Merge branch 'master' into tisaac/dmforest

directory layout changed again: merging to switching branches back and forth
doesn't cause reconfigure to have a hard time

* master: (357 commits)
remov

Merge branch 'master' into tisaac/dmforest

directory layout changed again: merging to switching branches back and forth
doesn't cause reconfigure to have a hard time

* master: (357 commits)
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
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
add a test for MatPtAP()
small cleanup; add tests
cleanup MatPtAPSymbolic_MPIAIJ_MPIAIJ()
Fix nonzerostate tracking in all MATMPI types.
update location of test matrices in faq.html file
unused variable still declared
Fix for MatLoad_MPIDense() from sparsely stored matrix also fix for MatLoad_MPIDense_DenseInFile() when matrix has not had its local sizes preset by user
Preserve the B nonzerostate during disassembly.
TSEvent: Fix arch-mswin nightly errors due to declaring variables in the middle of a function.
Fix error in parallel loading of dense format matrix
removed KSPSetNullSpace() since mat already carries that information and having two locations for it is confusing, unnecessary and prone to error added MatSetTransposeNullSpace() for providing the null space of the transpose of the matrix and added support in KSPSolve() to remove this null space from the right handside of the linear system thus making the system consistent.
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Merge branch 'master' into knepley/feature-composable-callbacks

* master: (151 commits)
PetscMalloc: Fix handling of zero-sized allocations
add note to DMGetLocal/GlobalVector() about intended s

Merge branch 'master' into knepley/feature-composable-callbacks

* master: (151 commits)
PetscMalloc: Fix handling of zero-sized allocations
add note to DMGetLocal/GlobalVector() about intended short-time usage of the vectors.
sf: use patched openmpi tarball that has a potential fix for sf example hang
SNES problems that set VI bounds must use a VI solver since the other solvers ignore the bounds
pounders viewer did not cast PetscReal to double in printf nor use %D instead of %d
fix ts ex20adj
fix ts theta
fixed another variable declaration in the middle of a code block
example main() had PetscInt return type and argument that should be int
DMDAVTKWriteAll_VTS: Fix handling of higher-dimension coordinates
fixed example that declared variables in the middle of a function
C programs do not return PetscInt nor do they take an argument that is PetscInt, fixed example that did
You cannot declare variables in the middle of functions in PETSc.
add ierr checking to PetscOptionsBegin/End() in example
configure: add error check if user specifies PETSC_ARCH=-dbg [i.e starts with a '-']
scale norm of vector difference by norm of vector to insure it is small enough to consider the two vectors equal
missing PetscViewerDestroy() added
MatNestGetISs: use custom fortranstub to handle PETSC_NULL_OBJECT
update location of open-mx website on FAQ page
If the user sets bounds and calls a solver that does not support them, throw an error.
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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'

updated PETSc directory layout to match standard packaging strategies

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

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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Merge branch 'knepley/feature-harmonic-advection'

* knepley/feature-harmonic-advection: (86 commits)
SNES: Some docs for NASM
TS: Added view for MIMEX
Plex: Silence compiler warnings
Builder

Merge branch 'knepley/feature-harmonic-advection'

* knepley/feature-harmonic-advection: (86 commits)
SNES: Some docs for NASM
TS: Added view for MIMEX
Plex: Silence compiler warnings
Builder: Check for missing numProcs was wrong
PetscFE: Turn off Fortran binding for PetscFECompositeGetMapping()
Plex: Fix big bug in DMPlexGetGlobalFieldOffset_Internal() - If offset is negative (dof is on another proc), then we must have end < start
Builder: Allow override of numProcs
Plex: Fix Fortran wrappers for DMLabelView() and DMPlexDistribute()
Plex+Label: Added Fortran wrapper for DMPlexCreateLabel()
Plex: Dammit, how did this not get checked in?
Plex: Refiner check for hybrid cells must use hybrid faces as well - Ghost cells in FV method are hybrid
TS: MIMEX now uses work vectors for correct grid
Plex: Adding support for FV in automatic interpolator construction - Notice that the injector cannot do the right thing until we scrap VecScatter
Plex+FEM: Using PetscFVGetDualSpace()
SNES+Doc: Added Options Database keys
PetscFV: Added PetscFVRefine() - This allows interpolation to finer grids needed for FAS
PetscFV: Added a dual space for calculating projections
DM: Better error checking in DMCoarsen()
DMDT+PetscFE: Added PetscQuadratureExpandComposite() - Replaces PetscFECompositeExpandQuadrature() - Added PetscFECompositeGetMapping()
Plex: Fixed complex type error
...

Conflicts:
src/dm/impls/plex/ftn-custom/makefile
src/ts/interface/ts.c

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Plex: Fix Fortran wrappers for DMLabelView() and DMPlexDistribute()

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 barry/clean-gamg

Need updates to KSPCHEBYSHEV since I will be adding to them

Merge branch 'mlange/feature-plex-fluent'

* mlange/feature-plex-fluent:
Plex+Fluent: Fixed cast
Plex+Fluent: Fixed PetscBool handling
Plex ex1: Add Fluent reader tests for binary and pseudo-mi

Merge branch 'mlange/feature-plex-fluent'

* mlange/feature-plex-fluent:
Plex+Fluent: Fixed cast
Plex+Fluent: Fixed PetscBool handling
Plex ex1: Add Fluent reader tests for binary and pseudo-mixed sections
Plex-Fluent: Use a single-level meet to mark interior faces
Plex-Fluent: Face-type 5 also requires dynamic derivation of data size
Plex-Fluent: Add custom Fortran wrapper for DMPlexCreateFluentFromFile
Plex ex1: Add sequential and parallel tests for Fluent .cas reader
Plex-Fluent: Add support for binary sections in Fluent reader
Plex-Fluent: Mark faces with provided zoneIDs
Plex-Fluent: Dynamically derive data size for "mixed" sections
Plex-Fluent: Add coordinates to the generated Plex
Plex-Fluent: Build Plex topology from face connectivity
Plex-Fluent: Add skeleton reader for ANSYS Fluent mesh files

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Plex-Fluent: Add custom Fortran wrapper for DMPlexCreateFluentFromFile

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' into stefano_zampini/pcbddc-adaptive-selection

Merge branch 'tisaac/feature-gamg-extensible' into barry/experiment

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

Merge branch 'mlange/feature-plex-gmsh-fortran'

* mlange/feature-plex-gmsh-fortran:
SF: Activate Fortran wrapper for PetscSFDestroy()
Plex-Gmsh: Loosen the version requirement for .msh files
P

Merge branch 'mlange/feature-plex-gmsh-fortran'

* mlange/feature-plex-gmsh-fortran:
SF: Activate Fortran wrapper for PetscSFDestroy()
Plex-Gmsh: Loosen the version requirement for .msh files
Plex-Gmsh: Add custom Fortran wrapper for DMPlexCreateGmshFromFile

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