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outdated example that doesn't match coding style removed and buggy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 'prbrune/pcgamg-fixscatteruse'

* prbrune/pcgamg-fixscatteruse:
PCGAMGClassical: Fix PetscInt passed to MPI function.

PCGAMGClassical: Fix PetscInt passed to MPI function.

Reported-by: Matthew Knepley <knepley@gmail.com>

Merge branch 'prbrune/pcgamg-fixscatteruse'

* prbrune/pcgamg-fixscatteruse:
PCGAMG: More cleanup after the switch
PCGAMG: Remove scatter use for indices from Standard interpolation
PCGAMG: Rem

Merge branch 'prbrune/pcgamg-fixscatteruse'

* prbrune/pcgamg-fixscatteruse:
PCGAMG: More cleanup after the switch
PCGAMG: Remove scatter use for indices from Standard interpolation
PCGAMG: Remove use of matrix-internal scatter context from Direct interpolation
Mat: Added MatGetLayouts() which allows for access to row and column layouts.

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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

PCGAMG: More cleanup after the switch

PCGAMG: Remove scatter use for indices from Standard interpolation

PCGAMG: Remove use of matrix-internal scatter context from Direct interpolation

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 'master' into barry/ts-rhsjacobian-only

convert to PetscMalloc1()
better handling of string viewer when running out of space

Merge branch 'master' into balay/tao-to-petsc

Conflicts:
include/makefile

Merge branch 'master' into knepley/feature-mat-zerorowscols-baij

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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Merged petsc/petsc into master

Merge branch 'prbrune/pcgamg-classicalinterpolationstrategies'

Merge branch 'master' into knepley/feature-dmda-section

* master: (319 commits)
SNESGS: Fix for uninitialized variable warning in gssecant.c
DMPlex: Fix for orientation in Gmsh files - Fixed tes

Merge branch 'master' into knepley/feature-dmda-section

* master: (319 commits)
SNESGS: Fix for uninitialized variable warning in gssecant.c
DMPlex: Fix for orientation in Gmsh files - Fixed test output
do not use C99 struct initialization code in PETSc
Nightly Summary: Added time taken to each of the tests in the dashboard.
ASCII printing of floating point numbers must cast to (double) to support quad precision
configure: check fortranDatatypes only when fortran is enabled [this fixes configure crash with --with-fc=0]
don't use non-portable and also dependent on floating point precision system level math constants
picky compilers
fix a couple compiler warnings/errors (depending on compiler) for Matlab engine code
DMPlex: More fixup from bad rebase, moved to DMGet/SetCoordinateSection()
DM: Added DMGet/SetCoordinateSection()
Fuckup: Fix for merge that is still untangling bad rebase from Oct. 17th 2013 - Fixed const in declarations - Fixed merge from PetscFE - Fixed 2 mallocs
replace all echo in test/tutorial makefiles with printf since echo behaves differently on different systems
DMDA: Missing header - Damn rebase
DMPlex ex3: Added 2D Q_1 and 3D P_2 tests
DMDA: Added DMDAProjectFunction() and DMDAComputeL2Diff()
DMDA: Fixed 2D geometry - Should reuse DMPlex routines
DMDA: Fix bug in 2D closure operation for cells
DMDA: Make closure operations also return the size
DMDA: Changed DMDACreateSection() to emulate DMPlexCreateSection()
...

Conflicts:
config/builder.py
include/petscdmda.h
src/dm/dt/interface/dtfe.c
src/dm/impls/da/dageometry.c
src/dm/impls/da/dalocal.c
src/dm/impls/plex/plexgeometry.c

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PCGAMG_Classical: Fix for Windows complex build errors

classical.c
C:\cygwin\home\sbalay\PETSC~2.CLO\src\ksp\pc\impls\gamg\classical.c(639) : error C2784: '_Ty __cdecl std::abs(const class std::comp

PCGAMG_Classical: Fix for Windows complex build errors

classical.c
C:\cygwin\home\sbalay\PETSC~2.CLO\src\ksp\pc\impls\gamg\classical.c(639) : error C2784: '_Ty __cdecl std::abs(const class std::complex<_Ty> &)' : could not deduce template argument for 'const class std::complex<_Ty> &' from 'double'
C:\cygwin\home\sbalay\PETSC~2.CLO\src\ksp\pc\impls\gamg\classical.c(640) : error C2784: '_Ty __cdecl std::abs(const class std::complex<_Ty> &)' : could not deduce template argument for 'const class std::complex<_Ty> &' from 'double'
C:\cygwin\home\sbalay\PETSC~2.CLO\src\ksp\pc\impls\gamg\classical.c(1127) : error C2440: '=' : cannot convert from 'int (__cdecl *)(struct _p_PC *,struct _p_Mat *,struct _p_Mat ** )' to 'int (__cdecl *)(struct _p_PC *,struct _p_Mat *const ,struct _p_Mat ** )'
This conversion requires a reinterpret_cast, a C-style cast or function-style cast
gmakefile:135: recipe for target 'arch-mswin-cxx-cmplx/obj/src/ksp/pc/impls/gamg/classical.o' failed

Reported-by: Satish Balay <balay@mcs.anl.gov>

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Merged in madams/gamg-destroy (pull request #112)

fixed bug with not cleaning AGG subtype when setting to another type (classical).

Merged petsc/petsc into master