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-adaptive-selection

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

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

Merge branch 'master' of bitbucket.org:petsc/petsc into mark/gamg-crs-ksp2

manual merge of conflict

Three directory namespace changes for better --prefix install support

1) include/finclude becomes include/petsc-finclude
2) include/mpiuni becomes include/petsc-mpiuni
3) conf (both $PETSC_DIR/conf

Three directory namespace changes for better --prefix install support

1) include/finclude becomes include/petsc-finclude
2) include/mpiuni becomes include/petsc-mpiuni
3) conf (both $PETSC_DIR/conf and $PETSC_DIR/$PETSC_ARCH/conf become) lib/petsc-conf

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Merge branch 'master' into shri/ts-events

Conflicts:
src/ts/interface/ts.c

Merge branch 'master' into barry/xcode

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

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

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
s

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
src/snes/impls/composite/snescomposite.c
src/snes/impls/gs/snesgs.c
src/snes/impls/nasm/nasm.c
src/snes/impls/ngmres/snesngmres.c

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

* master: (287 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib e

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

* master: (287 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

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Merge remote-tracking branch 'origin/master' into stefano_zampini/pcbddc-improvelocalsolvers

Merge remote-tracking branch 'origin/master' into stefano_zampini/pcbddc-mirrorsfix

Merge remote-tracking branch 'origin/master' into stefano_zampini/pcbddc-constraintssetupimproved

Merge branch 'paulmullowney/txpetscgpu-package-removal'

CUDA: CUSPARSE still includes CUSP headers, so change the guards

Removal of TXPETSCGPU package from the SEQAIJCUSPARSE class

In this commit, I've removed the dependence of the SEQAIJCUSPARSE
class on the TXPETSCGPU package. However, other classes such as
SEQAIJCU

Removal of TXPETSCGPU package from the SEQAIJCUSPARSE class

In this commit, I've removed the dependence of the SEQAIJCUSPARSE
class on the TXPETSCGPU package. However, other classes such as
SEQAIJCUSP, VECCUSP, and MPIAIJCUSPARSE, and MPIAIJCUSP still depend
on that package. These dependencies will be removed in subsequent
commits once the design and structure is agreed upon.

The reason for this dependency removal is that SEQAIJCUSPARSE only
depends on the Nvidia CUSPARSE library which comes standard with CUDA.
Thus, the SEQAIJCUSPARSE class should be built whenever PETSc is
built with CUDA support. This will be far more maintanable in the
long term. Lastly, most of the CUSP dependencies have been removed
from this class. The only remaining CUSP dependencies are in the
vector data structures used in MatMult* and MatSolve* methods.
These will be removed in a subsequent branch as it is not clear
what the architecture should be yet.

In order to accomodate all the different functionality for various
Krylov solves, two new data structures were defined in cusparsematimpl.h.
The first is a Mat_SeqAIJCUSPARSEMultStruct struct. This contains an opaque pointer
for a matrix, a MatDescription data structure, and indices vector which will
be useful in MatMultAdd functions. The second new data structure is a
Mat_SeqAIJCUSPARSETriFactorStruct struct. This contains an CSR Matrix pointer,
a MatDescription data structure, a solve analysis data structure and an
operation type.

Next, Mat_SeqAIJCUSPARSETriFactors was redefined to hold pointers
to up to 4 different Mat_SeqAIJCUSPARSETriFactorStruct structs: one for lower
and one for upper solves for both ILU and ICC. Two more for lower and upper
solves in algorithms that require a transpose, such as BiCG. The
latter two are necessary, as far as I can tell, because one doesn't
know until runtime if data structures for the transpose are needed
Thus, those are created on demand. Indexing vectors for reorderings
are also stored in Mat_SeqAIJCUSPARSETriFactors.

Lastly, Mat_SeqAIJCUSPARSE is the data structure that holds the
data needed in multiply. There are 2 pointers to Mat_SeqAIJCUSPARSEMultStruct
structs for MatMult and MatMultTranspose. Several auxilliary data
structures like workvectors and few other necessary data for MatMult
are also stored in here. One important variable, the cudaStream_t,
is stored here but it is not owned. Streams are necessary for the parallel
SpMV (a subsequent commit will add code setting stream variables from
the MPIAIJCUSPARSE class) and the matrices used in the MatMult and
MatMultAdd will then use the same stream identifier to attain optimal
performance. The MPIAIJCUSPARSE class will own the stream variable which
is then used in the SEQAIJCUSPARSE methods.

In matregis.c as well as the petscmat.h and finclude/petscmat.h,
I've changed the dependency of SEQAIJCUSPARSE to be on CUDA and
not TXPETSCGPU.

The test series TESTEXAMPLES_TXPETSCGPU has been changed to
TESTEXAMPLES_CUDA since SEQAIJCUSPARSE only depends on CUDA as
discussed above. ksp/ksp/examples/tests/ex43-aijcusparse.c has
been renamed to ksp/ksp/examples/tests/ex43.c, the targets in
the makefile have been changed appropriately and the results
fiels are renamed. Two new test targets were added in
ksp/ksp/examples/tests/makefile that test aijcusparse using
bicg (and thus the MatSolveTranspose and MatMultTranspose methods) as well as
bicg with reordering. The previous results for runex43_2.out (formerly
runex43-aijcusparse_2.out) were wrong and so I'm committing
new results that agree with CPU based computation. The code is
valgrind clean and cuda-memcheck clean.

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Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

merge PetscSF implementation

Hg-commit: 98dccc99445b69cb7a66312149eb16fec359e294

removed trailing spaces from all files

Hg-commit: 1cfa55059afe46c5145e0e830cd797b97216abfb

commit after merge

Hg-commit: d0f613618ca66a5aeb1aac97d210d2cc29755d3d

reemove OBJSC and OBJSF from invididual makefiles and auto-define in conf/variables

Hg-commit: 2f01c17f3c19dc4b89aaf306cfd60a12312c270d

Merge

Hg-commit: 8f74ca6da3dda2e92c9063777436a7e360bcc637