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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removed Mat option for skipping checking of compressed row format since it is now free using the nonzerorowcnt previously introduced

Merge branch 'paulmullowney/txpetscgpu-package-removal2'

Merge branch 'hzhang/mat-redundant'

rm psubcomm from MatGetRedundantMatrix() because Jed does not like it :-(

add 'psubcomm' as an input for MatGetRedundantMatrix(): user can provide his own subcomm, or psubsomm, or nsubcomm

rm mlocal_red from MatGetRedundantMatrix()
set defaults in PetscSubcommCreate()

Removing unused enumerated parapeters from MatCUSP/CUSPARSEFormatOperation

I remove MAT_CUSP_SOLVE from MatCUSPFormatOperation
and MAT_CUSPARSE_SOLVE from MatCUSPARSEFormatOperation as
potential par

Removing unused enumerated parapeters from MatCUSP/CUSPARSEFormatOperation

I remove MAT_CUSP_SOLVE from MatCUSPFormatOperation
and MAT_CUSPARSE_SOLVE from MatCUSPARSEFormatOperation as
potential parameters for choosing the storage of the matrix
for tirangular solve. In particular, the triangular
solves was always using csr format so this parameter had
no effect. Moreover, I never found a case where
an ellpack/hybrid format worked better. Thus I remove this
as a potential parameter. However, I think it is important
to keep MatCUSP/CUSPARSEFormatOperation in the code. In the
future I can see a MAT_CUSPARSE_FACTOR option which uses
CUSPARSE to do ilu0/ic0 factorization on the GPU.

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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'

Adding PREPROCESSOR directives to protect ELL and HYB storage formats.

I've added preprocessor directives around all code using the cusparse
hybrid (or ellpack) format to only build when CUDA 4.2 or

Adding PREPROCESSOR directives to protect ELL and HYB storage formats.

I've added preprocessor directives around all code using the cusparse
hybrid (or ellpack) format to only build when CUDA 4.2 or beyond is
being used. I've also changed the documentation in a few places to
reflect this. In a few places, protections were required for CUDA
5.0 (hyb2csr conversion and in the stream creation in veccusp.cu).

Also adding code to the init.c that 1) checks cuda error codes and
2) sets the device flags so that memory can be registered as paged-
locked via : cudaSetDeviceFlags(cudaDeviceMapHost). This should be
valid for all 1.3 devices and later. Moreover, these changes allow
multiple MPI threads to work on 1 GPU using cuda streams in a thread
safe manner.

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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 'prbrune/dm-coordinaterestrict' into prbrune/snes-elasticityexample

Merge branch 'jed/mat-factor-shift'

* jed/mat-factor-shift:
Mat PCFactor: include MatFactorShiftType in PCView_Factor output

Merge branch 'karlrupp/feature-viennacl'

Merged petsc/petsc into rmills/petsc master.

Merge branch 'jed/matnullspaceremove-inplace'

* jed/matnullspaceremove-inplace:
Mat: remove 'vec' member of MatNullSpace
Mat: remove third argument to MatNullSpaceRemove

Merge branch 'barry/fix-docs-regarding-xxxtype'

Removed the ability of XXXType to be the string name of a library and function in that library but forgot to remove this form from all the XXXAType manual pages

Mat PCFactor: include MatFactorShiftType in PCView_Factor output

Consolidates the detailed shift string and updates all output files,
including a couple that have not been run in a long time and hav

Mat PCFactor: include MatFactorShiftType in PCView_Factor output

Consolidates the detailed shift string and updates all output files,
including a couple that have not been run in a long time and have other
problems.

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Mat: remove third argument to MatNullSpaceRemove

Out of place removals were dangerous because the MatNullSpace held the
only reference to the resulting Vec, which is dangerous. This use case
is rar

Mat: remove third argument to MatNullSpaceRemove

Out of place removals were dangerous because the MatNullSpace held the
only reference to the resulting Vec, which is dangerous. This use case
is rare (never used in PETSc itself) and can easily be accomplished:

VecDuplicate(x,&y);
VecCopy(x,y);
MatNullSpaceRemove(nullsp,y);

Suggested-by: Tobin Isaac <tisaac@ices.utexas.edu>

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ViennaCL: Added sequential AIJ matrix.

Compiles, 'make test' passes. Further testing required.
Injects similar to PETSC_HAVE_CUSP into existing functions.
A general concept for dealing with accelera

ViennaCL: Added sequential AIJ matrix.

Compiles, 'make test' passes. Further testing required.
Injects similar to PETSC_HAVE_CUSP into existing functions.
A general concept for dealing with accelerators is required here, but postponed after release 3.4.
aijAssemble.cpp is a stub, also row-compressed CSR is not yet supported.

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Merge branch 'barry/fix-xxxviewsetfromoptions'

* barry/fix-xxxviewsetfromoptions:
*ViewFromOptions: update documentation, providing disabled man pages
fixed bug where XXXViewFromOptions() used p

Merge branch 'barry/fix-xxxviewsetfromoptions'

* barry/fix-xxxviewsetfromoptions:
*ViewFromOptions: update documentation, providing disabled man pages
fixed bug where XXXViewFromOptions() used prefix of object rather than appropriate prefix of KSP or SNES

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