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' of bitbucket.org:petsc/petsc

Merge branch 'master' of bitbucket.org:petsc/petsc into mark/gamg-remove-eig-est

Merge branch 'tisaac/fix-makefile-allgtags'

`make allgtags` should now work on more platforms

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 'maint'

Conflicts:
config/BuildSystem/config/packages/ml.py

makefile: update stream target to pass PETSC_DIR and PETSC_ARCH

fixes and improvements to a variety of manual pages

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

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

makefile: allgtags made more portable

Remove OS X specific -E flag and brace expansion

Merge branch 'knepley/feature-dm-sf-local-copy' into knepley/feature-ts-fem+fvm-example

* knepley/feature-dm-sf-local-copy:
DM: Added support for INSERT_VALUES in DMLocalToGlobal() with an SF, whe

Merge branch 'knepley/feature-dm-sf-local-copy' into knepley/feature-ts-fem+fvm-example

* knepley/feature-dm-sf-local-copy:
DM: Added support for INSERT_VALUES in DMLocalToGlobal() with an SF, where it just does a local copy
fortranstubs: do not process files in .git
setup.py: Fix install of package's __init__.py file
f2cblaslapack: use correct location to copy tmpmakefile for subsequent self.installNeeded() to work.
doc: exclude tutorials/HandsOnExercise.html from 'docsetdate'
setup.py: Better handling of $PETSC_CONFIGURE_OPTIONS
setup.py: Simplify code to support just pip install
Don't install $PETSC_ARCH/lib/.DIR
Move install.py and gmakegen.py from lib/petsc-conf/ to config/
updated gamg tests
fixed squaring graph on all levels in GAMG
fixed gamg coarse grid to be general

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

Merged in dalcinl/pip-install (pull request #247)

Update support for pip install

Merge branch 'maint'

doc: exclude tutorials/HandsOnExercise.html from 'docsetdate'

Move install.py and gmakegen.py from lib/petsc-conf/ to config/