Merge branch 'barry/remove-unneeded-paren-petscmalloc'

Conflicts:
src/mat/impls/baij/seq/baij.c

Merge branch 'master' into mlange/refactor-plex-distribute

Conflicts:
src/dm/impls/plex/examples/tests/output/ex12_1.out
src/dm/impls/plex/examples/tests/output/ex12_2.out

convert some PetscMalloc() to PetscMalloc1()
remove unneeded () in first argument to PetscMalloc/Calloc1()
fixes for MATLAB examples

Plex: Enabling parallel re-partitioning via DMPlexDistribute

This commit adds several fixes that allow DMPlexDistribute to be used on
an already distributed plex. It fixes the partition graph genera

Plex: Enabling parallel re-partitioning via DMPlexDistribute

This commit adds several fixes that allow DMPlexDistribute to be used on
an already distributed plex. It fixes the partition graph generation
and stratifies the migration SF used in DMPlexDistribute.

It also changes the point ordering again by always putting local points
first in DMPlexPartitionLabelInvert. This is done to deal with ParMetis
always returning the cell partitioning in local numbers.

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Plex: Create parallel partitions that ParMetis accepts

For this we need to convert the cell graph into (positive) global numbers
and drop all overlap cells.

Plex: Re-implement routine to create partitioner graph

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 remote-tracking branch 'lawrence/petscpartitioner-doc'

* lawrence/petscpartitioner-doc:
Fix docstring of PetscPartitionerShellSetPartition

Merge remote-tracking branch 'lawrence/petscpartitioner-set'

* lawrence/petscpartitioner-set:
Note refcounting in DMPlexGetPartitioner
Add programmatic interface to set partitioner on DMPlex

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.

Fix docstring of PetscPartitionerShellSetPartition

Note refcounting in DMPlexGetPartitioner

Add programmatic interface to set partitioner on DMPlex

Counterpart to DMPlexGetPartitioner.

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-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: Added DMPlexGetPartitioner() and PetscPartitionerShellSetPartition()

Plex: Fixed Fortran stub

Plex: Create partition overlap from distributed non-overlapping DM

This commit adds DMPlexDistributeOverlap, which computes the partition
overlap from an already distributed non-overlapping DM and b

Plex: Create partition overlap from distributed non-overlapping DM

This commit adds DMPlexDistributeOverlap, which computes the partition
overlap from an already distributed non-overlapping DM and builds the
correct parallel DM and it's pointSF. This is significantly faster when
FEM adjacency is used with overlap=1.

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