Refactor of PetscViewerBinary code.

Commencing reorganisation of PetscViewerBinary to
have a more consistent way of setting and using
option prefixes and allowing mpi-io to be used
on specific viewe

Refactor of PetscViewerBinary code.

Commencing reorganisation of PetscViewerBinary to
have a more consistent way of setting and using
option prefixes and allowing mpi-io to be used
on specific viewers.

This commit:
( i) introduces a setupcalled flag into the binary
context
( ii) adds an empty SetUp function
(iii) adds a SetFromOptions_Binary function which
combines all options (skip header, skipinfo, etc)
within a PetscOptionsHead()/PetscOptionsTail()
block so that option prefixes are used.

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Modified for consistency with maint and not
master.

Fixed typos, printf mistake and some petsc coding style issues

(i) Small cleanup of the makefile.
(ii) added serial/parallel tests for header less write/read using PetscViewer binary
(iii) added parallel write/read test for header less PetscViewer binary + mpiio.

Small updates such the text written to stdout
can be robustly diff'd on different platforms.

Added test code for binary files written or filled
using VecView()/VecLoad().

To verify the headerless write/read has occurred
correctly, we load the file originally written
with VecView using P

Added test code for binary files written or filled
using VecView()/VecLoad().

To verify the headerless write/read has occurred
correctly, we load the file originally written
with VecView using PetscBinaryRead().
If the entries obtained using PetscBinaryRead()
match the known values, we conclude that the
headerless read/write was successful.

To test mpiio binary read/write, run ex3 with the
command line option -usempiio

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Fixed errors in manual page documentation including formating.
Fixed rank argument for DMCreateRedundant() to be PetscMPIInt

Reported-by: Dave May <dave.mayhem23@gmail.com>

Merge branch 'karpeev/fix-ksp-matgetschurcomplement-pmatreuse' into barry/experiment

Conflicts:
src/ksp/ksp/utils/schurm.c

minor fixes to PetscInfo() formating

simplify option object names

moved PetscOptionsObject from global variable to local variable in functions

manual merge of conflict

mv include/finclude to include/petsc-finclude for namespacing in installs

Merge branch 'master' into barry/ksp-converged-reason-viewer

Conflicts:
src/sys/objects/options.c

when using quad precision allow vtk binary output to work

Merge branch 'barry/fix-hdf5'

-ksp_richardson_scale was ignored when PCApplyRichardson() was used
Fix: turn off PCApplyRichardson() when scale is not 1 and print PetscInfo warning

Reported-by: Mark Adams <mfadams@lbl.gov>

Fixed

-ksp_richardson_scale was ignored when PCApplyRichardson() was used
Fix: turn off PCApplyRichardson() when scale is not 1 and print PetscInfo warning

Reported-by: Mark Adams <mfadams@lbl.gov>

Fixed missing carriage return in uses of PetscInfo() and missing ierr CHKERRQ() usage

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Changing -snes_converged_reason and -ksp_converged_reason to take a general viewer argument

moved the rest of the HDF5 calls behind PetscStackCall's

added PetscStackCallHDF5() and test usage

Remove XXXRegisterAll() from public interface

This means we are relying on packages to be well behaved, to set
themselves up properly. Passes testexamples in my builds (haven't tried
complex).

Remove XXXRegisterAllCalled from public interface.

All XXXRegisterAll() methods are now idempotent, so a boolean indicating
whether they can be called or not is no longer necessary.

Merge branch 'mlange/plex-gmsh-binary'

* mlange/plex-gmsh-binary:
Viewer: Fix 64-bit integer parse
Plex-Gmsh: Improve error handling
Viewer: Use %lld to parse 64-bit integers
Plex-Gmsh: Fixe

Merge branch 'mlange/plex-gmsh-binary'

* mlange/plex-gmsh-binary:
Viewer: Fix 64-bit integer parse
Plex-Gmsh: Improve error handling
Viewer: Use %lld to parse 64-bit integers
Plex-Gmsh: Fixes for 64-bit integer mode
Plex-Gmsh: Fix and test parallel Gmsh reads
Plex-Gmsh: Add new Gmsh tests based on 2D square
Plex-Gmsh: Add DMPlexCreateGmshFromFile, which determines file type
Plex-Gmsh: Enabling binary mesh file reads in DMPlexCreateGmsh
Viewer: Add PetscViewerRead()
Plex-Gmsh: Adding PetscViewerASCIIRead()
Plex-Gmsh: Read gmsh elements into memory for repeated file traversal.
Plex-Gmsh: Fix cell and dimension counting

Conflicts:
src/dm/impls/plex/plexgmsh.c

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Viewer: Fix 64-bit integer parse

Viewer: Use %lld to parse 64-bit integers