Merge branch 'master' into jed/process-options-handler

Merge branch 'tisaac/dmplex-stable-tet-refinement' into tisaac/plex-feature-tree-fv

This feature branch also changed the topology of nonconforming examples:
I am merging so that I can make the regre

Merge branch 'tisaac/dmplex-stable-tet-refinement' into tisaac/plex-feature-tree-fv

This feature branch also changed the topology of nonconforming examples:
I am merging so that I can make the regression output that should be
correct in master and next

* tisaac/dmplex-stable-tet-refinement: (594 commits)
plex: added tet shape regression test
plexrefine: remove replaced code
plex: update test output for new tet refinement order
plex: fix tet refinement for stable element shape
DMPlex: added test of shape quality to ex1
Better to use the proper error handling version of PetscViewerASCIIGetStdout() instead of PETSC_VIEWER_STDOUT_()
Generate a very useful error message if PetscLogView(), PetscLogEventGetPerfInfo() or PetscLogEventGetFlops() is called with a preceeding call to PetscLogBegin() and friends (also -log_summary which triggers a PetscLogBegin())
fix compile warnings
Plex: Fix bug with bcComps initialization
Turn off elemental shared libraries if --with-shared-libraries=0 is used
Bib: Added refs
Bib: Fixed a bunch of errors
add warning/error flag for '-mat_superlu_dist_parsymbfact' when MatInputMode=GLOBAL
makefile: fix format
tests: add back ex6f, runex6f targets - that got removed in 2f1d3d565a6a43067e6df75b043e6343b05fcd1d
accessing option that may never have been set
typo in DMNetworkSetNumVariables() reported by Sean Shahkarami
superlu_dist: update to using latest 4.1 version
fix compile warnings
Generate an error message when trying to overwrite default options of CN and BEULER
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DMPlex: added DMPlexReconstructGradientsFVM()

Merge branch 'master' into barry/fix-petscviewer-attempt-2

Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of

Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of git. I think it is not justified to ever have anything in next for more than a few weeks at most.
Either take it out of next if it is broken or put it in master if it is not broken. Hanging around in next but
not master for ever is not a good policy.

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Merge branch 'pr345/anriseth/anriseth/ngmres-reset-xm-increase/master'

NGMRES: option to restart on F_M increase

Merge remote-tracking branch 'petsc/master' into matpartitioning-hierach

Merge remote-tracking branch 'petsc/master' into mat-increaseoverlap

Merge branch 'master' into knepley/feature-snes-deflation

* master: (32 commits)
MatGetSubmatrix() could hang when some processes thought the entire matrix as being selected and others did not.

Merge branch 'master' into knepley/feature-snes-deflation

* master: (32 commits)
MatGetSubmatrix() could hang when some processes thought the entire matrix as being selected and others did not.
PetscOptionsStringToScalar() and hence PetscOptionsScalarArray() did not work correctly for complex numbers with negative imaginary part
Have SNESCOMPOSITE honour -snes_max_fail for the number of inner solver failures it will tolerate.
fiat: add fallback url
added Stefano and Lisandro to PETSc authors list updated PETSc version number to 3.6 and year of publication to 2015 in the users manuals
deeper cleanup of matrix when the type is reset
need to call KSPSetFromOptions() after KSPSetOperators() so that command line null space is attached to correct matrix updated example output for null space not attached to KSP
Doc: Acknowledge Patrick
bugs in example that should never have gotten into next bug in code calling VecGetArray() on read only vector
doc: seperate -> separate
configure: help - prevent from printing duplcate sections - all PACAKGENAMEs should be CAPS
remove C99 code from example update output from example
updated list of PETSc enum objects that bfort will treat as native for generating Fortran stubs
-help would print the various -xxx_type values on multiple lines making a | grep -ksp_type (for example) not list all the possible options
fix memory leak as reported by the nightly tests
print help message for PetscOptionsGetViewer() the message is rather long
removed dead code about PETSc web server
removed unneeded custom XXXViewFromOptions() functions and updated to use PetscObject as second argument calling sequence
changed second argument of PetscObjectViewFromOptions() to PetscObject and all routines that use this routine
bugfix as reported by PETSc blame digest (next) 2015-05-25
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Merge branch 'master' of bitbucket.org:petsc/petsc

