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outdated example that doesn't match coding style removed and buggy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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gmakefile: fix multiline variable for make-3.81

make-3.82 and later interpret

define multiline =
more than
one line
endef

as a variable with two lines, but make-3.81 does not understan

gmakefile: fix multiline variable for make-3.81

make-3.82 and later interpret

define multiline =
more than
one line
endef

as a variable with two lines, but make-3.81 does not understand "define
multiline =" (or "define multiline :=", etc) syntax, so it interprets
the above as an empty variable. For 3.81 compatibility, we must be less
precise by writing

define multiline
more than
one line
endef

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Merge branch 'master' into shri/ts-events

Conflicts:
src/ts/interface/ts.c

Merge branch 'master' into shri/feature-dm-circuit

Conflicts:
src/dm/impls/makefile

Merge branch 'master' into prbrune/matcoloring-greedy

Merge branch 'master' into knepley/feature-plex-fas

* master: (863 commits)
Revert "mpich: use latest mpich tarball with gcov but use '--enable-coverage' mpich configure option."
MatCreateTransp

Merge branch 'master' into knepley/feature-plex-fas

* master: (863 commits)
Revert "mpich: use latest mpich tarball with gcov but use '--enable-coverage' mpich configure option."
MatCreateTranspose: fix for lazy block size
mpich: use latest mpich tarball with gcov but use '--enable-coverage' mpich configure option.
configure: add FC_DEFINE_FLAG to petscvariables
added a citation for pounders, Stefan finally came through
update to latest netcdf fixes bug that did not allow building on recent Mac OS X
DMPlex: Fixes for CGNS - Fixed loop bounds since CGNS uses closed intervals - Bug with mixed cell types - Typo with coordinates
final updates from nightly tests
fix for countcfunction
removed outdated docs and comments on MatStructure usage removed SAME_PRECONDITIONER since no longer used removed unneed use of MatStructure in Schur complement matrix
removed MatStructure arguments from Tao
fixes for Sundials and fun3d cannot use MPIU_SUM for integer arrays
inplace ILU factorization must update state of inplace matrix to prevent infinite recursion of updating PC
fixes for BDDC by the way not having BDDC always in the testing is going to lead to trouble
the compute Jacobian functions for SNES and TS now do not take a MatStructure flag
KSPSetOperators() no longer has the MatStructure argument. The Mat objects now track that information themselves. Use KPS/PCSetReusePreconditioner() to prevent the recomputation of the preconditioner if the operator changed in the way that SAME_PRECONDITIONER did with KSPSetOperators()
tracks when Mat's have a change in nonzero structure this information can be used by PC to determine how preconditioners must be rebuilt currently only does an error check if the user said same nonzero pattern but actually changed the pattern
completed cleanup of removal of matrix pointers to compute jacobian routines
makefile: Added 'make includegraph' to create an inclusion dependency graph.
Contrib: Updated include-graph.sh script to ignore *.hh files
...

Conflicts:
src/dm/dt/interface/dt.c

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Merging master with feature-dmmoab. Only conflict was with SOURCECXX specification under impls/moab/makefile.

Merged petsc/petsc into master

Merge branch 'master' into prbrune/snes-fascontinuation

Conflicts:
include/petscsnesfas.h

Merge branch 'jed/elemental-int64'

* jed/elemental-int64:
Elemental: disable Qt5 so we don't have to pass -I for those include paths
nightlybuilds: disable elemental build when conflicting with

Merge branch 'jed/elemental-int64'

* jed/elemental-int64:
Elemental: disable Qt5 so we don't have to pass -I for those include paths
nightlybuilds: disable elemental build when conflicting with hdf5
elemental: update nightly builds. [add with-cxx-dialect=C++11 to linux - disable elsewere]
Elemental: use self.framework.getCompilerFlags()
Elemental: add support for 64-bit indices
Elemental: upgrade to development version that requires C++11
config: add with-cxx-dialect and check for C++11
Elemental: fix setting of CMAKE_CXX_FLAGS
config: write CXX_FLAGS for building C++ even when clanguage=C

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Merge branch 'master' into barry/ts-rhsjacobian-only

make: hide library symlinking

Presumably the user is not interested in seeing this. It should just
work.

make shared: use leading 0 to indicate development version

These are distinct sonames on Linux. Apple -compatibility_version is
unaffected because they convert to a 32-bit integer, so the leading 0

make shared: use leading 0 to indicate development version

These are distinct sonames on Linux. Apple -compatibility_version is
unaffected because they convert to a 32-bit integer, so the leading 0
vanishes.

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make shared: pass path to SL_LINKER_FUNCTION

OS-X needs -install_name to contain the full path (similar to RPATH on
other unixy systems except it is set be the library rather than the
executable/dep

make shared: pass path to SL_LINKER_FUNCTION

OS-X needs -install_name to contain the full path (similar to RPATH on
other unixy systems except it is set be the library rather than the
executable/dependent.)

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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

Uses $(eval ...) to eliminate some redundancy between packages.

Reported-by: Barry Smith <bsmith@mcs.anl.gov>

Merge branch 'shri/update-SuiteSparse' into shri/external-package-KLU

Conflicts:
conf/test
config/examples/arch-linux-pkgs-dbg-ftn-interfaces.py
config/examples/arch-linux-pkgs-opt.py

make shared: default SL_LINKER_FUNCTION (revert before release)

This default allows old petscvariables to work while we transition to
using this function for linking. This commit should be reverted

make shared: default SL_LINKER_FUNCTION (revert before release)

This default allows old petscvariables to work while we transition to
using this function for linking. This commit should be reverted before
v3.5.

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make shared: use configure to determine shared linking

Now supports OS-X -dynamiclib instead of less portable -shared (which
apparently does not work with Intel 14.0).

Reported-by: Blaise A Bourdin

make shared: use configure to determine shared linking

Now supports OS-X -dynamiclib instead of less portable -shared (which
apparently does not work with Intel 14.0).

Reported-by: Blaise A Bourdin <bourdin@lsu.edu>

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Merge branch 'balay/tao-to-petsc'

Conflicts:
src/snes/impls/fas/fasfunc.c
src/snes/impls/fas/fasgalerkin.c

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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