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

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

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

Merge branch 'barry/experiment'

Merge branch 'tisaac/feature-gamg-extensible' into barry/experiment

Conflicts:
src/ksp/pc/impls/gamg/gamg.h

Move MG and GAMG implementation headers to petsc-private

I want to be able to register GAMG plugins. I considered a few options:

a) Move the implementation headers to petsc-private so they can be

Move MG and GAMG implementation headers to petsc-private

I want to be able to register GAMG plugins. I considered a few options:

a) Move the implementation headers to petsc-private so they can be
installed

b) Make Get/Set methods for all of the GAMGOps: graph, coarsen,
optprol, etc.

c) Add a PCGAMGGet/SetOperation like MatShellGet/SetOperation for each
of these operations.

The easiest was (a), and the GAMG methods are so context-specific I'm
not sure who would benefit from their being part of the public petsc
interface. If GAMG get's refactored to where the operations are easier
to understand on their own, then maybe (b) or (c) would be a better
option.

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Merge branch 'master' into shri/ts-events

Conflicts:
src/ts/interface/ts.c

Merge branch 'master' into barry/xcode

Merge branch 'master' into barry/wirth-fusion-materials

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

PCMG: Fixed Fortran binding
- Jed, don't you test before checkin :)

Merge branch 'prbrune/dm-coordinaterestrict' into prbrune/snes-elasticityexample

Merge branch 'jed/pcmg-residual-underscore' (early part) into maint

* 'jed/pcmg-residual-underscore' (early part):
Fortran: PCMGResidual_Default needs to handle double-underscore

Merge branch 'jed/pcmg-residual-underscore'

* jed/pcmg-residual-underscore:
PCMGResidualDefault: fix fortran def [error on windows build]
PCMGResidualDefault: deprecate old semi-private name and

Merge branch 'jed/pcmg-residual-underscore'

* jed/pcmg-residual-underscore:
PCMGResidualDefault: fix fortran def [error on windows build]
PCMGResidualDefault: deprecate old semi-private name and make public
Fortran: PCMGResidual_Default needs to handle double-underscore

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PCMGResidualDefault: deprecate old semi-private name and make public

Fortran: PCMGResidual_Default needs to handle double-underscore

When PETSC_HAVE_FORTRAN_UNDERSCORE_UNDERSCORE, we must append two
underscores. If this function is to be public (as it seems to be
ac

Fortran: PCMGResidual_Default needs to handle double-underscore

When PETSC_HAVE_FORTRAN_UNDERSCORE_UNDERSCORE, we must append two
underscores. If this function is to be public (as it seems to be
according to the man page), it should be named PCMGResidualDefault.

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Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

Automerge.

Hg-commit: 81500f7e84c8ec0c4dcae9cb31d1cb32892d545d