feature-parallel-partition:
Plex: Silence compiler warning
Plex: Needs custom Fortran binding
Plex: Fix distribution for meshes with

Merge branch 'knepley/feature-parallel-partition'

* knepley/feature-parallel-partition:
Plex: Silence compiler warning
Plex: Needs custom Fortran binding
Plex: Fix distribution for meshes without coordinates
Plex ex12: Added test from Michael
Plex: Added methods to support distributed overlap calculation - Added DMPlexCreateTwoSidedProcessSF() - Added DMPlexDistributeOwnership() - Added DMPlexCreateOverlap()
PetscSF: Fix ComputeDegree and GetMultiSF for sparse SFs
Plex: Added DMPlexDistributeFieldIS() - Small doc fix
Plex: DMPlexCreateProcessSF() is now documented and the outputs are optional - The root space is also correct
PetscSF: The declaration of PetscSFNode should be in the types header
Plex ex12: Add overlap
Plex ex12: Added test for parallel partitioning
SNES ex12: Misspelling
Plex ex1: Typo
Plex: Fix LaTeX mesh output

Conflicts:
include/petscdmplex.h

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Plex+Label: Fix logic for label distribution
- It is restrictive now, but doing it right would mean a ton of infrastructure I think

Plex: Only call SetFromOptions() after Distribute, since we cannot avoid it

Plex: If using FVM adjacency, we must include the closure in the overlap

Plex+Label: All processes with a valid label should participate in label distribution
- Formerly it was just proc 0

Plex: Add check that parallel renumbering fully covers the cone points

Plex: For one level adjacency, include the point itself since this makes sense when looking in parallel from the overlap

Plex: Cannot Malloc2() the arrays passed to PetscSFSetGraph()

Merge branch 'knepley/feature-plex-partitioner-shell' into mlange/feature-parallel-distribute

* knepley/feature-plex-partitioner-shell:
Plex: Cleanup of examples to use new interfaces
Plex: Adde

Merge branch 'knepley/feature-plex-partitioner-shell' into mlange/feature-parallel-distribute

* knepley/feature-plex-partitioner-shell:
Plex: Cleanup of examples to use new interfaces
Plex: Added DMPlexCreateFromFile() - Dispatches to the right constructor based on extension
Plex ex1: Added test partitioner
Plex: Added DMPlexGetPartitioner() and PetscPartitionerShellSetPartition()
PetscSection: Added PetscSectionCopy()
Plex ex1: Cleaned up mesh creation - Now use -dm_refine for uniform refinement
Plex: Remove superfluous argument from DMPlexDisitrbute()
Plex: Fixed Fortran stub

Conflicts:
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexdistribute.c

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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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Plex: Fix leaks

Plex: Silence compiler warning