Merge branch 'master' of bitbucket.org:petsc/petsc

Merge branch 'tisaac/dm-locate-points-sf'

* tisaac/dm-locate-points-sf:
Plex: missed in IS
DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

A PetscSF is a more natural return value from DMLocatePoints() because:
- In the event that the mesh has overlapping

DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

A PetscSF is a more natural return value from DMLocatePoints() because:
- In the event that the mesh has overlapping cells, it's clearer which
in which process/cell the point is located.
- A natural next step after DMLocatePoints() is to send each point to
its cell for some local computation. With a PetscSF this is easy with
PetscSFGatherBegin()/PetscSFGatherEnd().

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Merge branch 'master' into barry/add-pcfieldsplit-logevent

Merge branch 'master' into barry/add-pcreset-hypre-for-master

Needed to move PCDestroy_HYPRE() added to master to PCReset_HYPRE() since that was introduced
as a bug fix for maint

Merge branch 'master' into barry-allow-vecset-nan-3.6

Merge branch 'master' into pr263/PierreBdR/ts-domain-error-in-stage/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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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 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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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 'master' of bitbucket.org:petsc/petsc

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

* master: (206 commits)
Bib: Added ref
fix the output file for the ts example ex20adj
Bugfix: setting post-step function in ztsf.c
f

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

* master: (206 commits)
Bib: Added ref
fix the output file for the ts example ex20adj
Bugfix: setting post-step function in ztsf.c
fix makefile format error with 'all-legacy'
doc: handle missing dev.html in a release tarball
doc: add in petscistypes.h to doc sourcefile list
Increase patchlevel to 3.6.1
update some example output files
Doc+Vec: Fixed VecSetValuesBlocked() Reported by: Shao-Ching Huang <huangsc@gmail.com>
clarify that PETSc's "thread safe" code only works with OpenMP
allow adjoint integration over split time intervals
DT: Goddman it. Why are people stepping on my commits
Bib: Added ref
fix the bug in the endpoint version of discrete adjoint theta and correct the affected example outputs
SNES: Added SNESQN types to Fortran Reported-by: Chris Bradley <c.bradley@auckland.ac.nz>
fix: buggy change in 33da457b864643cfcac2768e47197c286471a5a4
updated petscthreads.html with information on thread per object model
fix for ex56
removed the dead links to threads.html
send petsc repository messages to Karl no longer from his mcs address
...

Conflicts:
config/builder.py
src/dm/impls/plex/examples/tests/ex3.c
src/dm/impls/plex/examples/tests/makefile
src/dm/impls/plex/makefile

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Merge branch 'master' into knepley/feature-plex-point-location

* master: (202 commits)
Bib: Added ref
fix makefile format error with 'all-legacy'
Increase patchlevel to 3.6.1
update some exa

Merge branch 'master' into knepley/feature-plex-point-location

* master: (202 commits)
Bib: Added ref
fix makefile format error with 'all-legacy'
Increase patchlevel to 3.6.1
update some example output files
Doc+Vec: Fixed VecSetValuesBlocked() Reported by: Shao-Ching Huang <huangsc@gmail.com>
clarify that PETSc's "thread safe" code only works with OpenMP
allow adjoint integration over split time intervals
DT: Goddman it. Why are people stepping on my commits
Bib: Added ref
fix the bug in the endpoint version of discrete adjoint theta and correct the affected example outputs
SNES: Added SNESQN types to Fortran Reported-by: Chris Bradley <c.bradley@auckland.ac.nz>
fix: buggy change in 33da457b864643cfcac2768e47197c286471a5a4
updated petscthreads.html with information on thread per object model
fix for ex56
removed the dead links to threads.html
send petsc repository messages to Karl no longer from his mcs address
Plex: Fix for all the hidebound morons living with c89. Good luck doing computational science in the 80s!
DT: Fix tanh-sinh - Removed wrong var
SNES: Added SNESQN types to Fortran Reported-by: Chris Bradley <c.bradley@auckland.ac.nz>
Bib: More refs
...

Conflicts:
config/builder.py

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Merge branch 'mesgarnejad/feature-plex-globaltonatural'

* mesgarnejad/feature-plex-globaltonatural:
Plex ex15: This requires HDF5
Plex ex15: Fixed variable type
Plex: Fixed variable init
Ple

Merge branch 'mesgarnejad/feature-plex-globaltonatural'

* mesgarnejad/feature-plex-globaltonatural:
Plex ex15: This requires HDF5
Plex ex15: Fixed variable type
Plex: Fixed variable init
Plex ex15: Added test for reading and writing HDF5 in native format
Vec: Straighten out defines for VECOP
DM: Reminder to handle g2n in DMCreateSubDM()
Plex ex15: One test of g2n working
Plex: Fixed global to natural mapping creation
Plex: When creating g2n map, must use parallel DM
PetscSF: Corrected bug in PetscSFCreateInverseSF() for sparse leaves - Have to index over entire leaf space
PetscSection: PetscSectionCreateGlobalSection() now allows the user to keep local offsets - This is useful is all you want is to filter out the constrained points
Plex: Create the global to natural mapping during distribution if the flag is set
Plex: Added viewing in native format using the global to natural mapping
Plex: Added global to natural ordering support - The natural ordering is the one you have before distribution - Added DMPlexCreateGlobalToNaturalSF() - Added DMPlexGlobalToNaturalBegin/End() - Added DMPlexNaturaToGloballBegin/End()
SF: Added PetscSFCreateEmbeddedLeafSF() - This name sucks, but it subsets on leaves instead of roots
DM: Added an SF for the global to local mapping and a flag to enable its construction - Added DMGet/SetUseNatural() - Should hook this up to DMDA
SF: Added Fortran binding for SFView()
DM: Automatic Fortran binding should work for DMCreateSubDM()
SF: Added PetscSFCompose()
SF: Added PetscSFCreateFromZero()

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SF: Added PetscSFCreateEmbeddedLeafSF()
- This name sucks, but it subsets on leaves instead of roots

SF: Added PetscSFCompose()

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
...

Conflicts:
config/builder.py

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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 '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 stefano_zampini/pcbddc-adaptive-selection

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