To add a space to all comments I have made before. Barry pointed out
that a comment without a space right after '/*' may cause bfort to crash

Merge remote-tracking branch 'petsc/master' into fixed-c

To add a space to all comments I have made before. Barry pointed out
that a comment without a space right after '/*' may cause bfort to crash

Merge remote-tracking branch 'petsc/master' into fixed-comment-space

Conflicts:
include/petsc/finclude/petscmat.h
include/petscmat.h
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiaij.h

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Merge branch 'pr329/master/Fande-Kong/matpartitioning-hierarch' into pr361/master/Fande-Kong/pcgasm-increaseoverlap: need hierarch to build GASM subdomains.

Conflicts:
src/mat/examples/tests/makefi

Merge branch 'pr329/master/Fande-Kong/matpartitioning-hierarch' into pr361/master/Fande-Kong/pcgasm-increaseoverlap: need hierarch to build GASM subdomains.

Conflicts:
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiaij.h

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Merge branch 'master' into pr352/dmay/pctelescope/master

Merge branch 'master' into pr358/buptphyphy/addmatcreatenormalhermitian/master

Merge branch 'tisaac/plex-feature-tree-fv'

Make the PetscFV gradient reconstruction method work for the
non-conforming meshes introduced by the Tree extension to DMPlex.

* tisaac/plex-feature-tree-

Merge branch 'tisaac/plex-feature-tree-fv'

Make the PetscFV gradient reconstruction method work for the
non-conforming meshes introduced by the Tree extension to DMPlex.

* tisaac/plex-feature-tree-fv: (52 commits)
Plex ex3: make test that works for single precision
PlexSNES: address compiler warning
DMPlex ex3: make test output PASS/FAIL rather than precision specific
Plex: fix type punning problem stuffing (PetscFECellGeom *) in a Vec
Plex: allow ex3 testFVgrad examples in complex
PetscFV: allow SVD pseudoinverse least squares gradient calculation for complex.
Plex ex3: put fv tensor examples in C_NoComplex tests
Plex ex3: update regression output for nonconforming examples
Plex ex3: make separate fe and fv tests
Plex ex3: use MPIU_MAX, not MPI_MAX
DMPlex: added DMPlexReconstructGradientsFVM()
Plex: fix typo in change to cohesive cell creation
Plex: add ex4 and ex5 to makefile so they can be used for regression tests
DMPlex: remove overzealous error condition from FV gradient reconstruction
DMPlex: correct pointSF size in new point shift approach
DMPlexMigrate(): use correct global indices when migrating tree
DMPlexMigrate(): Don't invalidate old DM by overwriting cones
Plex ex3: use DMPlexDistributeOverlap()
DMPlexPartitionLabelClosure: traverse the tree up and down
PetscPartitionerSimple: work in parallel
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PlexSNES: address compiler warning

Merge branch 'tisaac/dt-fix-geom-punning' into tisaac/plex-feature-tree-fv

Pull in a fix to FE geometry that affects the complex,64bit case

* tisaac/dt-fix-geom-punning: (240 commits)
Plex: fix t

Merge branch 'tisaac/dt-fix-geom-punning' into tisaac/plex-feature-tree-fv

Pull in a fix to FE geometry that affects the complex,64bit case

* tisaac/dt-fix-geom-punning: (240 commits)
Plex: fix type punning problem stuffing (PetscFECellGeom *) in a Vec
PGI compiler cannot handle [restrict] usage therefor disable restrict for PGI compiler Fix ex48.c to use PETSc standard way of marking restrict
PETSC_UNUSED must occur before the typename. With PGI compilers they error if it is after the type name
on solaris in TSAdaptChoose_Basic() negative root for zero could produce -infinity thus causing time step to be decreased even though the error estimate was zero
MatGetSchurComplement: revert test from LUMP back to DIAG and update output
there are no tests for opencl or viennacl so prevent warning message: make[2]: *** No rule to make target `testexamples_OPENCL', needed by `tree'. Stop. make[2]: *** No rule to make target `testexamples_VIENNACL', needed by `tree'. Stop.
incorrect initial conditions function that could produce floating point exception value (and does on windows) due to squareroot of non-negative number
forgot to fix rule for building ex194
move ex193.c to ex194 because someone else created a 193
remove outdate manual page comment
add missing VecRestoreArray()
add missing VecRestoreArray()
missing restore array in example
formating for print statements of test example with __float128 precision
fix example for __float128 precision by using PETSc math macros and casting PetscReal in print statements
remove Tao example custom monitor that produced different results for __float128 precision
all PETSc built in monitors require a valid PetscViewer, NULL is not acceptable
PETSc built in monitors always require viewers to be passed in, no longer support a NULL viewer
use tigher haptol for minres for quad precision because otherwise false positive of indefinite matrix appeared in example
check for PetscMPIInt overflow in ISAllGather()
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Plex: fix type punning problem stuffing (PetscFECellGeom *) in a Vec

If (sizeof(PetscFECellGeom) % sizeof(PetscScalar)), then the array of
geometries read from the Vec is not packed, which sucks.

I

Plex: fix type punning problem stuffing (PetscFECellGeom *) in a Vec

If (sizeof(PetscFECellGeom) % sizeof(PetscScalar)), then the array of
geometries read from the Vec is not packed, which sucks.

I am not a fan of stuffing geometries into Vecs for this reason.

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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()

DMPlexSNES: fix recursive limiter application

Only recur on faces, not on lower dimensional children

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

added error checking for when PetscViewer is not passed to the standard monitor routines

Reported-by: Garth N. Wells <gnw20@cam.ac.uk>

Removed outdated output in example test file

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 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 'master' of bitbucket.org:petsc/petsc

Merge branch 'knepley/feature-plex-assembly-cellrange'

* knepley/feature-plex-assembly-cellrange:
Plex: DMPlexComputeJacobian_Internal() defined - Give both t and X_tShift arguments - Give cell ra

Merge branch 'knepley/feature-plex-assembly-cellrange'

* knepley/feature-plex-assembly-cellrange:
Plex: DMPlexComputeJacobian_Internal() defined - Give both t and X_tShift arguments - Give cell range - Put in declaration
Plex: Now DMPlexComputeResidual_Internal() explicitly takes [cStart, cEnd)

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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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