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 'knepley/feature-dt-fem' into knepley/feature-fem-dgspace

* knepley/feature-dt-fem: (123 commits)
SNES ex12: Fix buggy checkin
Builder: strip test output before comparing
PetscDua

Merge branch 'knepley/feature-dt-fem' into knepley/feature-fem-dgspace

* knepley/feature-dt-fem: (123 commits)
SNES ex12: Fix buggy checkin
Builder: strip test output before comparing
PetscDualSpace: Pointer check barfs for function pointer
Sys: Add ability to turn off CUBLAS initialization - This continually SEGVs on my Air
SNES ex62: Updated test output - Matrix now prints attached nullspace indicator - 3D tests are wierdly different, they need to be verified by hand
SNES ex12: Updated test output - Mostly for completed labels
SNES ex12/62: Changed to new DMPlexProjectFunction() interface - Took DM out of main struct
SNES ex12/62: Complete boundary label - Puts in edges in 3D - Perhaps should be moved to the creation routine
PetscDualSpace: Fixed orientation of reference tetrahedron - Now this does not match FIAT
PetscDualSpace: Fixed numDof for P0
PetscDualSpace: Added PetscDualSpaceApply() for the action of a functional - Declared PetscDualSpaceGetFunctional()
DMPlex: Updated ProjectFunction() to use PetscDualSpace for generic projection - Has not been tested with moment dofs - Accommodates vector functions
DMPlex: Added support for INSERT_BC_VALUES in VecSetClosure()
DMPlex: Fixed missing RestoreTransitiveClosure()
DMPlex: Fixed optimized portion of VecGetClosure() for NULL input array
DMPlex: Allow NULL array as input to DMPlexVecGetClosure()
DMPlex: Fix VecGetClosure() when the array is input
PetscFE: OpenCL is hardcoded for P0 coefficients right now
SNES ex12: Added test cases for variable coefficient Laplace - The P1 tests reproduce the analytic linear coefficient
PetscFE: Added auxiliary fields to PetscFEIntegrateJacobian() - Hooked it up to DMPlexComputeJacobian()
...

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Merge branch 'master' into knepley/feature-dt-fem

* master: (211 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries

Merge branch 'master' into knepley/feature-dt-fem

* master: (211 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
...

Conflicts:
config/builder.py
src/dm/impls/plex/plexgeometry.c

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Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (273 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (273 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
...

Conflicts:
include/petscdmplex.h

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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 branch 'knepley/feature-benchmark-example'

* knepley/feature-benchmark-example:
Benchmark: Corrected processing of parallel flops
Benchmark: Improve interaction with batch system - Look at

Merge branch 'knepley/feature-benchmark-example'

* knepley/feature-benchmark-example:
Benchmark: Corrected processing of parallel flops
Benchmark: Improve interaction with batch system - Look at environment for some qsub options
Benchmark: Get size of parallel mesh properly
Benchmark: Use PETSC_DIR to run generation script
Benchmark: Adding cwd to path since summary module is written there
Benchmark: Added plotEventScaling() to benchamrkExample

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Merge branch 'karlrupp/feature-snes-ex52-OpenCL' into knepley/feature-dt-fem

* karlrupp/feature-snes-ex52-OpenCL:
SNES ex52: OpenCL integration now natively supports double precision as well.
SN

Merge branch 'karlrupp/feature-snes-ex52-OpenCL' into knepley/feature-dt-fem

* karlrupp/feature-snes-ex52-OpenCL:
SNES ex52: OpenCL integration now natively supports double precision as well.
SNES ex52: Added option to switch between OpenCL and CUDA backends.
SNES ex52: Added test for multiple regular parallel refinements
SNES ex52: Fixed output flag for residual printing
SNES ex52: Added -refinement_rounds to allow multiple regular parallel refinements
SNES ex52: Added uniform parallel refinement - Added test
DMPlex: Uniform refinement does not work on uninterpolated meshes
SNES ex52: Changed output for 3D tests
SNES ex52: Fixed Makefile to support compilation of both the OpenCL and the CUDA version
SNES ex52: OpenCL version can now deal with multiple parallel blocks.
SNES ex52: Fixed OpenCL vector-type initialization for Laplacian as well.
SNES ex52: Fixed static initialization issue in OpenCL kernel for the AMD SDK.
SNES ex52: Fixed OpenCL test suite, added reference output
SNES ex52: Now builder runs for OpenCL are separate
SNES ex52: Unify dispatch function for CUDA and OpenCL - Now only one function works at a time (I think this is alright in the example) - Remove -opencl flag
SNES ex52: Added OpenCL profiling information.
SNES ex52: Now supporting elasticity in 2d via OpenCL.
SNES ex52: Updated OpenCL version such that spatial dimension is now a runtime parameter.
Added OpenCL version of SNES ex52 for the Laplacian.
Builder: Fixed problems for snes/ex52: "Cuda" -> "cuda", stripping "\r" from output for comparison with reference.

Conflicts:
src/snes/examples/tutorials/ex52.c

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Benchmark: Corrected processing of parallel flops

Benchmark: Improve interaction with batch system
- Look at environment for some qsub options

Benchmark: Get size of parallel mesh properly

Benchmark: Use PETSC_DIR to run generation script

Benchmark: Adding cwd to path since summary module is written there

Benchmark: Added plotEventScaling() to benchamrkExample

SNES ex52: Added option to switch between OpenCL and CUDA backends.

commit after merge

Hg-commit: 719627a6cee54b4367ab263a30985c06b3d9399d

Allow examples to be run in daemon mode

Hg-commit: ddfa6347477721e02bbee13d4f8e2b93163c7078

commit after merge

Hg-commit: 8bbde4c6a68210736fec1b806d9ca592257e9fc9

More examples

Hg-commit: a8e2f2c193198ad16433626d241c31b4edea9570

commit after merge

Hg-commit: e8d19a834d936a4816c3abf3af0b68733c00be11

Improvements to plotting for benchmarkExample

Hg-commit: 7a93eb0d3fa2e4662884869729a840dd9c164245

commit after merge

Hg-commit: ad9064ecab6663bf6a24da505dd949d26e524f4c

Fixing example benchmarking
- Now uses block size correctly for time plots

Hg-commit: 9654a35303f7ce99cb313313d4af3cb9238afbaf

commit after merge

Hg-commit: 0db928480d979c13a2377936075c7720438182bd

Fix syntax in benchmarkExample.py

Hg-commit: 5ad65589ae654a618e4bc1a29f0c742dd72b587d

commit after merge

Hg-commit: fb27d03db297d0e9b4ef73082c64edf0fc429f9e