Merge branch 'master' into barry/always-mark-floats

Needed to merge in master to resolve conflicts that will appear when this branch is merged with master

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c

Merge branch 'master' into tisaac/dmforest

Get 3.6.2 patches

* master: (1360 commits)
remove nasty memory leak with CUDA code when using block Jacobi with multiple blocks per process
print abs

Merge branch 'master' into tisaac/dmforest

Get 3.6.2 patches

* master: (1360 commits)
remove nasty memory leak with CUDA code when using block Jacobi with multiple blocks per process
print abs in Fortran test example in order to have same result with real and complex builds
changed outdate mpirun and -np to mpiexec and -n
force sqrt to be taken in the precision of PetscReal in fortran examples
continuation line too soon for some compilers
stop configure if user selected C++ clanguage, single precision, complex combination since we do not support it
fixes for Fortran examples to compile cleanly in single precision that do not involve complex numbers
fixes to Fortran examples to compile cleanly in single precision complex
fix previous mistake
must cast 1. to PetscScalar before dividing by a PetscScalar (C++ complex class is terrible)
must cast 0.0 to PetscScalar before comparison with a PetscScalar
changed order of suggested locations of downloadable PETSc to Barry's preference
Increase patchlevel to 3.6.2
remove debug print statement from two commits before
remove debug print statements I accidently left in the last commit
PetscDraw: Fix dummy definition of PetscDrawCollective{Begin|End}()
remove cleanupMumps flag from MatDestroy_Mumps() it should always free the memory it allocated Bug detected while adding features to libMesh
improved viewing of fractional counts in xml nested log viewing fixed bug in output of doubles to xml nested log files
chombo: build only libs - not examples
fix typo. 'gcc-4.8 --with-cxx-dialect=C++11' gives a warning with this line - even though its in a #ifdef thats never enabled.
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Merge branch 'knepley/feature-label-empty-stratum'

* knepley/feature-label-empty-stratum:
Plex ex11: Added code to test empty strata in DMLabel
Plex: Check the depth label state - If the depth l

Merge branch 'knepley/feature-label-empty-stratum'

* knepley/feature-label-empty-stratum:
Plex ex11: Added code to test empty strata in DMLabel
Plex: Check the depth label state - If the depth label is user managed, then send it when distributing labels
DMLabel: Now has a state - Why are these not PetscObjects?
Plex: If we remove the depth label, clear the optimized access
DMLabel: Check for empty stratum
DMLabel: Make DMLabelAddStratum() public

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To refactor the comments to follow petsc style.

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

Conflicts:
include/petsc/finclude/petscmat.h
src/mat/examples/tests/makefile

To refactor the comments to follow petsc style.

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

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

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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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Plex: Check the depth label state
- If the depth label is user managed, then send it when distributing labels

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

Merge in Barry's fix to synchonized print out of plex objects into
updated output files.

* master: (31 commits)
fix %nd for plex printf that

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

Merge in Barry's fix to synchonized print out of plex objects into
updated output files.

* master: (31 commits)
fix %nd for plex printf that should be %nD
PGI compiler requires cast to char* of this array for some reason
Incorrect use of %d for %D in viewing of PetscSection
update output for suitesparse examples with new KSP view data
changed boomeramg advanced smoother output files to use short format so there are less differences with different systems
fix some issues with PetscViewerFlush() and PetscViewerASCIIPushSynchronized() within the plex object viewing
incorrectly used stride value instead of local size in check that ISSTRIDE has same layout as columns of matrix
try using int(w) for Fortran case to integer instead of int(w,integer) since the latter failed on most systems claiming integer was not a constant. Very unclear to me what that second argument is suppose to be
SNES function evaluations were not counted for certain Jacobian computations
nightlybuilds: fix vec/ex7,ex7f link issue by using the correct LIBS option
nightlybuilds: move location of petsc.clone(s) on bb44 from nfs to /sandbox
nightlybuilds: arch-linux-complex-gcov -> arch-linux-cmplx-gcov to be consistant with other config tests
add __float128 data file neeed by test example 10 otherwise test example crashes with --with-precision=__float128 builds
cast fortran integer that may be 64bit with int() to prevent compiler warning about Warning: Possible change of value in conversion from INTEGER(8) to INTEGER(4) at (1)
removed unneeded definition of Sqr in example since PetscSqr should be used, and was in other parts of the same example!
nightlybuilds: run 'git gc' in the build clones
opensolaris: use 'FFLAGS=-ftrap=%none' this way fortran examples on solaris do not crash in lapack during 'div by zero' Also use the updated path to mpich
when I swapped the role of coulping and rest in fieldsplit I missed a place
cannot use PetscMalloc2() on arrays that will be freed as two seperate arrays
C++ cannot handle [PETSC_RESTRICT]
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Merge branch 'master' into mark/eigen-rand

fix some issues with PetscViewerFlush() and PetscViewerASCIIPushSynchronized() within the plex object viewing

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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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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PlexTree: protect against truncated sections when computing anchors

I had only tested on sections that included all points before.
Testing on the gradients generated in FVM exposed this.

