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

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

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

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

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

Don't install $PETSC_ARCH/lib/.DIR

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

reorge of PETSc "utilities" config files into "options" since all of these are user setable options

Merge branch 'jed/config-re.sub' into maint

* jed/config-re.sub:
config: prefer str.replace(...) over re.sub(re.escape(...))
config: simplify regex

Merge branch 'jed/config-re.sub'

* jed/config-re.sub:
config: prefer str.replace(...) over re.sub(re.escape(...))
config: simplify regex

config: prefer str.replace(...) over re.sub(re.escape(...))

Some instances were not escaped, leading to failure when paths contain
special characters. Combining re.sub with re.escape is rather perv

config: prefer str.replace(...) over re.sub(re.escape(...))

Some instances were not escaped, leading to failure when paths contain
special characters. Combining re.sub with re.escape is rather perverse,
so just use str.replace instead.

Reported-by: David Moxey <d.moxey@imperial.ac.uk>

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

Merge branch 'maint'

build: update 'make test' instructions for prefix build to avoid error
egrep: /home/balay/tmp/petsc-install/arch-mpich/include/petscconf.h: No such file or directory

Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]

Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]
gfortran: remove 132 char limit from f90 free-form
SNES: Set up matrix-free *after* copying the user Jacobian to snes->pc
DMPlex-Gmsh: Use trueNumCells when building the coordinate section
Sys: Got guard logic reversed
Sys: The #define guard for PetscMalloc*() must match the one for PetscFree*()
PetscFV: I hate fucking complex
removed ltog scatter from DMDA since functionality can be obtained with gtol scatter and less memory
fix test of DMLocalToGlobalBegin/End and add actual test cases
improve object memory logging for DA, ISLocalToGlobal and ISBLOCK
lower high water mark of constructing parallel scatter by allocating only as much room in svalues as needed
owner in VecScatter construction is the rank, therefor can use PetscMPIInt to hold it do not PetscInt
another reuse of allocated array in 2d/3d DMDA create
improved high water mark of DMDASetups by implementing and using PETSC_USE_POINTER for ISCreateBlock()
PetscFV: Another complex fix
DMPlex+TS: Fixing types
ISIdentity() was wrong for block IS! Indices are NOT scaled by bs
PetscFV: Straighten out complex types
TS ex11: Fix casts and remove unused variable
...

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Merge branch 'master' into barry/saws-options

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bdd

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddcprivate.c

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Merge remote-tracking branch 'origin/master' into feature-dmmoab

Merged petsc/petsc into master

Merge branch 'master' into knepley/feature-plex-hdf5-parallel-load

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this wa

Merge branch 'master' into knepley/feature-plex-hdf5-parallel-load

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this was really bad)
outdated example that doesn't match coding style removed and buggy
petscversion.h: workaround ifort -cpp lack of referential transparency
configure: ignore AR, MAKEFLAGS [if set in env]
incorrect first entry in array being zeroed in example
sizeof.c: remove dependence on petsc [and fix syntax error]
nightlybuilds: use consistant PETSC_ARCH, machine names
TS: Allow viewing of TS solutions
DMPlex: Fix comparison for complex
change MPIVersion streams to use MPI_Wtime() to be portable to Windows do not use scalar square root on real number; it upsets Microsoft
cannot use I in PETSc code because in complex it sometimes represents imaginary number cannot pass PetscScalar * to VecNorm()
in dashboard don't warn about SSL and BOI deprecated
TS ex11: Fixed output formatting
Doc+DMPlex: Added function documentation for some refinement functions
streams: translate code from 'bash' to 'sh' [fix freebsd]
barry is an idiot who doesn't have a clue as to what he is doing (and git's unfriendlyness doesn't help matters)
don't list examples under C that don't work with complex!
forgotten output file
removed valgrind warning about sending uninitialized data
nightly builds ignore unrecognized pragma and .c file as C++ code
...

Conflicts:
include/petsc-private/dmpleximpl.h

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Merge branch 'jed/gnumake'

Shared library versioning and less redundancy in gmakefile

* jed/gnumake:
gmakefile: fix multiline variable for make-3.81
make: hide library symlinking
make shared:

Merge branch 'jed/gnumake'

Shared library versioning and less redundancy in gmakefile

* jed/gnumake:
gmakefile: fix multiline variable for make-3.81
make: hide library symlinking
make shared: use leading 0 to indicate development version
make shared: pass path to SL_LINKER_FUNCTION
make: simply list objects as dependencies instead of via target-specific var
make shared: link directly to the actual library rather than via soname
make shared: symlink without directory and install by recreating symlinks
make shared: fix library versioning, sonames, and symbolic linking
make shared: default SL_LINKER_FUNCTION (revert before release)
make shared: use configure to determine shared linking

Conflicts:
gmakefile

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Merge branch 'master' into shri/ts-events

Conflicts:
src/ts/interface/ts.c

make shared: symlink without directory and install by recreating symlinks

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

Conflicts:
src/ts/examples/tutorials/advection-dif

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

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

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Merge branch 'master' into barry/xcode