MatMUMPS: add support for Schur complement computation during factorization phase

the same changes were also commited to stefano_zampini/pcbddc-adaptive-selection
Committed also in a separate branch

MatMUMPS: add support for Schur complement computation during factorization phase

the same changes were also commited to stefano_zampini/pcbddc-adaptive-selection
Committed also in a separate branch to make repository history cleaner

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Fixed function declaration/definition mismatch: PetscMPIInt —> PetscInt.

MatGetSubMatricesParallel —> MatGetSubMatricesMPI. Implementation rewritten, tests added.

Merge branch 'pr192/Fande-Kong/scalable-matincreaseoverlap/master' of https://bitbucket.org/petsc/petsc

Merged petsc/petsc into master

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/mat/impls/aij/mpi/mumps/mumps.c
s

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/mat/impls/aij/mpi/mumps/mumps.c
src/mat/impls/is/matis.h

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Merged master into semihozmen/ksp-fcg-eigen-comp-support

Merge branch 'master' into pr192/Fande-Kong/scalable-matincreaseoverlap/master

Needed to merge master to update to new calling sequence PetscCommBuildTwoSided

Merged petsc/petsc into master

Merge branch 'barry/fix-directory-layout'

typo in include file prototype of MatMPIAIJSetUseScalableIncreaseOverlap()

do some refactoring of the scalable MatIncreaseOverlap() code for MPIAIJ to respect PETSc style
in particular not having an options database in the compute code; it should be handled in MatSetFromOpt

do some refactoring of the scalable MatIncreaseOverlap() code for MPIAIJ to respect PETSc style
in particular not having an options database in the compute code; it should be handled in MatSetFromOptions()
and use standard inheritence of replacing a method with a new derived method

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updated PETSc directory layout to match standard packaging strategies

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

Merge branch 'pr291/andrewspott/andrewspott/MatCreateHTranspose/master'

Conflicts:
src/mat/examples/tests/makefile

Merge branch 'barry/optimize-matshift'

Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
thi

Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
this branch. Matt's and my fixes in DMPlex will also be relevant.

* master: (1557 commits)
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 ex3: For want of a semicolon, the kingdom was lost
MatSetValuesMPISBAIJ will now print correct global indices when error generated due to new nonzero location
completed basic use of MatSetValuesBlocked_SeqBAIJ_Inlined() by MatSetValuesBlocked_MPIBAIJ() to allow proper global indices being printed when error generated by new nonzero locations.
Added inline version of MatSetValuesBlocked_SeqBAIJ() to be used by MatSetValuesBlocked_MPIBAIJ() to print error message for nonzero block with global indices
...

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Optimized MatShift() for a completely empty matrix since this is commonly used with SLEPc to produce diagonal matrices

Reported-by: Jose Roman <jroman@dsic.upv.es>

Added support for a "MatCreateHermitianTranspose" that acts the same as "MatCreateTranspose".

Currently, both matrices have type "transpose", I'm not sure if this is the correct way to do this. Als

Added support for a "MatCreateHermitianTranspose" that acts the same as "MatCreateTranspose".

Currently, both matrices have type "transpose", I'm not sure if this is the correct way to do this. Also added support for duplication of a transposed matrix (which just calls "MatTranspose" or similar). Tests for the hermitian transpose version have been added as ex175 in src/mat/examples/tests.

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Merge branch 'master' into shri/ts-is-for-differential-variables

Conflicts:
include/petsc-private/tsimpl.h
src/ts/impls/eimex/eimex.c
src/ts/interface/ts.c

Merge branch 'barry/clean-gamg'

Conflicts:
src/ksp/pc/impls/gamg/gamg.c

Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

Merge branch 'master' into barry/clean-gamg

Need updates to KSPCHEBYSHEV since I will be adding to them

There is no verbose in PETSc!

Removed the verbose mechanism from GAMG code and used PetscInfo() for reports instead.

Merge branch 'balay/update-Elemental-0.85'

MatStash BTS: add MAT_SUBSET_OFF_PROC_ENTRIES, impl with neighbor-only comm

Add MatOption to imprint a communication pattern on the first assembly
and reuse on subsequent assemblies. Messages of si

MatStash BTS: add MAT_SUBSET_OFF_PROC_ENTRIES, impl with neighbor-only comm

Add MatOption to imprint a communication pattern on the first assembly
and reuse on subsequent assemblies. Messages of size 0 are sent if no
values need to be communicated to that rank. Since there are no
collectives (even Ibarrier) and no separate headers, this should be more
efficient for large process counts. The BTS implementation must
currently be activated via the -matstash_bts option.

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