DM: move Get/SetCoarseDM from DMPlex into DM

Merge branch 'tisaac/dm-label-promote' into tisaac/dmforest

* tisaac/dm-label-promote: (319 commits)
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part o

Merge branch 'tisaac/dm-label-promote' into tisaac/dmforest

* tisaac/dm-label-promote: (319 commits)
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part of all DMs
builder: update regression tests
builder: update some missing package requirements
DM: set coordinate vector name
ts tutorials ex11_sa: make it compile
mark variable as unused so compiler doesn't warn about unused value
configure: use 'git cat-file -e' to check for existance of a commit in localrepo. ['git rev-parse' does not give error for a hash thats not in repo]
petsc4py: revert to manually syncing petsc4py with petsc master changes
configure: revert gitcommit default value to Null. If a pacakge using giturl does not change this value - raise an error
fix: revert change in a44bcdf that breaks with pgf90
update test output for fixed to hypre interface that now actually pass the interp vectors to BoomerAMG
Error message should say use negative threshold value to prevent filtering out zeros
Calls to HYPRE_BoomerAMGSetInterpVectors() did not actually copy the vector data pointer from the PETSc vector to the hypre vector thus resulting in the hypre interp vectors being identically zero and hence not affecting the quality of the AMG hierarchy produced/
DMPlex: Silence overzealous compiler warnings
add row/col orientation to MatConvert_Elemental_Dense
fix formatting error in previous commit [broke nightlybuilds]
fix formating of TSTHETA manual page and add missing command line option
run hwloc with MPIEXEC and binding so it runs on the correct machine
fix: memory leaks [in valgrind test]
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DM: make DMLabel labels a part of all DMs

Most DMLabel routines do not depend on the internals of DMPlex, and I
want to reuse them in other DM types

DM: puth depthLabel in DM

I know that this is s

DM: make DMLabel labels a part of all DMs

Most DMLabel routines do not depend on the internals of DMPlex, and I
want to reuse them in other DM types

DM: puth depthLabel in DM

I know that this is something that's only used by plex, but I'm not sure
how else to do this.

DM: move MarkBoundaryFaces back to plex

DM: add reference counting to label linked list for cloning purposes

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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 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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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 knepley/feature-label-empty-stratum

* master: (151 commits)
moved PCTELESCOPE comment into users manual since no one will see the comment
message in makefile about hyp

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

* master: (151 commits)
moved PCTELESCOPE comment into users manual since no one will see the comment
message in makefile about hypre bugs causing test crashes
remove use of some unitialized variables, remove use of "dummy" entries in Vec and IS since Dave May thought they could not be of size zero. Now three telescope tests give no valgrind errors
code sent unitialized data via MPI and allocated too large space for creating indices
Force generateetags.py to use /usr/local/bin/ctags before using ctags because the ctags provided with Apple XCode gets confused by function usage in .tex files and does not make proper tags for TSSolve() and many many others
Optimized version of snes/examples/tutorials/ex1f.F produced incorrect results when lx_v() and lf_v() were declared as of dimension 1 with optimzed builds only. Cannot explain exactly why this happens but since we are using VecGetArray() from Fortran we are gambling with the compiler regardless
make the PetscRandom object used in GAMG to be a public object that can be controlled via the options database. This allows the same example to produce the same results with real and complex numbers by using the option -pc_gamg_random_no_imaginary_part
added parallel tester for examples. Crude but it reduces a basic alltests on my laptop from 25 minutes to 7 1/2 minutes.
remove unneccessary if
fix the problem for ex9 which involves multiple TSSolve calls
shortened the time of several test examples
decrease dramatically the time used by several test examples that take more than a minute on may machine with debug mode
Some of the vectors created in MatNullSpaceCreateRigidBody() were not normalized to 1
fix strange PCTelescope struct name of P which caused duplicate symbol error on some systems cleanup use of PetscMalloc and PetscFree for telescope for modern PETSc standards replace semiredundat to telescope in makefile that runs test examples
SNESUpdateCheckJacobian: make relative norm output syntactically correct
DMCompositeGetGlobalISs: document Fortran interface
fix warnings on bsd. Also fix usage of PetscFunctionBegin/Return
Making an even bigger mess, I cannot explain why this is not in the branch
hypre: update with "Bug fix for Parasails; src/ksp/ksp/examples/tutorials/ex10.c runex10_16"
decrease duration of ex22 by factor of 10 to decrease testing time
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Merge branch 'pr352/dmay/pctelescope/master'

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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DM interfaces: New API's introduced
* Added the methods DMAppendOptionsPrefix() and DMGetOptionsPrefix()

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

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

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

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