Merge branch 'stefano_zampini/pcbddc-reusebddc' into stefano_zampini/pcbddc-multilevel-improvement

Merge branch 'master' into knepley/feature-fem-dgspace

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key

Merge branch 'master' into knepley/feature-fem-dgspace

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
SNESQN: only monitor real part of dot product (fails with C++ complex)
Corrected the #include statement in the man pages for the PetscObjectComposedDataSet/Getwhatever routines.
DMPlex: Added doc for DMPlexGetHybridBounds()
winzip: detect if winzip is used to extract petsc.tar.gz and error out.
configure: remove self.archIndependent as its not being used. [it is used to create externalpackages/package/arch dir which is unused]
configure: fix packages using package-dir/PETSC_ARCH as out-of-source-build location Perhaps this should be changed to package-dir/build?
configure: remove dead code previously used to download BuildSystem
configure: check if compilerDefines [and compilerFixes] exist in framework before using them
configure: save/restore reconfigure.py when --with-clean is used
configure: add --with-clean option to delete buildfiles/externalpackages in PETSC_DIR/PETSC_ARCH and potential externalpackages in --with-external-package-dir/PETSC_ARCH
configure: With --with-externalpackages-dir=dir store/build packages in dir/PETSC_ARCH
Add MatSeqSBAIJSetPreallocationCSR()
configure: switch to using PETSC_DIR/PETSC_ARCH/externalpackages by updating package.py to use externalpackages.py as the externalPackagesDirProvider
configure: move dead code configureExternalPackagesDir() from petscdir.py to externalpackagesdir.py Also set PETSC_DIR/PETSC_ARCH/externalpackages as the externalpackagesdir
...

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PCBDDC: remove trailing whitespaces from source

Merge branch 'master' into barry/saws

Conflicts:
src/ksp/pc/impls/gamg/gamg.c
src/sys/classes/viewer/impls/ams/ams.c
src/sys/objects/pinit.c

PCBDDC: solved compilation error with complex build

Merge branch 'stefano_zampini/pcbddc-baijfixes'

* stefano_zampini/pcbddc-baijfixes:
PCBDDC: updated example using local to global mapping generated by DMDA
PCBDDC: solved a bug when multiple con

Merge branch 'stefano_zampini/pcbddc-baijfixes'

* stefano_zampini/pcbddc-baijfixes:
PCBDDC: updated example using local to global mapping generated by DMDA
PCBDDC: solved a bug when multiple constraints are present and some are eliminated by SVD
PCBDDC: index set for R nodes now stores block size information
PCBDDC: updated todo list
PCBDDC: updated bddc example with sbaij matrix type
PCBDDC: updated man pages
PCBDDC: bddc now works with sbaij matrices.
PCBDDC: added field in bddc data struct to determine if fields splitting has been provided by the user
PCIS: add support for sbaij matrices
PCBDDC: updated example using local to global mapping generated by DMDA
PCBDDC: solved a bug when multiple constraints are present and some are eliminated by SVD
PCBDDC: index set for R nodes now stores block size information
PCBDDC: updated todo list
PCBDDC: updated bddc example with sbaij matrix type
PCBDDC: updated man pages
PCBDDC: bddc now works with sbaij matrices.
PCBDDC: added field in bddc data struct to determine if fields splitting has been provided by the user
PCIS: add support for sbaij matrices

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PCBDDC: introduce a new variable in PCBDDC data stucture to store the actual number of current vertices (corners with constraints with basis changed)

removed calls to PCBDDCGetPrimalVerticesLocalIdx

PCBDDC: introduce a new variable in PCBDDC data stucture to store the actual number of current vertices (corners with constraints with basis changed)

removed calls to PCBDDCGetPrimalVerticesLocalIdx which are no longer needed

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PCBDDC: make BtoNmap a member of bddc data struct (created once after PCISSetUp)

Use GlobalToLocalMapping to map local to boundary indices
Inserted some memcpy to speed up memory movement

PCBDDC: check of dirichlet and neumann solvers is not needed if pcbddc->NullSpace is not present

Added some PetscSynchronizedAllow since on some machines the verbose output is broken otherwise

PCBDDC: improved reuse of coarse matrix

MatCovert_IS_AIJ renamed in MatISGetMPIXAIJ (MatConvert does not support out-of-place reuse of destination matrix)
Added some lines in MATIS code (commented).

PCBDDC: better management of primal space. Now a coarse numbering is computed if and only if the primal space has been really changed

PCBDDC: allow different customization of dirichlet and neumann boundary indices among successive linear solves

PCBDDC: now PCBDDC reuses part of its private data if NearNullSpace customization is changed between different linear solves

I know it is a large commit, but this is the minimal set of changes to ge

PCBDDC: now PCBDDC reuses part of its private data if NearNullSpace customization is changed between different linear solves

I know it is a large commit, but this is the minimal set of changes to get it working

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PCBDDC: local work vectors should be created only if new constraints are created and the relevant sizes are different

PCBDDC/PCIS: make vec4_D a member of pcis, not pcbddc

PCBDDC: demand object destruction to setup routines for BDDCGraph and constraints

PCBDDC: solved a bug when multiple constraints are present and some are eliminated by SVD

change_of_basis flag should be set AFTER SVD has recognized independent components
Some minor modications to

PCBDDC: solved a bug when multiple constraints are present and some are eliminated by SVD

change_of_basis flag should be set AFTER SVD has recognized independent components
Some minor modications to the code (due to broken MatMult_BAIJ with compressed rows)

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PCBDDC: index set for R nodes now stores block size information

When IS block size is equal to Mat block size, there's no need to convert local matrices anymore

PCBDDC: updated todo list

added a further guard before calling SVDs

PCBDDC: bddc now works with sbaij matrices.

This is a partial solution, since in practice the Neumann problem matrix will always be seqaij

Implemented user switch for field split

PCBDDC: solved a bug when multiple constraints are present and some are eliminated by SVD

change_of_basis flag should be set AFTER SVD has recognized independent components
Some minor modications to

PCBDDC: solved a bug when multiple constraints are present and some are eliminated by SVD

change_of_basis flag should be set AFTER SVD has recognized independent components
Some minor modications to the code (due to broken MatMult_BAIJ with compressed rows)

show more ...

PCBDDC: index set for R nodes now stores block size information

When IS block size is equal to Mat block size, there's no need to convert local matrices anymore

PCBDDC: updated todo list

added a further guard before calling SVDs

PCBDDC: bddc now works with sbaij matrices.

This is a partial solution, since in practice the Neumann problem matrix will always be seqaij

Implemented user switch for field split

Merge branch 'master' into barry/wirth-fusion-materials

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c