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

accidently removed the C symbol in previous edits

Merge remote-tracking branch 'origin/master' into knepley/fix-plex-examples

* origin/master:
Matt needs to learn the difference between %d and %D and test with --with-64-bit-indices before pushing

Merge remote-tracking branch 'origin/master' into knepley/fix-plex-examples

* origin/master:
Matt needs to learn the difference between %d and %D and test with --with-64-bit-indices before pushing to next and master. This fixes a few of his %d mistakes.
update to no change output for indefinite problem
update to no change output due to change in format of mat nullspace attachment
update to no change test output for formating of has null space
update no change output
test example should only output message if error else verbose confusing nightly build message
example output should have 1 for line search termination value of success %d should be used with a (int) cast
fix minor issue with unused options printed into test output file
since clang __attribute doesn't handle const args properly we need to turn off this test until the fix it. to prevent spurious warnings

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Matt needs to learn the difference between %d and %D and test with --with-64-bit-indices before pushing to next and master. This fixes a few of his %d mistakes.

Merge branch 'master' into knepley/fix-plex-examples

* master: (75 commits)
increase the size of the ex25.c multigrid example so that the eigenestimator does not produce numbers that depend on mac

Merge branch 'master' into knepley/fix-plex-examples

* master: (75 commits)
increase the size of the ex25.c multigrid example so that the eigenestimator does not produce numbers that depend on machine roundoff and thus are different on different OS/hardware and produce different test restults. Previously the GMRES converged to 16 digits in 4 iterations and spent the next 6 churning but that churning produced different eigenvalues which produced different convergence for the multigrid method
Bib: More references
example used int and double !
added long forgotten test output file
removed tao test example run that uses random numbers since not reproducable on different systems
Jason changed a default TAO tolerance but did not update example test output that viewer the tolerance
Plex: Correct complex problem
Plex ex12: Now PCMG monitor creates its own coarse solutions
Plex ex12: Put in working setting for PCMG coarsening test
XDMF: Now take a bunch of files as input
SNES ex12: Use monitors instead of brute force to monitor errors
SNES ex12: Renumber meshes to match MG numbering
PC+SNES: Attach a level id to subsolvers in a multilevel solve - We should have done this years ago
Plex: Added epsilon to point location check
Plex ex12: Added error output on each level
Plex: Added DMPlexComputeL2DiffVec() - This puts cellwise error integrals in a Vec
Plex: Fix complex conversion
Plex: Fix variable init
Add an option to ex12 to dump the coarsened hierarchy to disk.
Plex: Fixed unused variables
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Merge remote-tracking branch 'origin/knepley/feature-snes-deflation'

* origin/knepley/feature-snes-deflation: (55 commits)
Plex: Correct complex problem
Plex ex12: Now PCMG monitor creates its o

Merge remote-tracking branch 'origin/knepley/feature-snes-deflation'

* origin/knepley/feature-snes-deflation: (55 commits)
Plex: Correct complex problem
Plex ex12: Now PCMG monitor creates its own coarse solutions
Plex ex12: Put in working setting for PCMG coarsening test
XDMF: Now take a bunch of files as input
SNES ex12: Use monitors instead of brute force to monitor errors
SNES ex12: Renumber meshes to match MG numbering
PC+SNES: Attach a level id to subsolvers in a multilevel solve - We should have done this years ago
Plex ex12: Added error output on each level
Plex: Added DMPlexComputeL2DiffVec() - This puts cellwise error integrals in a Vec
Plex: Fix variable init
Add an option to ex12 to dump the coarsened hierarchy to disk.
Plex: Fixed unused variables
Plex: Fixed PetscScalar conversion problem
Plex: Fixed function header
Profile DMCreateInterpolation (nontrivial cost for nonnested meshes)
Replace the arguments for coarsening in ex12 with correct ones
Plex: Using a refinement function
Plex: Added DMPlexGet/SetRefinementFunction() - Use to do non-uniform refinement
Events for DMCoarsen and DMLocatePoints
Update the pragmatic build script to use master, not my branch
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Merge remote-tracking branch 'origin/knepley/feature-plex-point-location'

* origin/knepley/feature-plex-point-location:
Plex: Added epsilon to point location check
Plex: Fix complex conversion

Merge remote-tracking branch 'origin/knepley/feature-plex-point-location'

* origin/knepley/feature-plex-point-location:
Plex: Added epsilon to point location check
Plex: Fix complex conversion
Plex: Now check whether a cell edge intersects a box edge as well - Added DMPlexGetLineIntersection_2D_Internal()
Plex: Fix marking of boxes enclosing cell vertices
Plex: Added error if point is not found - Might remove this later
Plex: Fixed initialization in point location
Plex: Removed unused vars, Initialized vars
Plex: Fixed signature for PetscGridHashGetEnclosingBox()
Plex ex17: Tests point location - One test which locates cell centroids right now
Plex: Replaced brute force search with grid hashing for point location
Plex: Now every Plex has a PetscGridHash
PetscGridHash: Added a simple regular point location data structure
DMLabel: Added DMLabelConvertToSection() - This routine converts a label to a Section+IS
Doc+Plex: Fixed function name

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