This branch reorganizes the API of mat-mat operations: A*B, At*B, A*Bt, PtAP, RARt, A*B*C
- See matproduct.c for detailed description of new API
- removed API function XXXSymbolic() and XXXNumeric()

This branch reorganizes the API of mat-mat operations: A*B, At*B, A*Bt, PtAP, RARt, A*B*C
- See matproduct.c for detailed description of new API
- removed API function XXXSymbolic() and XXXNumeric()
- removed subroutines MatMatMult_xxx, MatPtAP_xxx, ...
- modified MatxxxSymbolic_XXX() prototype (product is an input now)
- selection of algorithm is in MatProductSetFromOptions_xxx()

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Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maint

Obtain changed (v3.5) handling of MatMPIBAIJSetPreallocationCSR to match
documentation.

Merge branch 'master' into knepley/feature-adaptor-plex

* master: (56 commits)
test: Disable TS ex19 with single precision
PETSCVIEWERGLVIS: Support DMView_DA() out of VecView_GLVis()
test: Fi

Merge branch 'master' into knepley/feature-adaptor-plex

* master: (56 commits)
test: Disable TS ex19 with single precision
PETSCVIEWERGLVIS: Support DMView_DA() out of VecView_GLVis()
test: Fix TS ex19 time drift issue with quad precision
testing
Minor edit to 3.8 changes log for AIJMKL/BAIJMKL.
Bib: Added ref
Plex: Change initializers for C89
small update as complained by nightly tests
doc: fix missing from 0e50f9e530a7b78427514d3e384f6941d4a9cc62
small fix for nightly tests
PetscDualSpaceApplyFVM(): Fix for change in dual space semantics
Plex: All tests now passing after DMPlexCreateBoxMesh() update
cleanup MatPtAP_MPIAIJ_MPIAIJ; rm MatPtAPXXX_MPIAIJ_MPIAIJ_ptap()
update MatView_MUMPS()
PFLOW: Bug-fix in parser.
PFLOW: Bug-fix in parser.
Plex: Small fix for box meshing
Plex: Unified box mesh creation to DMPlexCreateBoxMesh() - Makes simplices and tensor cells - Does not work for all combinations, but gives correct error
Plex: Added bounds and faces in each dim to DMPlexCreateBoxMesh()
Plex: Added domain bounds to HexBoxMesh()
...

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Merge branch 'hzhang/opt-ptap'

optimize sequential MatPtAP -- ues rap as default

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
ini

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
initialize ap as complained by the nightly tests
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
SNES ex12: Mix misnaming Nf --> Nc
update tests
add tests
add MatView_SeqXAIJ_ASCII_structonly(); enable A->structure_only in MatSetValuesBlocked_SeqBAIJ
typo
fill-in some references
Bib: Fixed ref
Plex: Added PLY to file support
Plex: Adding PLY support
PetscDS: Turn off Fortran bindings for Constants
Plex tests: Updated to new point function API
SNES ex56: Moved tests to new format
DM: Allow field projection functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tutorials/ex63.c

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Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes

Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
superlu: libray is installed in PREFIX/lib64 - fix this to use PREFIX/lib
backport fixes cc105cc3 2b35c90a - required for 3bf428d - that was backported from master - 80c96bb
'echo -n' fails on opensolaris/osx - so avoid using it.
fix diffs in nightlybuilds due to options in ~/.petscrc
add Kelley03 to src/docs/tex/petsc.bib
build: determine moudles, mpi.h used during buildtime and print in 'info'
fix analyzer warnings
fix build failure on opensolaris - where -lm from flibs is removed due to -lm in cxxlibs. But then - only flib gets used for some configure tests [blaslapack, parms]
config: prefer __restrict over C99 restrict keyword
...

