PetscViewerHDF5ReadSelectHyperslab_Internal impl.

HDF5ReadCtx: added timestep,complexVal,dim2 attributes

PetscViewerHDF5ReadSizes_Internal: renamed variables

PetscViewerHDF5ReadSizes_Internal: update PetscLayout instead of returning N,bs

PetscViewerHDF5ReadSizes_Internal: removed bsDimInd,lenDimInd,dim2 out args)

PetscViewerHDF5ReadInitialize_Internal: fail for complex data and non-complex petsc

PetscViewerHDF5ReadSizes: factored out PetscViewerHDF5Read{Initialize,Size,Finalize}_Internal

PetscViewerHDF5ReadSizes: support vectors stored as 1D array

PetscViewerHDF5ReadSizes moved from vecio.c to hdf5v.c

added PetscViewerHDF5OpenGroup documentation

PetscViewerHDF5OpenGroup moved from vecio.c to hdf5v.c

examples that use function whose API has changed.

Commit-type: bug-fix, testing-fix, example

Complete support for individual PETSc objects to use their own options database with PetscObjectSetOptions()

Commit-type: feature, example
Reported-by: "Blondel, Sophie" <sblondel@utk.edu>

PetscViewerBinary: open a new file if we have been asked to append to a non-existing one

Note that the ASCII format already supports this, since fopen(filename,'a') opens the file when not present

GLVis: Refactor implementation for DMs and Vec

* Do not use nonlocal returns (setjmp/longjmp) for I/O error handling.
* Add PetscGLVisCollective{Begin|End}() to handle closed windows.
* Remove dupli

GLVis: Refactor implementation for DMs and Vec

* Do not use nonlocal returns (setjmp/longjmp) for I/O error handling.
* Add PetscGLVisCollective{Begin|End}() to handle closed windows.
* Remove duplicated code in Plex and DA, use instead a routine
with a callback in charge of dumping data to the GLVis server.

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GLVis: Add command line options to send arbitrary keys and commands

GLVis: Change visualization defaults for 1D/2D mesh/solution

GLVis: Add command line options

Remove memory leaks of XXXRegister() is called but XXX object is never used

This means adding YYYInitialPackage() at the beginning of XXXRegister() routines

Minor fixes of missing prototypes

Commi

Remove memory leaks of XXXRegister() is called but XXX object is never used

This means adding YYYInitialPackage() at the beginning of XXXRegister() routines

Minor fixes of missing prototypes

Commit-type: style-fix
Reported-by: Jed Brown <jed@jedbrown.org>
Thanks-to: Fande Kong <fande.kong@inl.gov>

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Merge remote-tracking branch 'origin/barry/adios'

adios: fixes

- fix configure to pass in MPI compilers [instead of --with-mpi=DIR. Similarly attempt to use PETSc configure detected values for hdf5, netcdf, zlib etc..
- fix compiler error with usin

adios: fixes

- fix configure to pass in MPI compilers [instead of --with-mpi=DIR. Similarly attempt to use PETSc configure detected values for hdf5, netcdf, zlib etc..
- fix compiler error with using '0' for ADIOS_STATISTICS_FLAG
- declare Petsc_adios_group as PETSC_EXTERN - this way its useable from -lpetscvec [with-visibility=1]
- also move Petsc_adios_group to petscimpl.h - to avoid duplicate definitions
- fix fortran examples [by adding adios initialization to fortran interface
- fix compile error with ex10

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Fix cut and paste from when generating adios2 stub locations from adios1

Commit-type: bug-fix

Added the stub code for ADIOS VecView() and VecLoad()

Fails link examples due to "missing libadios2_atl.dylib on my Mac. Posted issue on github

Commit-type: feature

Merge branch 'psanan/vtk-viewer-dmda-dof' [PR #1029]

* psanan/vtk-viewer-dmda-dof:
DMDA VTK viewing: output multiple-dof fields

This continues a discussion on petsc-dev: https://lists.mcs.anl.gov/p

Merge branch 'psanan/vtk-viewer-dmda-dof' [PR #1029]

* psanan/vtk-viewer-dmda-dof:
DMDA VTK viewing: output multiple-dof fields

This continues a discussion on petsc-dev: https://lists.mcs.anl.gov/pipermail/petsc-dev/2018-June/023142.html
The aim is to allow one to view both scalar and vector fields in the same .vtr or .vts file, by viewing vectors associated with two compatible (but not identical because of differing dof/node) DMDAs.
This allows one to create an easy-to-load-into-Paraview file with the solution to the Stokes system, where the velocity is loaded as vector data (not a collection of scalar fields as before, where you’d have to use the Calculator to do things like plot streamlines).
This is accomplished here by:
- Adding a new argument to PetscViewerVTKAddField() to allow skipping the existing check that all vectors come from the same DM
- Adding a new function PetscViewerVTKGetDM()
- When viewing a vector associated with a DMDA, using the two changes above to skip the check and perform a check with DMGetCompatibility()
- Changing the behavior of DMDA viewing, when dof > 1, to write a single multi-dof field instead of multiple scalar fields (thanks to @Boris Kaus for the original code for this)

Some additional tests are added, based on DM test ex42.

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Options: Code reorganization and faster option lookup

* Speedup option lookup by using a auxiliary hash table.
* Move many routines around to make the implementation easier to follow.
Eventually,

Options: Code reorganization and faster option lookup

* Speedup option lookup by using a auxiliary hash table.
* Move many routines around to make the implementation easier to follow.
Eventually, we may split options.c in two, all of the query routines
PetscOptionsGetXXX() do not need (and should not have) access to the
PetscOptions data structure.
* Restore proper handling of monitors in set/clear option events.
* Add PetscOptionsHasHelp(), eventually we may add a "category" argument
to do special handling of let say `-help <package>`
* Change PetscOptionsReject() to handle option prefix, this makes the call
easier to use in XXXSetFromOptions() implementations.

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