Merge branch 'barry/fix-petscobjectviewfromoptions'

changed second argument of PetscObjectViewFromOptions() to PetscObject and all routines that use this routine

Merged petsc/petsc into master

Merge branch 'knepley/feature-plex-bc'

* knepley/feature-plex-bc:
TS: Take out unnecessary declaration
XDMF: Allow missing time dimension
MatSchur: Better check for missing D matrix
TAO ex1:

Merge branch 'knepley/feature-plex-bc'

* knepley/feature-plex-bc:
TS: Take out unnecessary declaration
XDMF: Allow missing time dimension
MatSchur: Better check for missing D matrix
TAO ex1: Updated to new Plex interface
Plex: Fixed bug for FV BCs in DMCreateSection_Plex()
Plex+TS: FIxed DMPlexTSCheckFromOptions()
Plex: Changed the signature of pointwise input functions - Now the spatial dimension and number of fields is passed in
Plex: Fixed bugs with DMPlexCreateSection() - F90 declaration - Do not constrain more than the dog
DM: Can view the global section using -global_section_view
Plex: Now DMPlexCreateSection() also takes the constrained components
Plex: Now BC take constrained field components as well - Changed DMPlexAdd/GetBoundary() - Can use -bc_<name>_comp <nums> to override
Plex: Now -dm_plex_separate_marker works correctly in DMPlexCreateSquareBoundary()
DMLabel: Added DMLabelInsertIS()
SNES: Added DMSNESCheckFromOptions() - Should simplify examples

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Merge branch 'knepley/feature-plex-bc' into knepley/solkx

* knepley/feature-plex-bc:
TS: Take out unnecessary declaration
XDMF: Allow missing time dimension
MatSchur: Better check for missing

Merge branch 'knepley/feature-plex-bc' into knepley/solkx

* knepley/feature-plex-bc:
TS: Take out unnecessary declaration
XDMF: Allow missing time dimension
MatSchur: Better check for missing D matrix
TAO ex1: Updated to new Plex interface
Plex: Fixed bug for FV BCs in DMCreateSection_Plex()
Plex+TS: FIxed DMPlexTSCheckFromOptions()
Plex: Changed the signature of pointwise input functions - Now the spatial dimension and number of fields is passed in
Plex: Fixed bugs with DMPlexCreateSection() - F90 declaration - Do not constrain more than the dog
DM: Can view the global section using -global_section_view
Plex: Now DMPlexCreateSection() also takes the constrained components
Plex: Now BC take constrained field components as well - Changed DMPlexAdd/GetBoundary() - Can use -bc_<name>_comp <nums> to override
Plex: Now -dm_plex_separate_marker works correctly in DMPlexCreateSquareBoundary()
DMLabel: Added DMLabelInsertIS()
SNES: Added DMSNESCheckFromOptions() - Should simplify examples

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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
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Conflicts:
config/builder.py

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Add SNESLineSearchReason to fortran includes
Also truncate names to fit 32 char fortran limit

And fix typo MATOP_TRANSPOSE_MATM_ULT_NUMER

Merged petsc/petsc into master

Plex: Changed the signature of pointwise input functions
- Now the spatial dimension and number of fields is passed in

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 'barry/propagate-pcsetup-failures'

SNES: Added DMSNESCheckFromOptions()
- Should simplify examples

Infrastructure that allows failures in PCSetUp(), PCApply(), MatMult() etc due to, for example a zero pivot or function evaluation outside its domain, to propagate up and become a KSP_DIVERGED inste

Infrastructure that allows failures in PCSetUp(), PCApply(), MatMult() etc due to, for example a zero pivot or function evaluation outside its domain, to propagate up and become a KSP_DIVERGED instead of generating an error that stops the program. In response to Issue 96. This includes failures in MatCreateSNESMF() applications due to domain errors. The mechanism to propagate some errors is by setting Info or Nan into the output vector and using the norm or inner product reductions in SNES or KSP to propagate the error condition to all processes and then handling them immediately after the norm or inner product.

This allows, for example, ODE integrators to try again with a smaller time-step if the PCSetUp failed instead of requiring a complete restart of the run with other options.

Currently some error conditions, such as function domain error in a line search may not get progated up using the correct SNESConvergedReason

See src/snes/examples/tests/ex69.c for the handling of several conditions

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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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