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Merge branch 'barry/remove-funct'

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-t

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-to: Andreas Mang <andreas@ices.utexas.edu>

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Merge branch 'stefano_zampini/feature-usehyprematmatops'

Added support for MatMatMatMult_transpose_aij_aij

actually, boomerAMGBuildCoarseOperator needs Rt and not R to perform RAP.
Removed HYPRE support from MatMatMatMult_AIJ_AIJ_AIJ and added the compose

Added support for MatMatMatMult_transpose_aij_aij

actually, boomerAMGBuildCoarseOperator needs Rt and not R to perform RAP.
Removed HYPRE support from MatMatMatMult_AIJ_AIJ_AIJ and added the composed to the AIJ objects

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MatSeqAIJ and MatMPIAIJ: added support for MatMatMatMult using HYPRE

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax error with error message
SNES ex5: Correct Jacobian handling on patches
SNES ex5: Stupid complex fixes
DMP4est: fix transfer of labels to parents
petsc4py: update to latest snapshot. Fixes da example breakage in petsc4py test suite
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logging in interpolator creation
Plex: Correct use of tabs in ASCII viewer
DM: Shorten long event name
Plex ex12: Create boundary label automatically at all levels of mesh hierarchy
Plex ex12: Change PetscViewerSetFormat --> PetscViewerPushFormat - Fix order of SetMode and SetFilename
Plex ex12: Change all functions to static
Since DMDA with periodic boundary conditions does support P0 interpolation remove checks that error out under those conditions
ascem-io.py and amanzi.py need to handle self.hdf5.include being None correctly
fix MPI Uni to recycle communicators so it won't run out like with the petsc4py tests also fix check for location of python shared library on mac to check all cases each time
Switch back to Sherry's version since she accepted by pull request
PetscDraw: Update help messages for -draw_save* options
...

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

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Merged petsc/petsc into master

Merge branch 'barry/fix-private-functions'

made a few more private symbols private
make checking for turning on symbol visibility the default

Merge branch 'master' into knepley/solkx

* master: (6933 commits)
Bib: Added reference
Includegraph: Updated for compatibility with new folder layout.
Add SNESLineSearchReason to fortran inclu

Merge branch 'master' into knepley/solkx

* master: (6933 commits)
Bib: Added reference
Includegraph: Updated for compatibility with new folder layout.
Add SNESLineSearchReason to fortran includes Also truncate names to fit 32 char fortran limit
fix compile warnings /usr/home/balay/petsc.clone-2/src/vec/vec/interface/vector.c:1944: warning: division by zero in '1.0e+0 / 0.' /usr/home/balay/petsc.clone-2/src/ksp/ksp/interface/itfunc.c:508: warning: 'vec_rhs' may be used uninitialized in this function
updated output for new trust region initial size
initial size of the trust region is set as a percent of the norm of the initial guess, it should not be related to the initial norm of the function (which is kind of nuts).
The default bounds for SNESVISetVariableBounds() in the manual page were reversed from correct values
Bib: Added refs
Bib: Update MPICH webpage
Plex: Forgot to close file
removed nonexistent ex46f from makefile test rule
Revert "fixed bad merge into master"
fixed bad merge into master
fix memory leak in mkl_pardiso fix some formatting in mkl_pardiso code
mv runex111 from TESTEXAMPLES_C to TESTEXAMPLES_DATAFILESPATH
Mat+Doc: More Fortran docs
Plex ex3: Run tests with the correct number of field components
Bib: Added TetGen cite
parmetis: make sure 'ldd libparmetis.so' points to the correct libmetis.so that its linked with.
small fix as reported by the nightly test
...

Conflicts:
config/builder.py

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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 '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 stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bdd

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

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddcprivate.c

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Merge branch 'master' into shri/ts-events

Conflicts:
src/ts/interface/ts.c

Merge branch 'master' into shri/feature-dm-circuit

Conflicts:
src/dm/impls/makefile

Merge branch 'master' into prbrune/snes-fascontinuation

Conflicts:
include/petscsnesfas.h

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

Conflicts:
src/ts/examples/tutorials/advection-dif

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

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

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