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' of bitbucket.org:petsc/petsc

Merge branch 'knepley/fix-compiler-warnings'

* knepley/fix-compiler-warnings:
Fixed compiler warnings
Fix compiler warnings about unreachable code

Fixed compiler warnings

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

Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

Merge branch 'tisaac/dm-plex-fix-nonconforming'

Changes to DMPlexMigrate() broke the nonconforming examples. The fix was
simple (reintroduce tree/closure traversal when computing partition labels),

Merge branch 'tisaac/dm-plex-fix-nonconforming'

Changes to DMPlexMigrate() broke the nonconforming examples. The fix was
simple (reintroduce tree/closure traversal when computing partition labels),
but the bigger problem was that I didn't have the nonconforming examples in
the test suite. To test in as many environments as possible, I made the
nonconforming tests independent of the partitioning packages available
(several don't support 64bit indices), and I had to make
PetscFEGetTabulation() work with complex scalars.

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Plex: account for tree in DMPlexPartitionLabelClosure()

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

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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Merge branch 'tisaac/simplify-register-all'

Removed the XXXRegisterAll() functions from the public interface. These should now only be handled by the package intialization functions.

Merge branch 'knepley/feature-partitioner-simple'

* knepley/feature-partitioner-simple:
Plex: Removed unused variable
Partitioner: Added tests for simple partitioner
Plex: Added a simple parti

Merge branch 'knepley/feature-partitioner-simple'

* knepley/feature-partitioner-simple:
Plex: Removed unused variable
Partitioner: Added tests for simple partitioner
Plex: Added a simple partitioner

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Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

Plex: Removed unused variable

Plex: Added a simple partitioner

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

Merge branch 'master' into barry/ksp-converged-reason-viewer

Conflicts:
src/sys/objects/options.c

Merge branch 'mlange/refactor-plex-distribute'

* mlange/refactor-plex-distribute: (31 commits)
Plex: MS compilers do not allow declarations in the middle of a block
DMLabel: Add DMLabelMakeAllVa

Merge branch 'mlange/refactor-plex-distribute'

* mlange/refactor-plex-distribute: (31 commits)
Plex: MS compilers do not allow declarations in the middle of a block
DMLabel: Add DMLabelMakeAllValid_Private
Plex ex12: Add fixed re-partitioning for load balance test
DMLabel: Validate/build point arrays per stratum
Plex: Remove obsolete partitioning routines
Plex: Fix deadlock in DMPlexCreatePointNumbering
Plex: Fix dynamic check for one-to-all pattern in DMPlexMigrate
Plex: Add missing header entries
Plex ex12: Enable L2-overlap test and switch to ascii_info_detail
Plex ex1: Fix overlap tests and switch to ascii_info_detail
Plex: Fix and clean up DMPlexCreatePointSF
Plex: Correctly restore closure in DMPlexPartitionLabelClosure
Plex: Let SegBuffer allocate partition graph to avoid memory corruption
Plex ex12: Enabling parallel re-partitioning test via scii_latex output
Plex: Enabling parallel re-partitioning via DMPlexDistribute
Plex ex12: Add new test for parallel re-partitioning
Plex: Add DMPlexCreatePointSF utility
Plex: Fix overlap point SF generation
Plex: Build complete overlap label and stratify resulting SF.
Plex: Create parallel partitions that ParMetis accepts
...

Conflicts:
config/builder.py
src/dm/impls/plex/examples/tests/output/ex1_13.out
src/dm/impls/plex/examples/tests/output/ex1_14.out
src/dm/impls/plex/plexlabel.c
src/dm/impls/plex/plexpartition.c

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Remove XXXRegisterAllCalled from public interface.

All XXXRegisterAll() methods are now idempotent, so a boolean indicating
whether they can be called or not is no longer necessary.

Plex: Remove obsolete partitioning routines

Removed:
* DMPlexEnlargePartition
* DMPlexMarkTreeClosure
* DMPlexCreatePartitionClosure
* PetscSFConvertPartition

Plex: Correctly restore closure in DMPlexPartitionLabelClosure

Plex: Let SegBuffer allocate partition graph to avoid memory corruption