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

PCBDDC: added reuse of coarse subassembling information

In order to do do, I had to change the MATIS class (I dont know why there was a guard for is->mapping in matis code)

Solved a couple of bugs

PCBDDC: added reuse of coarse subassembling information

In order to do do, I had to change the MATIS class (I dont know why there was a guard for is->mapping in matis code)

Solved a couple of bugs when doing multilevel and a dbg_viewer on a single level only

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

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fi

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

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fix for TSGetRHSMats_Private() in the creation of the Arhs and Brhs matrices
protect logging of objects (which uses global variables) with PETSC_USE_LOG
error handler API had been previously changed but this example was not updated to new API.
DMPlex: Fixed bug in coordinate permutation
PetscSection: Doc fix for permutation
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bugfix of MatCreateSeqAIJFromTriple() contributed by Nicolas Marsic <nicolas.marsic@montefiore.ulg.ac.be>
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
completed removing server code that was not removed in previous commit
removed PETSc webserver and configure package files that supported it
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
fix outdated PetscOptionsList
SNESQN: only monitor real part of dot product (fails with C++ complex)
Fix for multiple definitions in mat/color/interface/ custom fortran bindings
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/da/dageometry.c
src/dm/impls/plex/examples/tests/ex4.c
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexinterpolate.c

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PCBDDC: added FETIDPMatMultTranspose and PCApplyTranspose (for Dirichlet FETIDP preconditioner)

PCBDDC: support for PCApplyTranspose completed by solving the transpose of the coarse operator in PCBDDCApplyInterfacePreconditioner.

Function pointer is now set during object creation

PCBDDC: added second parameter to PCBDDCApplyInterfacePreconditioner to determine if the interface preconditioner should be applied tranposed or not

The main reason for this is to avoid code duplica

PCBDDC: added second parameter to PCBDDCApplyInterfacePreconditioner to determine if the interface preconditioner should be applied tranposed or not

The main reason for this is to avoid code duplication

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PCBDDC: added initial implementation of PCApplyTranspose_BDDC

PCBDDC: set compute topography to true with new field split

PCBDDC: set compute topography to true also when Local version of the boundaries API is invoked

Merge branch 'stefano_zampini/pcbddc-globalordering-api' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcprivate.c

PCBDDC: provide APIs for setting field split in global ordering

previous API moved to PCBDDCSetDofsSplittingLocal

For consistency with updated man pages, which_dof values should default to -1;
this

PCBDDC: provide APIs for setting field split in global ordering

previous API moved to PCBDDCSetDofsSplittingLocal

For consistency with updated man pages, which_dof values should default to -1;
this way, unlisted nodes in field split will belong to a different subset

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PCBDDC: provide API for setting Dirichlet/Neumann boundaries in global ordering

PCBDDC: replace SetXXXBoundaries with SetXXXBoundariesLocal (better logic)

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 unneeded code to check nearnullspace

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: 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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