large over allocation of work array for determine matrix preallocation for AIJ matrices for large dof in DMDA

Reported-by: Sophie Blondel <blondels@ornl.gov>

DMDACnvertToCell spelled incorrectly in function macro definition

Reported-by: Mark L. Stowell <stowell1@llnl.gov>

Add size checks for static arrays of assumed max size [-Warray-bounds]

Plex: Changed the signature of pointwise input functions
- Now the spatial dimension and number of fields is passed in

Merge branch 'maint'

DMDAVTKWriteAll_VTS: Fix handling of higher-dimension coordinates

Doc: Fixed collective designation for DMDAVecGetArray() and friends

Add the possibility of writing HDF5 data in single precision

This commit adds the possibility for the user, at run-time,
select to write single precision data into the HDF5 file.
This is useful in m

Add the possibility of writing HDF5 data in single precision

This commit adds the possibility for the user, at run-time,
select to write single precision data into the HDF5 file.
This is useful in many cases, as one often stop the (iterative)
solver when an approximate answer is found, thus not utilizing
full double precision. Using single precision for IO can then
save you half the disk space (or give you the possibility of
writeing twice the amount of data on the same space).

The HDF5 library takes care of the type conversion, hence the
required changes to the IO routines are very small.

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VecLoad_HDF5_DA() accept 1-sized dimension for dof

VecLoad_HDF5_DA() can now read datasets written both with and
without a 1-sized dimension for the dof. This is handled with
the same kind of logic

VecLoad_HDF5_DA() accept 1-sized dimension for dof

VecLoad_HDF5_DA() can now read datasets written both with and
without a 1-sized dimension for the dof. This is handled with
the same kind of logic as VecLoad_HDF5(), and is completely
transparent to the user.

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fixed missing CHKERRQ() detected by clang's --analyze

updated PETSc directory layout to match standard packaging strategies

include/petsc finclude,private,mpiuni
lib/petsc conf
bin/petsc*

Merge branch 'knepley/feature-viewer-partial-read'

* knepley/feature-viewer-partial-read:
Viewer: Fixed initialization
TS: Updated example to new interface
Plex: Fix compiler warning
Viewer:

Merge branch 'knepley/feature-viewer-partial-read'

* knepley/feature-viewer-partial-read:
Viewer: Fixed initialization
TS: Updated example to new interface
Plex: Fix compiler warning
Viewer: Now ViewerRead() takes an extra argument to return the number of items read - An error is thrown for insufficient data unless the extra argument is non-NULL
Viewer: Fixes for new Read interface - Fixed example - Fixed Fortran 90 binding - Fixed type
Builder: Allow a local dictionary for run parameters
Viewer: PetscViewerRead() should return the number of items actually read - This also applies to all its implementations

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when MPIU_REAL or MPIU_SCALAR is used then MPIU_SUM/MAX/MIN must be used

these bugs are why plex as crashing in quad precision

Viewer: Now ViewerRead() takes an extra argument to return the number of items read
- An error is thrown for insufficient data unless the extra argument is non-NULL

Merge branch 'master' into knepley/feature-viewer-partial-read

* master: (48 commits)
ViennaCL: Fixes memory leak when destructing an aijviennacl matrix.
MatLoad_MPIDense() always allocated arra

Merge branch 'master' into knepley/feature-viewer-partial-read

* master: (48 commits)
ViennaCL: Fixes memory leak when destructing an aijviennacl matrix.
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: Reorganized PlexPoint interface - Added DMPlexGetPointLocalField() and DMPlexGetPointGlobalField() - Now the DMPlexGetLocalOffset*_Private() functions return start and end - Uniformly use private functions
Plex: Put in explicit cast
MatSetValuesMPISBAIJ will now print correct global indices when error generated due to new nonzero location
...

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

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PETSc Vecs with a bs of 1, coming from a generic VecCreate() or DMCreateGlobalVector() with a DMDA
will NOT have an extra dimension attached to them in HDF5 files created with VecView() with HDF5 vie

PETSc Vecs with a bs of 1, coming from a generic VecCreate() or DMCreateGlobalVector() with a DMDA
will NOT have an extra dimension attached to them in HDF5 files created with VecView() with HDF5 viewers,
to have that extra dimension even if the bs is on use either PetscViewerHDF5SetBaseDimension2() or
-viewer_hdf5_base_dimension2. Similarly to handle VecLoad() you need to set this value in the viewer if the
file has the extra dimension

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Viewer: PetscViewerRead() should return the number of items actually read
- This also applies to all its implementations

added PetscDrawMarkerType
changed VecView_MPI_Draw_DA1d() to use PetscDrawMarker() to mark points
added XIO handling to VecView_MPI_Draw_DA1d()

removed generation of automatic matrix name when viewing parallel matrices
removed double printing of matrix header when printing matrices associated with DAs

updates to docs for extchemfield.c for visualizing solutions in various ways

added DMDASetFieldNames() and DMDAGetFieldNames to allow handling the names of DMDAs with many fields easier

troubles with running extchemfield.c on two processes

tchem example with more than 1 cell is now working

mistakenly used hsize_t for return type from an HDF5 function that returns int
fix code formatting

Merge branch 'maint'

Conflicts:
src/dm/impls/da/gr2.c
src/vec/vec/utils/vecio.c